Soma-notes - User contributions [en]

BioSec 2012: Consolidated Notes

2012-05-08T00:33:02Z

Dsouza3190: /* Malicious code/organisms */

Below is a summary of what was discussed in the 2012 run of Biological Approaches to Computer Security, organized by topic.

(Cheryl: I think a topical organization is easiest and clearest, but if you have other ideas feel free to go with them. I just made up some topics off the top of my head, please use ones that make sense based on the notes you find. Look at all of the pages linked to from the top-level biosec page: the notes for the first weeks, the misc notes pages, and the individual student pages. Please condense or drop stuff that is too detailed (particularly notes on evolution).)

==Evolution==
''The origin of species'' by Charles Darwin is one of the most well known and respected pieces of literature to this day, even through today, it is half a century old. It has changed the way we as humans see and perceive the world as we know it. Darwin's theory on evolution challenged all the past and present views of how species came about. This not only includes theories in science, but also religion - where many believe in natural theology. That is species are created by a creator and a species' adaptation to their environment is nothing but `intelligent design'. Although still very much a controversial piece of literature as it was in Darwin's time; the theory of evolution has stood the test of time in the scientific realm and still remains to be the most accepted scientific explanation for the origin of species of all living organisms.

===Summary of ''The origin of species''===
The entire argument that Darwin formulated throughout this piece of literature is based on variation. It should be noted that variations in a particular species is present irrespective of whether or not that particular species is domesticated. Each species is distinguishable from the other due to the numerous different adaptations and traits it poses. The variations in a particular species are present in either one, or a combination of physical, chemical and biological traits. These traits are often inherited from one generation to the next (hereditary) and is rooted in the species adapting to change in their environment at some point in history. To support this hypothesis Darwin gives numerous examples of remarkable adaptions that permitted different species to survive and in some cases thrive in their environment. A couple of these examples include: the beak of the woodpecker that allows it to better collect it's prey - insects, and the wings of the bat that permits it to fly. Furthermore small variations seen within a particular species directly correlated to variations seen across different species. Thus, Darwin's entire theory of evolution attempts to explain with proof of observation that variation is the entire cause of ''the origin of species''.

Key to Darwin's argument is the notion of natural selection which explains how variation can eventually lead to the evolution of the particular species. In order to understand this concept, one needs to first understand the concept of struggle for existence. In chapter three through to chapter seven of \textit{the origin of species}, Darwin explains the struggle for existence as the reason why some species' characteristics survive and others go extinct. In addition, he notes that the huge amount of variation in species has permitted for species to adapt very well to their environments. That is, due to the unique characteristics that certain organisms have developed they can thrive in their specific environment. In addition, Darwin notes that only the characteristics that prove to be most advantageous (variations that permit a species to adapt to their environment better than other species) is passed from one generation onto the next (hereditary). This is when the concept of natural selection comes to play. Natural selection allows for the species that have best adapted to the environment to survive and/or prosper. However, at the same time the species that do not possess variations that are advantageous struggle for their existence, but do not succeed, thus becoming extinct.

In other words, natural selection is basically the mechanism that drives what we refer to as evolution. Living organisms continue to pass genes from one organism to another. These genes are not all the same, some carry variations, some do not. The variations in the genes can prove to be either advantageous or disadvantageous to future generations. This is due to the fact that only advantageous genes are naturally selected and thus survive. Implying that living organisms with the advantageous genes continue to reproduce passing their genes from one generation to the next. Eventually, this variation causes this group of living organisms to be branch off from their original species and become a species of their own. The continual branching of species into new species suggests that all species can be traced back to one single parent species. Moreover, this theory provides a simple but profound explanation as to why many species are very similar to each other. The reason behind which is that the species either evolved from one another or they have a closely related common parent.

Another concept that go hand in hand with natural selection is the limits of population increase. Nature can provide enough food and shelter for all the species that is inhabitants and at the same time be very destructive (natural disasters, animals prey on other species, etc.). This in turn causes species to struggle for their lives, and essentially prohibits some organisms to survive. The concept of limits of population increase (borrowed from Thomas Malthus) basically states that each generation increases the population of the species exponentially, which in turn implies that the population of the entire world is increasing constantly. However, this poses the problem of the world running out of room for the species to occupy. That is if the birth rate increases exponentially while the death rate remains the same from one generation to the next. This is not the case in reality, thus there must exist a limit that nature imposes on the total number of inhabitants. This in turn gives rise to competition, where each species must compete with each other in order to ensure that they survive thus threatening the survival of the other species.

The rest of this piece of literature is devoted to Darwin defending his theory against possible criticisms from other known scientists of that time, and still some today. For example, the existence of fossil records proves not to link the chains of evolution from one parent species. Darwin's argument in this case is that, many of the fossil fuels found today, are not perfect, their original conditions have been destroyed. In addition Darwin argues that geographical isolation proves to be a fundamental component to his theory. That is because his theory suggests that all living organisms develop from one or a handful of `original' parent species, there was a need for species to travel and immigrate to different areas of the world. However, this was easier said than done, especially when barriers such as water (oceans), height (hills and mountains), etc. highly restricts the possibility of living organisms to immigrate to another region of the world. Thus, the few that were able to escape their birth place and immigrate to another region shaped the rest of the species in that particular geographical area.

===Computer security perspective===
A lot can be said about applying computer security to Darwin's approach. To begin with, a lot of questions needs to be answered. For example, although Darwin's approach of evolution seems to be a fool proof way of doing things, it is really slow. In order for biology to get to the stage where it is at, it took billions of years. How are we supposed to replicate this billions of years worth of work in a matter of few days or months or even years? In addition, following Darwin's approach, we need to be able to accept failure most of the time. That is, biology has gotten to where it is currently at by accepting failure, which is present when species become extinct because they did not adapt a advantageous variation. Lastly, in Darwin's theory, a species survival was highly dependent on that of the environment. Although this might have worked within the realm of biology, we do not have the luxury of exploiting this in the realm of computer security. That is, computer security needs to work accurately irrespective of the environment it is in.\\

==Diversity==

''Diversity'' can be defined as a variation. This variation can take place in many different form. In the previous chapter diversity among different species was briefly mentioned. This chapter discuss biological diversity and software diversity that is currently present today. The chapter then concludes with a brief section about how this all relates to computer security.

===Biological diversity===
''Biodiversity'', also known as biological diversity is the variety of different living organisms and all its processes found on Earth. This broad category is further divided into three categories: genetic diversity, species diversity and ecosystem diversity. ''Genetic diversity'' is basically the total amount of different genes found in the entire population of one species. ''Species diversity'' is the diversity of species within a particular region (i.e. the total number of different species that inhabit a particular area). ''Ecosystem diversity'' the total number of different habitats that are encompasses within a region. Needless to say, there is an abundance of diversity that is present in biology. This is mainly because of evolution. As explained in the previous chapter, the theory of evolution basically states that all organisms descended from one or a hand-full of common ancestors. This thus implies that they all share common features. At the very same time due to natural selection species need to continue to evolve and change over time to adapt to their specific environment. Thus, as each species changes and evolves into another, they add to the biodiversity that is already existent. This is because when a species evolves substantially, it becomes it's own `new species' which adds to the species diversity and subsequently adds to genetic diversity and ecosystem diversity.

With biodiversity comes a lot of dependence. That is different species depend on each other for food, thus in turn affecting the entire population of the species. For example, parasitism and mutualism. ''Parasitism'' is the symbiotic relationship between two organisms, where one organism benefits at the expense of the other organism. ''Mutualism'' is also a symbiotic relationship between two organisms, however the difference is that both organisms benefit from this relationship. This interdependence in biological systems means that if something were to happen, it would strain an entire species, or a couple of species, depending on the actual gene that it affects. However, the chances of one `virus' killing all the living organisms in the world is very slim. Unless it attacks the three aspects that are common to all living organisms: ATP, DNA or plasma membrane. Even if this is the case, all living organisms have a general mechanism of dealing with unknown dangers. This is in addition to the other various mechanisms that are more specific and deal with known dangers. Thus, diversity increase the probability that at some level in the headachy or organisms, at least one member, if not not many will be able to withstand a major attack.

===Software diversity===
From the days where computers were just affordable and in almost every office and house, ''Microsoft'' has dominated the operating system market. Although today, the use of other operating systems such as Linux, Mac OS X, etc. have increased in popularity, Microsoft dominates the current market. But unlike the past, security measures such as network access, anti-virus, etc. has been improving at a remarkable rate. However, this is improvement is driven by the need to always be one step ahead of the community that attacks these systems (hackers). Nevertheless, the problem is still very much prevalent in today. This is because of the lack of diversity. When hackers create a virus, unless they are attacking a specific system, they normally try to meet the following criteria:
# A OS/system that is most widely used so as to attack the most number of people at once
# A OS/system that has good documentation, thus permitting the virus to be created easily
# A OS/system that is not secure, and hence is extremely venerable, thus permitting a virus to propagate

===Computer security perspective===
With respect to computer security, diversity would imply aspects such as automatic scanning all the time which would then make it extremely difficult for attacks to propagate though a given system. Furthermore, the fact that a given script can easily attack many computer systems indicates that a computer system is in fact homogenous. Thus, diversifying the entire internal system of a computer by adding `junk' code/introns could provide an additional level of security against unknown attacks/threats. Currently, computer systems are protected against known attacks, and a very general methodology that is very low level and easily bypassed.

However, at the same time, there are disadvantages of making such a system. To begin with there is always the brute force method incase some part of a system is randomized. Hence, there needs to be some sort limit as to how many tries a given piece of software can utilize certain areas of the computer system. Additionally, creating an number of computer systems that are so diverse that they offer a lot of protection against attacks is not as straightforward as it seems. This is because biological systems have a huge genetic adaptation, but, the number of potential operating systems/applications is considerably small. In addition, currently all systems that are currently existent are vulnerable to more than one known attack. Thus, replacing a multitude of relatively homogeneous systems with equally vulnerable but diverse systems (diversity will result from modifying/randomizing a certain aspect of an `original' system) does not in any way increase security. Moreover, although the security aspect of a system would be satisfied, it would not be practically in terms of creating additional programs/applications.

Therefore,further research must be done in order to evaluate the various way of creating a diverse system. However, to start of with some parallels could be drawn from biodiversity. For example, parasitism/predator-prey relationships: - one can imagine the predators as the attackers/hackers. In order to simplify things, this could be seen as one whole group. However, a more complicated version of this model could be that the attackers/hackers are separated into different categories based on various characteristics such as skill. This is very similar to many predators after the same prey, some more harmful than others, but nevertheless they all exist. The prey could be viewed as the software itself. For simplicity this could start off being characterized by operating system. However, could potentially be more complicated and be based of different programs/applications, etc. In addition with this, various other concepts such as competition and extinction come into play.

==Malicious organisms and code==

The immune system is one of the best systems (and most obvious systems) that computer security should adopt. It has a multilevel security system that is put in place to protect the entire organism. In addition to protecting the organism, the immune system also cleans up after the battle/attack. The immune system is comprised of may little organisms. Antigens, proteins that are not native to the body, are recognized by the organism's antibodies (organism's `immune system's detectors'). The key here is that these antibodies have receptors that are extremely specific to certain antigens. If any other antigen even attempts to bind to these antibodies, an alarm goes off. This `alarm' then triggers a whole mechanism that ultimately causes the antigen that does not belong to be destroyed.

===Malicious organisms===
One of the most well studied immune cells are called T cells. The production of these cells involves a ''negative selection process''. Like any of the other antibodies, T cells also have receptors that are highly specific. Any antigen that is present within the organism and it does not fit one of these receptors, is a ''malicious organism''. Thus, it can be concluded that the receptors of these cells are designed in such a way that the it never identifies its own self as a antigen.

The ''negative selection process'' is is the process by which any cell that reacts with other cells that are part of the organism are automatically filtered out. An example of this process is the production of T cells. The cells are produced through a pseudo random genetical process. Once this is done, any cell that recognizes it's self (the organism that it is in) is eliminated through the ''negative selection process''. The rest of the antibodies that are created are distributed throughout the organism which is then looks for potential ''malicious organisms''. Another key aspect of the immune system is that it has the potential to react with both antigens it has never been in contact with and antigens that it has been in contact with before. Once it has come in contact with the antigen before, it has the ability of remembering that antigen for more than 70 years, i.e. potentially the rest of a human's life. Moreover, the response of the immune system to antigens it has seen/has contact with before is much quicker than its response to antigens it is in contact with for the first time.

===Malicious code===
''Malicious code'' is basically the same thing as malicious organisms, but with respect to computer systems. That is, malicious code is code that is `intruding' the system and is not supposed to be there. A common example of malicious code is malware (malicious software). Malware, is software designed specifically to damage or disrupt a system. This disruption could potentially take over the entire system and kill it. An example of such a software is a Trojan Horse. The current problem that people who are trying to defend these system are facing is that current methods of virus detection do not detect polymorphic malware. That is, malware that uses a defence mechanism such as encryption to avoid detection. The problem is that even if there was a anti-virus that could potentially detect itself the malware, the system does not have sufficient time to respond. In addition there are malware that makes it next to impossible to detect until the damage is done. An example of such a system is serendipitious seeding of malware. Thus the only key to accurately detect these viruses in time is to recognize the fact that these mechanisms under go evolution constantly.

===Computer security perspective===
It is a well known fact that security of any kind works in three stages: prevention, detection and response. Although prevention is most cost effective way of dealing with security, it could potentially be very harmful if one replies only this method. This is because if prevention fails at any given time, it could potentially be very costly to fix the system. Moreover, preventing intrusion on a highly complex machine can be a daunting task. However, there are ways such as a multiple level security system that could make it just a little bit easier. On the other hand, detection is a much easier goal to achieve than prevention altogether. It is key to have an excellent detection and response procedure in order to defend any system from attackers both within and outside a given system.

==Homeostasis/feedback==
===Cell Communication===
'''Hormone:''' messenger molecule/small chemical messages
* creates localized state change
* kind of an interface to the cell
* hormones mediate reactions
* used for regulating homeostasis
* work with the nervous system to communicate throughout the body
* hormones aren't surface bound, they go into the cell
* they are global signals, and can have systemic effects
* there are different hormone receptors and mechanisms
** they induce change on the inside of cells instead of triggering reactions from the outside
* seem to be an early evolutionary construct
** sort of a blunt stick form of communication
** govern emotions, fight or flight-type reactions, growth
** they have systemic and far-reaching effects
* hormones are sort of like datagrams
* only about 50 hormones exist
** they don't convey much information, or much interpretation
** however, concentrations don't need to be high for them to have effects
*one-to-many communication

'''Crosstalk:'''
* different hormones interfere with each other
* a given receptor can be activated by different molecules
* a molecule can activate different receptors
* the network begins as a fully connected graph, and then connections are pruned away
* crosstalk is why drugs have complicated and unpredictable side effects

We could consider the "drug discovery problem" to be equivalent to the "computer security problem".

* Engineering challenge
** every input is connected to every output
** through trial and error, select for the pathways that work
*moral of the story: there needs to be more coupling than we think in computer
** we need to allow for feedback loops, running parallel to the main operations

* Metabolic diseases are really receptor diseases
** the question is "what receptor does it target?"
** this is why viruses only affect certain tissues: the tissues where the receptors are located are affected
* some diseases (such as avian flu) can be caught by humans from animals, but not spread between humans

In this chapter the differences between cellular communication and the communication that takes place in computer programs was discussed. In cellular communication, the process seems to be top down: all links are established, then some are pared away. In computer programs, the process is bottom up: links are established on an as-needed basis. My first thought is that having more links could be a security problem - if you want information to stay where it's put, not having many links seems to make sense. However, having a system with more links could allow for more feedback and could potentially better support an evolutionary system.

BioSec 2012: Consolidated Notes

2012-05-08T00:29:37Z

Dsouza3190:

Below is a summary of what was discussed in the 2012 run of Biological Approaches to Computer Security, organized by topic.

(Cheryl: I think a topical organization is easiest and clearest, but if you have other ideas feel free to go with them. I just made up some topics off the top of my head, please use ones that make sense based on the notes you find. Look at all of the pages linked to from the top-level biosec page: the notes for the first weeks, the misc notes pages, and the individual student pages. Please condense or drop stuff that is too detailed (particularly notes on evolution).)

==Evolution==
''The origin of species'' by Charles Darwin is one of the most well known and respected pieces of literature to this day, even through today, it is half a century old. It has changed the way we as humans see and perceive the world as we know it. Darwin's theory on evolution challenged all the past and present views of how species came about. This not only includes theories in science, but also religion - where many believe in natural theology. That is species are created by a creator and a species' adaptation to their environment is nothing but `intelligent design'. Although still very much a controversial piece of literature as it was in Darwin's time; the theory of evolution has stood the test of time in the scientific realm and still remains to be the most accepted scientific explanation for the origin of species of all living organisms.

===Summary of ''The origin of species''===
The entire argument that Darwin formulated throughout this piece of literature is based on variation. It should be noted that variations in a particular species is present irrespective of whether or not that particular species is domesticated. Each species is distinguishable from the other due to the numerous different adaptations and traits it poses. The variations in a particular species are present in either one, or a combination of physical, chemical and biological traits. These traits are often inherited from one generation to the next (hereditary) and is rooted in the species adapting to change in their environment at some point in history. To support this hypothesis Darwin gives numerous examples of remarkable adaptions that permitted different species to survive and in some cases thrive in their environment. A couple of these examples include: the beak of the woodpecker that allows it to better collect it's prey - insects, and the wings of the bat that permits it to fly. Furthermore small variations seen within a particular species directly correlated to variations seen across different species. Thus, Darwin's entire theory of evolution attempts to explain with proof of observation that variation is the entire cause of ''the origin of species''.

Key to Darwin's argument is the notion of natural selection which explains how variation can eventually lead to the evolution of the particular species. In order to understand this concept, one needs to first understand the concept of struggle for existence. In chapter three through to chapter seven of \textit{the origin of species}, Darwin explains the struggle for existence as the reason why some species' characteristics survive and others go extinct. In addition, he notes that the huge amount of variation in species has permitted for species to adapt very well to their environments. That is, due to the unique characteristics that certain organisms have developed they can thrive in their specific environment. In addition, Darwin notes that only the characteristics that prove to be most advantageous (variations that permit a species to adapt to their environment better than other species) is passed from one generation onto the next (hereditary). This is when the concept of natural selection comes to play. Natural selection allows for the species that have best adapted to the environment to survive and/or prosper. However, at the same time the species that do not possess variations that are advantageous struggle for their existence, but do not succeed, thus becoming extinct.

In other words, natural selection is basically the mechanism that drives what we refer to as evolution. Living organisms continue to pass genes from one organism to another. These genes are not all the same, some carry variations, some do not. The variations in the genes can prove to be either advantageous or disadvantageous to future generations. This is due to the fact that only advantageous genes are naturally selected and thus survive. Implying that living organisms with the advantageous genes continue to reproduce passing their genes from one generation to the next. Eventually, this variation causes this group of living organisms to be branch off from their original species and become a species of their own. The continual branching of species into new species suggests that all species can be traced back to one single parent species. Moreover, this theory provides a simple but profound explanation as to why many species are very similar to each other. The reason behind which is that the species either evolved from one another or they have a closely related common parent.

Another concept that go hand in hand with natural selection is the limits of population increase. Nature can provide enough food and shelter for all the species that is inhabitants and at the same time be very destructive (natural disasters, animals prey on other species, etc.). This in turn causes species to struggle for their lives, and essentially prohibits some organisms to survive. The concept of limits of population increase (borrowed from Thomas Malthus) basically states that each generation increases the population of the species exponentially, which in turn implies that the population of the entire world is increasing constantly. However, this poses the problem of the world running out of room for the species to occupy. That is if the birth rate increases exponentially while the death rate remains the same from one generation to the next. This is not the case in reality, thus there must exist a limit that nature imposes on the total number of inhabitants. This in turn gives rise to competition, where each species must compete with each other in order to ensure that they survive thus threatening the survival of the other species.

The rest of this piece of literature is devoted to Darwin defending his theory against possible criticisms from other known scientists of that time, and still some today. For example, the existence of fossil records proves not to link the chains of evolution from one parent species. Darwin's argument in this case is that, many of the fossil fuels found today, are not perfect, their original conditions have been destroyed. In addition Darwin argues that geographical isolation proves to be a fundamental component to his theory. That is because his theory suggests that all living organisms develop from one or a handful of `original' parent species, there was a need for species to travel and immigrate to different areas of the world. However, this was easier said than done, especially when barriers such as water (oceans), height (hills and mountains), etc. highly restricts the possibility of living organisms to immigrate to another region of the world. Thus, the few that were able to escape their birth place and immigrate to another region shaped the rest of the species in that particular geographical area.

===Computer security perspective===
A lot can be said about applying computer security to Darwin's approach. To begin with, a lot of questions needs to be answered. For example, although Darwin's approach of evolution seems to be a fool proof way of doing things, it is really slow. In order for biology to get to the stage where it is at, it took billions of years. How are we supposed to replicate this billions of years worth of work in a matter of few days or months or even years? In addition, following Darwin's approach, we need to be able to accept failure most of the time. That is, biology has gotten to where it is currently at by accepting failure, which is present when species become extinct because they did not adapt a advantageous variation. Lastly, in Darwin's theory, a species survival was highly dependent on that of the environment. Although this might have worked within the realm of biology, we do not have the luxury of exploiting this in the realm of computer security. That is, computer security needs to work accurately irrespective of the environment it is in.\\

==Diversity==

''Diversity'' can be defined as a variation. This variation can take place in many different form. In the previous chapter diversity among different species was briefly mentioned. This chapter discuss biological diversity and software diversity that is currently present today. The chapter then concludes with a brief section about how this all relates to computer security.

===Biological diversity===
''Biodiversity'', also known as biological diversity is the variety of different living organisms and all its processes found on Earth. This broad category is further divided into three categories: genetic diversity, species diversity and ecosystem diversity. ''Genetic diversity'' is basically the total amount of different genes found in the entire population of one species. ''Species diversity'' is the diversity of species within a particular region (i.e. the total number of different species that inhabit a particular area). ''Ecosystem diversity'' the total number of different habitats that are encompasses within a region. Needless to say, there is an abundance of diversity that is present in biology. This is mainly because of evolution. As explained in the previous chapter, the theory of evolution basically states that all organisms descended from one or a hand-full of common ancestors. This thus implies that they all share common features. At the very same time due to natural selection species need to continue to evolve and change over time to adapt to their specific environment. Thus, as each species changes and evolves into another, they add to the biodiversity that is already existent. This is because when a species evolves substantially, it becomes it's own `new species' which adds to the species diversity and subsequently adds to genetic diversity and ecosystem diversity.

With biodiversity comes a lot of dependence. That is different species depend on each other for food, thus in turn affecting the entire population of the species. For example, parasitism and mutualism. ''Parasitism'' is the symbiotic relationship between two organisms, where one organism benefits at the expense of the other organism. ''Mutualism'' is also a symbiotic relationship between two organisms, however the difference is that both organisms benefit from this relationship. This interdependence in biological systems means that if something were to happen, it would strain an entire species, or a couple of species, depending on the actual gene that it affects. However, the chances of one `virus' killing all the living organisms in the world is very slim. Unless it attacks the three aspects that are common to all living organisms: ATP, DNA or plasma membrane. Even if this is the case, all living organisms have a general mechanism of dealing with unknown dangers. This is in addition to the other various mechanisms that are more specific and deal with known dangers. Thus, diversity increase the probability that at some level in the headachy or organisms, at least one member, if not not many will be able to withstand a major attack.

===Software diversity===
From the days where computers were just affordable and in almost every office and house, ''Microsoft'' has dominated the operating system market. Although today, the use of other operating systems such as Linux, Mac OS X, etc. have increased in popularity, Microsoft dominates the current market. But unlike the past, security measures such as network access, anti-virus, etc. has been improving at a remarkable rate. However, this is improvement is driven by the need to always be one step ahead of the community that attacks these systems (hackers). Nevertheless, the problem is still very much prevalent in today. This is because of the lack of diversity. When hackers create a virus, unless they are attacking a specific system, they normally try to meet the following criteria:
# A OS/system that is most widely used so as to attack the most number of people at once
# A OS/system that has good documentation, thus permitting the virus to be created easily
# A OS/system that is not secure, and hence is extremely venerable, thus permitting a virus to propagate

===Computer security perspective===
With respect to computer security, diversity would imply aspects such as automatic scanning all the time which would then make it extremely difficult for attacks to propagate though a given system. Furthermore, the fact that a given script can easily attack many computer systems indicates that a computer system is in fact homogenous. Thus, diversifying the entire internal system of a computer by adding `junk' code/introns could provide an additional level of security against unknown attacks/threats. Currently, computer systems are protected against known attacks, and a very general methodology that is very low level and easily bypassed.

However, at the same time, there are disadvantages of making such a system. To begin with there is always the brute force method incase some part of a system is randomized. Hence, there needs to be some sort limit as to how many tries a given piece of software can utilize certain areas of the computer system. Additionally, creating an number of computer systems that are so diverse that they offer a lot of protection against attacks is not as straightforward as it seems. This is because biological systems have a huge genetic adaptation, but, the number of potential operating systems/applications is considerably small. In addition, currently all systems that are currently existent are vulnerable to more than one known attack. Thus, replacing a multitude of relatively homogeneous systems with equally vulnerable but diverse systems (diversity will result from modifying/randomizing a certain aspect of an `original' system) does not in any way increase security. Moreover, although the security aspect of a system would be satisfied, it would not be practically in terms of creating additional programs/applications.

Therefore,further research must be done in order to evaluate the various way of creating a diverse system. However, to start of with some parallels could be drawn from biodiversity. For example, parasitism/predator-prey relationships: - one can imagine the predators as the attackers/hackers. In order to simplify things, this could be seen as one whole group. However, a more complicated version of this model could be that the attackers/hackers are separated into different categories based on various characteristics such as skill. This is very similar to many predators after the same prey, some more harmful than others, but nevertheless they all exist. The prey could be viewed as the software itself. For simplicity this could start off being characterized by operating system. However, could potentially be more complicated and be based of different programs/applications, etc. In addition with this, various other concepts such as competition and extinction come into play.

==Malicious code/organisms==

==Homeostasis/feedback==
===Cell Communication===
'''Hormone:''' messenger molecule/small chemical messages
* creates localized state change
* kind of an interface to the cell
* hormones mediate reactions
* used for regulating homeostasis
* work with the nervous system to communicate throughout the body
* hormones aren't surface bound, they go into the cell
* they are global signals, and can have systemic effects
* there are different hormone receptors and mechanisms
** they induce change on the inside of cells instead of triggering reactions from the outside
* seem to be an early evolutionary construct
** sort of a blunt stick form of communication
** govern emotions, fight or flight-type reactions, growth
** they have systemic and far-reaching effects
* hormones are sort of like datagrams
* only about 50 hormones exist
** they don't convey much information, or much interpretation
** however, concentrations don't need to be high for them to have effects
*one-to-many communication

'''Crosstalk:'''
* different hormones interfere with each other
* a given receptor can be activated by different molecules
* a molecule can activate different receptors
* the network begins as a fully connected graph, and then connections are pruned away
* crosstalk is why drugs have complicated and unpredictable side effects

We could consider the "drug discovery problem" to be equivalent to the "computer security problem".

* Engineering challenge
** every input is connected to every output
** through trial and error, select for the pathways that work
*moral of the story: there needs to be more coupling than we think in computer
** we need to allow for feedback loops, running parallel to the main operations

* Metabolic diseases are really receptor diseases
** the question is "what receptor does it target?"
** this is why viruses only affect certain tissues: the tissues where the receptors are located are affected
* some diseases (such as avian flu) can be caught by humans from animals, but not spread between humans

In this chapter the differences between cellular communication and the communication that takes place in computer programs was discussed. In cellular communication, the process seems to be top down: all links are established, then some are pared away. In computer programs, the process is bottom up: links are established on an as-needed basis. My first thought is that having more links could be a security problem - if you want information to stay where it's put, not having many links seems to make sense. However, having a system with more links could allow for more feedback and could potentially better support an evolutionary system.

BioSec 2012: Consolidated Notes

2012-05-08T00:28:12Z

Dsouza3190: /* Biological diversity */

Below is a summary of what was discussed in the 2012 run of Biological Approaches to Computer Security, organized by topic.

(Cheryl: I think a topical organization is easiest and clearest, but if you have other ideas feel free to go with them. I just made up some topics off the top of my head, please use ones that make sense based on the notes you find. Look at all of the pages linked to from the top-level biosec page: the notes for the first weeks, the misc notes pages, and the individual student pages. Please condense or drop stuff that is too detailed (particularly notes on evolution).)

==Evolution==
''The origin of species'' by Charles Darwin is one of the most well known and respected pieces of literature to this day, even through today, it is half a century old. It has changed the way we as humans see and perceive the world as we know it. Darwin's theory on evolution challenged all the past and present views of how species came about. This not only includes theories in science, but also religion - where many believe in natural theology. That is species are created by a creator and a species' adaptation to their environment is nothing but `intelligent design'. Although still very much a controversial piece of literature as it was in Darwin's time; the theory of evolution has stood the test of time in the scientific realm and still remains to be the most accepted scientific explanation for the origin of species of all living organisms.

===Summary of ''The origin of species''===
The entire argument that Darwin formulated throughout this piece of literature is based on variation. It should be noted that variations in a particular species is present irrespective of whether or not that particular species is domesticated. Each species is distinguishable from the other due to the numerous different adaptations and traits it poses. The variations in a particular species are present in either one, or a combination of physical, chemical and biological traits. These traits are often inherited from one generation to the next (hereditary) and is rooted in the species adapting to change in their environment at some point in history. To support this hypothesis Darwin gives numerous examples of remarkable adaptions that permitted different species to survive and in some cases thrive in their environment. A couple of these examples include: the beak of the woodpecker that allows it to better collect it's prey - insects, and the wings of the bat that permits it to fly. Furthermore small variations seen within a particular species directly correlated to variations seen across different species. Thus, Darwin's entire theory of evolution attempts to explain with proof of observation that variation is the entire cause of ''the origin of species''.

Key to Darwin's argument is the notion of natural selection which explains how variation can eventually lead to the evolution of the particular species. In order to understand this concept, one needs to first understand the concept of struggle for existence. In chapter three through to chapter seven of \textit{the origin of species}, Darwin explains the struggle for existence as the reason why some species' characteristics survive and others go extinct. In addition, he notes that the huge amount of variation in species has permitted for species to adapt very well to their environments. That is, due to the unique characteristics that certain organisms have developed they can thrive in their specific environment. In addition, Darwin notes that only the characteristics that prove to be most advantageous (variations that permit a species to adapt to their environment better than other species) is passed from one generation onto the next (hereditary). This is when the concept of natural selection comes to play. Natural selection allows for the species that have best adapted to the environment to survive and/or prosper. However, at the same time the species that do not possess variations that are advantageous struggle for their existence, but do not succeed, thus becoming extinct.

In other words, natural selection is basically the mechanism that drives what we refer to as evolution. Living organisms continue to pass genes from one organism to another. These genes are not all the same, some carry variations, some do not. The variations in the genes can prove to be either advantageous or disadvantageous to future generations. This is due to the fact that only advantageous genes are naturally selected and thus survive. Implying that living organisms with the advantageous genes continue to reproduce passing their genes from one generation to the next. Eventually, this variation causes this group of living organisms to be branch off from their original species and become a species of their own. The continual branching of species into new species suggests that all species can be traced back to one single parent species. Moreover, this theory provides a simple but profound explanation as to why many species are very similar to each other. The reason behind which is that the species either evolved from one another or they have a closely related common parent.

Another concept that go hand in hand with natural selection is the limits of population increase. Nature can provide enough food and shelter for all the species that is inhabitants and at the same time be very destructive (natural disasters, animals prey on other species, etc.). This in turn causes species to struggle for their lives, and essentially prohibits some organisms to survive. The concept of limits of population increase (borrowed from Thomas Malthus) basically states that each generation increases the population of the species exponentially, which in turn implies that the population of the entire world is increasing constantly. However, this poses the problem of the world running out of room for the species to occupy. That is if the birth rate increases exponentially while the death rate remains the same from one generation to the next. This is not the case in reality, thus there must exist a limit that nature imposes on the total number of inhabitants. This in turn gives rise to competition, where each species must compete with each other in order to ensure that they survive thus threatening the survival of the other species.

The rest of this piece of literature is devoted to Darwin defending his theory against possible criticisms from other known scientists of that time, and still some today. For example, the existence of fossil records proves not to link the chains of evolution from one parent species. Darwin's argument in this case is that, many of the fossil fuels found today, are not perfect, their original conditions have been destroyed. In addition Darwin argues that geographical isolation proves to be a fundamental component to his theory. That is because his theory suggests that all living organisms develop from one or a handful of `original' parent species, there was a need for species to travel and immigrate to different areas of the world. However, this was easier said than done, especially when barriers such as water (oceans), height (hills and mountains), etc. highly restricts the possibility of living organisms to immigrate to another region of the world. Thus, the few that were able to escape their birth place and immigrate to another region shaped the rest of the species in that particular geographical area.

===Computer security perspective===
A lot can be said about applying computer security to Darwin's approach. To begin with, a lot of questions needs to be answered. For example, although Darwin's approach of evolution seems to be a fool proof way of doing things, it is really slow. In order for biology to get to the stage where it is at, it took billions of years. How are we supposed to replicate this billions of years worth of work in a matter of few days or months or even years? In addition, following Darwin's approach, we need to be able to accept failure most of the time. That is, biology has gotten to where it is currently at by accepting failure, which is present when species become extinct because they did not adapt a advantageous variation. Lastly, in Darwin's theory, a species survival was highly dependent on that of the environment. Although this might have worked within the realm of biology, we do not have the luxury of exploiting this in the realm of computer security. That is, computer security needs to work accurately irrespective of the environment it is in.\\

==Diversity==

''Diversity'' can be defined as a variation. This variation can take place in many different form. In the previous chapter diversity among different species was briefly mentioned. This chapter discuss biological diversity and software diversity that is currently present today. The chapter then concludes with a brief section about how this all relates to computer security.

===Biological diversity===
''Biodiversity'', also known as biological diversity is the variety of different living organisms and all its processes found on Earth. This broad category is further divided into three categories: genetic diversity, species diversity and ecosystem diversity. ''Genetic diversity'' is basically the total amount of different genes found in the entire population of one species. ''Species diversity'' is the diversity of species within a particular region (i.e. the total number of different species that inhabit a particular area). ''Ecosystem diversity'' the total number of different habitats that are encompasses within a region. Needless to say, there is an abundance of diversity that is present in biology. This is mainly because of evolution. As explained in the previous chapter, the theory of evolution basically states that all organisms descended from one or a hand-full of common ancestors. This thus implies that they all share common features. At the very same time due to natural selection species need to continue to evolve and change over time to adapt to their specific environment. Thus, as each species changes and evolves into another, they add to the biodiversity that is already existent. This is because when a species evolves substantially, it becomes it's own `new species' which adds to the species diversity and subsequently adds to genetic diversity and ecosystem diversity.

With biodiversity comes a lot of dependence. That is different species depend on each other for food, thus in turn affecting the entire population of the species. For example, parasitism and mutualism. ''Parasitism'' is the symbiotic relationship between two organisms, where one organism benefits at the expense of the other organism. ''Mutualism'' is also a symbiotic relationship between two organisms, however the difference is that both organisms benefit from this relationship. This interdependence in biological systems means that if something were to happen, it would strain an entire species, or a couple of species, depending on the actual gene that it affects. However, the chances of one `virus' killing all the living organisms in the world is very slim. Unless it attacks the three aspects that are common to all living organisms: ATP, DNA or plasma membrane. Even if this is the case, all living organisms have a general mechanism of dealing with unknown dangers. This is in addition to the other various mechanisms that are more specific and deal with known dangers. Thus, diversity increase the probability that at some level in the headachy or organisms, at least one member, if not not many will be able to withstand a major attack.

===Software diversity===
From the days where computers were just affordable and in almost every office and house, ''Microsoft'' has dominated the operating system market. Although today, the use of other operating systems such as Linux, Mac OS X, etc. have increased in popularity, Microsoft dominates the current market. But unlike the past, security measures such as network access, anti-virus, etc. has been improving at a remarkable rate. However, this is improvement is driven by the need to always be one step ahead of the community that attacks these systems (hackers). Nevertheless, the problem is still very much prevalent in today. This is because of the lack of diversity. When hackers create a virus, unless they are attacking a specific system, they normally try to meet the following criteria:
# A OS/system that is most widely used so as to attack the most number of people at once
# A OS/system that has good documentation, thus permitting the virus to be created easily
# A OS/system that is not secure, and hence is extremely venerable, thus permitting a virus to propagate

===Computer security perspective===
With respect to computer security, diversity would imply aspects such as automatic scanning all the time which would then make it extremely difficult for attacks to propagate though a given system. Furthermore, the fact that a given script can easily attack many computer systems indicates that a computer system is in fact homogenous. Thus, diversifying the entire internal system of a computer by adding `junk' code/introns could provide an additional level of security against unknown attacks/threats. Currently, computer systems are protected against known attacks, and a very general methodology that is very low level and easily bypassed.

However, at the same time, there are disadvantages of making such a system. To begin with there is always the brute force method incase some part of a system is randomized. Hence, there needs to be some sort limit as to how many tries a given piece of software can utilize certain areas of the computer system. Additionally, creating an number of computer systems that are so diverse that they offer a lot of protection against attacks is not as straightforward as it seems. This is because biological systems have a huge genetic adaptation, but, the number of potential operating systems/applications is considerably small. In addition, currently all systems that are currently existent are vulnerable to more than one known attack. Thus, replacing a multitude of relatively homogeneous systems with equally vulnerable but diverse systems (diversity will result from modifying/randomizing a certain aspect of an `original' system) does not in any way increase security. Moreover, although the security aspect of a system would be satisfied, it would not be practically in terms of creating additional programs/applications.

Therefore,further research must be done in order to evaluate the various way of creating a diverse system. However, to start of with some parallels could be drawn from biodiversity. For example, parasitism/predator-prey relationships: - one can imagine the predators as the attackers/hackers. In order to simplify things, this could be seen as one whole group. However, a more complicated version of this model could be that the attackers/hackers are separated into different categories based on various characteristics such as skill. This is very similar to many predators after the same prey, some more harmful than others, but nevertheless they all exist. The prey could be viewed as the software itself. For simplicity this could start off being characterized by operating system. However, could potentially be more complicated and be based of different programs/applications, etc. In addition with this, various other concepts such as competition and extinction come into play.

==Software Diversity==

==Malicious code/organisms==

==Homeostasis/feedback==
===Cell Communication===
'''Hormone:''' messenger molecule/small chemical messages
* creates localized state change
* kind of an interface to the cell
* hormones mediate reactions
* used for regulating homeostasis
* work with the nervous system to communicate throughout the body
* hormones aren't surface bound, they go into the cell
* they are global signals, and can have systemic effects
* there are different hormone receptors and mechanisms
** they induce change on the inside of cells instead of triggering reactions from the outside
* seem to be an early evolutionary construct
** sort of a blunt stick form of communication
** govern emotions, fight or flight-type reactions, growth
** they have systemic and far-reaching effects
* hormones are sort of like datagrams
* only about 50 hormones exist
** they don't convey much information, or much interpretation
** however, concentrations don't need to be high for them to have effects
*one-to-many communication

'''Crosstalk:'''
* different hormones interfere with each other
* a given receptor can be activated by different molecules
* a molecule can activate different receptors
* the network begins as a fully connected graph, and then connections are pruned away
* crosstalk is why drugs have complicated and unpredictable side effects

We could consider the "drug discovery problem" to be equivalent to the "computer security problem".

* Engineering challenge
** every input is connected to every output
** through trial and error, select for the pathways that work
*moral of the story: there needs to be more coupling than we think in computer
** we need to allow for feedback loops, running parallel to the main operations

* Metabolic diseases are really receptor diseases
** the question is "what receptor does it target?"
** this is why viruses only affect certain tissues: the tissues where the receptors are located are affected
* some diseases (such as avian flu) can be caught by humans from animals, but not spread between humans

In this chapter the differences between cellular communication and the communication that takes place in computer programs was discussed. In cellular communication, the process seems to be top down: all links are established, then some are pared away. In computer programs, the process is bottom up: links are established on an as-needed basis. My first thought is that having more links could be a security problem - if you want information to stay where it's put, not having many links seems to make sense. However, having a system with more links could allow for more feedback and could potentially better support an evolutionary system.

BioSec 2012: Consolidated Notes

2012-05-08T00:27:32Z

Dsouza3190: /* Biological Diversity */

Below is a summary of what was discussed in the 2012 run of Biological Approaches to Computer Security, organized by topic.

(Cheryl: I think a topical organization is easiest and clearest, but if you have other ideas feel free to go with them. I just made up some topics off the top of my head, please use ones that make sense based on the notes you find. Look at all of the pages linked to from the top-level biosec page: the notes for the first weeks, the misc notes pages, and the individual student pages. Please condense or drop stuff that is too detailed (particularly notes on evolution).)

==Evolution==
''The origin of species'' by Charles Darwin is one of the most well known and respected pieces of literature to this day, even through today, it is half a century old. It has changed the way we as humans see and perceive the world as we know it. Darwin's theory on evolution challenged all the past and present views of how species came about. This not only includes theories in science, but also religion - where many believe in natural theology. That is species are created by a creator and a species' adaptation to their environment is nothing but `intelligent design'. Although still very much a controversial piece of literature as it was in Darwin's time; the theory of evolution has stood the test of time in the scientific realm and still remains to be the most accepted scientific explanation for the origin of species of all living organisms.

===Summary of ''The origin of species''===
The entire argument that Darwin formulated throughout this piece of literature is based on variation. It should be noted that variations in a particular species is present irrespective of whether or not that particular species is domesticated. Each species is distinguishable from the other due to the numerous different adaptations and traits it poses. The variations in a particular species are present in either one, or a combination of physical, chemical and biological traits. These traits are often inherited from one generation to the next (hereditary) and is rooted in the species adapting to change in their environment at some point in history. To support this hypothesis Darwin gives numerous examples of remarkable adaptions that permitted different species to survive and in some cases thrive in their environment. A couple of these examples include: the beak of the woodpecker that allows it to better collect it's prey - insects, and the wings of the bat that permits it to fly. Furthermore small variations seen within a particular species directly correlated to variations seen across different species. Thus, Darwin's entire theory of evolution attempts to explain with proof of observation that variation is the entire cause of ''the origin of species''.

Key to Darwin's argument is the notion of natural selection which explains how variation can eventually lead to the evolution of the particular species. In order to understand this concept, one needs to first understand the concept of struggle for existence. In chapter three through to chapter seven of \textit{the origin of species}, Darwin explains the struggle for existence as the reason why some species' characteristics survive and others go extinct. In addition, he notes that the huge amount of variation in species has permitted for species to adapt very well to their environments. That is, due to the unique characteristics that certain organisms have developed they can thrive in their specific environment. In addition, Darwin notes that only the characteristics that prove to be most advantageous (variations that permit a species to adapt to their environment better than other species) is passed from one generation onto the next (hereditary). This is when the concept of natural selection comes to play. Natural selection allows for the species that have best adapted to the environment to survive and/or prosper. However, at the same time the species that do not possess variations that are advantageous struggle for their existence, but do not succeed, thus becoming extinct.

In other words, natural selection is basically the mechanism that drives what we refer to as evolution. Living organisms continue to pass genes from one organism to another. These genes are not all the same, some carry variations, some do not. The variations in the genes can prove to be either advantageous or disadvantageous to future generations. This is due to the fact that only advantageous genes are naturally selected and thus survive. Implying that living organisms with the advantageous genes continue to reproduce passing their genes from one generation to the next. Eventually, this variation causes this group of living organisms to be branch off from their original species and become a species of their own. The continual branching of species into new species suggests that all species can be traced back to one single parent species. Moreover, this theory provides a simple but profound explanation as to why many species are very similar to each other. The reason behind which is that the species either evolved from one another or they have a closely related common parent.

Another concept that go hand in hand with natural selection is the limits of population increase. Nature can provide enough food and shelter for all the species that is inhabitants and at the same time be very destructive (natural disasters, animals prey on other species, etc.). This in turn causes species to struggle for their lives, and essentially prohibits some organisms to survive. The concept of limits of population increase (borrowed from Thomas Malthus) basically states that each generation increases the population of the species exponentially, which in turn implies that the population of the entire world is increasing constantly. However, this poses the problem of the world running out of room for the species to occupy. That is if the birth rate increases exponentially while the death rate remains the same from one generation to the next. This is not the case in reality, thus there must exist a limit that nature imposes on the total number of inhabitants. This in turn gives rise to competition, where each species must compete with each other in order to ensure that they survive thus threatening the survival of the other species.

The rest of this piece of literature is devoted to Darwin defending his theory against possible criticisms from other known scientists of that time, and still some today. For example, the existence of fossil records proves not to link the chains of evolution from one parent species. Darwin's argument in this case is that, many of the fossil fuels found today, are not perfect, their original conditions have been destroyed. In addition Darwin argues that geographical isolation proves to be a fundamental component to his theory. That is because his theory suggests that all living organisms develop from one or a handful of `original' parent species, there was a need for species to travel and immigrate to different areas of the world. However, this was easier said than done, especially when barriers such as water (oceans), height (hills and mountains), etc. highly restricts the possibility of living organisms to immigrate to another region of the world. Thus, the few that were able to escape their birth place and immigrate to another region shaped the rest of the species in that particular geographical area.

===Computer security perspective===
A lot can be said about applying computer security to Darwin's approach. To begin with, a lot of questions needs to be answered. For example, although Darwin's approach of evolution seems to be a fool proof way of doing things, it is really slow. In order for biology to get to the stage where it is at, it took billions of years. How are we supposed to replicate this billions of years worth of work in a matter of few days or months or even years? In addition, following Darwin's approach, we need to be able to accept failure most of the time. That is, biology has gotten to where it is currently at by accepting failure, which is present when species become extinct because they did not adapt a advantageous variation. Lastly, in Darwin's theory, a species survival was highly dependent on that of the environment. Although this might have worked within the realm of biology, we do not have the luxury of exploiting this in the realm of computer security. That is, computer security needs to work accurately irrespective of the environment it is in.\\

==Diversity==

''Diversity'' can be defined as a variation. This variation can take place in many different form. In the previous chapter diversity among different species was briefly mentioned. This chapter discuss biological diversity and software diversity that is currently present today. The chapter then concludes with a brief section about how this all relates to computer security.

===Biological diversity===
''Biodiversity'', also known as biological diversity is the variety of different living organisms and all its processes found on Earth. This broad category is further divided into three categories: genetic diversity, species diversity and ecosystem diversity. ''Genetic diversity'' is basically the total amount of different genes found in the entire population of one species. ''Species diversity'' is the diversity of species within a particular region (i.e. the total number of different species that inhabit a particular area). \textit{Ecosystem diversity} the total number of different habitats that are encompasses within a region. Needless to say, there is an abundance of diversity that is present in biology. This is mainly because of evolution. As explained in the previous chapter, the theory of evolution basically states that all organisms descended from one or a hand-full of common ancestors. This thus implies that they all share common features. At the very same time due to natural selection species need to continue to evolve and change over time to adapt to their specific environment. Thus, as each species changes and evolves into another, they add to the biodiversity that is already existent. This is because when a species evolves substantially, it becomes it's own `new species' which adds to the species diversity and subsequently adds to genetic diversity and ecosystem diversity.

With biodiversity comes a lot of dependence. That is different species depend on each other for food, thus in turn affecting the entire population of the species. For example, parasitism and mutualism. \textit{Parasitism} is the symbiotic relationship between two organisms, where one organism benefits at the expense of the other organism. ''Mutualism'' is also a symbiotic relationship between two organisms, however the difference is that both organisms benefit from this relationship. This interdependence in biological systems means that if something were to happen, it would strain an entire species, or a couple of species, depending on the actual gene that it affects. However, the chances of one `virus' killing all the living organisms in the world is very slim. Unless it attacks the three aspects that are common to all living organisms: ATP, DNA or plasma membrane. Even if this is the case, all living organisms have a general mechanism of dealing with unknown dangers. This is in addition to the other various mechanisms that are more specific and deal with known dangers. Thus, diversity increase the probability that at some level in the headachy or organisms, at least one member, if not not many will be able to withstand a major attack.

===Software diversity===
From the days where computers were just affordable and in almost every office and house, ''Microsoft'' has dominated the operating system market. Although today, the use of other operating systems such as Linux, Mac OS X, etc. have increased in popularity, Microsoft dominates the current market. But unlike the past, security measures such as network access, anti-virus, etc. has been improving at a remarkable rate. However, this is improvement is driven by the need to always be one step ahead of the community that attacks these systems (hackers). Nevertheless, the problem is still very much prevalent in today. This is because of the lack of diversity. When hackers create a virus, unless they are attacking a specific system, they normally try to meet the following criteria:
# A OS/system that is most widely used so as to attack the most number of people at once
# A OS/system that has good documentation, thus permitting the virus to be created easily
# A OS/system that is not secure, and hence is extremely venerable, thus permitting a virus to propagate

===Computer security perspective===
With respect to computer security, diversity would imply aspects such as automatic scanning all the time which would then make it extremely difficult for attacks to propagate though a given system. Furthermore, the fact that a given script can easily attack many computer systems indicates that a computer system is in fact homogenous. Thus, diversifying the entire internal system of a computer by adding `junk' code/introns could provide an additional level of security against unknown attacks/threats. Currently, computer systems are protected against known attacks, and a very general methodology that is very low level and easily bypassed.

However, at the same time, there are disadvantages of making such a system. To begin with there is always the brute force method incase some part of a system is randomized. Hence, there needs to be some sort limit as to how many tries a given piece of software can utilize certain areas of the computer system. Additionally, creating an number of computer systems that are so diverse that they offer a lot of protection against attacks is not as straightforward as it seems. This is because biological systems have a huge genetic adaptation, but, the number of potential operating systems/applications is considerably small. In addition, currently all systems that are currently existent are vulnerable to more than one known attack. Thus, replacing a multitude of relatively homogeneous systems with equally vulnerable but diverse systems (diversity will result from modifying/randomizing a certain aspect of an `original' system) does not in any way increase security. Moreover, although the security aspect of a system would be satisfied, it would not be practically in terms of creating additional programs/applications.

Therefore,further research must be done in order to evaluate the various way of creating a diverse system. However, to start of with some parallels could be drawn from biodiversity. For example, parasitism/predator-prey relationships: - one can imagine the predators as the attackers/hackers. In order to simplify things, this could be seen as one whole group. However, a more complicated version of this model could be that the attackers/hackers are separated into different categories based on various characteristics such as skill. This is very similar to many predators after the same prey, some more harmful than others, but nevertheless they all exist. The prey could be viewed as the software itself. For simplicity this could start off being characterized by operating system. However, could potentially be more complicated and be based of different programs/applications, etc. In addition with this, various other concepts such as competition and extinction come into play.

==Software Diversity==

==Malicious code/organisms==

==Homeostasis/feedback==
===Cell Communication===
'''Hormone:''' messenger molecule/small chemical messages
* creates localized state change
* kind of an interface to the cell
* hormones mediate reactions
* used for regulating homeostasis
* work with the nervous system to communicate throughout the body
* hormones aren't surface bound, they go into the cell
* they are global signals, and can have systemic effects
* there are different hormone receptors and mechanisms
** they induce change on the inside of cells instead of triggering reactions from the outside
* seem to be an early evolutionary construct
** sort of a blunt stick form of communication
** govern emotions, fight or flight-type reactions, growth
** they have systemic and far-reaching effects
* hormones are sort of like datagrams
* only about 50 hormones exist
** they don't convey much information, or much interpretation
** however, concentrations don't need to be high for them to have effects
*one-to-many communication

'''Crosstalk:'''
* different hormones interfere with each other
* a given receptor can be activated by different molecules
* a molecule can activate different receptors
* the network begins as a fully connected graph, and then connections are pruned away
* crosstalk is why drugs have complicated and unpredictable side effects

We could consider the "drug discovery problem" to be equivalent to the "computer security problem".

* Engineering challenge
** every input is connected to every output
** through trial and error, select for the pathways that work
*moral of the story: there needs to be more coupling than we think in computer
** we need to allow for feedback loops, running parallel to the main operations

* Metabolic diseases are really receptor diseases
** the question is "what receptor does it target?"
** this is why viruses only affect certain tissues: the tissues where the receptors are located are affected
* some diseases (such as avian flu) can be caught by humans from animals, but not spread between humans

In this chapter the differences between cellular communication and the communication that takes place in computer programs was discussed. In cellular communication, the process seems to be top down: all links are established, then some are pared away. In computer programs, the process is bottom up: links are established on an as-needed basis. My first thought is that having more links could be a security problem - if you want information to stay where it's put, not having many links seems to make sense. However, having a system with more links could allow for more feedback and could potentially better support an evolutionary system.

BioSec 2012: Consolidated Notes

2012-05-08T00:22:52Z

Dsouza3190: /* Evolution */

BioSec 2012: Consolidated Notes

2012-04-28T17:30:54Z

Dsouza3190: /* Cell Communication */

BioSec 2012: Consolidated Notes

2012-04-28T16:37:07Z

Dsouza3190: /* Cell Communication */

BioSec 2012: Consolidated Notes

2012-04-28T16:36:28Z

Dsouza3190: /* Homeostasis/feedback */

BioSec 2012: Cheryl

2012-04-23T21:38:15Z

Dsouza3190: /* Trying to tie Computer Security into all of this */

=Trying to tie Computer Security into all of this=
Using Darwin’s approach
*'''Really slow:''' it took biology billions of years to get to the efficiency it now is at. How are we supposed to compete with that?
*If we follow the same process we are setting up for '''failure most of the time'''…species getting extinct because they failed most of the time
*Species '''survival is highly dependent on environment'''…computer security needs to basically work all the time independent of its environment …how is this going to work?

Programs = genotype (code/result)
.exe = phenotype (produce)
Exons= stuff that’s transcribed (5% or so) = spaghetti code
Introns= junk stuff (95% or so) = comments

----

So for things to work:
*there needs be a lot of '''redundant''' stuff:
**Genes – redundant ways to get an amino acid
**Genome – copies of the same genes
**Pathways – many regulators
*'''diversity'''
**Biology is so good because there aren’t two things that are really the same…they have a lot in common…but there is that one small aspect that sets them apart…if they were all the same then one small thing just wipes all of them out
**Can this be done with computers…randomize things by adding ''introns'' (junk code)?
* Relationship to cell cycle
** To enhance computer security, the cell (program) must learn to commit suicide (apoptosis). That is they need to learn how to recognize that they have been infected by a virus or something abnormal and then remove themselves from the entire network.

----

=Textbook Notes=
==Chapter 1: Light and Life==
* Light
# source of information and energy
# Defined as EM radiation
# Wave of photons
# Can be absorbed by pigments and then used
# Colour = light that is not absorbed by pigment
* Electrons become excited when absorbed by light which in turn then becomes potential energy (photosynthesis)
* Photoreceptor
# light-sensing system
# made up of pigment molecule bound to protein
# eye = organ of animals to sense light
* Problem:
# most light driven processes can only process a certain part of the EM spectrum
# source of energy…too much can cause deadly effects
# pigment melanin in our skin absorbs UV (high energy and can be damaging)
* Circadian rhythms (body clock) the daily cycle of most living organisms have evolved to adapt to the change in light (night and day…plant use photosynthesis during the day and night break glucose)
* Some animals prefer the dark (nocturnal animals like moths)
* Some animals have ancestors that had functional eyes but are not blind (blind mole rat)
* bioluminescent: organisms that use chemical energy to make their own light to attract a mate, camouflage, attract prey or communicate
==Chapter 2: Origins of Life==
* life defined by seven characteristics:
# '''Display order:''' high ordered structures
# '''Harness and utilize energy:''' getting and using chemical energy to power the organism’s activities
# '''Reproduce:''' ability to reproduce their own kind
# '''Respond to stimuli:''' ability to respond environmental stimuli
# '''Exhibit homeostasis:''' ability to control an organism’s internal environment within the limits to sustain life
# '''Growth and development:''' consistent growth and development (DNA inheritance)
# '''Evolve:''' adapt to environments over many generations to have better reproducibility and survival of the species.
* Cell theory
# All living organisms are composed of cells
# Cells are the functional units of life
# New cells come only from preexisting cells (division)
* Eukaryotic Cells

{| style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; border-color: #000; padding: 0"
|-
! style="border-style: solid; border-width: 0 1px 1px 0"| Function
! style="border-style: solid; border-width: 0 0 1px 0"| Organelles/Structures involved
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Genetic control of the cell
| style="border-style: solid; border-width: 0"| Nucleus and ribosomes
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Manufacture, distribution, and breakdown of molecules.
| style="border-style: solid; border-width: 0"| Endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles, and peroxisomes
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Energy processing
| style="border-style: solid; border-width: 0"| Mitochondria (plus chloroplasts in plant cells)
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Structural support, movement, and communication between cells
| style="border-style: solid; border-width: 0"| Structural support, movement, and communication between cells
|}
* Mitochondria and chloroplasts evolved by endosymbiosis which suggests mitochondria and chloroplasts were small prokaryotes and they began living within larger cells
* '''Cytoskeleton:'''
** network of protein fibers in the cells
** functions in structural support and mobility
** interacts with motor proteins resulting in mobility and cellular respiration
** composed of three kinds of fibers:
# '''Microfilaments:''' (actin filaments) support the cell’s shape and are involved in mobility
# '''Intermediated filaments:''' (not present in plant cells) reinforces the cell shape and provides and anchor for the organelles
# '''Microtubules:''' (made from tubulin) responsible for cell rigidity and guiding the organelle’s movement
==Chapter 3: Selection, Biodiversity and Biosphere==
* Biological organization:
[[File:Chapter3.png]]
* Categorizing organisms on how they obtain carbon
# '''Autotrophs:''' create their energy-containing organic carbon molecules (glucose) from inorganic carbon molecules (sunlight). Example: plants using photosynthesis
# '''Heterotrophs:''' get energy-containing organic carbon molecules (glucose) by consuming other organisms. Example: animals eating plants or other animals.
* Categorizing organisms on how they obtain energy
# '''Phototrophs:''' obtain energy from light
# '''Chemotrophs:''' obtains energy by oxidizing inorganic or organic substances
* '''Theory of evolution:''' all organisms descended from one common ancestor, thus share common features. At the same time due to natural selection species change over time to adapt to their specific environment
* All living organisms have three essential components:
# ATP for energy
# DNA for genetics
# Plasma membrane
* Parasitism = symbiotic relationship where one organism benefits at the expense of the other
* Mutualism = symbiotic relationship where both organism benefit
* ''Interesting: The genetic barcode that is embedded in almost every cell is the mitochondrial cytochrome c oxidase 1''
===Computer security aspect===
* diversity
** Biology is so good because there aren’t two things that are really the same…they have a lot in common…but there is that one small aspect that sets them apart…if they were all the same then one small thing just wipes all of them out
** Can this be done with computers…randomize things by adding introns (junk code)?
==Chapter 4: Energy and Enzymes==
* Cells can be basically thought of as a chemical factory (millions of chemical reaction take place in a cell)
** Chemical reactions used for cell maintenance, manufacture of cell parts and cell replication
* Energy is the capacity to do work
* Two kinds of energy
# Kinetic Energy: energy of motion
# Potential Energy: energy that is stored as a result of its location or structure
* Thermodynamics
** the study of energy transformations that occur between a system (matter under study) and its surroundings (rest of the universe)
** Two law of thermodynamics:
:# Energy in the universe is constant
:# Energy conversion increase entropy (measure of disorder/randomness)
* Spontaneous reactions take place without having to input any energy from its surroundings and releases free energy that is influenced by two factors:
** The changes in energy content
** Entropy of the system
* Chemical reactions either release or store energy
** Exergonic reactions: release energy (ex: Cellular respiration - uses some of the released energy to produce ATP)
** Endergonic reactions: stores energy or requires an input of energy; products have high potential energy (ex: photosynthesis – reactants = carbon dioxide and water (low energy), once absorbed energy from the sunlight produces products that are high in energy such as sugar)
* Cells also couple energies, which uses the energy released from exergonic reactions to drive key endergonic reaction. This process usually uses the energy stored in ATP molecules.
* ATP (Adenosine TriPhosphate) drives cellular work by energy coupling
** Powers all cellular work
** Is made up of: nitrogen base (adenine), sugar (ribose) and three phosphate groups
** Phosphorylation is the hydrolysis of ATP which releases energy by transferring the third phosphate from ATP to some other molecule
** ATP is a cycle – energy is released in an exergonic reaction (break down glucose) and is used in endergonic reaction (generation of ATP)
* Biological molecules have a lot of potential energy, but it is not spontaneously released. Thus an energy barrier must be overcome before a chemical reaction can begin (Activation energy, EA )
* Activation energy is the amount of energy that is needed for the reactants to move to a higher energy that is very unstable, thus forcing it to move to a lower energy that is stable.
* There are many ways in which a reaction could be sped up:
** '''Heat:''' makes sure the bonds between atoms break easier thus a allowing the reaction to proceed, but this could kill the entire cell
** '''Enzymes:''' acts as a catalyst that lowers the activation energy needed for a reaction to begin thus speeding up the cell’s chemical reactions. This method increases the rate of a reaction without being consumed by the reaction.
*** Enzymes are very selective in the reaction it catalyzes and are specific determined by its shape (active site fits only specific substrate molecules)
*** Substrate: is the specific reactant that an enzyme acts on
*** Active site: a region of the enzyme that a substrate fits into
*** Every enzyme is most effective under optimal conditions such as temperature and pH. For example: at optimal temperature, the contact between the reactants and enzyme’s active site is at the peak.
*** Many enzymes also include '''cofactors''', which are helpers that are inorganic ions (zinc, iron, copper) or organic nonprotien (called coenzymes such as vitamins). They bind to the active site and play a role in catalysis.
*** Regulation of enzyme activity is done by enzyme inhibitors, which is a chemical that interferes with an enzyme’s activity. There are two types of inhibitors:
::# '''Competitive inhibitors:''' blocks substrates from entering the active site, which in turn reduces the enzyme’s productivity.
::# '''Noncompetitive inhibitors:''' binds to the enzyme somewhere other than the active site which in turn changes the shape of the active site and thus preventing the substrate from binding to the enzyme.
::* '''Feedback inhibition''' occurs when the product acts as an inhibitor to one of the enzymes in the pathway that produced it.
==Chapter 5: Membranes and Transport==
* '''Fluid mosaic model:''' a membrane structure that is composed of a bilayer of phospholipids with attached and embedded proteins.

BioSec 2012: Cheryl

2012-04-23T21:37:00Z

Dsouza3190: /* Textbook Notes */

=Trying to tie Computer Security into all of this=
Using Darwin’s approach
*'''Really slow:''' it took biology billions of years to get to the efficiency it now is at. How are we supposed to compete with that?
*If we follow the same process we are setting up for '''failure most of the time'''…species getting extinct because they failed most of the time
*Species '''survival is highly dependent on environment'''…computer security needs to basically work all the time independent of its environment …how is this going to work?

----

So for things to work:
*there needs be a lot of '''redundant''' stuff:
**Genes – redundant ways to get an amino acid
**Genome – copies of the same genes
**Pathways – many regulators
*'''diversity'''
**Biology is so good because there aren’t two things that are really the same…they have a lot in common…but there is that one small aspect that sets them apart…if they were all the same then one small thing just wipes all of them out
**Can this be done with computers…randomize things by adding ''introns'' (junk code)?

----
=Textbook Notes=
==Chapter 1: Light and Life==
* Light
# source of information and energy
# Defined as EM radiation
# Wave of photons
# Can be absorbed by pigments and then used
# Colour = light that is not absorbed by pigment
* Electrons become excited when absorbed by light which in turn then becomes potential energy (photosynthesis)
* Photoreceptor
# light-sensing system
# made up of pigment molecule bound to protein
# eye = organ of animals to sense light
* Problem:
# most light driven processes can only process a certain part of the EM spectrum
# source of energy…too much can cause deadly effects
# pigment melanin in our skin absorbs UV (high energy and can be damaging)
* Circadian rhythms (body clock) the daily cycle of most living organisms have evolved to adapt to the change in light (night and day…plant use photosynthesis during the day and night break glucose)
* Some animals prefer the dark (nocturnal animals like moths)
* Some animals have ancestors that had functional eyes but are not blind (blind mole rat)
* bioluminescent: organisms that use chemical energy to make their own light to attract a mate, camouflage, attract prey or communicate
==Chapter 2: Origins of Life==
* life defined by seven characteristics:
# '''Display order:''' high ordered structures
# '''Harness and utilize energy:''' getting and using chemical energy to power the organism’s activities
# '''Reproduce:''' ability to reproduce their own kind
# '''Respond to stimuli:''' ability to respond environmental stimuli
# '''Exhibit homeostasis:''' ability to control an organism’s internal environment within the limits to sustain life
# '''Growth and development:''' consistent growth and development (DNA inheritance)
# '''Evolve:''' adapt to environments over many generations to have better reproducibility and survival of the species.
* Cell theory
# All living organisms are composed of cells
# Cells are the functional units of life
# New cells come only from preexisting cells (division)
* Eukaryotic Cells

{| style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; border-color: #000; padding: 0"
|-
! style="border-style: solid; border-width: 0 1px 1px 0"| Function
! style="border-style: solid; border-width: 0 0 1px 0"| Organelles/Structures involved
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Genetic control of the cell
| style="border-style: solid; border-width: 0"| Nucleus and ribosomes
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Manufacture, distribution, and breakdown of molecules.
| style="border-style: solid; border-width: 0"| Endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles, and peroxisomes
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Energy processing
| style="border-style: solid; border-width: 0"| Mitochondria (plus chloroplasts in plant cells)
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Structural support, movement, and communication between cells
| style="border-style: solid; border-width: 0"| Structural support, movement, and communication between cells
|}
* Mitochondria and chloroplasts evolved by endosymbiosis which suggests mitochondria and chloroplasts were small prokaryotes and they began living within larger cells
* '''Cytoskeleton:'''
** network of protein fibers in the cells
** functions in structural support and mobility
** interacts with motor proteins resulting in mobility and cellular respiration
** composed of three kinds of fibers:
# '''Microfilaments:''' (actin filaments) support the cell’s shape and are involved in mobility
# '''Intermediated filaments:''' (not present in plant cells) reinforces the cell shape and provides and anchor for the organelles
# '''Microtubules:''' (made from tubulin) responsible for cell rigidity and guiding the organelle’s movement
==Chapter 3: Selection, Biodiversity and Biosphere==
* Biological organization:
[[File:Chapter3.png]]
* Categorizing organisms on how they obtain carbon
# '''Autotrophs:''' create their energy-containing organic carbon molecules (glucose) from inorganic carbon molecules (sunlight). Example: plants using photosynthesis
# '''Heterotrophs:''' get energy-containing organic carbon molecules (glucose) by consuming other organisms. Example: animals eating plants or other animals.
* Categorizing organisms on how they obtain energy
# '''Phototrophs:''' obtain energy from light
# '''Chemotrophs:''' obtains energy by oxidizing inorganic or organic substances
* '''Theory of evolution:''' all organisms descended from one common ancestor, thus share common features. At the same time due to natural selection species change over time to adapt to their specific environment
* All living organisms have three essential components:
# ATP for energy
# DNA for genetics
# Plasma membrane
* Parasitism = symbiotic relationship where one organism benefits at the expense of the other
* Mutualism = symbiotic relationship where both organism benefit
* ''Interesting: The genetic barcode that is embedded in almost every cell is the mitochondrial cytochrome c oxidase 1''
===Computer security aspect===
* diversity
** Biology is so good because there aren’t two things that are really the same…they have a lot in common…but there is that one small aspect that sets them apart…if they were all the same then one small thing just wipes all of them out
** Can this be done with computers…randomize things by adding introns (junk code)?
==Chapter 4: Energy and Enzymes==
* Cells can be basically thought of as a chemical factory (millions of chemical reaction take place in a cell)
** Chemical reactions used for cell maintenance, manufacture of cell parts and cell replication
* Energy is the capacity to do work
* Two kinds of energy
# Kinetic Energy: energy of motion
# Potential Energy: energy that is stored as a result of its location or structure
* Thermodynamics
** the study of energy transformations that occur between a system (matter under study) and its surroundings (rest of the universe)
** Two law of thermodynamics:
:# Energy in the universe is constant
:# Energy conversion increase entropy (measure of disorder/randomness)
* Spontaneous reactions take place without having to input any energy from its surroundings and releases free energy that is influenced by two factors:
** The changes in energy content
** Entropy of the system
* Chemical reactions either release or store energy
** Exergonic reactions: release energy (ex: Cellular respiration - uses some of the released energy to produce ATP)
** Endergonic reactions: stores energy or requires an input of energy; products have high potential energy (ex: photosynthesis – reactants = carbon dioxide and water (low energy), once absorbed energy from the sunlight produces products that are high in energy such as sugar)
* Cells also couple energies, which uses the energy released from exergonic reactions to drive key endergonic reaction. This process usually uses the energy stored in ATP molecules.
* ATP (Adenosine TriPhosphate) drives cellular work by energy coupling
** Powers all cellular work
** Is made up of: nitrogen base (adenine), sugar (ribose) and three phosphate groups
** Phosphorylation is the hydrolysis of ATP which releases energy by transferring the third phosphate from ATP to some other molecule
** ATP is a cycle – energy is released in an exergonic reaction (break down glucose) and is used in endergonic reaction (generation of ATP)
* Biological molecules have a lot of potential energy, but it is not spontaneously released. Thus an energy barrier must be overcome before a chemical reaction can begin (Activation energy, EA )
* Activation energy is the amount of energy that is needed for the reactants to move to a higher energy that is very unstable, thus forcing it to move to a lower energy that is stable.
* There are many ways in which a reaction could be sped up:
** '''Heat:''' makes sure the bonds between atoms break easier thus a allowing the reaction to proceed, but this could kill the entire cell
** '''Enzymes:''' acts as a catalyst that lowers the activation energy needed for a reaction to begin thus speeding up the cell’s chemical reactions. This method increases the rate of a reaction without being consumed by the reaction.
*** Enzymes are very selective in the reaction it catalyzes and are specific determined by its shape (active site fits only specific substrate molecules)
*** Substrate: is the specific reactant that an enzyme acts on
*** Active site: a region of the enzyme that a substrate fits into
*** Every enzyme is most effective under optimal conditions such as temperature and pH. For example: at optimal temperature, the contact between the reactants and enzyme’s active site is at the peak.
*** Many enzymes also include '''cofactors''', which are helpers that are inorganic ions (zinc, iron, copper) or organic nonprotien (called coenzymes such as vitamins). They bind to the active site and play a role in catalysis.
*** Regulation of enzyme activity is done by enzyme inhibitors, which is a chemical that interferes with an enzyme’s activity. There are two types of inhibitors:
::# '''Competitive inhibitors:''' blocks substrates from entering the active site, which in turn reduces the enzyme’s productivity.
::# '''Noncompetitive inhibitors:''' binds to the enzyme somewhere other than the active site which in turn changes the shape of the active site and thus preventing the substrate from binding to the enzyme.
::* '''Feedback inhibition''' occurs when the product acts as an inhibitor to one of the enzymes in the pathway that produced it.
==Chapter 5: Membranes and Transport==
* '''Fluid mosaic model:''' a membrane structure that is composed of a bilayer of phospholipids with attached and embedded proteins.

BioSec 2012: Cheryl

2012-04-23T21:36:46Z

Dsouza3190: /* Textbook Notes */

=Trying to tie Computer Security into all of this=
Using Darwin’s approach
*'''Really slow:''' it took biology billions of years to get to the efficiency it now is at. How are we supposed to compete with that?
*If we follow the same process we are setting up for '''failure most of the time'''…species getting extinct because they failed most of the time
*Species '''survival is highly dependent on environment'''…computer security needs to basically work all the time independent of its environment …how is this going to work?

----

So for things to work:
*there needs be a lot of '''redundant''' stuff:
**Genes – redundant ways to get an amino acid
**Genome – copies of the same genes
**Pathways – many regulators
*'''diversity'''
**Biology is so good because there aren’t two things that are really the same…they have a lot in common…but there is that one small aspect that sets them apart…if they were all the same then one small thing just wipes all of them out
**Can this be done with computers…randomize things by adding ''introns'' (junk code)?

----
=Textbook Notes=
Chapter 1: Light and Life==
* Light
# source of information and energy
# Defined as EM radiation
# Wave of photons
# Can be absorbed by pigments and then used
# Colour = light that is not absorbed by pigment
* Electrons become excited when absorbed by light which in turn then becomes potential energy (photosynthesis)
* Photoreceptor
# light-sensing system
# made up of pigment molecule bound to protein
# eye = organ of animals to sense light
* Problem:
# most light driven processes can only process a certain part of the EM spectrum
# source of energy…too much can cause deadly effects
# pigment melanin in our skin absorbs UV (high energy and can be damaging)
* Circadian rhythms (body clock) the daily cycle of most living organisms have evolved to adapt to the change in light (night and day…plant use photosynthesis during the day and night break glucose)
* Some animals prefer the dark (nocturnal animals like moths)
* Some animals have ancestors that had functional eyes but are not blind (blind mole rat)
* bioluminescent: organisms that use chemical energy to make their own light to attract a mate, camouflage, attract prey or communicate
==Chapter 2: Origins of Life==
* life defined by seven characteristics:
# '''Display order:''' high ordered structures
# '''Harness and utilize energy:''' getting and using chemical energy to power the organism’s activities
# '''Reproduce:''' ability to reproduce their own kind
# '''Respond to stimuli:''' ability to respond environmental stimuli
# '''Exhibit homeostasis:''' ability to control an organism’s internal environment within the limits to sustain life
# '''Growth and development:''' consistent growth and development (DNA inheritance)
# '''Evolve:''' adapt to environments over many generations to have better reproducibility and survival of the species.
* Cell theory
# All living organisms are composed of cells
# Cells are the functional units of life
# New cells come only from preexisting cells (division)
* Eukaryotic Cells

{| style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; border-color: #000; padding: 0"
|-
! style="border-style: solid; border-width: 0 1px 1px 0"| Function
! style="border-style: solid; border-width: 0 0 1px 0"| Organelles/Structures involved
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Genetic control of the cell
| style="border-style: solid; border-width: 0"| Nucleus and ribosomes
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Manufacture, distribution, and breakdown of molecules.
| style="border-style: solid; border-width: 0"| Endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles, and peroxisomes
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Energy processing
| style="border-style: solid; border-width: 0"| Mitochondria (plus chloroplasts in plant cells)
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Structural support, movement, and communication between cells
| style="border-style: solid; border-width: 0"| Structural support, movement, and communication between cells
|}
* Mitochondria and chloroplasts evolved by endosymbiosis which suggests mitochondria and chloroplasts were small prokaryotes and they began living within larger cells
* '''Cytoskeleton:'''
** network of protein fibers in the cells
** functions in structural support and mobility
** interacts with motor proteins resulting in mobility and cellular respiration
** composed of three kinds of fibers:
# '''Microfilaments:''' (actin filaments) support the cell’s shape and are involved in mobility
# '''Intermediated filaments:''' (not present in plant cells) reinforces the cell shape and provides and anchor for the organelles
# '''Microtubules:''' (made from tubulin) responsible for cell rigidity and guiding the organelle’s movement
==Chapter 3: Selection, Biodiversity and Biosphere==
* Biological organization:
[[File:Chapter3.png]]
* Categorizing organisms on how they obtain carbon
# '''Autotrophs:''' create their energy-containing organic carbon molecules (glucose) from inorganic carbon molecules (sunlight). Example: plants using photosynthesis
# '''Heterotrophs:''' get energy-containing organic carbon molecules (glucose) by consuming other organisms. Example: animals eating plants or other animals.
* Categorizing organisms on how they obtain energy
# '''Phototrophs:''' obtain energy from light
# '''Chemotrophs:''' obtains energy by oxidizing inorganic or organic substances
* '''Theory of evolution:''' all organisms descended from one common ancestor, thus share common features. At the same time due to natural selection species change over time to adapt to their specific environment
* All living organisms have three essential components:
# ATP for energy
# DNA for genetics
# Plasma membrane
* Parasitism = symbiotic relationship where one organism benefits at the expense of the other
* Mutualism = symbiotic relationship where both organism benefit
* ''Interesting: The genetic barcode that is embedded in almost every cell is the mitochondrial cytochrome c oxidase 1''
===Computer security aspect===
* diversity
** Biology is so good because there aren’t two things that are really the same…they have a lot in common…but there is that one small aspect that sets them apart…if they were all the same then one small thing just wipes all of them out
** Can this be done with computers…randomize things by adding introns (junk code)?
==Chapter 4: Energy and Enzymes==
* Cells can be basically thought of as a chemical factory (millions of chemical reaction take place in a cell)
** Chemical reactions used for cell maintenance, manufacture of cell parts and cell replication
* Energy is the capacity to do work
* Two kinds of energy
# Kinetic Energy: energy of motion
# Potential Energy: energy that is stored as a result of its location or structure
* Thermodynamics
** the study of energy transformations that occur between a system (matter under study) and its surroundings (rest of the universe)
** Two law of thermodynamics:
:# Energy in the universe is constant
:# Energy conversion increase entropy (measure of disorder/randomness)
* Spontaneous reactions take place without having to input any energy from its surroundings and releases free energy that is influenced by two factors:
** The changes in energy content
** Entropy of the system
* Chemical reactions either release or store energy
** Exergonic reactions: release energy (ex: Cellular respiration - uses some of the released energy to produce ATP)
** Endergonic reactions: stores energy or requires an input of energy; products have high potential energy (ex: photosynthesis – reactants = carbon dioxide and water (low energy), once absorbed energy from the sunlight produces products that are high in energy such as sugar)
* Cells also couple energies, which uses the energy released from exergonic reactions to drive key endergonic reaction. This process usually uses the energy stored in ATP molecules.
* ATP (Adenosine TriPhosphate) drives cellular work by energy coupling
** Powers all cellular work
** Is made up of: nitrogen base (adenine), sugar (ribose) and three phosphate groups
** Phosphorylation is the hydrolysis of ATP which releases energy by transferring the third phosphate from ATP to some other molecule
** ATP is a cycle – energy is released in an exergonic reaction (break down glucose) and is used in endergonic reaction (generation of ATP)
* Biological molecules have a lot of potential energy, but it is not spontaneously released. Thus an energy barrier must be overcome before a chemical reaction can begin (Activation energy, EA )
* Activation energy is the amount of energy that is needed for the reactants to move to a higher energy that is very unstable, thus forcing it to move to a lower energy that is stable.
* There are many ways in which a reaction could be sped up:
** '''Heat:''' makes sure the bonds between atoms break easier thus a allowing the reaction to proceed, but this could kill the entire cell
** '''Enzymes:''' acts as a catalyst that lowers the activation energy needed for a reaction to begin thus speeding up the cell’s chemical reactions. This method increases the rate of a reaction without being consumed by the reaction.
*** Enzymes are very selective in the reaction it catalyzes and are specific determined by its shape (active site fits only specific substrate molecules)
*** Substrate: is the specific reactant that an enzyme acts on
*** Active site: a region of the enzyme that a substrate fits into
*** Every enzyme is most effective under optimal conditions such as temperature and pH. For example: at optimal temperature, the contact between the reactants and enzyme’s active site is at the peak.
*** Many enzymes also include '''cofactors''', which are helpers that are inorganic ions (zinc, iron, copper) or organic nonprotien (called coenzymes such as vitamins). They bind to the active site and play a role in catalysis.
*** Regulation of enzyme activity is done by enzyme inhibitors, which is a chemical that interferes with an enzyme’s activity. There are two types of inhibitors:
::# '''Competitive inhibitors:''' blocks substrates from entering the active site, which in turn reduces the enzyme’s productivity.
::# '''Noncompetitive inhibitors:''' binds to the enzyme somewhere other than the active site which in turn changes the shape of the active site and thus preventing the substrate from binding to the enzyme.
::* '''Feedback inhibition''' occurs when the product acts as an inhibitor to one of the enzymes in the pathway that produced it.
==Chapter 5: Membranes and Transport==
* '''Fluid mosaic model:''' a membrane structure that is composed of a bilayer of phospholipids with attached and embedded proteins.

BioSec 2012: Cheryl

2012-04-23T21:36:23Z

Dsouza3190: /* Chapter 4: Energy and Enzymes */

=Trying to tie Computer Security into all of this=
Using Darwin’s approach
*'''Really slow:''' it took biology billions of years to get to the efficiency it now is at. How are we supposed to compete with that?
*If we follow the same process we are setting up for '''failure most of the time'''…species getting extinct because they failed most of the time
*Species '''survival is highly dependent on environment'''…computer security needs to basically work all the time independent of its environment …how is this going to work?

----

So for things to work:
*there needs be a lot of '''redundant''' stuff:
**Genes – redundant ways to get an amino acid
**Genome – copies of the same genes
**Pathways – many regulators
*'''diversity'''
**Biology is so good because there aren’t two things that are really the same…they have a lot in common…but there is that one small aspect that sets them apart…if they were all the same then one small thing just wipes all of them out
**Can this be done with computers…randomize things by adding ''introns'' (junk code)?

----
=Textbook Notes=
Chapter 1: Light and Life==
* Light
# source of information and energy
# Defined as EM radiation
# Wave of photons
# Can be absorbed by pigments and then used
# Colour = light that is not absorbed by pigment
* Electrons become excited when absorbed by light which in turn then becomes potential energy (photosynthesis)
* Photoreceptor
# light-sensing system
# made up of pigment molecule bound to protein
# eye = organ of animals to sense light
* Problem:
# most light driven processes can only process a certain part of the EM spectrum
# source of energy…too much can cause deadly effects
# pigment melanin in our skin absorbs UV (high energy and can be damaging)
* Circadian rhythms (body clock) the daily cycle of most living organisms have evolved to adapt to the change in light (night and day…plant use photosynthesis during the day and night break glucose)
* Some animals prefer the dark (nocturnal animals like moths)
* Some animals have ancestors that had functional eyes but are not blind (blind mole rat)
* bioluminescent: organisms that use chemical energy to make their own light to attract a mate, camouflage, attract prey or communicate
==Chapter 2: Origins of Life==
* life defined by seven characteristics:
# '''Display order:''' high ordered structures
# '''Harness and utilize energy:''' getting and using chemical energy to power the organism’s activities
# '''Reproduce:''' ability to reproduce their own kind
# '''Respond to stimuli:''' ability to respond environmental stimuli
# '''Exhibit homeostasis:''' ability to control an organism’s internal environment within the limits to sustain life
# '''Growth and development:''' consistent growth and development (DNA inheritance)
# '''Evolve:''' adapt to environments over many generations to have better reproducibility and survival of the species.
* Cell theory
# All living organisms are composed of cells
# Cells are the functional units of life
# New cells come only from preexisting cells (division)
* Eukaryotic Cells

{| style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; border-color: #000; padding: 0"
|-
! style="border-style: solid; border-width: 0 1px 1px 0"| Function
! style="border-style: solid; border-width: 0 0 1px 0"| Organelles/Structures involved
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Genetic control of the cell
| style="border-style: solid; border-width: 0"| Nucleus and ribosomes
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Manufacture, distribution, and breakdown of molecules.
| style="border-style: solid; border-width: 0"| Endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles, and peroxisomes
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Energy processing
| style="border-style: solid; border-width: 0"| Mitochondria (plus chloroplasts in plant cells)
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Structural support, movement, and communication between cells
| style="border-style: solid; border-width: 0"| Structural support, movement, and communication between cells
|}
* Mitochondria and chloroplasts evolved by endosymbiosis which suggests mitochondria and chloroplasts were small prokaryotes and they began living within larger cells
* '''Cytoskeleton:'''
** network of protein fibers in the cells
** functions in structural support and mobility
** interacts with motor proteins resulting in mobility and cellular respiration
** composed of three kinds of fibers:
# '''Microfilaments:''' (actin filaments) support the cell’s shape and are involved in mobility
# '''Intermediated filaments:''' (not present in plant cells) reinforces the cell shape and provides and anchor for the organelles
# '''Microtubules:''' (made from tubulin) responsible for cell rigidity and guiding the organelle’s movement
==Chapter 3: Selection, Biodiversity and Biosphere==
* Biological organization:
[[File:Chapter3.png]]
* Categorizing organisms on how they obtain carbon
# '''Autotrophs:''' create their energy-containing organic carbon molecules (glucose) from inorganic carbon molecules (sunlight). Example: plants using photosynthesis
# '''Heterotrophs:''' get energy-containing organic carbon molecules (glucose) by consuming other organisms. Example: animals eating plants or other animals.
* Categorizing organisms on how they obtain energy
# '''Phototrophs:''' obtain energy from light
# '''Chemotrophs:''' obtains energy by oxidizing inorganic or organic substances
* '''Theory of evolution:''' all organisms descended from one common ancestor, thus share common features. At the same time due to natural selection species change over time to adapt to their specific environment
* All living organisms have three essential components:
# ATP for energy
# DNA for genetics
# Plasma membrane
* Parasitism = symbiotic relationship where one organism benefits at the expense of the other
* Mutualism = symbiotic relationship where both organism benefit
* ''Interesting: The genetic barcode that is embedded in almost every cell is the mitochondrial cytochrome c oxidase 1''
===Computer security aspect===
* diversity
** Biology is so good because there aren’t two things that are really the same…they have a lot in common…but there is that one small aspect that sets them apart…if they were all the same then one small thing just wipes all of them out
** Can this be done with computers…randomize things by adding introns (junk code)?
==Chapter 4: Energy and Enzymes==
* Cells can be basically thought of as a chemical factory (millions of chemical reaction take place in a cell)
** Chemical reactions used for cell maintenance, manufacture of cell parts and cell replication
* Energy is the capacity to do work
* Two kinds of energy
# Kinetic Energy: energy of motion
# Potential Energy: energy that is stored as a result of its location or structure
* Thermodynamics
** the study of energy transformations that occur between a system (matter under study) and its surroundings (rest of the universe)
** Two law of thermodynamics:
:# Energy in the universe is constant
:# Energy conversion increase entropy (measure of disorder/randomness)
* Spontaneous reactions take place without having to input any energy from its surroundings and releases free energy that is influenced by two factors:
** The changes in energy content
** Entropy of the system
* Chemical reactions either release or store energy
** Exergonic reactions: release energy (ex: Cellular respiration - uses some of the released energy to produce ATP)
** Endergonic reactions: stores energy or requires an input of energy; products have high potential energy (ex: photosynthesis – reactants = carbon dioxide and water (low energy), once absorbed energy from the sunlight produces products that are high in energy such as sugar)
* Cells also couple energies, which uses the energy released from exergonic reactions to drive key endergonic reaction. This process usually uses the energy stored in ATP molecules.
* ATP (Adenosine TriPhosphate) drives cellular work by energy coupling
** Powers all cellular work
** Is made up of: nitrogen base (adenine), sugar (ribose) and three phosphate groups
** Phosphorylation is the hydrolysis of ATP which releases energy by transferring the third phosphate from ATP to some other molecule
** ATP is a cycle – energy is released in an exergonic reaction (break down glucose) and is used in endergonic reaction (generation of ATP)
* Biological molecules have a lot of potential energy, but it is not spontaneously released. Thus an energy barrier must be overcome before a chemical reaction can begin (Activation energy, EA )
* Activation energy is the amount of energy that is needed for the reactants to move to a higher energy that is very unstable, thus forcing it to move to a lower energy that is stable.
* There are many ways in which a reaction could be sped up:
** '''Heat:''' makes sure the bonds between atoms break easier thus a allowing the reaction to proceed, but this could kill the entire cell
** '''Enzymes:''' acts as a catalyst that lowers the activation energy needed for a reaction to begin thus speeding up the cell’s chemical reactions. This method increases the rate of a reaction without being consumed by the reaction.
*** Enzymes are very selective in the reaction it catalyzes and are specific determined by its shape (active site fits only specific substrate molecules)
*** Substrate: is the specific reactant that an enzyme acts on
*** Active site: a region of the enzyme that a substrate fits into
*** Every enzyme is most effective under optimal conditions such as temperature and pH. For example: at optimal temperature, the contact between the reactants and enzyme’s active site is at the peak.
*** Many enzymes also include '''cofactors''', which are helpers that are inorganic ions (zinc, iron, copper) or organic nonprotien (called coenzymes such as vitamins). They bind to the active site and play a role in catalysis.
*** Regulation of enzyme activity is done by enzyme inhibitors, which is a chemical that interferes with an enzyme’s activity. There are two types of inhibitors:
::# '''Competitive inhibitors:''' blocks substrates from entering the active site, which in turn reduces the enzyme’s productivity.
::# '''Noncompetitive inhibitors:''' binds to the enzyme somewhere other than the active site which in turn changes the shape of the active site and thus preventing the substrate from binding to the enzyme.
::* '''Feedback inhibition''' occurs when the product acts as an inhibitor to one of the enzymes in the pathway that produced it.

BioSec 2012: Cheryl

2012-04-23T21:35:12Z

Dsouza3190: /* Chapter 4: Energy and Enzymes */

=Trying to tie Computer Security into all of this=
Using Darwin’s approach
*'''Really slow:''' it took biology billions of years to get to the efficiency it now is at. How are we supposed to compete with that?
*If we follow the same process we are setting up for '''failure most of the time'''…species getting extinct because they failed most of the time
*Species '''survival is highly dependent on environment'''…computer security needs to basically work all the time independent of its environment …how is this going to work?

----

So for things to work:
*there needs be a lot of '''redundant''' stuff:
**Genes – redundant ways to get an amino acid
**Genome – copies of the same genes
**Pathways – many regulators
*'''diversity'''
**Biology is so good because there aren’t two things that are really the same…they have a lot in common…but there is that one small aspect that sets them apart…if they were all the same then one small thing just wipes all of them out
**Can this be done with computers…randomize things by adding ''introns'' (junk code)?

----
=Textbook Notes=
Chapter 1: Light and Life==
* Light
# source of information and energy
# Defined as EM radiation
# Wave of photons
# Can be absorbed by pigments and then used
# Colour = light that is not absorbed by pigment
* Electrons become excited when absorbed by light which in turn then becomes potential energy (photosynthesis)
* Photoreceptor
# light-sensing system
# made up of pigment molecule bound to protein
# eye = organ of animals to sense light
* Problem:
# most light driven processes can only process a certain part of the EM spectrum
# source of energy…too much can cause deadly effects
# pigment melanin in our skin absorbs UV (high energy and can be damaging)
* Circadian rhythms (body clock) the daily cycle of most living organisms have evolved to adapt to the change in light (night and day…plant use photosynthesis during the day and night break glucose)
* Some animals prefer the dark (nocturnal animals like moths)
* Some animals have ancestors that had functional eyes but are not blind (blind mole rat)
* bioluminescent: organisms that use chemical energy to make their own light to attract a mate, camouflage, attract prey or communicate
==Chapter 2: Origins of Life==
* life defined by seven characteristics:
# '''Display order:''' high ordered structures
# '''Harness and utilize energy:''' getting and using chemical energy to power the organism’s activities
# '''Reproduce:''' ability to reproduce their own kind
# '''Respond to stimuli:''' ability to respond environmental stimuli
# '''Exhibit homeostasis:''' ability to control an organism’s internal environment within the limits to sustain life
# '''Growth and development:''' consistent growth and development (DNA inheritance)
# '''Evolve:''' adapt to environments over many generations to have better reproducibility and survival of the species.
* Cell theory
# All living organisms are composed of cells
# Cells are the functional units of life
# New cells come only from preexisting cells (division)
* Eukaryotic Cells

{| style="border-collapse: separate; border-spacing: 0; border-width: 1px; border-style: solid; border-color: #000; padding: 0"
|-
! style="border-style: solid; border-width: 0 1px 1px 0"| Function
! style="border-style: solid; border-width: 0 0 1px 0"| Organelles/Structures involved
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Genetic control of the cell
| style="border-style: solid; border-width: 0"| Nucleus and ribosomes
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Manufacture, distribution, and breakdown of molecules.
| style="border-style: solid; border-width: 0"| Endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles, and peroxisomes
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Energy processing
| style="border-style: solid; border-width: 0"| Mitochondria (plus chloroplasts in plant cells)
|-
| style="border-style: solid; border-width: 0 1px 0 0"| Structural support, movement, and communication between cells
| style="border-style: solid; border-width: 0"| Structural support, movement, and communication between cells
|}
* Mitochondria and chloroplasts evolved by endosymbiosis which suggests mitochondria and chloroplasts were small prokaryotes and they began living within larger cells
* '''Cytoskeleton:'''
** network of protein fibers in the cells
** functions in structural support and mobility
** interacts with motor proteins resulting in mobility and cellular respiration
** composed of three kinds of fibers:
# '''Microfilaments:''' (actin filaments) support the cell’s shape and are involved in mobility
# '''Intermediated filaments:''' (not present in plant cells) reinforces the cell shape and provides and anchor for the organelles
# '''Microtubules:''' (made from tubulin) responsible for cell rigidity and guiding the organelle’s movement
==Chapter 3: Selection, Biodiversity and Biosphere==
* Biological organization:
[[File:Chapter3.png]]
* Categorizing organisms on how they obtain carbon
# '''Autotrophs:''' create their energy-containing organic carbon molecules (glucose) from inorganic carbon molecules (sunlight). Example: plants using photosynthesis
# '''Heterotrophs:''' get energy-containing organic carbon molecules (glucose) by consuming other organisms. Example: animals eating plants or other animals.
* Categorizing organisms on how they obtain energy
# '''Phototrophs:''' obtain energy from light
# '''Chemotrophs:''' obtains energy by oxidizing inorganic or organic substances
* '''Theory of evolution:''' all organisms descended from one common ancestor, thus share common features. At the same time due to natural selection species change over time to adapt to their specific environment
* All living organisms have three essential components:
# ATP for energy
# DNA for genetics
# Plasma membrane
* Parasitism = symbiotic relationship where one organism benefits at the expense of the other
* Mutualism = symbiotic relationship where both organism benefit
* ''Interesting: The genetic barcode that is embedded in almost every cell is the mitochondrial cytochrome c oxidase 1''
===Computer security aspect===
* diversity
** Biology is so good because there aren’t two things that are really the same…they have a lot in common…but there is that one small aspect that sets them apart…if they were all the same then one small thing just wipes all of them out
** Can this be done with computers…randomize things by adding introns (junk code)?
==Chapter 4: Energy and Enzymes==
* Cells can be basically thought of as a chemical factory (millions of chemical reaction take place in a cell)
** Chemical reactions used for cell maintenance, manufacture of cell parts and cell replication
* Energy is the capacity to do work
* Two kinds of energy
# Kinetic Energy: energy of motion
# Potential Energy: energy that is stored as a result of its location or structure
* Thermodynamics
** the study of energy transformations that occur between a system (matter under study) and its surroundings (rest of the universe)
** Two law of thermodynamics:
:# Energy in the universe is constant
:# Energy conversion increase entropy (measure of disorder/randomness)
* Spontaneous reactions take place without having to input any energy from its surroundings and releases free energy that is influenced by two factors:
** The changes in energy content
** Entropy of the system
* Chemical reactions either release or store energy
** Exergonic reactions: release energy (ex: Cellular respiration - uses some of the released energy to produce ATP)
** Endergonic reactions: stores energy or requires an input of energy; products have high potential energy (ex: photosynthesis – reactants = carbon dioxide and water (low energy), once absorbed energy from the sunlight produces products that are high in energy such as sugar)
* Cells also couple energies, which uses the energy released from exergonic reactions to drive key endergonic reaction. This process usually uses the energy stored in ATP molecules.
* ATP (Adenosine TriPhosphate) drives cellular work by energy coupling
** Powers all cellular work
** Is made up of: nitrogen base (adenine), sugar (ribose) and three phosphate groups
** Phosphorylation is the hydrolysis of ATP which releases energy by transferring the third phosphate from ATP to some other molecule
** ATP is a cycle – energy is released in an exergonic reaction (break down glucose) and is used in endergonic reaction (generation of ATP)
* Biological molecules have a lot of potential energy, but it is not spontaneously released. Thus an energy barrier must be overcome before a chemical reaction can begin (Activation energy, EA )
* Activation energy is the amount of energy that is needed for the reactants to move to a higher energy that is very unstable, thus forcing it to move to a lower energy that is stable.
* There are many ways in which a reaction could be sped up:
** '''Heat:''' makes sure the bonds between atoms break easier thus a allowing the reaction to proceed, but this could kill the entire cell
** '''Enzymes:''' acts as a catalyst that lowers the activation energy needed for a reaction to begin thus speeding up the cell’s chemical reactions. This method increases the rate of a reaction without being consumed by the reaction.
*** Enzymes are very selective in the reaction it catalyzes and are specific determined by its shape (active site fits only specific substrate molecules)
*** Substrate: is the specific reactant that an enzyme acts on
*** Active site: a region of the enzyme that a substrate fits into
*** Every enzyme is most effective under optimal conditions such as temperature and pH. For example: at optimal temperature, the contact between the reactants and enzyme’s active site is at the peak.
*** Many enzymes also include '''cofactors''', which are helpers that are inorganic ions (zinc, iron, copper) or organic nonprotien (called coenzymes such as vitamins). They bind to the active site and play a role in catalysis.
*** Regulation of enzyme activity is done by enzyme inhibitors, which is a chemical that interferes with an enzyme’s activity. There are two types of inhibitors:
::# '''Competitive inhibitors:''' blocks substrates from entering the active site, which in turn reduces the enzyme’s productivity.
::# '''Noncompetitive inhibitors:''' binds to the enzyme somewhere other than the active site which in turn changes the shape of the active site and thus preventing the substrate from binding to the enzyme.
*** '''Feedback inhibition''' occurs when the product acts as an inhibitor to one of the enzymes in the pathway that produced it.

BioSec 2012: Cheryl

2012-04-23T21:32:27Z

Dsouza3190: /* Chapter 4: Energy and Enzymes */

BioSec 2012: Cheryl

2012-04-23T21:31:31Z

Dsouza3190: /* Textbook Notes */

BioSec 2012: Cheryl

2012-04-23T21:31:02Z

Dsouza3190: /* Chapter 3: Selection, Biodiversity and Biosphere */

BioSec 2012: Cheryl

2012-04-23T21:29:28Z

Dsouza3190: /* Trying to tie Computer Security into all of this */

File:Chapter3.png

2012-04-23T21:29:01Z

Dsouza3190:

BioSec 2012: Cheryl

2012-04-23T21:04:30Z

Dsouza3190: /* Trying to tie Computer Security into all of this */

BioSec 2012: Cheryl

2012-02-08T16:22:48Z

Dsouza3190:

BioSec 2012: Cheryl

2012-02-07T19:50:30Z

Dsouza3190: /* Chapter 1: Light and Life */

BioSec 2012: Cheryl

2012-02-07T19:50:22Z

Dsouza3190: /* Chapter 2: origins of Life */

BioSec 2012: Cheryl

2012-02-07T19:25:27Z

Dsouza3190: /* Chapter2: origins of Life */

=Chapter 1: Light and Life=
*Light
**source of information and energy
**Defined as EM radiation
**Wave of photons
**Can be absorbed by pigments and then used
**Colour = light that is not absorbed by pigment
*Electrons become excited when absorbed by light which in turn then becomes potential energy (photosynthesis)
*Photoreceptor
**light-sensing system
**made up of pigment molecule bound to protein
**eye = organ of animals to sense light
*Problem:
**most light driven processes can only process a certain part of the EM spectrum
**source of energy…too much can cause deadly effects
**pigment melanin in our skin absorbs UV (high energy and can be damaging)
*Circadian rhythms (body clock) the daily cycle of most living organisms have evolved to adapt to the change in light (night and day…plant use photosynthesis during the day and night break glucose)
*Some animals prefer the dark (nocturnal animals like moths)
*Some animals have ancestors that had functional eyes but are not blind (blind mole rat)
*bioluminescent: organisms that use chemical energy to make their own light to attract a mate, camouflage, attract prey or communicate

=Chapter 2: origins of Life=
*life defined by seven characteristics:
#;Display order: high ordered structures
#Harness and utilize energy: getting and using chemical energy to power the organism’s activities
#Reproduce: ability to reproduce their own kind
#Respond to stimuli: ability to respond environmental stimuli
#Exhibit homeostasis: ability to control an organism’s internal environment within the limits to sustain life
#Growth and development: consistent growth and development (DNA inheritance)
#Evolve: adapt to environments over many generations to have better reproducibility and survival of the species.
*Cell theory
#All living organisms are composed of cells
#Cells are the functional units of life
#New cells come only from preexisting cells (division)
*Eukaryotic Cells

BioSec 2012: Cheryl

2012-02-07T19:22:58Z

Dsouza3190: /* Chapter 1: Light and Life */

=Chapter 1: Light and Life=
*Light
**source of information and energy
**Defined as EM radiation
**Wave of photons
**Can be absorbed by pigments and then used
**Colour = light that is not absorbed by pigment
*Electrons become excited when absorbed by light which in turn then becomes potential energy (photosynthesis)
*Photoreceptor
**light-sensing system
**made up of pigment molecule bound to protein
**eye = organ of animals to sense light
*Problem:
**most light driven processes can only process a certain part of the EM spectrum
**source of energy…too much can cause deadly effects
**pigment melanin in our skin absorbs UV (high energy and can be damaging)
*Circadian rhythms (body clock) the daily cycle of most living organisms have evolved to adapt to the change in light (night and day…plant use photosynthesis during the day and night break glucose)
*Some animals prefer the dark (nocturnal animals like moths)
*Some animals have ancestors that had functional eyes but are not blind (blind mole rat)
*bioluminescent: organisms that use chemical energy to make their own light to attract a mate, camouflage, attract prey or communicate

=Chapter2: origins of Life=
*life defined by seven characteristics:
#Display order: high ordered structures
#Harness and utilize energy: getting and using chemical energy to power the organism’s activities
#Reproduce: ability to reproduce their own kind
#Respond to stimuli: ability to respond environmental stimuli
#Exhibit homeostasis: ability to control an organism’s internal environment within the limits to sustain life
#Growth and development: consistent growth and development (DNA inheritance)
#Evolve: adapt to environments over many generations to have better reproducibility and survival of the species.
*Cell theory
#All living organisms are composed of cells
#Cells are the functional units of life
#New cells come only from preexisting cells (division)
*Eukaryotic Cells

BioSec 2012: Cheryl

2012-02-07T19:21:48Z

Dsouza3190: Created page with "=Chapter 1: Light and Life= *Light **source of information and energy **Defined as EM radiation **Wave of photons **Can be absorbed by pigments and then used **Colour = light t…"

BioSec: Evolution

2012-02-06T21:33:27Z

Dsouza3190: /* CHAPTER III. STRUGGLE FOR EXISTENCE */

For help in mediawiki formatting see reference: http://www.mediawiki.org/wiki/Help:Formatting

== Purpose: ==

To retell Darwin's argument associating the biological with the technological.

The sections are as follows:

== CHAPTER I - VARIATION UNDER DOMESTICATION. ==

=== Causes of Variability ====

(Luc)

*Conditions of Life:
**Quantity of food
**Type of food
**Climate
*Pre-existing tendency towards variation
*Nature of the Organism

"Indefinite Variations" sounds like observations made in ignorance of genetics. Though, to be fair, we still see variations that are not well understood (Twin research, knockout mice)

Darwin argues that nature exerts pressure on organisms to adapt. As conditions of life change, species will modify themselves to either streamline themselves to harsher conditions or to take advantage of conditions of abundance (domestication).

However, while nature can apply external pressure on species to adapt, the species themselves will determine which parameters to modify. Determining which parameters will change seemed to be, at least to Darwin, an exercise in futility as different organisms within the species will be observed with differently modified parameters.

Technology:

While I'm not sure I'd call desktop Linux distributions a species, they have all mostly existed in the same environment, with environmental pressures being fairly uniform. Yet, if one were to compare Fedora, Debian, Ubuntu, Arch, Gentoo, and SuSE, it becomes glaringly obvious that each has tried to survive using different (sometimes radically different) strategies. The same can be seen in window managers, shells, scripting languages, and browsers. I, for one, would not want to have to predict how vastly increased availability in network bandwidth, or the sudden stagnation of memory availability would change the evolution of browsers.

===Effects of Habit and the use or disuse of Parts ===
(Mohamed)

=== Correlated Variation ===
(Annie)

Darwin in this section was stating that you cannot breed selectively for only one type of trait, as traits come in groupings (of at least two). Single examples were stated such as one cannot have a long limbed animal without an elongated head, or cats with white hair and blue eyes are deaf, or long, coarse haired animals tend to have horns.

His conclusion stated: "Hence if man goes on selecting and thus augmenting, any peculiarity, he will almost certainly modify unintentionally other parts of the structure, owing to the mysterious laws of correlation. The results of the various, unknown or but dimly understood laws of variation are infinitely complex and diversified.... it is really surprising to note the endless points of structure and constitution in which the varieties and sub-varieties differ slightly from each other."

To a certain degree this still applies even with the case of genetic engineering. As I think that specific genes within DNA are known to affect multiple traits. Isolating those genes individually will still affect the "engineered" animal in potentially multiple ways, as it is not only the genes, it is their interactions which may be modified and potentially corrected? (totally guessing here)

Technology wise there is a certain correlation between the graphical user interface and the program of an application. This is not evolutionary however, as it is of course due to design. Change the purpose of the program, and the user interface will have to change as well to accommodate the change. (?)

=== Inheritance ===
(Cheryl)

Darwin comes to the conclusion that the only way to explain variation is reproduction, through which parent pass on specific variations to their offspring. Furthermore, these variations are then carried and passed on from one generation to the next. Darwin also admits that scientist do not completely understand the law s that govern inheritance. Thus, scientists cannot explain why some traits are inherited by the off springs and why some are not; or why some traits skip a generation. In addition, Darwin notes that it is not clear if the various species types are the offspring of one parent species or not. He studied different domestic pigeons and cross bread them. The offspring resulted in a “perfectly fertile” species. From this he concluded that the various species are the offspring from one parent. This is because the offspring of two parents would result in a sterile offspring.

From a computer science perspective, inheritance is seen in a number ways. For example different versions of the same software can be viewed as parents and their offspring. Where the original software is the “rock” parent and the subsequent versions are its offspring. Inheritance can also be seen in programming; where programmers generally reuse parts of code. Furthermore, in object-oriented programming (OOP), inheritance describes the ability of one class to use methods and properties of another class. Another example could possibly be polymorphic code which uses a polymorphic engine to mutate however keeping the original algorithms. This can be seen in computer viruses and worms.

=== Character of Domestic Varieties ===
(Annie)
In domestic varieties there is less uniformity of character than in true species
The monstrous character of domestic varieties is defined by the small differences in some respects while differing in an extreme degree in a specific part. This is determined upon close inspection with a sample of the wild stock versus the domestic stock, as well as domestic stock with one another.
Closely connected wild species of the same genus in nature still differ from one another, except those differences aren't as radical as when you compare the domesticated version to the wild species. This explains why some smart people believe that the domestic races of many animals and plants have been judged as the descendants of aboriginally distinct species and other smart people claim that they are just varieties of the same species. Naturalists have differing opinions in what determines which characters are of generic value; all such valuations being at present empirical.

!! NOTE: NOT FINISHED !!

=== Difficulty of distinguishing between Varieties and Species ===
(Annie)
=== Origin of Domestic Varieties from one or more Species ===
(Cheryl)

Darwin states that in the case of most domesticated species it is not possible to pin point their origins. Thus we are unsure if they are the offspring of one parent species or multiple parent species. However, Darwin believes that all the different breeds come from one common parent. But he does not any evidence to confirm this hypothesis.

The authors of the book “Domestication of Media and Technology” discuss innovations are ‘tamed or domesticated’ by users – that is how technology is no longer a novelty but an aspect of everyday life. For example computers are now ‘domesticated’ because they are used by almost everyone and it is part of everyday life. However, there are many different types of computers, each slightly distinct from the other, however they all have the same basic core components.

=== Domestic Pigeons, their Differences and Origin ===

(Dan)

In this section Darwin argues the common ancestry of a variety of Pigeon breeds. Using the Pigeon as a case study he develops an argument proposing that despite the high variance within Pigeon breeds it can be reasoned that the [http://en.wikipedia.org/wiki/Rock_Pigeon Rock Pigeon (Columba Livia)] is their aboriginal ancestor.

Darwin's choice of studying Pigeons was not arbitrary (though he admits a certain infatuation with the species); a large selection of pigeon breeds was available for study and there was a historical body of treatises on the species to draw from. He begins the case study by establishing the diversity of pigeon breeds, and the aspects by which they differ. Nearly every aspect of the species is variable when examined with sufficient scope. Notable differences included the size and shape of the beak, in-flight behavior, feather appearance, age at which maturity is achieved, and skeleton details such as size, shape and count of various bone structures.

With such a great level of diversity between breeds, and the striking physical differences this diversity brings, Darwin posits it would be easy for a naturalist to assume many unique ancestor species. Darwin's counter argument to this assumption builds on the absence of any candidate species to fill this ancestral role. In order to create the present breeds as anything other than sub-varieties of a common ancestor a parent species must exist for the unique traits that are to be merged. For instance, the Porter breed has a large [http://en.wikipedia.org/wiki/Crop_%28anatomy%29 crop] that would have to have been inherited in the multiple origin species hypothesis. The absence of such an origin species indicates that either ornithologists have yet to discover the species, or that it has gone extinct. Due to the proliferation of Pigeons Darwin finds both possibilities unlikely and considers this as evidence towards the common ancestor theory. Darwin points to the fertility of hybrid (mongrel) Pigeons as further evidence supporting his common ancestry theory. For such a large selection of Pigeon breeds to cross-breed successfully and produce fertile offspring their commonality must run quite deep.

Interestingly Darwin notes that the naturalists dedication to their area of study reduces their ability to accept the common ancestry theory. With a deep appreciation of the differences of each breed it is the naturalist's view that only several unique species could explain the diversity they so well understand.

From a computer science perspective I ponder the idea of an outside observer trying to establish the common ancestry of a handful of [http://en.wikipedia.org/wiki/POSIX POSIX] descendent operating systems. As a user the OSX, Linux and Solaris operating systems seem highly divergent from one another. Much like a naturalist would assume no historic relation between Pigeon breeds, so too would an end user not assume a unified ancestor for the unique operating systems. Yet, underneath there are well established commonalities. Darwin's argument related to the fertility of offspring born of hybrid Pigeons could be similarly established for POSIX operating systems by means of considering a program written to POSIX standard running on the divergent operating systems mentioned. For a single program to successfully execute on three very different operating systems without the notion of a common ancestor seems highly improbable.

=== Principles of Selection, anciently followed, their Effects ===
(Moe)

-The production of domestic species: Effects may be attributed to direct and definite action of the external conditions of life and some to habit.

-Adaptation seen in domesticated races is not necessarily in the species' own good but rather more to the benefit of the breeder.

-The key to variation of domestic species is man's power of accumulative selection.

-Nature gives successive variations, man adds them up in certain directions

-Continued selection of slight variations produces races different from each other.

=== Methodical and Unconscious Selection ===
(Elizabeth)

In discussing the selection process that takes place in the breeding of domesticated animals, Darwin distinguishes two kinds of selection: ''methodical selection'', where breeders start with an idea in mind and deliberately attempt to create a new and superior species; and ''unconscious selection'', where many people try to get ahold of the best animals and by doing so, improve the breed. Darwin is primarily interested in unconscious selection, and notes the importance of observation and documentation, so that these changes become noticeable.

In the world of computing, parallels of the process of unconscious selection can be seen in many situations. Some examples might be the process of code development – where the same task might be coded in several ways, and eventually unified into the most efficient process once all the possibilities have been explored. A more economically motivated example might be when multiple products are competing in a market. Though no particular consumer has any intention of improving the field of desktop publishing, all consumers want to use the product that creates the most beautiful documents. Thus, the program that most people buy gets further examination and development, leading to improvement.

<blockquote>“Man can hardly select, or only with much difficulty, any deviation of structure excepting such as is externally visible; and indeed he rarely cares for what is internal. He can never act by selection, excepting on variations which are first given to him in some slight degree by nature.”</blockquote>

Darwin reflects briefly on the nature of unconscious selection, and discusses how although humankind has shaped the development of various species, the ideas always come from nature, and humans must work within the limitations of the domain.

(How is this true of computing?)

=== Unknown Origin of our Domestic Productions ===
(Elizabeth)



Darwin briefly brings up a point about the unknown ancestors of domestic breeds. His point seems to be that the process of development through selection is slow, and individual changes are small, and this means that no one pays attention to the initial stages when the creature is undeveloped. At first glance, this section is not obviously true of computers. We know exactly where computers came from, and how they developed. However, the point about small changes sometimes leading to more important changes later is true of the development of computers. In a smaller context, it is easy to see that the reasons behind early changes are often lost, leaving behind no evidence of the program they were created to deal with.

=== Circumstances favourable to Man's power of Selection ===
(Elizabeth)

In the final section of the first chapter of “The Origin of Species”, Darwin discusses the kinds of circumstances that facilitate the successful domestic selection of animals. Several of the factors Darwin lists are contextual factors. He remarks that a high degree of variability in the population is needed to attempt selective breeding, and that someone must have access to and control over a large population. In addition, he remarks that there must be some obvious value in undertaking this challenge.

<blockquote>“… the animal or plant should be so highly valued by man, that the closest attention is paid to even the slightest deviations in its qualities or structure.”</blockquote>

From the perspective of facilitating the development and selection of computer programs, it seems possible that similar contextual factors are needed. In place of a high degree of population variation, we could perhaps substitute a high degree of knowledge, expertise and experience. It seems entirely sensible that an organization who has access to large amounts of expertise, experience, equipment (and presumably, budget) would be positioned to motivate and commission work in the area. Darwin’s remark that “... the [product] should be so highly valued by man, that the closest attention is paid to even the slightest deviations in its qualities or structures” can be directly applied to the construction of computer programs. It seems believable that development and evolution of computer products (whether hardware or software) are likely to be more successful when there is a clear need or use for the product.

(What kind of organizations will have these privileges? Large corporations, like Google, sure. But what about people developing open source software? Crowd-sourced efforts, like Wikipedia? )

Darwin also notes a few factors that affect selection that have more to do with the nature of the creature at hand. Clearly, determined selection will be much easier if the species can be easily crossed, but it is also necessary to be able to prevent species from crossing at will or at random. For computer products, these two factors seem relatively easy to accomplish. Programs usually change only in the way specified by the developers and programmers, and if left alone, most computer programs do not change, merge or reproduce. (What about computer viruses, things like that?)

Part of Darwin’s discussion is of the limits of natural selection – how far can selection be pushed? He acknowledges that some limitations are defined by the capability of the product, but he also notes that external pressures affect the limitations of development. For computers, I think these limitations include hardware limitations (presumably some products will be developed at the time that the hardware exists to implement them), but I think that the external limitations come not only from the perceived need for the product, but also from the need for someone to have an idea for the product. We cannot develop products we have not thought of, or have an idea of their use or necessity.

== CHAPTER II. VARIATION UNDER NATURE ==
(Cheryl)

In this chapter Darwin basically answers the question: Can variation in species that are present in nature be considered similar to variations that are present in domesticated species?

He starts answering this question by describing three types of variations. The first type is what he calls monstrosities. These are variations that occur naturally in nature but are not really helpful in terms of survival or development of the species. In some instances, these variations are even harmful for the particular species. In the second case, variations are said to be driven due to environmental change (i.e. climate, temperature, etc.). Lastly, variations are the result of a small variation in genes that are passed from parents to their offspring. Darwin states that the first two cases of variations are most likely not passed from parents to offspring, while the third is.

The problem lies when trying to differentiate variations within a species from variations that imply the existence of two distinct species. Darwin notes that it is next to impossible to distinguish between varieties within a species. The solution to the problem is somewhat vague but clear enough to distinguish between varieties: “The amount of difference between species must be greater than the amount of difference between varieties within the species”.

Lastly, Darwin concludes by noting that variations are more likely to occur in a large sample. He does this by arguing that each species is not an act of God. Because if it were an act of God, there would be no real difference in the amount of variety between the smaller and larger groups of species.

== CHAPTER III. STRUGGLE FOR EXISTENCE ==
(Cheryl)

In this chapter Darwin explains how different species are created. His entire argument is based on two concepts: the struggles for existence and natural selection.

He explains the struggle for existence is the reason why some species’ characteristics survive and other go extinct. In addition, he notes that the huge amount of variation in species has permitted for species to adapt very well to their environments. That is, due to the unique characteristics that certain organisms have developed they can thrive in their specific environment. In addition, Darwin notes that only the characteristics that prove to be most advantageous is passed from one generation onto the next. The second concept, natural selection, is the result of these particular advantageous characteristics still present.

Other concepts that Darwin explains in this chapter is the struggle for life and the limits of population increase. Nature can provide enough food and shelter for all the species that is inhabitants and at the same time be very destructive (natural disasters, animals prey on other species, etc.). This in turn causes species to struggle for their lives, and essentially prohibits some organisms to survive. The concept of limits of population increase (borrowed from Thomas Malthus) basically states that each generation of increases the population of the species exponentially, which in turn implies that the population of the entire world is increasing constantly. However, this poses the problem of the world running out of room for the species to occupy. That is if the birth rate increases exponentially while the death rate remains the same from one generation to the next. This is not the case in reality, thus there must exist a limit that nature imposes on the total number of inhabitants. This in turn gives rise to competition, where each species must compete with each other in order to ensure that they survive thus threatening the survival of the other species.

== CHAPTER IV. NATURAL SELECTION; OR THE SURVIVAL OF THE FITTEST ==
(Dan)

In this chapter Darwin discusses the force of natural selection and the concept of ''survival of the fittest''. He begins by pointing out a reminder that in artificial selection, man can not create varieties only preserve and accumulate the ones beneficial to their needs. Since changes can and do occur in nature, then there must too be a means by which nature accumulates changes according to some goal. The question of what the goal is leads to the notions of natural fitness.

Variations that are useful in adapting to the wild environment can accumulate in successive generations. Since more beings are born than survive even slight advantages can increase the chance of survival, and in turn the chance of procreation. Increased procreation leads to the passing on/accumulating of these variations. Conversely, "injurious" variations, those that harm survival, are likely to be quickly eliminated by these properties of natural selection. Natural selection can be boiled down to preserving beneficial variations, and eliminating detrimental ones. Variations with no affect on survival/reproduction are "fluctuations".

Darwin notes there is a tight coupling between species and that a change in a large number of inhabitants of an area will greatly affect the others even if they are not directly affected by the cause of the initial changes.

Darwin also discusses the fact that nature pays no heed to aesthetics except when they additional serve a functional purpose. While man operating artificially can only select based on properties he can observe, nature operates on all the ''machinery'' of life. Additionally, the scale of time at which natural selection operates affords it the ability to accumulate massive amounts of variation.

From a computer science perspective I consider the perspectives of a user and a programmer. A user selects software based on the surface level details they can perceive, usability, potentially speed of use, features, etc. A programmer may be selecting designs underlying the software based on much finer detail, memory usage, cpu cycles, elegance of component exchange, the ''machinery'' of the program. Probably not the best analogy but it's the first that comes to mind.

=== SEXUAL SELECTION ===
(Dan)

Darwin notes that often in nature artificial selection has created variation between sexes of the same species. He notes that in conjunction to the ''fitness'' of surviving, there is a ''fitness'' to reproducing. Intra-species struggles between individuals to find the best mate, or to have a chance to mate are common.

He notes this form of selection might be "less rigorous" in that you must survive to reproduce and so survival clearly plays a more significant role in selection than reproduction alone.

=== ILLUSTRATIONS OF THE ACTION OF NATURAL SELECTION, OR THE SURVIVAL OF THE FITTEST. ===
(Dan)

In this section Darwin talks of the idea that a local variation that has success can spread outwards, and often displace less adapted individuals/species. He notes that there is often a tight coupling between separate species that is exploited to a great degree, causing mutually beneficial variations to have great influence on the progression of evolution.

He gives the dependency between flowers and birds as an example. The bees benefit from increased pollen creation by a flower variation, and the flower benefits from a bees ability to travel greater distances or survive longer.

=== ON THE INTERCROSSING OF INDIVIDUALS. ===
(Dan)

Darwin notes that it is very important for members of a species to cross with one another to reproduce, that is, to not reproduce as single units in isolation by fertilising themselves. He states that close ''interbreeding'' diminishes fertility and vigour while crossing of separate individuals does the opposite. In support of these notions Darwin notes that relatively speaking there are few hermaphrodite species and even fewer that fertilise themselves.

Further evidence is given by the fact that many plant reproductive organs are placed very closely together. This arrangement would seemingly be optimised for self-fertilisation, but instead natural selection has lead to fairly advanced measures that prevent a plant from fertilising itself easily. Since natural selection only selects for beneficial attributes it must be reasoned that there is a reason self-fertilisation is so rare.

=== CIRCUMSTANCES FAVOURABLE FOR THE PRODUCTION OF NEW FORMS THROUGH NATURAL SELECTION. ===
(Dan)

In this section Darwin discusses some geographical constraints on selection. He notes that any one species that can't keep up with the adaptations of a competitor will be quickly exterminated.

Isolation plays an important role in natural selection in that it may prevent other species or variations from "swooping in" and taking a niche that might have been used by an existing species if given time to accumulate variations useful for that niche. He notes that confined areas tend to have more "uniform" life and that this life is operated on by selection in the same ways across the board.

Darwin is careful to clarify that time alone does nothing and that it merely allows for a greater chance of useful variations to occur, and be accumulated. Natural selection can only act when there is a niche to be filled by some new adaptation, otherwise things stagnate. These new "niches" are often caused by physical changes (climate, geography, etc) and are generally very slow acting.

=== EXTINCTION CAUSED BY NATURAL SELECTION. ===
(Dan)

Darwin talks about the geometric rate of increase for biological beings. Since this rate of increase is so large, geographic areas tend to be fully inhabited. As the number of ''favoured'' individuals in an area increases it is natural to conclude the number ''unfavoured'' individuals would decrease. Darwin posits that rarity is the precursor to extinction, and that as the number of a specific variation or species decreases so does it's chance of survival/propogation.

Darwin notes that the forms/variations that are closest in functionality to their competition are most at risk of extinction. In Computer Science terms I think this can be exemplified by the 'embrace/extend/extinguish' mentality shown by Microsoft in the late 90's. As products like Word Perfect were emulated/embraced by Microsoft their competitive advantages diminished. New adaptations by Word were then able to more easily displace the competing software, leading to an extinction.

=== DIVERGENCE OF CHARACTER. ===
(Dan)

Darwin poses the idea that varieties are species "under formation", what he calls "''incipient species''". He notes that as diversity increases, wildly different varieties have the chance to capitalise on very different niches in their environment. To the point where two variations of the same species can be exploiting very different environmental characteristics in order to succeed. Small areas open to immigration have the greatest diversity because one must be diverse in order to survive in the overcrowding. Unique variations might allow for access to resources not yet monopolised by the existing swath of inhabitants.

He poses that the idea of diversification of organisms in a region is similar to the physiological division of the organs in a body. For instance, the stomach is a highly specialised organ 'variety' that is very good at getting nutrients out of food.

=== THE PROBABLE EFFECTS OF THE ACTION OF NATURAL SELECTION THROUGH DIVERGENCE OF CHARACTER AND EXTINCTION, ON THE DESCENDANTS OF A COMMON ANCESTOR. ===
(Dan)

My version of the origin of species seems to be missing a diagram. The majority of this section of the chapter is based on discussing this diagram, so I've skipped it here. Someone else should feel free to fill this in if they can find the diagram!

=== ON THE DEGREE TO WHICH ORGANISATION TENDS TO ADVANCE. ===
(Dan)

This section notes that the amount of differentiation increases as organisms age. There is more specialisation to the parts of an organism as time progresses past birth. Accumulation of variation tends towards specialisation.

This leads to an interesting question of why there are so many ''lower'' forms still in existence if specialisation and greater levels of organisation/detail in an organism are better. I.e. why are there still tiny creatures when the large specialised creatures seem to do so well. Shouldn't natural selection have evolved everything to this point?

Darwin questions whether there is always a benefit to higher organisation that natural selection could exploit. Under some conditions such organization and specialisation might make a variation no better off than it's competition. It's even easy to see how it could hinder an organism living in highly volatile situations as the increased complexity might make it more vulnerable/delicate.

In Computer Science terms I think of this as analogous to the question of why some software is still very primitive/simple. It might be the case that increasing the complexity to add features might break it and cause devastating effects. The "KISS" (keep it simple, stupid) principle of software design is an example of this.

=== CONVERGENCE OF CHARACTER. ===
(Dan)

This section discusses reasons why there aren't an infinite number of variations in nature. If variations were always good, and specialisation is useful, why are there species with many individuals of so much similarity? Darwin notes an area can only support so many lifeforms. If the number of truly unique variations was very high then each variation would only have a few representative members.

With only a few representative members in an area, a variation would be prone to extinction from very slight fluctuations in the environment. In this case extermination could be very rapid, and Darwin has already argued why the creation of new species is slow. This imbalance would be quickly corrected or lead to total extinction.

== CHAPTER V. LAWS OF VARIATION ==
(Dan)

== CHAPTER VI. DIFFICULTIES OF THE THEORY ==
(Elizabeth)

In this chapter, Darwin notes some objections to his theory of natural selection, and gives a defense against the criticisms.

===ON THE ABSENCE OR RARITY OF TRANSITIONAL VARIETIES===

The first objection that Darwin addresses is a comment that in nature, we don't seem to ever see transitional varieties of animals. Darwin lists a few possible reasons for this, including pointing out that development progresses slowly, and the process does not necessarily include any period of chaotic variation. He remarks that variation is a slow process: how do we know that what we now see is not a developing version of some other thing?

He also gives some examples in nature that contradict criticisms of this type. He points out that we do see in nature a few variations of one species that show differences in structure, and this presumably is evidence of variation. Also, fossils show records of variation and development, but the record is somewhat flawed and inconsistent, meaning that we cannot see the whole picture.

===ON THE ORIGIN AND TRANSITION OF ORGANIC BEINGS WITH PECULIAR HABITS AND STRUCTURE===
(Elizabeth)

The criticism being addressed in this section is that creatures with odd habits and structural features could not have developed through the process of natural selection. The primary example given is the difference in development between an animal that breathes air, vs. one that is able to breathe underwater. The question is how can a transition have taken place from one species to another when they have features that appear to be mutually exclusive. Darwin's response is that there are several examples of animals with multiple abilities, and he delves into a deeper discussion of whether behaviour drives the development of structure, or whether changing structure propels the emergence of new behaviours.

<blockquote>"It is, however, difficult to decide and immaterial for us, whether habits generally change first and structure afterwards; or whether slight modifications of structure lead to changed habits; both probably often occurring almost simultaneously."</blockquote>

===ORGANS OF EXTREME PERFECTION AND COMPLICATION===
(Elizabeth)

Next, Darwin replies to objections about how complicated and precise organs could have developed. The main example given is the human eye, and the question raised is about how it could have naturally developed the sensitivity to light and ability to focus that have allowed it to be so useful to humans. Darwin points out some less advanced versions of the eye in other creatures, and notes that its evolutionary advantages are clear.

Another aspect of the section is somewhat more philosophical or theological in nature. Darwin mounts a few arguments against design by a creator. In the quote below, he discusses the dangers and inherent self-centredness that comes with assuming a creator would have behaved exactly as a human might.

<blockquote>"It is scarcely possible to avoid comparing the eye with a telescope. We know that this instrument has been perfected by the long-continued efforts of the highest human intellects; and we naturally infer that the eye has been formed by a somewhat analogous process. But may not this inference be presumptuous? Have we any right to assume that the Creator works by intellectual powers like those of man? If we must compare the eye to an optical instrucment, we ought in imagination to take a thick layer of transparent tissue, with spaces filled with fluid, and with a nerve sensitive to light beneath, and then suppose every part of this layer to be continually changing slowly in density, so as to separate into layers of different densities and thicknesses, placed at different distances from each other, and with the surfaces of each layer slowly changing in form. ... Let this process go on for millions of years; and instrument might thus be formed as superior to one of glass, as the works of the Creator are to those of man?"</blockquote>

===MODES OF TRANSITION===
(Elizabeth)

Darwin points out that to his knowledge, no example is known that contradicts his theory of natural selection. He acknowledges that if such an example existed, it would certainly knock down his theory. He also gives a few examples of how we should not be quick to conclude that something could not have been created with natural selection. As evidence against this kind of view, Darwin quotes "Natura non facit saltum" (nature does not make jumps), and points out that new organs never appear.

===SPECIAL DIFFICULTIES OF THE THEORY OF NATURAL SELECTION===
(Elizabeth)

In this section, Darwin discusses a number of examples of features where it is difficult to understand how they could have developed. The examples given are of animals with the ability to produce electric shocks - not only is this ability not universal, animals with the ability don't seem to even use it for the same purposes. An example with parallel properties is the ability of some insects to produce luminescence. It is not understood how such capacities could have developed, nor their evolutionary advantages. The other example given is of a type of orchid which has developed in such a way as to encourage bees to fall into its flower, and when they crawl out, they end up carrying the pollen on their backs, where they carry it to other flowers. This reproductive technique is extremely complicated, but works.

===ORGANS OF LITTLE APPARENT IMPORTANCE, AS AFFECTED BY NATURAL SELECTION===
(Elizabeth)

One objection to the theory of natural selection is that organs exist in creatures that are apparently unused in the current version of the organism. Darwin's response to this criticism is to point out that these organs were presumably of greater importance in previous versions of the creature, and that there may not have been any advantage in getting rid of these organs. Darwin also remarks that we might make errors in what we attribute to natural selection, and the reasons for this selection are not always clear to us. He gives an example of a (fictional) green woodpecker, and remarks that if it existed, we would think its green colour was an adaptive trait, evolved to hide it in the foliage from its enemies. Since we know woodpeckers are not free, we know that this is not the reason it has evolved the way it has.

===UTILITARIAN DOCTRINE, HOW FAR TRUE: BEAUTY, HOW ACQUIRED===
(Elizabeth)

One apparent objection to the theory of natural selection is that it makes no provision for things that have evolved solely to be beautiful. Darwin's reply is largely that beauty is in the eye of the beholder: different cultures and different people regard different items as being beautiful. Darwin points out that things we perceive as beautiful may not have been created for that purpose, and he goes on to point out that it is naive to believe humankind are the only beholders of the world.

Darwin also points out beauty, or distinctiveness, as an adaptive feature developed by natural selection. The example he gives is of flowers, which have become visually distinct from the green grass in order to attract insects. Flowers that do not rely on insects for their survival are not as brightly coloured, because there has been no evolutionary advantage in visual distinctiveness.

== CHAPTER VII. MISCELLANEOUS OBJECTIONS TO THE THEORY OF NATURAL SELECTION ==
(Elizabeth)

This chapter examines in further detail some more objections to Darwin's theory of natural selection, and Darwin's response and defence against the criticism. Most of the defences in this chapter are aimed at specific criticisms, and Darwin responds to specific authors. The bulk of the chapter is aimed at the criticisms of St. George Mivert, who took it upon himself to collect together objections to the theory. Most of Mivert's questions relate to the question of where the initial components of natural selection come from. Darwin's response is usually to give a collection of examples illustrating how the feature in question 'could' have developed, but in general, these are questions about the theory that have no clear answer.

== CHAPTER VIII. INSTINCT ==
=== Instincts comparable with habits, but different in their origin ===
=== Instincts graduated—Aphides and ants ===
=== Instincts variable—Domestic instincts, their origin===
=== Natural instincts of the cuckoo, molothrus, ostrich, and parasitic bees ===
=== Slave-making ants—Hive-bee, its cell-making instinct ===
=== Changes of instinct and structure not necessarily simultaneous ===
=== Difficulties of the theory of the Natural Selection of instincts ===
=== Neuter or sterile insects ===
=== Summary ===

No complex instinct can possibly be produced through natural selection, except by the slow and gradual accumulation of numerous, slight, yet profitable, variations.

Similarly no complex program can be produced in and of itself, at least well, except by adopting small accumulations of tiny programs. Each prototype version will have slight variations, that accomplish similar yet different tasks.

Similarly to how a cell engulfs and uses the properties of other organisms, so too can many programs adopt and make use of smaller programs, if instructed to do so.

How can we program instinctual behaviors into computer programs? Is this possible. The benefits are numerous. Security wise, if a program was to instinctually detect and react to a virus or malicious action, this would cause that particular application to be preferred over others. Similarly, operating systems that tend to be attacked more often, should logically not be used as much. (leading to the frustration of its' users) Unfortunately the human desire to continue to be productive, overrides most concern for security as a secondary task, if thought of at all.

It seems he talks more about adaptation than instinctual behaviour in this chapter. (example given instead of looking for pollen bees will accept the substitute of oatmeal in their search for food.)

Inherited instincts -

With cats, for instance, one naturally takes to catching rats, and another mice, and these tendencies are known to be inherited. One cat, according to Mr. St. John, always brought home game birds, another hares or rabbits, and another hunted on marshy ground and almost nightly caught woodcocks or snipes.

Whereby some cats have a natural tendency to give chase, others have a more calm quality and chase the affection of their owners instead. (Merlin vs. Pinga) Merlin given the chase will pounce after a laser pointer and will watch the mouse on the screen, whereas pinga will jump at any shadow and continually chase the mouse on the projector screen for hours.

Talk about instincts – what about the “robber cat” - seems to bring home any articles that it can lift up (from underwear / socks / children's toys) from the neighbourhood (learned this behaviour in order to impress it's owner?) This cat was videotaped at night to see if the rumors about it stealing things was correct.

What are we teaching these animals?

Should we make computers adapt similarly – instincts could be thought of as programs – we write programs to make our lives effectively easier – I would say that a program could be thought of as an instinct – if similar to a script that makes our life easier – now only if the computer could read our mind, and apply these instincts at the appropriate moment in time – for example if the user is in the habit of looking at a web page first thing in the morning and saving a particular image, perhaps opening and starting the web browser, going to that page automatically and downloading the image – might be an appropriate instinct for that user's computer to do. However based upon these instincts – once learning them could become a security risk. For if you knew that the computer would do those things – then you can as an attacker exploit the fact that you know what actions will be taken instinctually.
But let us look to the familiar case of the breeds of dogs: it cannot be doubted that young pointers (I have myself seen striking instances) will sometimes point and even back other dogs the very first time that they are taken out; retrieving is certainly in some degree inherited by retrievers; and a tendency to run round, instead of at, a flock of sheep, by shepherd-dogs.

Barking at the sound of a door – barking even before the person gets home, because they have a sense that they are coming home.

Tendancy to run around, when they are being aggressive, not just towards sheep, but other people and dogs as well. Still categories of instinctual behaviour – non-aggressive, passive, and aggressive.

Define domestic instincts – how do they differ from natural instints -

Domestic instincts, as they may be called, are certainly far less fixed than natural instincts; but they have been acted on by far less rigorous selection, and have been transmitted for an incomparably shorter period, under less fixed conditions of life.

When the first tendency to point was once displayed, methodical selection and the inherited effects of compulsory training in each successive generation would soon complete the work; and unconscious selection is still in progress, as each man tries to procure, without intending to improve the breed, dogs which stand and hunt best.
Hence, we may conclude that under domestication instincts have been acquired and natural instincts have been lost, partly by habit and partly by man selecting and accumulating, during successive generations, peculiar mental habits and actions, which at first appeared from what we must in our ignorance call an accident. In some cases compulsory habit alone has sufficed to produce inherited mental changes; in other cases compulsory habit has done nothing, and all has been the result of selection, pursued both methodically and unconsciously; but in most cases habit and selection have probably concurred.

Mockingly reproduce similar actions to these ( such as Gates' house where you walk into a room and your media follows you / the lights turn on, etc.) How are these habits going to affect our instincts?

Def: Nidification – act of building a nest.

== CHAPTER IX. HYBRIDISM ==
(Annie)

== CHAPTER X. ON THE IMPERFECTION OF THE GEOLOGICAL RECORD ==
(???)

== CHAPTER XI. ON THE GEOLOGICAL SUCCESSION OF ORGANIC BEINGS ==
(???)

== CHAPTER XII. GEOGRAPHICAL DISTRIBUTION ==

(Mohamed)

''' Present distribution cannot be accounted for by differences in physical conditions'''

-When considering the distribution of organic beings over the face of the globe, different climates and physical conditions in various regions are not the only factor that affects the similarity or dissimilarity of beings.

-Although the climatal conditions of to geographically distributed worlds could be very similar, their fauna/flora could be very different and the opposite is true as well (different conditions, closely related flora/fauna).

'''Importance of barriers'''

Obstacles to free migration, are related in a close and important manner to the differences between the productions of various regions.

'''Affinity of the productions of the same continent or of the same sea'''

-Throughout a single continent, species are specifically distinct though nearly related.

-Similarities of species is attributed to inheritance and their difference attributed to variation and natural selection and to a degree, the different physical conditions.

-Inheritance with modification through migration.

'''SINGLE CENTRES OF SUPPOSED CREATION'''

The idea that each species having been produced in one area alone, and having subsequently migrated from that area as far as its powers of migration and subsistence under past and present conditions permitted, is the most probable. The idea that all species had a single birth place seems to be the safest to assume.

'''MEANS OF DISPERSAL'''

-Different climate and geological patterns in the past could have enabled migration that is now not possible. (e.g Pangaea)

-Accidental dispersal such as a flood washing a fruit out to sea, birds, icebergs.

-Multiple birth origins can be explained by the glacial period.

-Glacial periods in one hemisphere coincides with a warmer period in the northern hemisphere. Thus Migration occurred.

== CHAPTER XIII. GEOGRAPHICAL DISTRIBUTION—continued ==
(???)

== CHAPTER XIV. MUTUAL AFFINITIES OF ORGANIC BEINGS ==
(???)

== CHAPTER XV. RECAPITULATION AND CONCLUSION ==
(???)

BioSec: Evolution

2012-02-06T21:27:14Z

Dsouza3190: /* CHAPTER II. VARIATION UNDER NATURE */

For help in mediawiki formatting see reference: http://www.mediawiki.org/wiki/Help:Formatting

== Purpose: ==

To retell Darwin's argument associating the biological with the technological.

The sections are as follows:

== CHAPTER I - VARIATION UNDER DOMESTICATION. ==

=== Causes of Variability ====

(Luc)

*Conditions of Life:
**Quantity of food
**Type of food
**Climate
*Pre-existing tendency towards variation
*Nature of the Organism

"Indefinite Variations" sounds like observations made in ignorance of genetics. Though, to be fair, we still see variations that are not well understood (Twin research, knockout mice)

Darwin argues that nature exerts pressure on organisms to adapt. As conditions of life change, species will modify themselves to either streamline themselves to harsher conditions or to take advantage of conditions of abundance (domestication).

However, while nature can apply external pressure on species to adapt, the species themselves will determine which parameters to modify. Determining which parameters will change seemed to be, at least to Darwin, an exercise in futility as different organisms within the species will be observed with differently modified parameters.

Technology:

While I'm not sure I'd call desktop Linux distributions a species, they have all mostly existed in the same environment, with environmental pressures being fairly uniform. Yet, if one were to compare Fedora, Debian, Ubuntu, Arch, Gentoo, and SuSE, it becomes glaringly obvious that each has tried to survive using different (sometimes radically different) strategies. The same can be seen in window managers, shells, scripting languages, and browsers. I, for one, would not want to have to predict how vastly increased availability in network bandwidth, or the sudden stagnation of memory availability would change the evolution of browsers.

===Effects of Habit and the use or disuse of Parts ===
(Mohamed)

=== Correlated Variation ===
(Annie)

Darwin in this section was stating that you cannot breed selectively for only one type of trait, as traits come in groupings (of at least two). Single examples were stated such as one cannot have a long limbed animal without an elongated head, or cats with white hair and blue eyes are deaf, or long, coarse haired animals tend to have horns.

His conclusion stated: "Hence if man goes on selecting and thus augmenting, any peculiarity, he will almost certainly modify unintentionally other parts of the structure, owing to the mysterious laws of correlation. The results of the various, unknown or but dimly understood laws of variation are infinitely complex and diversified.... it is really surprising to note the endless points of structure and constitution in which the varieties and sub-varieties differ slightly from each other."

To a certain degree this still applies even with the case of genetic engineering. As I think that specific genes within DNA are known to affect multiple traits. Isolating those genes individually will still affect the "engineered" animal in potentially multiple ways, as it is not only the genes, it is their interactions which may be modified and potentially corrected? (totally guessing here)

Technology wise there is a certain correlation between the graphical user interface and the program of an application. This is not evolutionary however, as it is of course due to design. Change the purpose of the program, and the user interface will have to change as well to accommodate the change. (?)

=== Inheritance ===
(Cheryl)

Darwin comes to the conclusion that the only way to explain variation is reproduction, through which parent pass on specific variations to their offspring. Furthermore, these variations are then carried and passed on from one generation to the next. Darwin also admits that scientist do not completely understand the law s that govern inheritance. Thus, scientists cannot explain why some traits are inherited by the off springs and why some are not; or why some traits skip a generation. In addition, Darwin notes that it is not clear if the various species types are the offspring of one parent species or not. He studied different domestic pigeons and cross bread them. The offspring resulted in a “perfectly fertile” species. From this he concluded that the various species are the offspring from one parent. This is because the offspring of two parents would result in a sterile offspring.

From a computer science perspective, inheritance is seen in a number ways. For example different versions of the same software can be viewed as parents and their offspring. Where the original software is the “rock” parent and the subsequent versions are its offspring. Inheritance can also be seen in programming; where programmers generally reuse parts of code. Furthermore, in object-oriented programming (OOP), inheritance describes the ability of one class to use methods and properties of another class. Another example could possibly be polymorphic code which uses a polymorphic engine to mutate however keeping the original algorithms. This can be seen in computer viruses and worms.

=== Character of Domestic Varieties ===
(Annie)
In domestic varieties there is less uniformity of character than in true species
The monstrous character of domestic varieties is defined by the small differences in some respects while differing in an extreme degree in a specific part. This is determined upon close inspection with a sample of the wild stock versus the domestic stock, as well as domestic stock with one another.
Closely connected wild species of the same genus in nature still differ from one another, except those differences aren't as radical as when you compare the domesticated version to the wild species. This explains why some smart people believe that the domestic races of many animals and plants have been judged as the descendants of aboriginally distinct species and other smart people claim that they are just varieties of the same species. Naturalists have differing opinions in what determines which characters are of generic value; all such valuations being at present empirical.

!! NOTE: NOT FINISHED !!

=== Difficulty of distinguishing between Varieties and Species ===
(Annie)
=== Origin of Domestic Varieties from one or more Species ===
(Cheryl)

Darwin states that in the case of most domesticated species it is not possible to pin point their origins. Thus we are unsure if they are the offspring of one parent species or multiple parent species. However, Darwin believes that all the different breeds come from one common parent. But he does not any evidence to confirm this hypothesis.

The authors of the book “Domestication of Media and Technology” discuss innovations are ‘tamed or domesticated’ by users – that is how technology is no longer a novelty but an aspect of everyday life. For example computers are now ‘domesticated’ because they are used by almost everyone and it is part of everyday life. However, there are many different types of computers, each slightly distinct from the other, however they all have the same basic core components.

=== Domestic Pigeons, their Differences and Origin ===

(Dan)

In this section Darwin argues the common ancestry of a variety of Pigeon breeds. Using the Pigeon as a case study he develops an argument proposing that despite the high variance within Pigeon breeds it can be reasoned that the [http://en.wikipedia.org/wiki/Rock_Pigeon Rock Pigeon (Columba Livia)] is their aboriginal ancestor.

Darwin's choice of studying Pigeons was not arbitrary (though he admits a certain infatuation with the species); a large selection of pigeon breeds was available for study and there was a historical body of treatises on the species to draw from. He begins the case study by establishing the diversity of pigeon breeds, and the aspects by which they differ. Nearly every aspect of the species is variable when examined with sufficient scope. Notable differences included the size and shape of the beak, in-flight behavior, feather appearance, age at which maturity is achieved, and skeleton details such as size, shape and count of various bone structures.

With such a great level of diversity between breeds, and the striking physical differences this diversity brings, Darwin posits it would be easy for a naturalist to assume many unique ancestor species. Darwin's counter argument to this assumption builds on the absence of any candidate species to fill this ancestral role. In order to create the present breeds as anything other than sub-varieties of a common ancestor a parent species must exist for the unique traits that are to be merged. For instance, the Porter breed has a large [http://en.wikipedia.org/wiki/Crop_%28anatomy%29 crop] that would have to have been inherited in the multiple origin species hypothesis. The absence of such an origin species indicates that either ornithologists have yet to discover the species, or that it has gone extinct. Due to the proliferation of Pigeons Darwin finds both possibilities unlikely and considers this as evidence towards the common ancestor theory. Darwin points to the fertility of hybrid (mongrel) Pigeons as further evidence supporting his common ancestry theory. For such a large selection of Pigeon breeds to cross-breed successfully and produce fertile offspring their commonality must run quite deep.

Interestingly Darwin notes that the naturalists dedication to their area of study reduces their ability to accept the common ancestry theory. With a deep appreciation of the differences of each breed it is the naturalist's view that only several unique species could explain the diversity they so well understand.

From a computer science perspective I ponder the idea of an outside observer trying to establish the common ancestry of a handful of [http://en.wikipedia.org/wiki/POSIX POSIX] descendent operating systems. As a user the OSX, Linux and Solaris operating systems seem highly divergent from one another. Much like a naturalist would assume no historic relation between Pigeon breeds, so too would an end user not assume a unified ancestor for the unique operating systems. Yet, underneath there are well established commonalities. Darwin's argument related to the fertility of offspring born of hybrid Pigeons could be similarly established for POSIX operating systems by means of considering a program written to POSIX standard running on the divergent operating systems mentioned. For a single program to successfully execute on three very different operating systems without the notion of a common ancestor seems highly improbable.

=== Principles of Selection, anciently followed, their Effects ===
(Moe)

-The production of domestic species: Effects may be attributed to direct and definite action of the external conditions of life and some to habit.

-Adaptation seen in domesticated races is not necessarily in the species' own good but rather more to the benefit of the breeder.

-The key to variation of domestic species is man's power of accumulative selection.

-Nature gives successive variations, man adds them up in certain directions

-Continued selection of slight variations produces races different from each other.

=== Methodical and Unconscious Selection ===
(Elizabeth)

In discussing the selection process that takes place in the breeding of domesticated animals, Darwin distinguishes two kinds of selection: ''methodical selection'', where breeders start with an idea in mind and deliberately attempt to create a new and superior species; and ''unconscious selection'', where many people try to get ahold of the best animals and by doing so, improve the breed. Darwin is primarily interested in unconscious selection, and notes the importance of observation and documentation, so that these changes become noticeable.

In the world of computing, parallels of the process of unconscious selection can be seen in many situations. Some examples might be the process of code development – where the same task might be coded in several ways, and eventually unified into the most efficient process once all the possibilities have been explored. A more economically motivated example might be when multiple products are competing in a market. Though no particular consumer has any intention of improving the field of desktop publishing, all consumers want to use the product that creates the most beautiful documents. Thus, the program that most people buy gets further examination and development, leading to improvement.

<blockquote>“Man can hardly select, or only with much difficulty, any deviation of structure excepting such as is externally visible; and indeed he rarely cares for what is internal. He can never act by selection, excepting on variations which are first given to him in some slight degree by nature.”</blockquote>

Darwin reflects briefly on the nature of unconscious selection, and discusses how although humankind has shaped the development of various species, the ideas always come from nature, and humans must work within the limitations of the domain.

(How is this true of computing?)

=== Unknown Origin of our Domestic Productions ===
(Elizabeth)



Darwin briefly brings up a point about the unknown ancestors of domestic breeds. His point seems to be that the process of development through selection is slow, and individual changes are small, and this means that no one pays attention to the initial stages when the creature is undeveloped. At first glance, this section is not obviously true of computers. We know exactly where computers came from, and how they developed. However, the point about small changes sometimes leading to more important changes later is true of the development of computers. In a smaller context, it is easy to see that the reasons behind early changes are often lost, leaving behind no evidence of the program they were created to deal with.

=== Circumstances favourable to Man's power of Selection ===
(Elizabeth)

In the final section of the first chapter of “The Origin of Species”, Darwin discusses the kinds of circumstances that facilitate the successful domestic selection of animals. Several of the factors Darwin lists are contextual factors. He remarks that a high degree of variability in the population is needed to attempt selective breeding, and that someone must have access to and control over a large population. In addition, he remarks that there must be some obvious value in undertaking this challenge.

<blockquote>“… the animal or plant should be so highly valued by man, that the closest attention is paid to even the slightest deviations in its qualities or structure.”</blockquote>

From the perspective of facilitating the development and selection of computer programs, it seems possible that similar contextual factors are needed. In place of a high degree of population variation, we could perhaps substitute a high degree of knowledge, expertise and experience. It seems entirely sensible that an organization who has access to large amounts of expertise, experience, equipment (and presumably, budget) would be positioned to motivate and commission work in the area. Darwin’s remark that “... the [product] should be so highly valued by man, that the closest attention is paid to even the slightest deviations in its qualities or structures” can be directly applied to the construction of computer programs. It seems believable that development and evolution of computer products (whether hardware or software) are likely to be more successful when there is a clear need or use for the product.

(What kind of organizations will have these privileges? Large corporations, like Google, sure. But what about people developing open source software? Crowd-sourced efforts, like Wikipedia? )

Darwin also notes a few factors that affect selection that have more to do with the nature of the creature at hand. Clearly, determined selection will be much easier if the species can be easily crossed, but it is also necessary to be able to prevent species from crossing at will or at random. For computer products, these two factors seem relatively easy to accomplish. Programs usually change only in the way specified by the developers and programmers, and if left alone, most computer programs do not change, merge or reproduce. (What about computer viruses, things like that?)

Part of Darwin’s discussion is of the limits of natural selection – how far can selection be pushed? He acknowledges that some limitations are defined by the capability of the product, but he also notes that external pressures affect the limitations of development. For computers, I think these limitations include hardware limitations (presumably some products will be developed at the time that the hardware exists to implement them), but I think that the external limitations come not only from the perceived need for the product, but also from the need for someone to have an idea for the product. We cannot develop products we have not thought of, or have an idea of their use or necessity.

== CHAPTER II. VARIATION UNDER NATURE ==
(Cheryl)

In this chapter Darwin basically answers the question: Can variation in species that are present in nature be considered similar to variations that are present in domesticated species?

He starts answering this question by describing three types of variations. The first type is what he calls monstrosities. These are variations that occur naturally in nature but are not really helpful in terms of survival or development of the species. In some instances, these variations are even harmful for the particular species. In the second case, variations are said to be driven due to environmental change (i.e. climate, temperature, etc.). Lastly, variations are the result of a small variation in genes that are passed from parents to their offspring. Darwin states that the first two cases of variations are most likely not passed from parents to offspring, while the third is.

The problem lies when trying to differentiate variations within a species from variations that imply the existence of two distinct species. Darwin notes that it is next to impossible to distinguish between varieties within a species. The solution to the problem is somewhat vague but clear enough to distinguish between varieties: “The amount of difference between species must be greater than the amount of difference between varieties within the species”.

Lastly, Darwin concludes by noting that variations are more likely to occur in a large sample. He does this by arguing that each species is not an act of God. Because if it were an act of God, there would be no real difference in the amount of variety between the smaller and larger groups of species.

== CHAPTER III. STRUGGLE FOR EXISTENCE ==
(Cheryl)

== CHAPTER IV. NATURAL SELECTION; OR THE SURVIVAL OF THE FITTEST ==
(Dan)

In this chapter Darwin discusses the force of natural selection and the concept of ''survival of the fittest''. He begins by pointing out a reminder that in artificial selection, man can not create varieties only preserve and accumulate the ones beneficial to their needs. Since changes can and do occur in nature, then there must too be a means by which nature accumulates changes according to some goal. The question of what the goal is leads to the notions of natural fitness.

Variations that are useful in adapting to the wild environment can accumulate in successive generations. Since more beings are born than survive even slight advantages can increase the chance of survival, and in turn the chance of procreation. Increased procreation leads to the passing on/accumulating of these variations. Conversely, "injurious" variations, those that harm survival, are likely to be quickly eliminated by these properties of natural selection. Natural selection can be boiled down to preserving beneficial variations, and eliminating detrimental ones. Variations with no affect on survival/reproduction are "fluctuations".

Darwin notes there is a tight coupling between species and that a change in a large number of inhabitants of an area will greatly affect the others even if they are not directly affected by the cause of the initial changes.

Darwin also discusses the fact that nature pays no heed to aesthetics except when they additional serve a functional purpose. While man operating artificially can only select based on properties he can observe, nature operates on all the ''machinery'' of life. Additionally, the scale of time at which natural selection operates affords it the ability to accumulate massive amounts of variation.

From a computer science perspective I consider the perspectives of a user and a programmer. A user selects software based on the surface level details they can perceive, usability, potentially speed of use, features, etc. A programmer may be selecting designs underlying the software based on much finer detail, memory usage, cpu cycles, elegance of component exchange, the ''machinery'' of the program. Probably not the best analogy but it's the first that comes to mind.

=== SEXUAL SELECTION ===
(Dan)

Darwin notes that often in nature artificial selection has created variation between sexes of the same species. He notes that in conjunction to the ''fitness'' of surviving, there is a ''fitness'' to reproducing. Intra-species struggles between individuals to find the best mate, or to have a chance to mate are common.

He notes this form of selection might be "less rigorous" in that you must survive to reproduce and so survival clearly plays a more significant role in selection than reproduction alone.

=== ILLUSTRATIONS OF THE ACTION OF NATURAL SELECTION, OR THE SURVIVAL OF THE FITTEST. ===
(Dan)

In this section Darwin talks of the idea that a local variation that has success can spread outwards, and often displace less adapted individuals/species. He notes that there is often a tight coupling between separate species that is exploited to a great degree, causing mutually beneficial variations to have great influence on the progression of evolution.

He gives the dependency between flowers and birds as an example. The bees benefit from increased pollen creation by a flower variation, and the flower benefits from a bees ability to travel greater distances or survive longer.

=== ON THE INTERCROSSING OF INDIVIDUALS. ===
(Dan)

Darwin notes that it is very important for members of a species to cross with one another to reproduce, that is, to not reproduce as single units in isolation by fertilising themselves. He states that close ''interbreeding'' diminishes fertility and vigour while crossing of separate individuals does the opposite. In support of these notions Darwin notes that relatively speaking there are few hermaphrodite species and even fewer that fertilise themselves.

Further evidence is given by the fact that many plant reproductive organs are placed very closely together. This arrangement would seemingly be optimised for self-fertilisation, but instead natural selection has lead to fairly advanced measures that prevent a plant from fertilising itself easily. Since natural selection only selects for beneficial attributes it must be reasoned that there is a reason self-fertilisation is so rare.

=== CIRCUMSTANCES FAVOURABLE FOR THE PRODUCTION OF NEW FORMS THROUGH NATURAL SELECTION. ===
(Dan)

In this section Darwin discusses some geographical constraints on selection. He notes that any one species that can't keep up with the adaptations of a competitor will be quickly exterminated.

Isolation plays an important role in natural selection in that it may prevent other species or variations from "swooping in" and taking a niche that might have been used by an existing species if given time to accumulate variations useful for that niche. He notes that confined areas tend to have more "uniform" life and that this life is operated on by selection in the same ways across the board.

Darwin is careful to clarify that time alone does nothing and that it merely allows for a greater chance of useful variations to occur, and be accumulated. Natural selection can only act when there is a niche to be filled by some new adaptation, otherwise things stagnate. These new "niches" are often caused by physical changes (climate, geography, etc) and are generally very slow acting.

=== EXTINCTION CAUSED BY NATURAL SELECTION. ===
(Dan)

Darwin talks about the geometric rate of increase for biological beings. Since this rate of increase is so large, geographic areas tend to be fully inhabited. As the number of ''favoured'' individuals in an area increases it is natural to conclude the number ''unfavoured'' individuals would decrease. Darwin posits that rarity is the precursor to extinction, and that as the number of a specific variation or species decreases so does it's chance of survival/propogation.

Darwin notes that the forms/variations that are closest in functionality to their competition are most at risk of extinction. In Computer Science terms I think this can be exemplified by the 'embrace/extend/extinguish' mentality shown by Microsoft in the late 90's. As products like Word Perfect were emulated/embraced by Microsoft their competitive advantages diminished. New adaptations by Word were then able to more easily displace the competing software, leading to an extinction.

=== DIVERGENCE OF CHARACTER. ===
(Dan)

Darwin poses the idea that varieties are species "under formation", what he calls "''incipient species''". He notes that as diversity increases, wildly different varieties have the chance to capitalise on very different niches in their environment. To the point where two variations of the same species can be exploiting very different environmental characteristics in order to succeed. Small areas open to immigration have the greatest diversity because one must be diverse in order to survive in the overcrowding. Unique variations might allow for access to resources not yet monopolised by the existing swath of inhabitants.

He poses that the idea of diversification of organisms in a region is similar to the physiological division of the organs in a body. For instance, the stomach is a highly specialised organ 'variety' that is very good at getting nutrients out of food.

=== THE PROBABLE EFFECTS OF THE ACTION OF NATURAL SELECTION THROUGH DIVERGENCE OF CHARACTER AND EXTINCTION, ON THE DESCENDANTS OF A COMMON ANCESTOR. ===
(Dan)

My version of the origin of species seems to be missing a diagram. The majority of this section of the chapter is based on discussing this diagram, so I've skipped it here. Someone else should feel free to fill this in if they can find the diagram!

=== ON THE DEGREE TO WHICH ORGANISATION TENDS TO ADVANCE. ===
(Dan)

This section notes that the amount of differentiation increases as organisms age. There is more specialisation to the parts of an organism as time progresses past birth. Accumulation of variation tends towards specialisation.

This leads to an interesting question of why there are so many ''lower'' forms still in existence if specialisation and greater levels of organisation/detail in an organism are better. I.e. why are there still tiny creatures when the large specialised creatures seem to do so well. Shouldn't natural selection have evolved everything to this point?

Darwin questions whether there is always a benefit to higher organisation that natural selection could exploit. Under some conditions such organization and specialisation might make a variation no better off than it's competition. It's even easy to see how it could hinder an organism living in highly volatile situations as the increased complexity might make it more vulnerable/delicate.

In Computer Science terms I think of this as analogous to the question of why some software is still very primitive/simple. It might be the case that increasing the complexity to add features might break it and cause devastating effects. The "KISS" (keep it simple, stupid) principle of software design is an example of this.

=== CONVERGENCE OF CHARACTER. ===
(Dan)

This section discusses reasons why there aren't an infinite number of variations in nature. If variations were always good, and specialisation is useful, why are there species with many individuals of so much similarity? Darwin notes an area can only support so many lifeforms. If the number of truly unique variations was very high then each variation would only have a few representative members.

With only a few representative members in an area, a variation would be prone to extinction from very slight fluctuations in the environment. In this case extermination could be very rapid, and Darwin has already argued why the creation of new species is slow. This imbalance would be quickly corrected or lead to total extinction.

== CHAPTER V. LAWS OF VARIATION ==
(Dan)

== CHAPTER VI. DIFFICULTIES OF THE THEORY ==
(Elizabeth)

In this chapter, Darwin notes some objections to his theory of natural selection, and gives a defense against the criticisms.

===ON THE ABSENCE OR RARITY OF TRANSITIONAL VARIETIES===

The first objection that Darwin addresses is a comment that in nature, we don't seem to ever see transitional varieties of animals. Darwin lists a few possible reasons for this, including pointing out that development progresses slowly, and the process does not necessarily include any period of chaotic variation. He remarks that variation is a slow process: how do we know that what we now see is not a developing version of some other thing?

He also gives some examples in nature that contradict criticisms of this type. He points out that we do see in nature a few variations of one species that show differences in structure, and this presumably is evidence of variation. Also, fossils show records of variation and development, but the record is somewhat flawed and inconsistent, meaning that we cannot see the whole picture.

===ON THE ORIGIN AND TRANSITION OF ORGANIC BEINGS WITH PECULIAR HABITS AND STRUCTURE===
(Elizabeth)

The criticism being addressed in this section is that creatures with odd habits and structural features could not have developed through the process of natural selection. The primary example given is the difference in development between an animal that breathes air, vs. one that is able to breathe underwater. The question is how can a transition have taken place from one species to another when they have features that appear to be mutually exclusive. Darwin's response is that there are several examples of animals with multiple abilities, and he delves into a deeper discussion of whether behaviour drives the development of structure, or whether changing structure propels the emergence of new behaviours.

<blockquote>"It is, however, difficult to decide and immaterial for us, whether habits generally change first and structure afterwards; or whether slight modifications of structure lead to changed habits; both probably often occurring almost simultaneously."</blockquote>

===ORGANS OF EXTREME PERFECTION AND COMPLICATION===
(Elizabeth)

Next, Darwin replies to objections about how complicated and precise organs could have developed. The main example given is the human eye, and the question raised is about how it could have naturally developed the sensitivity to light and ability to focus that have allowed it to be so useful to humans. Darwin points out some less advanced versions of the eye in other creatures, and notes that its evolutionary advantages are clear.

Another aspect of the section is somewhat more philosophical or theological in nature. Darwin mounts a few arguments against design by a creator. In the quote below, he discusses the dangers and inherent self-centredness that comes with assuming a creator would have behaved exactly as a human might.

<blockquote>"It is scarcely possible to avoid comparing the eye with a telescope. We know that this instrument has been perfected by the long-continued efforts of the highest human intellects; and we naturally infer that the eye has been formed by a somewhat analogous process. But may not this inference be presumptuous? Have we any right to assume that the Creator works by intellectual powers like those of man? If we must compare the eye to an optical instrucment, we ought in imagination to take a thick layer of transparent tissue, with spaces filled with fluid, and with a nerve sensitive to light beneath, and then suppose every part of this layer to be continually changing slowly in density, so as to separate into layers of different densities and thicknesses, placed at different distances from each other, and with the surfaces of each layer slowly changing in form. ... Let this process go on for millions of years; and instrument might thus be formed as superior to one of glass, as the works of the Creator are to those of man?"</blockquote>

===MODES OF TRANSITION===
(Elizabeth)

Darwin points out that to his knowledge, no example is known that contradicts his theory of natural selection. He acknowledges that if such an example existed, it would certainly knock down his theory. He also gives a few examples of how we should not be quick to conclude that something could not have been created with natural selection. As evidence against this kind of view, Darwin quotes "Natura non facit saltum" (nature does not make jumps), and points out that new organs never appear.

===SPECIAL DIFFICULTIES OF THE THEORY OF NATURAL SELECTION===
(Elizabeth)

In this section, Darwin discusses a number of examples of features where it is difficult to understand how they could have developed. The examples given are of animals with the ability to produce electric shocks - not only is this ability not universal, animals with the ability don't seem to even use it for the same purposes. An example with parallel properties is the ability of some insects to produce luminescence. It is not understood how such capacities could have developed, nor their evolutionary advantages. The other example given is of a type of orchid which has developed in such a way as to encourage bees to fall into its flower, and when they crawl out, they end up carrying the pollen on their backs, where they carry it to other flowers. This reproductive technique is extremely complicated, but works.

===ORGANS OF LITTLE APPARENT IMPORTANCE, AS AFFECTED BY NATURAL SELECTION===
(Elizabeth)

One objection to the theory of natural selection is that organs exist in creatures that are apparently unused in the current version of the organism. Darwin's response to this criticism is to point out that these organs were presumably of greater importance in previous versions of the creature, and that there may not have been any advantage in getting rid of these organs. Darwin also remarks that we might make errors in what we attribute to natural selection, and the reasons for this selection are not always clear to us. He gives an example of a (fictional) green woodpecker, and remarks that if it existed, we would think its green colour was an adaptive trait, evolved to hide it in the foliage from its enemies. Since we know woodpeckers are not free, we know that this is not the reason it has evolved the way it has.

===UTILITARIAN DOCTRINE, HOW FAR TRUE: BEAUTY, HOW ACQUIRED===
(Elizabeth)

One apparent objection to the theory of natural selection is that it makes no provision for things that have evolved solely to be beautiful. Darwin's reply is largely that beauty is in the eye of the beholder: different cultures and different people regard different items as being beautiful. Darwin points out that things we perceive as beautiful may not have been created for that purpose, and he goes on to point out that it is naive to believe humankind are the only beholders of the world.

Darwin also points out beauty, or distinctiveness, as an adaptive feature developed by natural selection. The example he gives is of flowers, which have become visually distinct from the green grass in order to attract insects. Flowers that do not rely on insects for their survival are not as brightly coloured, because there has been no evolutionary advantage in visual distinctiveness.

== CHAPTER VII. MISCELLANEOUS OBJECTIONS TO THE THEORY OF NATURAL SELECTION ==
(Elizabeth)

This chapter examines in further detail some more objections to Darwin's theory of natural selection, and Darwin's response and defence against the criticism. Most of the defences in this chapter are aimed at specific criticisms, and Darwin responds to specific authors. The bulk of the chapter is aimed at the criticisms of St. George Mivert, who took it upon himself to collect together objections to the theory. Most of Mivert's questions relate to the question of where the initial components of natural selection come from. Darwin's response is usually to give a collection of examples illustrating how the feature in question 'could' have developed, but in general, these are questions about the theory that have no clear answer.

== CHAPTER VIII. INSTINCT ==
=== Instincts comparable with habits, but different in their origin ===
=== Instincts graduated—Aphides and ants ===
=== Instincts variable—Domestic instincts, their origin===
=== Natural instincts of the cuckoo, molothrus, ostrich, and parasitic bees ===
=== Slave-making ants—Hive-bee, its cell-making instinct ===
=== Changes of instinct and structure not necessarily simultaneous ===
=== Difficulties of the theory of the Natural Selection of instincts ===
=== Neuter or sterile insects ===
=== Summary ===

No complex instinct can possibly be produced through natural selection, except by the slow and gradual accumulation of numerous, slight, yet profitable, variations.

Similarly no complex program can be produced in and of itself, at least well, except by adopting small accumulations of tiny programs. Each prototype version will have slight variations, that accomplish similar yet different tasks.

Similarly to how a cell engulfs and uses the properties of other organisms, so too can many programs adopt and make use of smaller programs, if instructed to do so.

How can we program instinctual behaviors into computer programs? Is this possible. The benefits are numerous. Security wise, if a program was to instinctually detect and react to a virus or malicious action, this would cause that particular application to be preferred over others. Similarly, operating systems that tend to be attacked more often, should logically not be used as much. (leading to the frustration of its' users) Unfortunately the human desire to continue to be productive, overrides most concern for security as a secondary task, if thought of at all.

It seems he talks more about adaptation than instinctual behaviour in this chapter. (example given instead of looking for pollen bees will accept the substitute of oatmeal in their search for food.)

Inherited instincts -

With cats, for instance, one naturally takes to catching rats, and another mice, and these tendencies are known to be inherited. One cat, according to Mr. St. John, always brought home game birds, another hares or rabbits, and another hunted on marshy ground and almost nightly caught woodcocks or snipes.

Whereby some cats have a natural tendency to give chase, others have a more calm quality and chase the affection of their owners instead. (Merlin vs. Pinga) Merlin given the chase will pounce after a laser pointer and will watch the mouse on the screen, whereas pinga will jump at any shadow and continually chase the mouse on the projector screen for hours.

Talk about instincts – what about the “robber cat” - seems to bring home any articles that it can lift up (from underwear / socks / children's toys) from the neighbourhood (learned this behaviour in order to impress it's owner?) This cat was videotaped at night to see if the rumors about it stealing things was correct.

What are we teaching these animals?

Should we make computers adapt similarly – instincts could be thought of as programs – we write programs to make our lives effectively easier – I would say that a program could be thought of as an instinct – if similar to a script that makes our life easier – now only if the computer could read our mind, and apply these instincts at the appropriate moment in time – for example if the user is in the habit of looking at a web page first thing in the morning and saving a particular image, perhaps opening and starting the web browser, going to that page automatically and downloading the image – might be an appropriate instinct for that user's computer to do. However based upon these instincts – once learning them could become a security risk. For if you knew that the computer would do those things – then you can as an attacker exploit the fact that you know what actions will be taken instinctually.
But let us look to the familiar case of the breeds of dogs: it cannot be doubted that young pointers (I have myself seen striking instances) will sometimes point and even back other dogs the very first time that they are taken out; retrieving is certainly in some degree inherited by retrievers; and a tendency to run round, instead of at, a flock of sheep, by shepherd-dogs.

Barking at the sound of a door – barking even before the person gets home, because they have a sense that they are coming home.

Tendancy to run around, when they are being aggressive, not just towards sheep, but other people and dogs as well. Still categories of instinctual behaviour – non-aggressive, passive, and aggressive.

Define domestic instincts – how do they differ from natural instints -

Domestic instincts, as they may be called, are certainly far less fixed than natural instincts; but they have been acted on by far less rigorous selection, and have been transmitted for an incomparably shorter period, under less fixed conditions of life.

When the first tendency to point was once displayed, methodical selection and the inherited effects of compulsory training in each successive generation would soon complete the work; and unconscious selection is still in progress, as each man tries to procure, without intending to improve the breed, dogs which stand and hunt best.
Hence, we may conclude that under domestication instincts have been acquired and natural instincts have been lost, partly by habit and partly by man selecting and accumulating, during successive generations, peculiar mental habits and actions, which at first appeared from what we must in our ignorance call an accident. In some cases compulsory habit alone has sufficed to produce inherited mental changes; in other cases compulsory habit has done nothing, and all has been the result of selection, pursued both methodically and unconsciously; but in most cases habit and selection have probably concurred.

Mockingly reproduce similar actions to these ( such as Gates' house where you walk into a room and your media follows you / the lights turn on, etc.) How are these habits going to affect our instincts?

Def: Nidification – act of building a nest.

== CHAPTER IX. HYBRIDISM ==
(Annie)

== CHAPTER X. ON THE IMPERFECTION OF THE GEOLOGICAL RECORD ==
(???)

== CHAPTER XI. ON THE GEOLOGICAL SUCCESSION OF ORGANIC BEINGS ==
(???)

== CHAPTER XII. GEOGRAPHICAL DISTRIBUTION ==

(Mohamed)

''' Present distribution cannot be accounted for by differences in physical conditions'''

-When considering the distribution of organic beings over the face of the globe, different climates and physical conditions in various regions are not the only factor that affects the similarity or dissimilarity of beings.

-Although the climatal conditions of to geographically distributed worlds could be very similar, their fauna/flora could be very different and the opposite is true as well (different conditions, closely related flora/fauna).

'''Importance of barriers'''

Obstacles to free migration, are related in a close and important manner to the differences between the productions of various regions.

'''Affinity of the productions of the same continent or of the same sea'''

-Throughout a single continent, species are specifically distinct though nearly related.

-Similarities of species is attributed to inheritance and their difference attributed to variation and natural selection and to a degree, the different physical conditions.

-Inheritance with modification through migration.

'''SINGLE CENTRES OF SUPPOSED CREATION'''

The idea that each species having been produced in one area alone, and having subsequently migrated from that area as far as its powers of migration and subsistence under past and present conditions permitted, is the most probable. The idea that all species had a single birth place seems to be the safest to assume.

'''MEANS OF DISPERSAL'''

-Different climate and geological patterns in the past could have enabled migration that is now not possible. (e.g Pangaea)

-Accidental dispersal such as a flood washing a fruit out to sea, birds, icebergs.

-Multiple birth origins can be explained by the glacial period.

-Glacial periods in one hemisphere coincides with a warmer period in the northern hemisphere. Thus Migration occurred.

== CHAPTER XIII. GEOGRAPHICAL DISTRIBUTION—continued ==
(???)

== CHAPTER XIV. MUTUAL AFFINITIES OF ORGANIC BEINGS ==
(???)

== CHAPTER XV. RECAPITULATION AND CONCLUSION ==
(???)

BioSec: Evolution

2012-02-06T21:27:05Z

Dsouza3190: /* CHAPTER II. VARIATION UNDER NATURE */

For help in mediawiki formatting see reference: http://www.mediawiki.org/wiki/Help:Formatting

== Purpose: ==

To retell Darwin's argument associating the biological with the technological.

The sections are as follows:

== CHAPTER I - VARIATION UNDER DOMESTICATION. ==

=== Causes of Variability ====

(Luc)

*Conditions of Life:
**Quantity of food
**Type of food
**Climate
*Pre-existing tendency towards variation
*Nature of the Organism

"Indefinite Variations" sounds like observations made in ignorance of genetics. Though, to be fair, we still see variations that are not well understood (Twin research, knockout mice)

Darwin argues that nature exerts pressure on organisms to adapt. As conditions of life change, species will modify themselves to either streamline themselves to harsher conditions or to take advantage of conditions of abundance (domestication).

However, while nature can apply external pressure on species to adapt, the species themselves will determine which parameters to modify. Determining which parameters will change seemed to be, at least to Darwin, an exercise in futility as different organisms within the species will be observed with differently modified parameters.

Technology:

While I'm not sure I'd call desktop Linux distributions a species, they have all mostly existed in the same environment, with environmental pressures being fairly uniform. Yet, if one were to compare Fedora, Debian, Ubuntu, Arch, Gentoo, and SuSE, it becomes glaringly obvious that each has tried to survive using different (sometimes radically different) strategies. The same can be seen in window managers, shells, scripting languages, and browsers. I, for one, would not want to have to predict how vastly increased availability in network bandwidth, or the sudden stagnation of memory availability would change the evolution of browsers.

===Effects of Habit and the use or disuse of Parts ===
(Mohamed)

=== Correlated Variation ===
(Annie)

Darwin in this section was stating that you cannot breed selectively for only one type of trait, as traits come in groupings (of at least two). Single examples were stated such as one cannot have a long limbed animal without an elongated head, or cats with white hair and blue eyes are deaf, or long, coarse haired animals tend to have horns.

His conclusion stated: "Hence if man goes on selecting and thus augmenting, any peculiarity, he will almost certainly modify unintentionally other parts of the structure, owing to the mysterious laws of correlation. The results of the various, unknown or but dimly understood laws of variation are infinitely complex and diversified.... it is really surprising to note the endless points of structure and constitution in which the varieties and sub-varieties differ slightly from each other."

To a certain degree this still applies even with the case of genetic engineering. As I think that specific genes within DNA are known to affect multiple traits. Isolating those genes individually will still affect the "engineered" animal in potentially multiple ways, as it is not only the genes, it is their interactions which may be modified and potentially corrected? (totally guessing here)

Technology wise there is a certain correlation between the graphical user interface and the program of an application. This is not evolutionary however, as it is of course due to design. Change the purpose of the program, and the user interface will have to change as well to accommodate the change. (?)

=== Inheritance ===
(Cheryl)

Darwin comes to the conclusion that the only way to explain variation is reproduction, through which parent pass on specific variations to their offspring. Furthermore, these variations are then carried and passed on from one generation to the next. Darwin also admits that scientist do not completely understand the law s that govern inheritance. Thus, scientists cannot explain why some traits are inherited by the off springs and why some are not; or why some traits skip a generation. In addition, Darwin notes that it is not clear if the various species types are the offspring of one parent species or not. He studied different domestic pigeons and cross bread them. The offspring resulted in a “perfectly fertile” species. From this he concluded that the various species are the offspring from one parent. This is because the offspring of two parents would result in a sterile offspring.

From a computer science perspective, inheritance is seen in a number ways. For example different versions of the same software can be viewed as parents and their offspring. Where the original software is the “rock” parent and the subsequent versions are its offspring. Inheritance can also be seen in programming; where programmers generally reuse parts of code. Furthermore, in object-oriented programming (OOP), inheritance describes the ability of one class to use methods and properties of another class. Another example could possibly be polymorphic code which uses a polymorphic engine to mutate however keeping the original algorithms. This can be seen in computer viruses and worms.

=== Character of Domestic Varieties ===
(Annie)
In domestic varieties there is less uniformity of character than in true species
The monstrous character of domestic varieties is defined by the small differences in some respects while differing in an extreme degree in a specific part. This is determined upon close inspection with a sample of the wild stock versus the domestic stock, as well as domestic stock with one another.
Closely connected wild species of the same genus in nature still differ from one another, except those differences aren't as radical as when you compare the domesticated version to the wild species. This explains why some smart people believe that the domestic races of many animals and plants have been judged as the descendants of aboriginally distinct species and other smart people claim that they are just varieties of the same species. Naturalists have differing opinions in what determines which characters are of generic value; all such valuations being at present empirical.

!! NOTE: NOT FINISHED !!

=== Difficulty of distinguishing between Varieties and Species ===
(Annie)
=== Origin of Domestic Varieties from one or more Species ===
(Cheryl)

Darwin states that in the case of most domesticated species it is not possible to pin point their origins. Thus we are unsure if they are the offspring of one parent species or multiple parent species. However, Darwin believes that all the different breeds come from one common parent. But he does not any evidence to confirm this hypothesis.

The authors of the book “Domestication of Media and Technology” discuss innovations are ‘tamed or domesticated’ by users – that is how technology is no longer a novelty but an aspect of everyday life. For example computers are now ‘domesticated’ because they are used by almost everyone and it is part of everyday life. However, there are many different types of computers, each slightly distinct from the other, however they all have the same basic core components.

=== Domestic Pigeons, their Differences and Origin ===

(Dan)

In this section Darwin argues the common ancestry of a variety of Pigeon breeds. Using the Pigeon as a case study he develops an argument proposing that despite the high variance within Pigeon breeds it can be reasoned that the [http://en.wikipedia.org/wiki/Rock_Pigeon Rock Pigeon (Columba Livia)] is their aboriginal ancestor.

Darwin's choice of studying Pigeons was not arbitrary (though he admits a certain infatuation with the species); a large selection of pigeon breeds was available for study and there was a historical body of treatises on the species to draw from. He begins the case study by establishing the diversity of pigeon breeds, and the aspects by which they differ. Nearly every aspect of the species is variable when examined with sufficient scope. Notable differences included the size and shape of the beak, in-flight behavior, feather appearance, age at which maturity is achieved, and skeleton details such as size, shape and count of various bone structures.

With such a great level of diversity between breeds, and the striking physical differences this diversity brings, Darwin posits it would be easy for a naturalist to assume many unique ancestor species. Darwin's counter argument to this assumption builds on the absence of any candidate species to fill this ancestral role. In order to create the present breeds as anything other than sub-varieties of a common ancestor a parent species must exist for the unique traits that are to be merged. For instance, the Porter breed has a large [http://en.wikipedia.org/wiki/Crop_%28anatomy%29 crop] that would have to have been inherited in the multiple origin species hypothesis. The absence of such an origin species indicates that either ornithologists have yet to discover the species, or that it has gone extinct. Due to the proliferation of Pigeons Darwin finds both possibilities unlikely and considers this as evidence towards the common ancestor theory. Darwin points to the fertility of hybrid (mongrel) Pigeons as further evidence supporting his common ancestry theory. For such a large selection of Pigeon breeds to cross-breed successfully and produce fertile offspring their commonality must run quite deep.

Interestingly Darwin notes that the naturalists dedication to their area of study reduces their ability to accept the common ancestry theory. With a deep appreciation of the differences of each breed it is the naturalist's view that only several unique species could explain the diversity they so well understand.

From a computer science perspective I ponder the idea of an outside observer trying to establish the common ancestry of a handful of [http://en.wikipedia.org/wiki/POSIX POSIX] descendent operating systems. As a user the OSX, Linux and Solaris operating systems seem highly divergent from one another. Much like a naturalist would assume no historic relation between Pigeon breeds, so too would an end user not assume a unified ancestor for the unique operating systems. Yet, underneath there are well established commonalities. Darwin's argument related to the fertility of offspring born of hybrid Pigeons could be similarly established for POSIX operating systems by means of considering a program written to POSIX standard running on the divergent operating systems mentioned. For a single program to successfully execute on three very different operating systems without the notion of a common ancestor seems highly improbable.

=== Principles of Selection, anciently followed, their Effects ===
(Moe)

-The production of domestic species: Effects may be attributed to direct and definite action of the external conditions of life and some to habit.

-Adaptation seen in domesticated races is not necessarily in the species' own good but rather more to the benefit of the breeder.

-The key to variation of domestic species is man's power of accumulative selection.

-Nature gives successive variations, man adds them up in certain directions

-Continued selection of slight variations produces races different from each other.

=== Methodical and Unconscious Selection ===
(Elizabeth)

In discussing the selection process that takes place in the breeding of domesticated animals, Darwin distinguishes two kinds of selection: ''methodical selection'', where breeders start with an idea in mind and deliberately attempt to create a new and superior species; and ''unconscious selection'', where many people try to get ahold of the best animals and by doing so, improve the breed. Darwin is primarily interested in unconscious selection, and notes the importance of observation and documentation, so that these changes become noticeable.

In the world of computing, parallels of the process of unconscious selection can be seen in many situations. Some examples might be the process of code development – where the same task might be coded in several ways, and eventually unified into the most efficient process once all the possibilities have been explored. A more economically motivated example might be when multiple products are competing in a market. Though no particular consumer has any intention of improving the field of desktop publishing, all consumers want to use the product that creates the most beautiful documents. Thus, the program that most people buy gets further examination and development, leading to improvement.

<blockquote>“Man can hardly select, or only with much difficulty, any deviation of structure excepting such as is externally visible; and indeed he rarely cares for what is internal. He can never act by selection, excepting on variations which are first given to him in some slight degree by nature.”</blockquote>

Darwin reflects briefly on the nature of unconscious selection, and discusses how although humankind has shaped the development of various species, the ideas always come from nature, and humans must work within the limitations of the domain.

(How is this true of computing?)

=== Unknown Origin of our Domestic Productions ===
(Elizabeth)



Darwin briefly brings up a point about the unknown ancestors of domestic breeds. His point seems to be that the process of development through selection is slow, and individual changes are small, and this means that no one pays attention to the initial stages when the creature is undeveloped. At first glance, this section is not obviously true of computers. We know exactly where computers came from, and how they developed. However, the point about small changes sometimes leading to more important changes later is true of the development of computers. In a smaller context, it is easy to see that the reasons behind early changes are often lost, leaving behind no evidence of the program they were created to deal with.

=== Circumstances favourable to Man's power of Selection ===
(Elizabeth)

In the final section of the first chapter of “The Origin of Species”, Darwin discusses the kinds of circumstances that facilitate the successful domestic selection of animals. Several of the factors Darwin lists are contextual factors. He remarks that a high degree of variability in the population is needed to attempt selective breeding, and that someone must have access to and control over a large population. In addition, he remarks that there must be some obvious value in undertaking this challenge.

<blockquote>“… the animal or plant should be so highly valued by man, that the closest attention is paid to even the slightest deviations in its qualities or structure.”</blockquote>

From the perspective of facilitating the development and selection of computer programs, it seems possible that similar contextual factors are needed. In place of a high degree of population variation, we could perhaps substitute a high degree of knowledge, expertise and experience. It seems entirely sensible that an organization who has access to large amounts of expertise, experience, equipment (and presumably, budget) would be positioned to motivate and commission work in the area. Darwin’s remark that “... the [product] should be so highly valued by man, that the closest attention is paid to even the slightest deviations in its qualities or structures” can be directly applied to the construction of computer programs. It seems believable that development and evolution of computer products (whether hardware or software) are likely to be more successful when there is a clear need or use for the product.

(What kind of organizations will have these privileges? Large corporations, like Google, sure. But what about people developing open source software? Crowd-sourced efforts, like Wikipedia? )

Darwin also notes a few factors that affect selection that have more to do with the nature of the creature at hand. Clearly, determined selection will be much easier if the species can be easily crossed, but it is also necessary to be able to prevent species from crossing at will or at random. For computer products, these two factors seem relatively easy to accomplish. Programs usually change only in the way specified by the developers and programmers, and if left alone, most computer programs do not change, merge or reproduce. (What about computer viruses, things like that?)

Part of Darwin’s discussion is of the limits of natural selection – how far can selection be pushed? He acknowledges that some limitations are defined by the capability of the product, but he also notes that external pressures affect the limitations of development. For computers, I think these limitations include hardware limitations (presumably some products will be developed at the time that the hardware exists to implement them), but I think that the external limitations come not only from the perceived need for the product, but also from the need for someone to have an idea for the product. We cannot develop products we have not thought of, or have an idea of their use or necessity.

== CHAPTER II. VARIATION UNDER NATURE ==
(Cheryl)
In this chapter Darwin basically answers the question: Can variation in species that are present in nature be considered similar to variations that are present in domesticated species?

He starts answering this question by describing three types of variations. The first type is what he calls monstrosities. These are variations that occur naturally in nature but are not really helpful in terms of survival or development of the species. In some instances, these variations are even harmful for the particular species. In the second case, variations are said to be driven due to environmental change (i.e. climate, temperature, etc.). Lastly, variations are the result of a small variation in genes that are passed from parents to their offspring. Darwin states that the first two cases of variations are most likely not passed from parents to offspring, while the third is.

The problem lies when trying to differentiate variations within a species from variations that imply the existence of two distinct species. Darwin notes that it is next to impossible to distinguish between varieties within a species. The solution to the problem is somewhat vague but clear enough to distinguish between varieties: “The amount of difference between species must be greater than the amount of difference between varieties within the species”.

Lastly, Darwin concludes by noting that variations are more likely to occur in a large sample. He does this by arguing that each species is not an act of God. Because if it were an act of God, there would be no real difference in the amount of variety between the smaller and larger groups of species.

== CHAPTER III. STRUGGLE FOR EXISTENCE ==
(Cheryl)

== CHAPTER IV. NATURAL SELECTION; OR THE SURVIVAL OF THE FITTEST ==
(Dan)

In this chapter Darwin discusses the force of natural selection and the concept of ''survival of the fittest''. He begins by pointing out a reminder that in artificial selection, man can not create varieties only preserve and accumulate the ones beneficial to their needs. Since changes can and do occur in nature, then there must too be a means by which nature accumulates changes according to some goal. The question of what the goal is leads to the notions of natural fitness.

Variations that are useful in adapting to the wild environment can accumulate in successive generations. Since more beings are born than survive even slight advantages can increase the chance of survival, and in turn the chance of procreation. Increased procreation leads to the passing on/accumulating of these variations. Conversely, "injurious" variations, those that harm survival, are likely to be quickly eliminated by these properties of natural selection. Natural selection can be boiled down to preserving beneficial variations, and eliminating detrimental ones. Variations with no affect on survival/reproduction are "fluctuations".

Darwin notes there is a tight coupling between species and that a change in a large number of inhabitants of an area will greatly affect the others even if they are not directly affected by the cause of the initial changes.

Darwin also discusses the fact that nature pays no heed to aesthetics except when they additional serve a functional purpose. While man operating artificially can only select based on properties he can observe, nature operates on all the ''machinery'' of life. Additionally, the scale of time at which natural selection operates affords it the ability to accumulate massive amounts of variation.

From a computer science perspective I consider the perspectives of a user and a programmer. A user selects software based on the surface level details they can perceive, usability, potentially speed of use, features, etc. A programmer may be selecting designs underlying the software based on much finer detail, memory usage, cpu cycles, elegance of component exchange, the ''machinery'' of the program. Probably not the best analogy but it's the first that comes to mind.

=== SEXUAL SELECTION ===
(Dan)

Darwin notes that often in nature artificial selection has created variation between sexes of the same species. He notes that in conjunction to the ''fitness'' of surviving, there is a ''fitness'' to reproducing. Intra-species struggles between individuals to find the best mate, or to have a chance to mate are common.

He notes this form of selection might be "less rigorous" in that you must survive to reproduce and so survival clearly plays a more significant role in selection than reproduction alone.

=== ILLUSTRATIONS OF THE ACTION OF NATURAL SELECTION, OR THE SURVIVAL OF THE FITTEST. ===
(Dan)

In this section Darwin talks of the idea that a local variation that has success can spread outwards, and often displace less adapted individuals/species. He notes that there is often a tight coupling between separate species that is exploited to a great degree, causing mutually beneficial variations to have great influence on the progression of evolution.

He gives the dependency between flowers and birds as an example. The bees benefit from increased pollen creation by a flower variation, and the flower benefits from a bees ability to travel greater distances or survive longer.

=== ON THE INTERCROSSING OF INDIVIDUALS. ===
(Dan)

Darwin notes that it is very important for members of a species to cross with one another to reproduce, that is, to not reproduce as single units in isolation by fertilising themselves. He states that close ''interbreeding'' diminishes fertility and vigour while crossing of separate individuals does the opposite. In support of these notions Darwin notes that relatively speaking there are few hermaphrodite species and even fewer that fertilise themselves.

Further evidence is given by the fact that many plant reproductive organs are placed very closely together. This arrangement would seemingly be optimised for self-fertilisation, but instead natural selection has lead to fairly advanced measures that prevent a plant from fertilising itself easily. Since natural selection only selects for beneficial attributes it must be reasoned that there is a reason self-fertilisation is so rare.

=== CIRCUMSTANCES FAVOURABLE FOR THE PRODUCTION OF NEW FORMS THROUGH NATURAL SELECTION. ===
(Dan)

In this section Darwin discusses some geographical constraints on selection. He notes that any one species that can't keep up with the adaptations of a competitor will be quickly exterminated.

Isolation plays an important role in natural selection in that it may prevent other species or variations from "swooping in" and taking a niche that might have been used by an existing species if given time to accumulate variations useful for that niche. He notes that confined areas tend to have more "uniform" life and that this life is operated on by selection in the same ways across the board.

Darwin is careful to clarify that time alone does nothing and that it merely allows for a greater chance of useful variations to occur, and be accumulated. Natural selection can only act when there is a niche to be filled by some new adaptation, otherwise things stagnate. These new "niches" are often caused by physical changes (climate, geography, etc) and are generally very slow acting.

=== EXTINCTION CAUSED BY NATURAL SELECTION. ===
(Dan)

Darwin talks about the geometric rate of increase for biological beings. Since this rate of increase is so large, geographic areas tend to be fully inhabited. As the number of ''favoured'' individuals in an area increases it is natural to conclude the number ''unfavoured'' individuals would decrease. Darwin posits that rarity is the precursor to extinction, and that as the number of a specific variation or species decreases so does it's chance of survival/propogation.

Darwin notes that the forms/variations that are closest in functionality to their competition are most at risk of extinction. In Computer Science terms I think this can be exemplified by the 'embrace/extend/extinguish' mentality shown by Microsoft in the late 90's. As products like Word Perfect were emulated/embraced by Microsoft their competitive advantages diminished. New adaptations by Word were then able to more easily displace the competing software, leading to an extinction.

=== DIVERGENCE OF CHARACTER. ===
(Dan)

Darwin poses the idea that varieties are species "under formation", what he calls "''incipient species''". He notes that as diversity increases, wildly different varieties have the chance to capitalise on very different niches in their environment. To the point where two variations of the same species can be exploiting very different environmental characteristics in order to succeed. Small areas open to immigration have the greatest diversity because one must be diverse in order to survive in the overcrowding. Unique variations might allow for access to resources not yet monopolised by the existing swath of inhabitants.

He poses that the idea of diversification of organisms in a region is similar to the physiological division of the organs in a body. For instance, the stomach is a highly specialised organ 'variety' that is very good at getting nutrients out of food.

=== THE PROBABLE EFFECTS OF THE ACTION OF NATURAL SELECTION THROUGH DIVERGENCE OF CHARACTER AND EXTINCTION, ON THE DESCENDANTS OF A COMMON ANCESTOR. ===
(Dan)

My version of the origin of species seems to be missing a diagram. The majority of this section of the chapter is based on discussing this diagram, so I've skipped it here. Someone else should feel free to fill this in if they can find the diagram!

=== ON THE DEGREE TO WHICH ORGANISATION TENDS TO ADVANCE. ===
(Dan)

This section notes that the amount of differentiation increases as organisms age. There is more specialisation to the parts of an organism as time progresses past birth. Accumulation of variation tends towards specialisation.

This leads to an interesting question of why there are so many ''lower'' forms still in existence if specialisation and greater levels of organisation/detail in an organism are better. I.e. why are there still tiny creatures when the large specialised creatures seem to do so well. Shouldn't natural selection have evolved everything to this point?

Darwin questions whether there is always a benefit to higher organisation that natural selection could exploit. Under some conditions such organization and specialisation might make a variation no better off than it's competition. It's even easy to see how it could hinder an organism living in highly volatile situations as the increased complexity might make it more vulnerable/delicate.

In Computer Science terms I think of this as analogous to the question of why some software is still very primitive/simple. It might be the case that increasing the complexity to add features might break it and cause devastating effects. The "KISS" (keep it simple, stupid) principle of software design is an example of this.

=== CONVERGENCE OF CHARACTER. ===
(Dan)

This section discusses reasons why there aren't an infinite number of variations in nature. If variations were always good, and specialisation is useful, why are there species with many individuals of so much similarity? Darwin notes an area can only support so many lifeforms. If the number of truly unique variations was very high then each variation would only have a few representative members.

With only a few representative members in an area, a variation would be prone to extinction from very slight fluctuations in the environment. In this case extermination could be very rapid, and Darwin has already argued why the creation of new species is slow. This imbalance would be quickly corrected or lead to total extinction.

== CHAPTER V. LAWS OF VARIATION ==
(Dan)

== CHAPTER VI. DIFFICULTIES OF THE THEORY ==
(Elizabeth)

In this chapter, Darwin notes some objections to his theory of natural selection, and gives a defense against the criticisms.

===ON THE ABSENCE OR RARITY OF TRANSITIONAL VARIETIES===

The first objection that Darwin addresses is a comment that in nature, we don't seem to ever see transitional varieties of animals. Darwin lists a few possible reasons for this, including pointing out that development progresses slowly, and the process does not necessarily include any period of chaotic variation. He remarks that variation is a slow process: how do we know that what we now see is not a developing version of some other thing?

He also gives some examples in nature that contradict criticisms of this type. He points out that we do see in nature a few variations of one species that show differences in structure, and this presumably is evidence of variation. Also, fossils show records of variation and development, but the record is somewhat flawed and inconsistent, meaning that we cannot see the whole picture.

===ON THE ORIGIN AND TRANSITION OF ORGANIC BEINGS WITH PECULIAR HABITS AND STRUCTURE===
(Elizabeth)

The criticism being addressed in this section is that creatures with odd habits and structural features could not have developed through the process of natural selection. The primary example given is the difference in development between an animal that breathes air, vs. one that is able to breathe underwater. The question is how can a transition have taken place from one species to another when they have features that appear to be mutually exclusive. Darwin's response is that there are several examples of animals with multiple abilities, and he delves into a deeper discussion of whether behaviour drives the development of structure, or whether changing structure propels the emergence of new behaviours.

<blockquote>"It is, however, difficult to decide and immaterial for us, whether habits generally change first and structure afterwards; or whether slight modifications of structure lead to changed habits; both probably often occurring almost simultaneously."</blockquote>

===ORGANS OF EXTREME PERFECTION AND COMPLICATION===
(Elizabeth)

Next, Darwin replies to objections about how complicated and precise organs could have developed. The main example given is the human eye, and the question raised is about how it could have naturally developed the sensitivity to light and ability to focus that have allowed it to be so useful to humans. Darwin points out some less advanced versions of the eye in other creatures, and notes that its evolutionary advantages are clear.

Another aspect of the section is somewhat more philosophical or theological in nature. Darwin mounts a few arguments against design by a creator. In the quote below, he discusses the dangers and inherent self-centredness that comes with assuming a creator would have behaved exactly as a human might.

<blockquote>"It is scarcely possible to avoid comparing the eye with a telescope. We know that this instrument has been perfected by the long-continued efforts of the highest human intellects; and we naturally infer that the eye has been formed by a somewhat analogous process. But may not this inference be presumptuous? Have we any right to assume that the Creator works by intellectual powers like those of man? If we must compare the eye to an optical instrucment, we ought in imagination to take a thick layer of transparent tissue, with spaces filled with fluid, and with a nerve sensitive to light beneath, and then suppose every part of this layer to be continually changing slowly in density, so as to separate into layers of different densities and thicknesses, placed at different distances from each other, and with the surfaces of each layer slowly changing in form. ... Let this process go on for millions of years; and instrument might thus be formed as superior to one of glass, as the works of the Creator are to those of man?"</blockquote>

===MODES OF TRANSITION===
(Elizabeth)

Darwin points out that to his knowledge, no example is known that contradicts his theory of natural selection. He acknowledges that if such an example existed, it would certainly knock down his theory. He also gives a few examples of how we should not be quick to conclude that something could not have been created with natural selection. As evidence against this kind of view, Darwin quotes "Natura non facit saltum" (nature does not make jumps), and points out that new organs never appear.

===SPECIAL DIFFICULTIES OF THE THEORY OF NATURAL SELECTION===
(Elizabeth)

In this section, Darwin discusses a number of examples of features where it is difficult to understand how they could have developed. The examples given are of animals with the ability to produce electric shocks - not only is this ability not universal, animals with the ability don't seem to even use it for the same purposes. An example with parallel properties is the ability of some insects to produce luminescence. It is not understood how such capacities could have developed, nor their evolutionary advantages. The other example given is of a type of orchid which has developed in such a way as to encourage bees to fall into its flower, and when they crawl out, they end up carrying the pollen on their backs, where they carry it to other flowers. This reproductive technique is extremely complicated, but works.

===ORGANS OF LITTLE APPARENT IMPORTANCE, AS AFFECTED BY NATURAL SELECTION===
(Elizabeth)

One objection to the theory of natural selection is that organs exist in creatures that are apparently unused in the current version of the organism. Darwin's response to this criticism is to point out that these organs were presumably of greater importance in previous versions of the creature, and that there may not have been any advantage in getting rid of these organs. Darwin also remarks that we might make errors in what we attribute to natural selection, and the reasons for this selection are not always clear to us. He gives an example of a (fictional) green woodpecker, and remarks that if it existed, we would think its green colour was an adaptive trait, evolved to hide it in the foliage from its enemies. Since we know woodpeckers are not free, we know that this is not the reason it has evolved the way it has.

===UTILITARIAN DOCTRINE, HOW FAR TRUE: BEAUTY, HOW ACQUIRED===
(Elizabeth)

One apparent objection to the theory of natural selection is that it makes no provision for things that have evolved solely to be beautiful. Darwin's reply is largely that beauty is in the eye of the beholder: different cultures and different people regard different items as being beautiful. Darwin points out that things we perceive as beautiful may not have been created for that purpose, and he goes on to point out that it is naive to believe humankind are the only beholders of the world.

Darwin also points out beauty, or distinctiveness, as an adaptive feature developed by natural selection. The example he gives is of flowers, which have become visually distinct from the green grass in order to attract insects. Flowers that do not rely on insects for their survival are not as brightly coloured, because there has been no evolutionary advantage in visual distinctiveness.

== CHAPTER VII. MISCELLANEOUS OBJECTIONS TO THE THEORY OF NATURAL SELECTION ==
(Elizabeth)

This chapter examines in further detail some more objections to Darwin's theory of natural selection, and Darwin's response and defence against the criticism. Most of the defences in this chapter are aimed at specific criticisms, and Darwin responds to specific authors. The bulk of the chapter is aimed at the criticisms of St. George Mivert, who took it upon himself to collect together objections to the theory. Most of Mivert's questions relate to the question of where the initial components of natural selection come from. Darwin's response is usually to give a collection of examples illustrating how the feature in question 'could' have developed, but in general, these are questions about the theory that have no clear answer.

== CHAPTER VIII. INSTINCT ==
=== Instincts comparable with habits, but different in their origin ===
=== Instincts graduated—Aphides and ants ===
=== Instincts variable—Domestic instincts, their origin===
=== Natural instincts of the cuckoo, molothrus, ostrich, and parasitic bees ===
=== Slave-making ants—Hive-bee, its cell-making instinct ===
=== Changes of instinct and structure not necessarily simultaneous ===
=== Difficulties of the theory of the Natural Selection of instincts ===
=== Neuter or sterile insects ===
=== Summary ===

No complex instinct can possibly be produced through natural selection, except by the slow and gradual accumulation of numerous, slight, yet profitable, variations.

Similarly no complex program can be produced in and of itself, at least well, except by adopting small accumulations of tiny programs. Each prototype version will have slight variations, that accomplish similar yet different tasks.

Similarly to how a cell engulfs and uses the properties of other organisms, so too can many programs adopt and make use of smaller programs, if instructed to do so.

How can we program instinctual behaviors into computer programs? Is this possible. The benefits are numerous. Security wise, if a program was to instinctually detect and react to a virus or malicious action, this would cause that particular application to be preferred over others. Similarly, operating systems that tend to be attacked more often, should logically not be used as much. (leading to the frustration of its' users) Unfortunately the human desire to continue to be productive, overrides most concern for security as a secondary task, if thought of at all.

It seems he talks more about adaptation than instinctual behaviour in this chapter. (example given instead of looking for pollen bees will accept the substitute of oatmeal in their search for food.)

Inherited instincts -

With cats, for instance, one naturally takes to catching rats, and another mice, and these tendencies are known to be inherited. One cat, according to Mr. St. John, always brought home game birds, another hares or rabbits, and another hunted on marshy ground and almost nightly caught woodcocks or snipes.

Whereby some cats have a natural tendency to give chase, others have a more calm quality and chase the affection of their owners instead. (Merlin vs. Pinga) Merlin given the chase will pounce after a laser pointer and will watch the mouse on the screen, whereas pinga will jump at any shadow and continually chase the mouse on the projector screen for hours.

Talk about instincts – what about the “robber cat” - seems to bring home any articles that it can lift up (from underwear / socks / children's toys) from the neighbourhood (learned this behaviour in order to impress it's owner?) This cat was videotaped at night to see if the rumors about it stealing things was correct.

What are we teaching these animals?

Should we make computers adapt similarly – instincts could be thought of as programs – we write programs to make our lives effectively easier – I would say that a program could be thought of as an instinct – if similar to a script that makes our life easier – now only if the computer could read our mind, and apply these instincts at the appropriate moment in time – for example if the user is in the habit of looking at a web page first thing in the morning and saving a particular image, perhaps opening and starting the web browser, going to that page automatically and downloading the image – might be an appropriate instinct for that user's computer to do. However based upon these instincts – once learning them could become a security risk. For if you knew that the computer would do those things – then you can as an attacker exploit the fact that you know what actions will be taken instinctually.
But let us look to the familiar case of the breeds of dogs: it cannot be doubted that young pointers (I have myself seen striking instances) will sometimes point and even back other dogs the very first time that they are taken out; retrieving is certainly in some degree inherited by retrievers; and a tendency to run round, instead of at, a flock of sheep, by shepherd-dogs.

Barking at the sound of a door – barking even before the person gets home, because they have a sense that they are coming home.

Tendancy to run around, when they are being aggressive, not just towards sheep, but other people and dogs as well. Still categories of instinctual behaviour – non-aggressive, passive, and aggressive.

Define domestic instincts – how do they differ from natural instints -

Domestic instincts, as they may be called, are certainly far less fixed than natural instincts; but they have been acted on by far less rigorous selection, and have been transmitted for an incomparably shorter period, under less fixed conditions of life.

When the first tendency to point was once displayed, methodical selection and the inherited effects of compulsory training in each successive generation would soon complete the work; and unconscious selection is still in progress, as each man tries to procure, without intending to improve the breed, dogs which stand and hunt best.
Hence, we may conclude that under domestication instincts have been acquired and natural instincts have been lost, partly by habit and partly by man selecting and accumulating, during successive generations, peculiar mental habits and actions, which at first appeared from what we must in our ignorance call an accident. In some cases compulsory habit alone has sufficed to produce inherited mental changes; in other cases compulsory habit has done nothing, and all has been the result of selection, pursued both methodically and unconsciously; but in most cases habit and selection have probably concurred.

Mockingly reproduce similar actions to these ( such as Gates' house where you walk into a room and your media follows you / the lights turn on, etc.) How are these habits going to affect our instincts?

Def: Nidification – act of building a nest.

== CHAPTER IX. HYBRIDISM ==
(Annie)

== CHAPTER X. ON THE IMPERFECTION OF THE GEOLOGICAL RECORD ==
(???)

== CHAPTER XI. ON THE GEOLOGICAL SUCCESSION OF ORGANIC BEINGS ==
(???)

== CHAPTER XII. GEOGRAPHICAL DISTRIBUTION ==

(Mohamed)

''' Present distribution cannot be accounted for by differences in physical conditions'''

-When considering the distribution of organic beings over the face of the globe, different climates and physical conditions in various regions are not the only factor that affects the similarity or dissimilarity of beings.

-Although the climatal conditions of to geographically distributed worlds could be very similar, their fauna/flora could be very different and the opposite is true as well (different conditions, closely related flora/fauna).

'''Importance of barriers'''

Obstacles to free migration, are related in a close and important manner to the differences between the productions of various regions.

'''Affinity of the productions of the same continent or of the same sea'''

-Throughout a single continent, species are specifically distinct though nearly related.

-Similarities of species is attributed to inheritance and their difference attributed to variation and natural selection and to a degree, the different physical conditions.

-Inheritance with modification through migration.

'''SINGLE CENTRES OF SUPPOSED CREATION'''

The idea that each species having been produced in one area alone, and having subsequently migrated from that area as far as its powers of migration and subsistence under past and present conditions permitted, is the most probable. The idea that all species had a single birth place seems to be the safest to assume.

'''MEANS OF DISPERSAL'''

-Different climate and geological patterns in the past could have enabled migration that is now not possible. (e.g Pangaea)

-Accidental dispersal such as a flood washing a fruit out to sea, birds, icebergs.

-Multiple birth origins can be explained by the glacial period.

-Glacial periods in one hemisphere coincides with a warmer period in the northern hemisphere. Thus Migration occurred.

== CHAPTER XIII. GEOGRAPHICAL DISTRIBUTION—continued ==
(???)

== CHAPTER XIV. MUTUAL AFFINITIES OF ORGANIC BEINGS ==
(???)

== CHAPTER XV. RECAPITULATION AND CONCLUSION ==
(???)

BioSec: Text: Unit 1: Setting the Stage

2012-01-27T18:19:00Z

Dsouza3190: /* The Chemical Basis of Cellular Respiration */

= Light and Life =

The book starts out talking about Monet, the French impressionist painter, and the reason why his later paintings lacked light blue, and appeared to be toned towards red-yellow. This was due to a physical ailment of cataracts. The opaqueness of a cataract affected lens causes it to absorb certain wavelengths of light.

The way in which you see the world is affected by biological processes. The way in which you view a computer is similar – an operating system on a machine is effectively a map to the internal workings of the machine. It gives you a perspective view of how to interact and process information stored within a computer.

== The Physical Nature of Light ==

Light functions:
Light is a source of energy that sustains life.
Light provides organisms with information about the physical world.

Photosynthesis – biological process to create energy rich molecules (algae)

Light is defined as the portion of the electromagnetic spectrum that humans can detect with their eyes. It is hard to characterize because it although it can be described as a wave it also behaves like a stream of energy particles.
When light interacts with matter three things can happen – it can be reflected off of the object, transmitted through the object or absorbed by the object. Absorption occurs when the energy of a photon is transferred to the electron of the pigment molecule.
Pigments are molecules that can absorb photons of light – each differ in the wavelengths that they can absorb. The feature critical to light absorption is a region where carbon atoms are covalently bonded with alternating single and double bonds (conjugated system) which results in the delocalization of electrons. A single photon results in the excitation of one and only one, electron in the pigment molecule and secondly the energy of the photon must match the energy difference between the ground state and one of the excited states in order for the photon to be absorbed.

Why is cholorophyll green in color? The color of a pigment is determined by the wavelengths of light it cannot absorb.

Photosynthesis sustains almost all life – uses the energy in sunlight to build sugar molecules from carbon dioxide and water – releasing oxygen as a by-product.

== Light as a Source of Energy ==
The excited electron state is a source of potential energy that can be used to do work. This energy is used to synthesize energy rich compounds (NADPH and ATP) which are used to convert CO2 into carbohydrates. Other biological molecules such as lipids, proteins, and nucleic acids from simple building blocks found in the environment.

== Light as a Source of Information ==
Organisms use light to sense their environment. Not every person – and not every species sees the world in the same way.
Rhodopsin - the most common photoreceptor found in nature – mystery as to why – perhaps it developed very early in the evolution of life
consists of a protein called opsin that binds a single pigment molecule called retinal
absorption of a photon causes the retinal pigment to change shape – causing chain reaction - alteration of protein, intracellular ion concentrations and electrical signals which are then sent to the brain
even things without eyes can sense light direction and intensity
eye – can be defined as the organ animals use to sense light – what distinguishes the eye from an eyespot of an invertibrate is the vision process – requires not only an eye but also a brain or simple nervous system that interprets signals sent from the eye

image forming eyes come in two varieties: compound eyes and single lens eyes -

compound eyes can be found in insects and crustaceans – hundreds to thousands of ommatidia units fitted closely together – each one samples only a small part of the visual field. Enables even slight motion detection.

Lens eyes (camera) – light enters through the transparent cornea – a lens concentrates the light and a layer of photoreceptors at the back of the eye, the retina – records the image.

Darwin proposed that the eye as it exists in humans and other animals did not appear suddenly but evolved by variation (mutation) and natural selection over time from a simple, primitive eye.

Any application during it's development life cycle evolves to hopefully become better at the task it was designed to perform. Not only programs, but operating systems, and hardware are selected and chosen by respective audiences somewhat based upon the usability, and performance of the system.

Computer scientists not only program, but attempt to imitate life in many ways as well. Robots were initially designed to perform specific tasks, but have evolved over time to complete more interesting behaviours. Sensors are designed to provide input in a variety of different ways to affect the behaviour of a robot. Cameras and photocells detect light. Touch screens, keyboards and mice provide the ability to provide stimuli.

“An optically refined eye is no good unless the brain of the organism improves at the same time, allowing for more advanced neural processing of the information being sent by the optic nerve.”

This makes me think of the case for an older camera driver for a newer model of video camera which is 1080 p enabled technically, but due to the old driver it can only process a lower resolution.

What can computer scientists learn from certain biological processes – don't throw out the old to replace with the new (as generally this type of thing doesn't work). Change can happen a lot but it doesn't completely waste what has already been created.

== Light can Damage Biological Molecules ==

Light is a form of energy that has the potential to damage biological molecules both directly and indirectly. All organisms have developed mechanisms to help prevent or repair damage once it occurs.
Carotenoids are accessory pigments that protect the photosynthetic apparatus from high light levels by absorbing extra light and converting the energy to heat.

Question: Plants unable to synthesize carotenoids turn white when exposed to light because the chlorophyll becomes oxidized and the light harvesting capabilities destroyed – (what about mushrooms – is this the same for fungus (plant or animal)?)

Melanin is a pigment that absorbs UV radiation. Melanin in cells prevents light from damaging the DNA in skin cells that is linked with cancer by preventing the destruction of B vitamin folate. Melanin cannot completely filter out all light rays because vitamin d is necessary for proper bone development.

Melanin is the “firewall” of light entering our bodies. A firewall being a device or set of devices designed to permit or deny network transmissions based on a set of rules used to protect networks from unauthorized access while permitting legitimate traffic. /ref{http://en.wikipedia.org/wiki/Firewall_%28computing%29}

== Role of Light in Ecology and Behaviour ==

circadian rythyms
nightly backups
nightly software updates / system upgrades
controlled by an internal clock – there are a lot of computational processes controlled by internal clock devices
normal operational behaviour – versus abnormal operational behaviour – logins that occur in the middle of the night to specific accounts

DNA replication only occurs at night. <- highly sensitive processing occurs nightly in order to avoid serious damaging errors.

Hormone – melatonin – secreted from the brain in order to control sleep wake cycles as it's synthesis is active at night.

Camouflage – works when an animal is indistinguishable to another in its current environment.

Separating the message from the noise. Microdots. Cryptography. (Ideas that come to mind within this context.)

Story of the industrial revolution moths – reminded me of the mac laptops in the classroom – one university professor noted that a certain year, there were many different types of laptops and one or two macs, and the following year it was all macs. (can't find the reference right now) now due to the emergence of better security (ahem - supposidely) on Windows 7, will the variety go back to the way that it was?

Using Color as signals – warnings / error messages – The effective ones are different colors or make different sounds when they occur. So many high tech security companies focus their marketing also around these stark contrast colors – Symantec Yellow / Black – Black / White / Red – McAfee – Avast Orange / Black – Norton Orange / Yellow / Black

== Life in the Dark ==

Even blind animals need to set their biological clocks to a circadian rythym. (Blind mole rat / Mexican cavefish)

== Organisms Making their own Light: Bioluminescence ==

This is a process by which the pigment transfers energy from an electron to a photon to assume a grounded state. This reaction in nature is highly efficient in order to ensure less heat production within an organism.

Most bioluminescence is found under the sea, and less on land animals – most often found at great depths, but also in algae / bacterial blooms near the surface. One great mystery surrounding this phenomenon is bioluminescent mushrooms.

= Origins of Life =

== What is Life? ==

The types of atoms and molecules found in living things is the same as those found in non living forms of matter. Living cells also obey the same fundamental laws of chemistry and physics as does the non living particles. Biochemical reactions that take place although complex are only modifications of reactions that take place by non living materials.

All forms of life share a set of attributes:

display order (cell fundamental unit – arranged in a highly ordered pattern)
harness and utilize energy (acquire energy and use it to maintain state)
reproduce (make more copies)
respond to stimuli (adjust structure, function or behaviour according to environment)
exhibit homeostasis (functions to maintain constant internal conditions)
growth and development (increase their size)
evolve (change over the course of generations to adapt to their environment)

Viruses are not alive because the lack the mechanisms required to produce proteins, and instead rely on highjacking the processes of a living cell to accomplish their replication.

3 Tenets of Cell Theory
1. Organisms are composed of one or more cells.

Single celled organisms are capable of carrying out all living activities. Multi-cellular organisms compartmentalize – that is, the activities are divided among groups of specialized cells.

2. The cell is the smallest unit that has the properties of life.
3. Cells arise only from growth and division of pre-existing cells.

== The Chemical Origins of Life ==

The key building blocks of life – nucleic acids and proteins – are not individually synthesized molecules called monomers – they are macromolecules built up from large numbers of subunit monomers coming together to produce polymers.
The synthesis of proteins and nucleic acids require protein-based catalysts (enzymes).

Clay – consists of very thin layers of minerals separated by thin layers of water. Present in evaporating tidal pools. The layered structure absorbs ions and organic molecules and promotes interactions (example: condensation).

Protobionts – first cells – abiotically produced organic molecules surrounded by a membrane.

== The Origins of Information and Metabolism ==

Critical events necessary for life development: one to store, replicate and translate information for protein synthesis and the other to develop metabolic pathways to capture and harness energy for life functions (metabolism).

Deoxyribonucleic acid (DNA) is a large double stranded, helical molecule that contains a unique alphabet that provides the instructions necessary for assembling many components of a cell organism from simpler molecules. DNA is copied onto molecules of a related substance (RNA) which is used to direct the production of proteins. Any changes to DNA are what contribute to evolutionary change over generations.

Group of RNA molecules called ribozymes can catalyze reactions on precursor RNA molecules that lead to their own synthesis and on related RNA molecules. (single stranded molecules that can bend into specialized shapes) A single type of molecule could serve as both a carrier of information and a catalyst.

Selection may have favored DNA for the following advantages over RNA:
Each strand is chemically more stable – due to the presence of the sugar deoxyribose instead of ribose.
Base uracil found in RNA was replaced by thymine which allows for the detection of a damaged cytosine
DNA is double stranded – in the case of a mutation / error – the complementary strand can be used to repair the damaged strand.

== Early Life ==

The earliest conclusive evidence of life are fossilized remains of structures called stromatolites – a type of layered rock that is formed when microorganisms bind particles of sediment together to form thin sheets.

Panspermia – hypothesis that forms of life are present in outer space and may have seeded early Earth.
Although life is complex it arose very quickly after the formation of the Earth. (The window for the development of life is very narrow)
life is more resilient than previously thought, and could survive for years in space. (Extremophiles which are mostly prokaryotes can thrive under harsh conditions of temperature, pressure and nutrients and might be able to survive in a dormant state in interstellar space.)

prokaryotic and eukaryotic cells are the two fundamental cell types all forms of life are based from.
Prokaryotic organsims exist in two domains: bacteria and Archaea.

Prokaryotic cells lack a nucleus (eukaryotic cells have a nucleus). All cells share fundamental features: - permeable plasma membrane (to separate external environment from cytoplasm (consisting of cytosol – mostly water, salts and various organic molecules, and structural features within the cell, including organelles)) – the membrane contains protein complexes that allow controlled transport of materials into and out of the cell.
In photosynthetic prokaryotic cells the plasma membrane is the site of photosynthetic electron transport chains which harvest light energy for the synthesis of energy rich molecules.
In eukaryotes mitochondria and chloroplasts perform energy transduction.

Prokaryotic cells have a nucleiod (central region) instead of a nucleus which is where the DNA of this organism is stored. They are 10 times smaller than a eukaryotic cell. They appear deceptively simple, as they are metabolically flexible which means they are able to use a variety of substances as energy and carbon sources to synthesize almost all of their required organic molecules from simple inorganic raw materials.

Where did oxygen come from? - Cyanobacteria could harness the electrons from water and when it split the water, Oxygen was a byproduct. The rise in oxygen in the atmosphere led to the evolution of prokaryotic cells. These cells were able to undergo aerobic respiration where energy is extracted from food molecules where oxygen acts as the final electron acceptor. Aerobic respiration enabled organisms to extract larger amounts of energy from food molecules than respiration that does not include oxygen. This was a key factor in the development of eukaryotic cells.

== Eukaryotic Cells ==

Distinguished characteristics that separate eukaryotic cells from prokaryotic cells:
separation of DNA and cytoplasm by nuclear envelope
membrane bound compartments with specialized functions (mitochondria, chloroplasts, endoplasmic reticulum, Golgi complex, etc)
highly specialized motor proteins that move cells and internal cell parts.

Membranes are connected directly or indirectly by vesicles – small membrane bound compartments that transfer substances between parts of the system. ER and Golgi complex serve the following functions:
synthesis and modification of proteins
protein transport into membranes or outside of the cell
synthesis of lipids
detoxification of harmful compounds
Endoplasmic Reticulum – ER – extensive interconnected network of membranous channels and vesicles – each vesicle is formed by a single membrane that surrounds an enclosed space called the lumen.
Rough er – ribosomes stud outer surface – destined for plasma membrane or release outside the cell
smooth er – lipid production

Golgi complex – stack of flattened membranous sacs located between the rough er and the plasma membrane that recieves and chemically modifies proteins made in the ER transported to the complex by vesicles.

Secretory vesicles release their contents to the exterior of the cell by exocitosis. Vesicles may also absorb molecules from outside the cell using endocitosis.

Established theory of endosymbiosis states that prokaryotic ancestors of modern mitochondria and chloroplasts were engulfed by larger prokaryotic cells forming a mutually advantageous relationship called symbiosis.
Mitochondria carry out aerobic respiration. Chloroplasts are thought to derive from endosymbiotic events involving cyanobacteria. Since cyanobacteria perform oxygenic photosynthesis – the host cell can easily supply the H20 necessary to drive photosynthesis. Only plants and algae have both mitochondria and chloroplasts.

The shape and internal organization of each type of cell are maintained by it's cytoskeleton (an interconnected system of protein fibers and tubes that extend throughout the cytoplasm). Three structural elements: microtubules (microscopic hollow tubes), intermediate filaments (fibres that occur singly, in parallel bundles and in interlinked networks) and microfilaments (thin fibres that consist of two rows of protein subunits wound around each other in a long spiral).

Flagella are long hairlike structures that project from the cell surface and function in cell movement.

“The internet is a series of Tubes” - unknown origin -

Structures that perform the same function but do not share a common evolutionary history are said to be analogous. If they do share history, they are homologous.

Division of labour – some cells specialize in harnessing energy – others for the motility of the organism. Cells no longer needed to be independent.

= Selection, Biodiversity, and Biosphere =

Air travel can affect the spread of viruses such as influenza A which kills 500000 people a year.
Since H3N2 was first reported in 1968 – it has undergone periods of relative stasis lasting 3 to 8 years followed by rapid changes. WHO has the opportunity to monitor the situation in East and SE Asia allowing vaccines to be developed against the most threatening strains.

== Biodiversity ==

Measured as the number of species of organisms, and reflects the reality that life exists from the ocean floor to the atmosphere. Other than taxonomic categories organisms are grouped based on how they obtain carbon.

Autotroph – self nourishing – synthesize organic carbon molecules using inorganic carbon (C02)
heterotrophs – they obtain carbon from organic molecules, either from living hosts or from organic molecules in the products, wastes or remains of dead organisms.
Chemotrophs – chemical nourishment – obtain energy by oxidizing inorganic or organic substances
phototrophs – obtain energy from light

chemoautotrophs – bacteria and archeans; not found in eukaryotes
chemoheterotrophs – found in some bacteria and archeans, also in proteins, fungi, animals, and plants
photoautotrophs – photosynthetic bacteria – in some proteins and some plants
photoheterotrophs – found in some photosynthetic bacteria

== Selection ==

Occurs when some force or phenomenon affects the survival of individual organisms, when a large population is exposed to a lethal factor and only resistant individuals survive to reproduce. If resistance is inherited, then the offspring of survivors will be resistant. If the resistant population is able to reproduce quickly, there is the potential for explosive growth of a population of individuals immune to the lethal factor.
Key factors – selective force and capacity for explosive population growth.

User interface adoption and product availability. (Economic comparison?)

== Evolution ==

Defined as a gradual change in the characteristics of a population of organisms over time, and can be a result of selection. Explains both the unity and diversity of life: all organisms alive today descended from a common ancestor – why all organisms share features such as the use of ATP (adenosine triphosphate) as a cellular energy source, DNA (deoxyribonucleic acid) as genetic material, and plasma membranes composed of lipid bilayers.
Darwin's central ideas to the theory of evolution by natural selection:
individual organisms in a population vary in many heritable traits.
Any population has the potential to produce far more offspring than the environment can support. Competition for limited resources means that only some individuals can survive.
Individuals may have traits that give them an advantage in their local environment; these are more likely to survive and reproduce.
These individuals pass on favorable traits to their offspring

Adaptive Radiation – these occur when an evolutionary breakthrough allows diversification of life.

The appearance of oxygenetic photosynthesis increased the concentrations of oxygen which led to aerobic respiration and the ozone layer, which allowed organisms to colonize terrestrial environments by blocking harmful (UV) rays. Changes caused by an increase in atmospheric oxygen triggered an extraordinary diversification of life.

Islands are seen as showcases of evolution – Hawaii, New Zealand, Madagascar, Mauritius, Galapagos Islands – also island populations of animals and plants can be vulnerable to extinction. (negative impact of humans on biodiversity)

Terrestrial animals used nontoxic excretory products (urea, uric acid), whereas aquatic ones still relied heavily on ammonia.

== The Biosphere ==

The area occupied by life on Earth. The various physical environments and their different abiotic factors (sunlight, temperature, humidity, wind speed, cloud cover and rainfall) influence the evolution and diversity of organisms.

Climate – weather conditions prevailing over an extended period of time.

== Biotic Factors ==
== Cumulative Impact on Biotic and Abiotic Factors ==

= Energy and Enzymes =
== Energy and the Laws of Thermodynamics ==
== Free Energy and Spontaneous Reactions ==
== The Energy Currency of the Cell: ATP ==
== The Role of Enzymes in Biological Reactions ==
== Conditions and Factors that Affect Enzyme Activity ==

(Mohamed)

Energy and Enzymes:

Catalyst called enzymes speed up the rates of reaction without the need for an increase in temperature.

Phosphatases: A group of enzymes catalyze the removal of phosphates groups from a range of molecules.

Energy: The capacity to do work e.g build a protein from a group of amino acids or pump sucrose across a cell membrane.

First law of thermodynamics: Energy can be transformed from one place to another, but it cannot be created or destroyed.

Second law of thermodynamics: The total disorder (entropy) of a system and its surroundings always increases.

It takes energy to maintain low entropy or the “orderness” of things.

Cells are always breaking down and new ones are always being created by the synthesis of a huge array of proteins, carbohydrates and lipid molecules.

Free energy: The portion of a system’s energy that is available to do work.

Spontaneous reactions:

1- Reactions tend to be spontaneous if the products have less potential energy than the reactants.

2- Reactions tend to be spontaneous when the products are less ordered than the reactants.

3- Change in free energy indicated whether a reaction is spontaneous. The free energy change as the system goes from initial to final states is the sum of the changes in the energy content and entropy.

Point of chemical equilibrium: a state in which reaction does not stop but rather a state in which the rate of the forward reaction equals the rate of the backward reactions.

The change in free energy of life is always negative as organisms constantly take in energy-rich molecules and use them to do work. Organisms reach equilibrium only when they die.

Exergonic reaction: A reaction that releases free energy. Products contain less free energy than the reactants

Endergonic reaction: The products contain more free energy than the reactants.The reactants involved in the reaction need to gain free energy from the surroundings to form products of the reaction.
Catabolic pathway: Energy is released by the breakdown of complex molecules to simpler compounds e.g. cellular respiration

Anabolic pathway: Energy is consumed to build complex molecules from more simple ones. e.g. photosynthesis.

Cells supplies energy to drive endergonic reactions using ATP (adenosine triphosphate)

ATP contains free enegry from high energy phosphate bonds.

Removal of one or two of the three phosphate groups is a spontaneous reaction that relieves the repulsion of the negatively charged phosphate groups and releases large amounts of free energy.

The breakdown of ATP is a hydrolysis reaction and results in the formation of ADP (adenosine diphosphate) and a molecule of inorganic phosphate.

Hydrolysis of ATP produces free energy (heat).

How do living cells link the hydrolysis of ATP to an endergonic reaction such that the energy is not wasted as heat?: Energy coupling: An enzyme brings ATP and the reactant molecule into close association.

Energy in carbohydrates, fats and proteins consumed in food is used in the energy requiring endergonic process that combines ADP and Pi.

The continued breakdown and resynthesis of ATP is called the ATP cycle.

A spontaneous reaction does not mean that it proceeds rapidly.

Activation Energy: initial energy required to start a reaction and tranform molecules into transition state where bonds are stable and are ready to be broken.

Enzymes act as a catalyst by lowering the activation energy required by molecules in reactants to start a reaction.

Enzymes speed-up the rate of spontaneous exergonic reactions.

Enzymes do not supply free energy to the reaction.

Three main mechanisms in which an Enzyme lowers activation Energy:

1- Bringing the reacting molecules together

2- Exposing the reactant molecule to altered charge environments that promote catalysis

3- Changing the shape of a substrate molecule

Temperature and pH levels have a significant effect on enzyme activity and thus the reaction rates. The optimum pH level for an enzyme depends on the pH level of its environment. If Temperature becomes too high the enzyme of denatured.

As the enzyme concentration increases the rate of catalysis increases.

Competitive Enzyme inhibition: enzyme inhibitors bind to the enzyme’s active site

Non-competitive inhibitors: enzyme inhibitors bind to a location on the enzyme other than the active site.

Enzyme inhibition is important to the cell since it controls the presence of multiple active enzymes at the same time. (allosteric regulation).

Feedback inhibition provides a mechanism to prevent the wasting of cell’s energy. If the concentration of the inhibitor increases the enzyme action is inhibited, if the concentration of the inhibitor decreases, the enzyme is activated.

= Membranes and Transport =
== An overview of the Structure of Membranes ==
== The Lipid Fabric of a Membrane ==
== Membrane Proteins ==
== Passive Membrane Transport ==
== Active Membrane Transport ==
== Exocytosis and Endocytosis ==

= Cellular Respiration =
== The Chemical Basis of Cellular Respiration ==
(Cheryl)

Cellular respiration allows organism to uses energy that is stored in chemical bonds of glucose (transferring electrons). This energy is then used to create ATP.

Redox reactions are a set of reactions that partially or completely transfer electrons. The reason they are called redox reactions is because they always occur in pairs – one oxidation and one reduction. The oxidation reaction is the reaction that releases an electron (increases in oxidation state). While the reduction reaction is the reaction that accepts this electron (decreases in oxidation state).

I think that redox reaction is extremely important and we see it almost everywhere. We use a battery for almost everything when we need a portable power source and it is an excellent example of redox reactions.

== Cellular Respiration: An Overview ==
== Glycolysis ==
== Pyruvate Oxidation and the Citric Acid Cycle ==
== Electron Transport and Chemiosmosis ==
== The Efficiency and Regulation of Cellular Respiration ==
== Oxygen and Cellular Respiration ==

BioSec: Text: Unit 1: Setting the Stage

2012-01-27T18:18:27Z

Dsouza3190: /* The Chemical Basis of Cellular Respiration */

= Light and Life =

The book starts out talking about Monet, the French impressionist painter, and the reason why his later paintings lacked light blue, and appeared to be toned towards red-yellow. This was due to a physical ailment of cataracts. The opaqueness of a cataract affected lens causes it to absorb certain wavelengths of light.

The way in which you see the world is affected by biological processes. The way in which you view a computer is similar – an operating system on a machine is effectively a map to the internal workings of the machine. It gives you a perspective view of how to interact and process information stored within a computer.

== The Physical Nature of Light ==

Light functions:
Light is a source of energy that sustains life.
Light provides organisms with information about the physical world.

Photosynthesis – biological process to create energy rich molecules (algae)

Light is defined as the portion of the electromagnetic spectrum that humans can detect with their eyes. It is hard to characterize because it although it can be described as a wave it also behaves like a stream of energy particles.
When light interacts with matter three things can happen – it can be reflected off of the object, transmitted through the object or absorbed by the object. Absorption occurs when the energy of a photon is transferred to the electron of the pigment molecule.
Pigments are molecules that can absorb photons of light – each differ in the wavelengths that they can absorb. The feature critical to light absorption is a region where carbon atoms are covalently bonded with alternating single and double bonds (conjugated system) which results in the delocalization of electrons. A single photon results in the excitation of one and only one, electron in the pigment molecule and secondly the energy of the photon must match the energy difference between the ground state and one of the excited states in order for the photon to be absorbed.

Why is cholorophyll green in color? The color of a pigment is determined by the wavelengths of light it cannot absorb.

Photosynthesis sustains almost all life – uses the energy in sunlight to build sugar molecules from carbon dioxide and water – releasing oxygen as a by-product.

== Light as a Source of Energy ==
The excited electron state is a source of potential energy that can be used to do work. This energy is used to synthesize energy rich compounds (NADPH and ATP) which are used to convert CO2 into carbohydrates. Other biological molecules such as lipids, proteins, and nucleic acids from simple building blocks found in the environment.

== Light as a Source of Information ==
Organisms use light to sense their environment. Not every person – and not every species sees the world in the same way.
Rhodopsin - the most common photoreceptor found in nature – mystery as to why – perhaps it developed very early in the evolution of life
consists of a protein called opsin that binds a single pigment molecule called retinal
absorption of a photon causes the retinal pigment to change shape – causing chain reaction - alteration of protein, intracellular ion concentrations and electrical signals which are then sent to the brain
even things without eyes can sense light direction and intensity
eye – can be defined as the organ animals use to sense light – what distinguishes the eye from an eyespot of an invertibrate is the vision process – requires not only an eye but also a brain or simple nervous system that interprets signals sent from the eye

image forming eyes come in two varieties: compound eyes and single lens eyes -

compound eyes can be found in insects and crustaceans – hundreds to thousands of ommatidia units fitted closely together – each one samples only a small part of the visual field. Enables even slight motion detection.

Lens eyes (camera) – light enters through the transparent cornea – a lens concentrates the light and a layer of photoreceptors at the back of the eye, the retina – records the image.

Darwin proposed that the eye as it exists in humans and other animals did not appear suddenly but evolved by variation (mutation) and natural selection over time from a simple, primitive eye.

Any application during it's development life cycle evolves to hopefully become better at the task it was designed to perform. Not only programs, but operating systems, and hardware are selected and chosen by respective audiences somewhat based upon the usability, and performance of the system.

Computer scientists not only program, but attempt to imitate life in many ways as well. Robots were initially designed to perform specific tasks, but have evolved over time to complete more interesting behaviours. Sensors are designed to provide input in a variety of different ways to affect the behaviour of a robot. Cameras and photocells detect light. Touch screens, keyboards and mice provide the ability to provide stimuli.

“An optically refined eye is no good unless the brain of the organism improves at the same time, allowing for more advanced neural processing of the information being sent by the optic nerve.”

This makes me think of the case for an older camera driver for a newer model of video camera which is 1080 p enabled technically, but due to the old driver it can only process a lower resolution.

What can computer scientists learn from certain biological processes – don't throw out the old to replace with the new (as generally this type of thing doesn't work). Change can happen a lot but it doesn't completely waste what has already been created.

== Light can Damage Biological Molecules ==

Light is a form of energy that has the potential to damage biological molecules both directly and indirectly. All organisms have developed mechanisms to help prevent or repair damage once it occurs.
Carotenoids are accessory pigments that protect the photosynthetic apparatus from high light levels by absorbing extra light and converting the energy to heat.

Question: Plants unable to synthesize carotenoids turn white when exposed to light because the chlorophyll becomes oxidized and the light harvesting capabilities destroyed – (what about mushrooms – is this the same for fungus (plant or animal)?)

Melanin is a pigment that absorbs UV radiation. Melanin in cells prevents light from damaging the DNA in skin cells that is linked with cancer by preventing the destruction of B vitamin folate. Melanin cannot completely filter out all light rays because vitamin d is necessary for proper bone development.

Melanin is the “firewall” of light entering our bodies. A firewall being a device or set of devices designed to permit or deny network transmissions based on a set of rules used to protect networks from unauthorized access while permitting legitimate traffic. /ref{http://en.wikipedia.org/wiki/Firewall_%28computing%29}

== Role of Light in Ecology and Behaviour ==

circadian rythyms
nightly backups
nightly software updates / system upgrades
controlled by an internal clock – there are a lot of computational processes controlled by internal clock devices
normal operational behaviour – versus abnormal operational behaviour – logins that occur in the middle of the night to specific accounts

DNA replication only occurs at night. <- highly sensitive processing occurs nightly in order to avoid serious damaging errors.

Hormone – melatonin – secreted from the brain in order to control sleep wake cycles as it's synthesis is active at night.

Camouflage – works when an animal is indistinguishable to another in its current environment.

Separating the message from the noise. Microdots. Cryptography. (Ideas that come to mind within this context.)

Story of the industrial revolution moths – reminded me of the mac laptops in the classroom – one university professor noted that a certain year, there were many different types of laptops and one or two macs, and the following year it was all macs. (can't find the reference right now) now due to the emergence of better security (ahem - supposidely) on Windows 7, will the variety go back to the way that it was?

Using Color as signals – warnings / error messages – The effective ones are different colors or make different sounds when they occur. So many high tech security companies focus their marketing also around these stark contrast colors – Symantec Yellow / Black – Black / White / Red – McAfee – Avast Orange / Black – Norton Orange / Yellow / Black

== Life in the Dark ==

Even blind animals need to set their biological clocks to a circadian rythym. (Blind mole rat / Mexican cavefish)

== Organisms Making their own Light: Bioluminescence ==

This is a process by which the pigment transfers energy from an electron to a photon to assume a grounded state. This reaction in nature is highly efficient in order to ensure less heat production within an organism.

Most bioluminescence is found under the sea, and less on land animals – most often found at great depths, but also in algae / bacterial blooms near the surface. One great mystery surrounding this phenomenon is bioluminescent mushrooms.

= Origins of Life =

== What is Life? ==

The types of atoms and molecules found in living things is the same as those found in non living forms of matter. Living cells also obey the same fundamental laws of chemistry and physics as does the non living particles. Biochemical reactions that take place although complex are only modifications of reactions that take place by non living materials.

All forms of life share a set of attributes:

display order (cell fundamental unit – arranged in a highly ordered pattern)
harness and utilize energy (acquire energy and use it to maintain state)
reproduce (make more copies)
respond to stimuli (adjust structure, function or behaviour according to environment)
exhibit homeostasis (functions to maintain constant internal conditions)
growth and development (increase their size)
evolve (change over the course of generations to adapt to their environment)

Viruses are not alive because the lack the mechanisms required to produce proteins, and instead rely on highjacking the processes of a living cell to accomplish their replication.

3 Tenets of Cell Theory
1. Organisms are composed of one or more cells.

Single celled organisms are capable of carrying out all living activities. Multi-cellular organisms compartmentalize – that is, the activities are divided among groups of specialized cells.

2. The cell is the smallest unit that has the properties of life.
3. Cells arise only from growth and division of pre-existing cells.

== The Chemical Origins of Life ==

The key building blocks of life – nucleic acids and proteins – are not individually synthesized molecules called monomers – they are macromolecules built up from large numbers of subunit monomers coming together to produce polymers.
The synthesis of proteins and nucleic acids require protein-based catalysts (enzymes).

Clay – consists of very thin layers of minerals separated by thin layers of water. Present in evaporating tidal pools. The layered structure absorbs ions and organic molecules and promotes interactions (example: condensation).

Protobionts – first cells – abiotically produced organic molecules surrounded by a membrane.

== The Origins of Information and Metabolism ==

Critical events necessary for life development: one to store, replicate and translate information for protein synthesis and the other to develop metabolic pathways to capture and harness energy for life functions (metabolism).

Deoxyribonucleic acid (DNA) is a large double stranded, helical molecule that contains a unique alphabet that provides the instructions necessary for assembling many components of a cell organism from simpler molecules. DNA is copied onto molecules of a related substance (RNA) which is used to direct the production of proteins. Any changes to DNA are what contribute to evolutionary change over generations.

Group of RNA molecules called ribozymes can catalyze reactions on precursor RNA molecules that lead to their own synthesis and on related RNA molecules. (single stranded molecules that can bend into specialized shapes) A single type of molecule could serve as both a carrier of information and a catalyst.

Selection may have favored DNA for the following advantages over RNA:
Each strand is chemically more stable – due to the presence of the sugar deoxyribose instead of ribose.
Base uracil found in RNA was replaced by thymine which allows for the detection of a damaged cytosine
DNA is double stranded – in the case of a mutation / error – the complementary strand can be used to repair the damaged strand.

== Early Life ==

The earliest conclusive evidence of life are fossilized remains of structures called stromatolites – a type of layered rock that is formed when microorganisms bind particles of sediment together to form thin sheets.

Panspermia – hypothesis that forms of life are present in outer space and may have seeded early Earth.
Although life is complex it arose very quickly after the formation of the Earth. (The window for the development of life is very narrow)
life is more resilient than previously thought, and could survive for years in space. (Extremophiles which are mostly prokaryotes can thrive under harsh conditions of temperature, pressure and nutrients and might be able to survive in a dormant state in interstellar space.)

prokaryotic and eukaryotic cells are the two fundamental cell types all forms of life are based from.
Prokaryotic organsims exist in two domains: bacteria and Archaea.

Prokaryotic cells lack a nucleus (eukaryotic cells have a nucleus). All cells share fundamental features: - permeable plasma membrane (to separate external environment from cytoplasm (consisting of cytosol – mostly water, salts and various organic molecules, and structural features within the cell, including organelles)) – the membrane contains protein complexes that allow controlled transport of materials into and out of the cell.
In photosynthetic prokaryotic cells the plasma membrane is the site of photosynthetic electron transport chains which harvest light energy for the synthesis of energy rich molecules.
In eukaryotes mitochondria and chloroplasts perform energy transduction.

Prokaryotic cells have a nucleiod (central region) instead of a nucleus which is where the DNA of this organism is stored. They are 10 times smaller than a eukaryotic cell. They appear deceptively simple, as they are metabolically flexible which means they are able to use a variety of substances as energy and carbon sources to synthesize almost all of their required organic molecules from simple inorganic raw materials.

Where did oxygen come from? - Cyanobacteria could harness the electrons from water and when it split the water, Oxygen was a byproduct. The rise in oxygen in the atmosphere led to the evolution of prokaryotic cells. These cells were able to undergo aerobic respiration where energy is extracted from food molecules where oxygen acts as the final electron acceptor. Aerobic respiration enabled organisms to extract larger amounts of energy from food molecules than respiration that does not include oxygen. This was a key factor in the development of eukaryotic cells.

== Eukaryotic Cells ==

Distinguished characteristics that separate eukaryotic cells from prokaryotic cells:
separation of DNA and cytoplasm by nuclear envelope
membrane bound compartments with specialized functions (mitochondria, chloroplasts, endoplasmic reticulum, Golgi complex, etc)
highly specialized motor proteins that move cells and internal cell parts.

Membranes are connected directly or indirectly by vesicles – small membrane bound compartments that transfer substances between parts of the system. ER and Golgi complex serve the following functions:
synthesis and modification of proteins
protein transport into membranes or outside of the cell
synthesis of lipids
detoxification of harmful compounds
Endoplasmic Reticulum – ER – extensive interconnected network of membranous channels and vesicles – each vesicle is formed by a single membrane that surrounds an enclosed space called the lumen.
Rough er – ribosomes stud outer surface – destined for plasma membrane or release outside the cell
smooth er – lipid production

Golgi complex – stack of flattened membranous sacs located between the rough er and the plasma membrane that recieves and chemically modifies proteins made in the ER transported to the complex by vesicles.

Secretory vesicles release their contents to the exterior of the cell by exocitosis. Vesicles may also absorb molecules from outside the cell using endocitosis.

Established theory of endosymbiosis states that prokaryotic ancestors of modern mitochondria and chloroplasts were engulfed by larger prokaryotic cells forming a mutually advantageous relationship called symbiosis.
Mitochondria carry out aerobic respiration. Chloroplasts are thought to derive from endosymbiotic events involving cyanobacteria. Since cyanobacteria perform oxygenic photosynthesis – the host cell can easily supply the H20 necessary to drive photosynthesis. Only plants and algae have both mitochondria and chloroplasts.

The shape and internal organization of each type of cell are maintained by it's cytoskeleton (an interconnected system of protein fibers and tubes that extend throughout the cytoplasm). Three structural elements: microtubules (microscopic hollow tubes), intermediate filaments (fibres that occur singly, in parallel bundles and in interlinked networks) and microfilaments (thin fibres that consist of two rows of protein subunits wound around each other in a long spiral).

Flagella are long hairlike structures that project from the cell surface and function in cell movement.

“The internet is a series of Tubes” - unknown origin -

Structures that perform the same function but do not share a common evolutionary history are said to be analogous. If they do share history, they are homologous.

Division of labour – some cells specialize in harnessing energy – others for the motility of the organism. Cells no longer needed to be independent.

= Selection, Biodiversity, and Biosphere =

Air travel can affect the spread of viruses such as influenza A which kills 500000 people a year.
Since H3N2 was first reported in 1968 – it has undergone periods of relative stasis lasting 3 to 8 years followed by rapid changes. WHO has the opportunity to monitor the situation in East and SE Asia allowing vaccines to be developed against the most threatening strains.

== Biodiversity ==

Measured as the number of species of organisms, and reflects the reality that life exists from the ocean floor to the atmosphere. Other than taxonomic categories organisms are grouped based on how they obtain carbon.

Autotroph – self nourishing – synthesize organic carbon molecules using inorganic carbon (C02)
heterotrophs – they obtain carbon from organic molecules, either from living hosts or from organic molecules in the products, wastes or remains of dead organisms.
Chemotrophs – chemical nourishment – obtain energy by oxidizing inorganic or organic substances
phototrophs – obtain energy from light

chemoautotrophs – bacteria and archeans; not found in eukaryotes
chemoheterotrophs – found in some bacteria and archeans, also in proteins, fungi, animals, and plants
photoautotrophs – photosynthetic bacteria – in some proteins and some plants
photoheterotrophs – found in some photosynthetic bacteria

== Selection ==

Occurs when some force or phenomenon affects the survival of individual organisms, when a large population is exposed to a lethal factor and only resistant individuals survive to reproduce. If resistance is inherited, then the offspring of survivors will be resistant. If the resistant population is able to reproduce quickly, there is the potential for explosive growth of a population of individuals immune to the lethal factor.
Key factors – selective force and capacity for explosive population growth.

User interface adoption and product availability. (Economic comparison?)

== Evolution ==

Defined as a gradual change in the characteristics of a population of organisms over time, and can be a result of selection. Explains both the unity and diversity of life: all organisms alive today descended from a common ancestor – why all organisms share features such as the use of ATP (adenosine triphosphate) as a cellular energy source, DNA (deoxyribonucleic acid) as genetic material, and plasma membranes composed of lipid bilayers.
Darwin's central ideas to the theory of evolution by natural selection:
individual organisms in a population vary in many heritable traits.
Any population has the potential to produce far more offspring than the environment can support. Competition for limited resources means that only some individuals can survive.
Individuals may have traits that give them an advantage in their local environment; these are more likely to survive and reproduce.
These individuals pass on favorable traits to their offspring

Adaptive Radiation – these occur when an evolutionary breakthrough allows diversification of life.

The appearance of oxygenetic photosynthesis increased the concentrations of oxygen which led to aerobic respiration and the ozone layer, which allowed organisms to colonize terrestrial environments by blocking harmful (UV) rays. Changes caused by an increase in atmospheric oxygen triggered an extraordinary diversification of life.

Islands are seen as showcases of evolution – Hawaii, New Zealand, Madagascar, Mauritius, Galapagos Islands – also island populations of animals and plants can be vulnerable to extinction. (negative impact of humans on biodiversity)

Terrestrial animals used nontoxic excretory products (urea, uric acid), whereas aquatic ones still relied heavily on ammonia.

== The Biosphere ==

The area occupied by life on Earth. The various physical environments and their different abiotic factors (sunlight, temperature, humidity, wind speed, cloud cover and rainfall) influence the evolution and diversity of organisms.

Climate – weather conditions prevailing over an extended period of time.

== Biotic Factors ==
== Cumulative Impact on Biotic and Abiotic Factors ==

= Energy and Enzymes =
== Energy and the Laws of Thermodynamics ==
== Free Energy and Spontaneous Reactions ==
== The Energy Currency of the Cell: ATP ==
== The Role of Enzymes in Biological Reactions ==
== Conditions and Factors that Affect Enzyme Activity ==

(Mohamed)

Energy and Enzymes:

Catalyst called enzymes speed up the rates of reaction without the need for an increase in temperature.

Phosphatases: A group of enzymes catalyze the removal of phosphates groups from a range of molecules.

Energy: The capacity to do work e.g build a protein from a group of amino acids or pump sucrose across a cell membrane.

First law of thermodynamics: Energy can be transformed from one place to another, but it cannot be created or destroyed.

Second law of thermodynamics: The total disorder (entropy) of a system and its surroundings always increases.

It takes energy to maintain low entropy or the “orderness” of things.

Cells are always breaking down and new ones are always being created by the synthesis of a huge array of proteins, carbohydrates and lipid molecules.

Free energy: The portion of a system’s energy that is available to do work.

Spontaneous reactions:

1- Reactions tend to be spontaneous if the products have less potential energy than the reactants.

2- Reactions tend to be spontaneous when the products are less ordered than the reactants.

3- Change in free energy indicated whether a reaction is spontaneous. The free energy change as the system goes from initial to final states is the sum of the changes in the energy content and entropy.

Point of chemical equilibrium: a state in which reaction does not stop but rather a state in which the rate of the forward reaction equals the rate of the backward reactions.

The change in free energy of life is always negative as organisms constantly take in energy-rich molecules and use them to do work. Organisms reach equilibrium only when they die.

Exergonic reaction: A reaction that releases free energy. Products contain less free energy than the reactants

Endergonic reaction: The products contain more free energy than the reactants.The reactants involved in the reaction need to gain free energy from the surroundings to form products of the reaction.
Catabolic pathway: Energy is released by the breakdown of complex molecules to simpler compounds e.g. cellular respiration

Anabolic pathway: Energy is consumed to build complex molecules from more simple ones. e.g. photosynthesis.

Cells supplies energy to drive endergonic reactions using ATP (adenosine triphosphate)

ATP contains free enegry from high energy phosphate bonds.

Removal of one or two of the three phosphate groups is a spontaneous reaction that relieves the repulsion of the negatively charged phosphate groups and releases large amounts of free energy.

The breakdown of ATP is a hydrolysis reaction and results in the formation of ADP (adenosine diphosphate) and a molecule of inorganic phosphate.

Hydrolysis of ATP produces free energy (heat).

How do living cells link the hydrolysis of ATP to an endergonic reaction such that the energy is not wasted as heat?: Energy coupling: An enzyme brings ATP and the reactant molecule into close association.

Energy in carbohydrates, fats and proteins consumed in food is used in the energy requiring endergonic process that combines ADP and Pi.

The continued breakdown and resynthesis of ATP is called the ATP cycle.

A spontaneous reaction does not mean that it proceeds rapidly.

Activation Energy: initial energy required to start a reaction and tranform molecules into transition state where bonds are stable and are ready to be broken.

Enzymes act as a catalyst by lowering the activation energy required by molecules in reactants to start a reaction.

Enzymes speed-up the rate of spontaneous exergonic reactions.

Enzymes do not supply free energy to the reaction.

Three main mechanisms in which an Enzyme lowers activation Energy:

1- Bringing the reacting molecules together

2- Exposing the reactant molecule to altered charge environments that promote catalysis

3- Changing the shape of a substrate molecule

Temperature and pH levels have a significant effect on enzyme activity and thus the reaction rates. The optimum pH level for an enzyme depends on the pH level of its environment. If Temperature becomes too high the enzyme of denatured.

As the enzyme concentration increases the rate of catalysis increases.

Competitive Enzyme inhibition: enzyme inhibitors bind to the enzyme’s active site

Non-competitive inhibitors: enzyme inhibitors bind to a location on the enzyme other than the active site.

Enzyme inhibition is important to the cell since it controls the presence of multiple active enzymes at the same time. (allosteric regulation).

Feedback inhibition provides a mechanism to prevent the wasting of cell’s energy. If the concentration of the inhibitor increases the enzyme action is inhibited, if the concentration of the inhibitor decreases, the enzyme is activated.

= Membranes and Transport =
== An overview of the Structure of Membranes ==
== The Lipid Fabric of a Membrane ==
== Membrane Proteins ==
== Passive Membrane Transport ==
== Active Membrane Transport ==
== Exocytosis and Endocytosis ==

= Cellular Respiration =
== The Chemical Basis of Cellular Respiration ==
(Cheryl)
Cellular respiration allows organism to uses energy that is stored in chemical bonds of glucose (transferring electrons). This energy is then used to create ATP.

Redox reactions are a set of reactions that partially or completely transfer electrons. The reason they are called redox reactions is because they always occur in pairs – one oxidation and one reduction. The oxidation reaction is the reaction that releases an electron (increases in oxidation state). While the reduction reaction is the reaction that accepts this electron (decreases in oxidation state).

I think that redox reaction is extremely important and we see it almost everywhere. We use a battery for almost everything when we need a portable power source and it is an excellent example of redox reactions.

== Cellular Respiration: An Overview ==
== Glycolysis ==
== Pyruvate Oxidation and the Citric Acid Cycle ==
== Electron Transport and Chemiosmosis ==
== The Efficiency and Regulation of Cellular Respiration ==
== Oxygen and Cellular Respiration ==

BioSec: Text: Unit 1: Setting the Stage

2012-01-27T15:10:27Z

Dsouza3190: /* The Chemical Basis of Cellular Respiration */

= Light and Life =

The book starts out talking about Monet, the French impressionist painter, and the reason why his later paintings lacked light blue, and appeared to be toned towards red-yellow. This was due to a physical ailment of cataracts. The opaqueness of a cataract affected lens causes it to absorb certain wavelengths of light.

The way in which you see the world is affected by biological processes. The way in which you view a computer is similar – an operating system on a machine is effectively a map to the internal workings of the machine. It gives you a perspective view of how to interact and process information stored within a computer.

== The Physical Nature of Light ==

Light functions:
Light is a source of energy that sustains life.
Light provides organisms with information about the physical world.

Photosynthesis – biological process to create energy rich molecules (algae)

Light is defined as the portion of the electromagnetic spectrum that humans can detect with their eyes. It is hard to characterize because it although it can be described as a wave it also behaves like a stream of energy particles.
When light interacts with matter three things can happen – it can be reflected off of the object, transmitted through the object or absorbed by the object. Absorption occurs when the energy of a photon is transferred to the electron of the pigment molecule.
Pigments are molecules that can absorb photons of light – each differ in the wavelengths that they can absorb. The feature critical to light absorption is a region where carbon atoms are covalently bonded with alternating single and double bonds (conjugated system) which results in the delocalization of electrons. A single photon results in the excitation of one and only one, electron in the pigment molecule and secondly the energy of the photon must match the energy difference between the ground state and one of the excited states in order for the photon to be absorbed.

Why is cholorophyll green in color? The color of a pigment is determined by the wavelengths of light it cannot absorb.

Photosynthesis sustains almost all life – uses the energy in sunlight to build sugar molecules from carbon dioxide and water – releasing oxygen as a by-product.

== Light as a Source of Energy ==
The excited electron state is a source of potential energy that can be used to do work. This energy is used to synthesize energy rich compounds (NADPH and ATP) which are used to convert CO2 into carbohydrates. Other biological molecules such as lipids, proteins, and nucleic acids from simple building blocks found in the environment.

== Light as a Source of Information ==
Organisms use light to sense their environment. Not every person – and not every species sees the world in the same way.
Rhodopsin - the most common photoreceptor found in nature – mystery as to why – perhaps it developed very early in the evolution of life
consists of a protein called opsin that binds a single pigment molecule called retinal
absorption of a photon causes the retinal pigment to change shape – causing chain reaction - alteration of protein, intracellular ion concentrations and electrical signals which are then sent to the brain
even things without eyes can sense light direction and intensity
eye – can be defined as the organ animals use to sense light – what distinguishes the eye from an eyespot of an invertibrate is the vision process – requires not only an eye but also a brain or simple nervous system that interprets signals sent from the eye

image forming eyes come in two varieties: compound eyes and single lens eyes -

compound eyes can be found in insects and crustaceans – hundreds to thousands of ommatidia units fitted closely together – each one samples only a small part of the visual field. Enables even slight motion detection.

Lens eyes (camera) – light enters through the transparent cornea – a lens concentrates the light and a layer of photoreceptors at the back of the eye, the retina – records the image.

Darwin proposed that the eye as it exists in humans and other animals did not appear suddenly but evolved by variation (mutation) and natural selection over time from a simple, primitive eye.

Any application during it's development life cycle evolves to hopefully become better at the task it was designed to perform. Not only programs, but operating systems, and hardware are selected and chosen by respective audiences somewhat based upon the usability, and performance of the system.

Computer scientists not only program, but attempt to imitate life in many ways as well. Robots were initially designed to perform specific tasks, but have evolved over time to complete more interesting behaviours. Sensors are designed to provide input in a variety of different ways to affect the behaviour of a robot. Cameras and photocells detect light. Touch screens, keyboards and mice provide the ability to provide stimuli.

“An optically refined eye is no good unless the brain of the organism improves at the same time, allowing for more advanced neural processing of the information being sent by the optic nerve.”

This makes me think of the case for an older camera driver for a newer model of video camera which is 1080 p enabled technically, but due to the old driver it can only process a lower resolution.

What can computer scientists learn from certain biological processes – don't throw out the old to replace with the new (as generally this type of thing doesn't work). Change can happen a lot but it doesn't completely waste what has already been created.

== Light can Damage Biological Molecules ==

Light is a form of energy that has the potential to damage biological molecules both directly and indirectly. All organisms have developed mechanisms to help prevent or repair damage once it occurs.
Carotenoids are accessory pigments that protect the photosynthetic apparatus from high light levels by absorbing extra light and converting the energy to heat.

Question: Plants unable to synthesize carotenoids turn white when exposed to light because the chlorophyll becomes oxidized and the light harvesting capabilities destroyed – (what about mushrooms – is this the same for fungus (plant or animal)?)

Melanin is a pigment that absorbs UV radiation. Melanin in cells prevents light from damaging the DNA in skin cells that is linked with cancer by preventing the destruction of B vitamin folate. Melanin cannot completely filter out all light rays because vitamin d is necessary for proper bone development.

Melanin is the “firewall” of light entering our bodies. A firewall being a device or set of devices designed to permit or deny network transmissions based on a set of rules used to protect networks from unauthorized access while permitting legitimate traffic. /ref{http://en.wikipedia.org/wiki/Firewall_%28computing%29}

== Role of Light in Ecology and Behaviour ==

circadian rythyms
nightly backups
nightly software updates / system upgrades
controlled by an internal clock – there are a lot of computational processes controlled by internal clock devices
normal operational behaviour – versus abnormal operational behaviour – logins that occur in the middle of the night to specific accounts

DNA replication only occurs at night. <- highly sensitive processing occurs nightly in order to avoid serious damaging errors.

Hormone – melatonin – secreted from the brain in order to control sleep wake cycles as it's synthesis is active at night.

Camouflage – works when an animal is indistinguishable to another in its current environment.

Separating the message from the noise. Microdots. Cryptography. (Ideas that come to mind within this context.)

Story of the industrial revolution moths – reminded me of the mac laptops in the classroom – one university professor noted that a certain year, there were many different types of laptops and one or two macs, and the following year it was all macs. (can't find the reference right now) now due to the emergence of better security (ahem - supposidely) on Windows 7, will the variety go back to the way that it was?

Using Color as signals – warnings / error messages – The effective ones are different colors or make different sounds when they occur. So many high tech security companies focus their marketing also around these stark contrast colors – Symantec Yellow / Black – Black / White / Red – McAfee – Avast Orange / Black – Norton Orange / Yellow / Black

== Life in the Dark ==

Even blind animals need to set their biological clocks to a circadian rythym. (Blind mole rat / Mexican cavefish)

== Organisms Making their own Light: Bioluminescence ==

This is a process by which the pigment transfers energy from an electron to a photon to assume a grounded state. This reaction in nature is highly efficient in order to ensure less heat production within an organism.

Most bioluminescence is found under the sea, and less on land animals – most often found at great depths, but also in algae / bacterial blooms near the surface. One great mystery surrounding this phenomenon is bioluminescent mushrooms.

= Origins of Life =

== What is Life? ==

The types of atoms and molecules found in living things is the same as those found in non living forms of matter. Living cells also obey the same fundamental laws of chemistry and physics as does the non living particles. Biochemical reactions that take place although complex are only modifications of reactions that take place by non living materials.

All forms of life share a set of attributes:

display order (cell fundamental unit – arranged in a highly ordered pattern)
harness and utilize energy (acquire energy and use it to maintain state)
reproduce (make more copies)
respond to stimuli (adjust structure, function or behaviour according to environment)
exhibit homeostasis (functions to maintain constant internal conditions)
growth and development (increase their size)
evolve (change over the course of generations to adapt to their environment)

Viruses are not alive because the lack the mechanisms required to produce proteins, and instead rely on highjacking the processes of a living cell to accomplish their replication.

3 Tenets of Cell Theory
1. Organisms are composed of one or more cells.

Single celled organisms are capable of carrying out all living activities. Multi-cellular organisms compartmentalize – that is, the activities are divided among groups of specialized cells.

2. The cell is the smallest unit that has the properties of life.
3. Cells arise only from growth and division of pre-existing cells.

== The Chemical Origins of Life ==

The key building blocks of life – nucleic acids and proteins – are not individually synthesized molecules called monomers – they are macromolecules built up from large numbers of subunit monomers coming together to produce polymers.
The synthesis of proteins and nucleic acids require protein-based catalysts (enzymes).

Clay – consists of very thin layers of minerals separated by thin layers of water. Present in evaporating tidal pools. The layered structure absorbs ions and organic molecules and promotes interactions (example: condensation).

Protobionts – first cells – abiotically produced organic molecules surrounded by a membrane.

== The Origins of Information and Metabolism ==

Critical events necessary for life development: one to store, replicate and translate information for protein synthesis and the other to develop metabolic pathways to capture and harness energy for life functions (metabolism).

Deoxyribonucleic acid (DNA) is a large double stranded, helical molecule that contains a unique alphabet that provides the instructions necessary for assembling many components of a cell organism from simpler molecules. DNA is copied onto molecules of a related substance (RNA) which is used to direct the production of proteins. Any changes to DNA are what contribute to evolutionary change over generations.

Group of RNA molecules called ribozymes can catalyze reactions on precursor RNA molecules that lead to their own synthesis and on related RNA molecules. (single stranded molecules that can bend into specialized shapes) A single type of molecule could serve as both a carrier of information and a catalyst.

Selection may have favored DNA for the following advantages over RNA:
Each strand is chemically more stable – due to the presence of the sugar deoxyribose instead of ribose.
Base uracil found in RNA was replaced by thymine which allows for the detection of a damaged cytosine
DNA is double stranded – in the case of a mutation / error – the complementary strand can be used to repair the damaged strand.

== Early Life ==

The earliest conclusive evidence of life are fossilized remains of structures called stromatolites – a type of layered rock that is formed when microorganisms bind particles of sediment together to form thin sheets.

Panspermia – hypothesis that forms of life are present in outer space and may have seeded early Earth.
Although life is complex it arose very quickly after the formation of the Earth. (The window for the development of life is very narrow)
life is more resilient than previously thought, and could survive for years in space. (Extremophiles which are mostly prokaryotes can thrive under harsh conditions of temperature, pressure and nutrients and might be able to survive in a dormant state in interstellar space.)

prokaryotic and eukaryotic cells are the two fundamental cell types all forms of life are based from.
Prokaryotic organsims exist in two domains: bacteria and Archaea.

Prokaryotic cells lack a nucleus (eukaryotic cells have a nucleus). All cells share fundamental features: - permeable plasma membrane (to separate external environment from cytoplasm (consisting of cytosol – mostly water, salts and various organic molecules, and structural features within the cell, including organelles)) – the membrane contains protein complexes that allow controlled transport of materials into and out of the cell.
In photosynthetic prokaryotic cells the plasma membrane is the site of photosynthetic electron transport chains which harvest light energy for the synthesis of energy rich molecules.
In eukaryotes mitochondria and chloroplasts perform energy transduction.

Prokaryotic cells have a nucleiod (central region) instead of a nucleus which is where the DNA of this organism is stored. They are 10 times smaller than a eukaryotic cell. They appear deceptively simple, as they are metabolically flexible which means they are able to use a variety of substances as energy and carbon sources to synthesize almost all of their required organic molecules from simple inorganic raw materials.

Where did oxygen come from? - Cyanobacteria could harness the electrons from water and when it split the water, Oxygen was a byproduct. The rise in oxygen in the atmosphere led to the evolution of prokaryotic cells. These cells were able to undergo aerobic respiration where energy is extracted from food molecules where oxygen acts as the final electron acceptor. Aerobic respiration enabled organisms to extract larger amounts of energy from food molecules than respiration that does not include oxygen. This was a key factor in the development of eukaryotic cells.

== Eukaryotic Cells ==

Distinguished characteristics that separate eukaryotic cells from prokaryotic cells:
separation of DNA and cytoplasm by nuclear envelope
membrane bound compartments with specialized functions (mitochondria, chloroplasts, endoplasmic reticulum, Golgi complex, etc)
highly specialized motor proteins that move cells and internal cell parts.

Membranes are connected directly or indirectly by vesicles – small membrane bound compartments that transfer substances between parts of the system. ER and Golgi complex serve the following functions:
synthesis and modification of proteins
protein transport into membranes or outside of the cell
synthesis of lipids
detoxification of harmful compounds
Endoplasmic Reticulum – ER – extensive interconnected network of membranous channels and vesicles – each vesicle is formed by a single membrane that surrounds an enclosed space called the lumen.
Rough er – ribosomes stud outer surface – destined for plasma membrane or release outside the cell
smooth er – lipid production

Golgi complex – stack of flattened membranous sacs located between the rough er and the plasma membrane that recieves and chemically modifies proteins made in the ER transported to the complex by vesicles.

Secretory vesicles release their contents to the exterior of the cell by exocitosis. Vesicles may also absorb molecules from outside the cell using endocitosis.

Established theory of endosymbiosis states that prokaryotic ancestors of modern mitochondria and chloroplasts were engulfed by larger prokaryotic cells forming a mutually advantageous relationship called symbiosis.
Mitochondria carry out aerobic respiration. Chloroplasts are thought to derive from endosymbiotic events involving cyanobacteria. Since cyanobacteria perform oxygenic photosynthesis – the host cell can easily supply the H20 necessary to drive photosynthesis. Only plants and algae have both mitochondria and chloroplasts.

The shape and internal organization of each type of cell are maintained by it's cytoskeleton (an interconnected system of protein fibers and tubes that extend throughout the cytoplasm). Three structural elements: microtubules (microscopic hollow tubes), intermediate filaments (fibres that occur singly, in parallel bundles and in interlinked networks) and microfilaments (thin fibres that consist of two rows of protein subunits wound around each other in a long spiral).

Flagella are long hairlike structures that project from the cell surface and function in cell movement.

“The internet is a series of Tubes” - unknown origin -

Structures that perform the same function but do not share a common evolutionary history are said to be analogous. If they do share history, they are homologous.

Division of labour – some cells specialize in harnessing energy – others for the motility of the organism. Cells no longer needed to be independent.

= Selection, Biodiversity, and Biosphere =

Air travel can affect the spread of viruses such as influenza A which kills 500000 people a year.
Since H3N2 was first reported in 1968 – it has undergone periods of relative stasis lasting 3 to 8 years followed by rapid changes. WHO has the opportunity to monitor the situation in East and SE Asia allowing vaccines to be developed against the most threatening strains.

== Biodiversity ==

Measured as the number of species of organisms, and reflects the reality that life exists from the ocean floor to the atmosphere. Other than taxonomic categories organisms are grouped based on how they obtain carbon.

Autotroph – self nourishing – synthesize organic carbon molecules using inorganic carbon (C02)
heterotrophs – they obtain carbon from organic molecules, either from living hosts or from organic molecules in the products, wastes or remains of dead organisms.
Chemotrophs – chemical nourishment – obtain energy by oxidizing inorganic or organic substances
phototrophs – obtain energy from light

chemoautotrophs – bacteria and archeans; not found in eukaryotes
chemoheterotrophs – found in some bacteria and archeans, also in proteins, fungi, animals, and plants
photoautotrophs – photosynthetic bacteria – in some proteins and some plants
photoheterotrophs – found in some photosynthetic bacteria

== Selection ==

Occurs when some force or phenomenon affects the survival of individual organisms, when a large population is exposed to a lethal factor and only resistant individuals survive to reproduce. If resistance is inherited, then the offspring of survivors will be resistant. If the resistant population is able to reproduce quickly, there is the potential for explosive growth of a population of individuals immune to the lethal factor.
Key factors – selective force and capacity for explosive population growth.

User interface adoption and product availability. (Economic comparison?)

== Evolution ==

Defined as a gradual change in the characteristics of a population of organisms over time, and can be a result of selection. Explains both the unity and diversity of life: all organisms alive today descended from a common ancestor – why all organisms share features such as the use of ATP (adenosine triphosphate) as a cellular energy source, DNA (deoxyribonucleic acid) as genetic material, and plasma membranes composed of lipid bilayers.
Darwin's central ideas to the theory of evolution by natural selection:
individual organisms in a population vary in many heritable traits.
Any population has the potential to produce far more offspring than the environment can support. Competition for limited resources means that only some individuals can survive.
Individuals may have traits that give them an advantage in their local environment; these are more likely to survive and reproduce.
These individuals pass on favorable traits to their offspring

Adaptive Radiation – these occur when an evolutionary breakthrough allows diversification of life.

The appearance of oxygenetic photosynthesis increased the concentrations of oxygen which led to aerobic respiration and the ozone layer, which allowed organisms to colonize terrestrial environments by blocking harmful (UV) rays. Changes caused by an increase in atmospheric oxygen triggered an extraordinary diversification of life.

Islands are seen as showcases of evolution – Hawaii, New Zealand, Madagascar, Mauritius, Galapagos Islands – also island populations of animals and plants can be vulnerable to extinction. (negative impact of humans on biodiversity)

Terrestrial animals used nontoxic excretory products (urea, uric acid), whereas aquatic ones still relied heavily on ammonia.

== The Biosphere ==

The area occupied by life on Earth. The various physical environments and their different abiotic factors (sunlight, temperature, humidity, wind speed, cloud cover and rainfall) influence the evolution and diversity of organisms.

Climate – weather conditions prevailing over an extended period of time.

== Biotic Factors ==
== Cumulative Impact on Biotic and Abiotic Factors ==

= Energy and Enzymes =
== Energy and the Laws of Thermodynamics ==
== Free Energy and Spontaneous Reactions ==
== The Energy Currency of the Cell: ATP ==
== The Role of Enzymes in Biological Reactions ==
== Conditions and Factors that Affect Enzyme Activity ==

(Mohamed)

Energy and Enzymes:

Catalyst called enzymes speed up the rates of reaction without the need for an increase in temperature.

Phosphatases: A group of enzymes catalyze the removal of phosphates groups from a range of molecules.

Energy: The capacity to do work e.g build a protein from a group of amino acids or pump sucrose across a cell membrane.

First law of thermodynamics: Energy can be transformed from one place to another, but it cannot be created or destroyed.

Second law of thermodynamics: The total disorder (entropy) of a system and its surroundings always increases.

It takes energy to maintain low entropy or the “orderness” of things.

Cells are always breaking down and new ones are always being created by the synthesis of a huge array of proteins, carbohydrates and lipid molecules.

Free energy: The portion of a system’s energy that is available to do work.

Spontaneous reactions:

1- Reactions tend to be spontaneous if the products have less potential energy than the reactants.

2- Reactions tend to be spontaneous when the products are less ordered than the reactants.

3- Change in free energy indicated whether a reaction is spontaneous. The free energy change as the system goes from initial to final states is the sum of the changes in the energy content and entropy.

Point of chemical equilibrium: a state in which reaction does not stop but rather a state in which the rate of the forward reaction equals the rate of the backward reactions.

The change in free energy of life is always negative as organisms constantly take in energy-rich molecules and use them to do work. Organisms reach equilibrium only when they die.

Exergonic reaction: A reaction that releases free energy. Products contain less free energy than the reactants

Endergonic reaction: The products contain more free energy than the reactants.The reactants involved in the reaction need to gain free energy from the surroundings to form products of the reaction.
Catabolic pathway: Energy is released by the breakdown of complex molecules to simpler compounds e.g. cellular respiration

Anabolic pathway: Energy is consumed to build complex molecules from more simple ones. e.g. photosynthesis.

Cells supplies energy to drive endergonic reactions using ATP (adenosine triphosphate)

ATP contains free enegry from high energy phosphate bonds.

Removal of one or two of the three phosphate groups is a spontaneous reaction that relieves the repulsion of the negatively charged phosphate groups and releases large amounts of free energy.

The breakdown of ATP is a hydrolysis reaction and results in the formation of ADP (adenosine diphosphate) and a molecule of inorganic phosphate.

Hydrolysis of ATP produces free energy (heat).

How do living cells link the hydrolysis of ATP to an endergonic reaction such that the energy is not wasted as heat?: Energy coupling: An enzyme brings ATP and the reactant molecule into close association.

Energy in carbohydrates, fats and proteins consumed in food is used in the energy requiring endergonic process that combines ADP and Pi.

The continued breakdown and resynthesis of ATP is called the ATP cycle.

A spontaneous reaction does not mean that it proceeds rapidly.

Activation Energy: initial energy required to start a reaction and tranform molecules into transition state where bonds are stable and are ready to be broken.

Enzymes act as a catalyst by lowering the activation energy required by molecules in reactants to start a reaction.

Enzymes speed-up the rate of spontaneous exergonic reactions.

Enzymes do not supply free energy to the reaction.

Three main mechanisms in which an Enzyme lowers activation Energy:

1- Bringing the reacting molecules together

2- Exposing the reactant molecule to altered charge environments that promote catalysis

3- Changing the shape of a substrate molecule

Temperature and pH levels have a significant effect on enzyme activity and thus the reaction rates. The optimum pH level for an enzyme depends on the pH level of its environment. If Temperature becomes too high the enzyme of denatured.

As the enzyme concentration increases the rate of catalysis increases.

Competitive Enzyme inhibition: enzyme inhibitors bind to the enzyme’s active site

Non-competitive inhibitors: enzyme inhibitors bind to a location on the enzyme other than the active site.

Enzyme inhibition is important to the cell since it controls the presence of multiple active enzymes at the same time. (allosteric regulation).

Feedback inhibition provides a mechanism to prevent the wasting of cell’s energy. If the concentration of the inhibitor increases the enzyme action is inhibited, if the concentration of the inhibitor decreases, the enzyme is activated.

= Membranes and Transport =
== An overview of the Structure of Membranes ==
== The Lipid Fabric of a Membrane ==
== Membrane Proteins ==
== Passive Membrane Transport ==
== Active Membrane Transport ==
== Exocytosis and Endocytosis ==

= Cellular Respiration =
== The Chemical Basis of Cellular Respiration ==
Cellular respiration allows organism to uses energy that is stored in chemical bonds of glucose (transferring electrons). This energy is then used to create ATP.

Redox reactions are a set of reactions that partially or completely transfer electrons. The reason they are called redox reactions is because they always occur in pairs – one oxidation and one reduction. The oxidation reaction is the reaction that releases an electron (increases in oxidation state). While the reduction reaction is the reaction that accepts this electron (decreases in oxidation state).

I think that redox reaction is extremely important and we see it almost everywhere. We use a battery for almost everything when we need a portable power source and it is an excellent example of redox reactions.

== Cellular Respiration: An Overview ==
== Glycolysis ==
== Pyruvate Oxidation and the Citric Acid Cycle ==
== Electron Transport and Chemiosmosis ==
== The Efficiency and Regulation of Cellular Respiration ==
== Oxygen and Cellular Respiration ==

BioSec: Text: Unit 1: Setting the Stage

2012-01-27T15:01:15Z

Dsouza3190: /* The Chemical Basis of Cellular Respiration */

= Light and Life =

The book starts out talking about Monet, the French impressionist painter, and the reason why his later paintings lacked light blue, and appeared to be toned towards red-yellow. This was due to a physical ailment of cataracts. The opaqueness of a cataract affected lens causes it to absorb certain wavelengths of light.

The way in which you see the world is affected by biological processes. The way in which you view a computer is similar – an operating system on a machine is effectively a map to the internal workings of the machine. It gives you a perspective view of how to interact and process information stored within a computer.

== The Physical Nature of Light ==

Light functions:
Light is a source of energy that sustains life.
Light provides organisms with information about the physical world.

Photosynthesis – biological process to create energy rich molecules (algae)

Light is defined as the portion of the electromagnetic spectrum that humans can detect with their eyes. It is hard to characterize because it although it can be described as a wave it also behaves like a stream of energy particles.
When light interacts with matter three things can happen – it can be reflected off of the object, transmitted through the object or absorbed by the object. Absorption occurs when the energy of a photon is transferred to the electron of the pigment molecule.
Pigments are molecules that can absorb photons of light – each differ in the wavelengths that they can absorb. The feature critical to light absorption is a region where carbon atoms are covalently bonded with alternating single and double bonds (conjugated system) which results in the delocalization of electrons. A single photon results in the excitation of one and only one, electron in the pigment molecule and secondly the energy of the photon must match the energy difference between the ground state and one of the excited states in order for the photon to be absorbed.

Why is cholorophyll green in color? The color of a pigment is determined by the wavelengths of light it cannot absorb.

Photosynthesis sustains almost all life – uses the energy in sunlight to build sugar molecules from carbon dioxide and water – releasing oxygen as a by-product.

== Light as a Source of Energy ==
The excited electron state is a source of potential energy that can be used to do work. This energy is used to synthesize energy rich compounds (NADPH and ATP) which are used to convert CO2 into carbohydrates. Other biological molecules such as lipids, proteins, and nucleic acids from simple building blocks found in the environment.

== Light as a Source of Information ==
Organisms use light to sense their environment. Not every person – and not every species sees the world in the same way.
Rhodopsin - the most common photoreceptor found in nature – mystery as to why – perhaps it developed very early in the evolution of life
consists of a protein called opsin that binds a single pigment molecule called retinal
absorption of a photon causes the retinal pigment to change shape – causing chain reaction - alteration of protein, intracellular ion concentrations and electrical signals which are then sent to the brain
even things without eyes can sense light direction and intensity
eye – can be defined as the organ animals use to sense light – what distinguishes the eye from an eyespot of an invertibrate is the vision process – requires not only an eye but also a brain or simple nervous system that interprets signals sent from the eye

image forming eyes come in two varieties: compound eyes and single lens eyes -

compound eyes can be found in insects and crustaceans – hundreds to thousands of ommatidia units fitted closely together – each one samples only a small part of the visual field. Enables even slight motion detection.

Lens eyes (camera) – light enters through the transparent cornea – a lens concentrates the light and a layer of photoreceptors at the back of the eye, the retina – records the image.

Darwin proposed that the eye as it exists in humans and other animals did not appear suddenly but evolved by variation (mutation) and natural selection over time from a simple, primitive eye.

Any application during it's development life cycle evolves to hopefully become better at the task it was designed to perform. Not only programs, but operating systems, and hardware are selected and chosen by respective audiences somewhat based upon the usability, and performance of the system.

Computer scientists not only program, but attempt to imitate life in many ways as well. Robots were initially designed to perform specific tasks, but have evolved over time to complete more interesting behaviours. Sensors are designed to provide input in a variety of different ways to affect the behaviour of a robot. Cameras and photocells detect light. Touch screens, keyboards and mice provide the ability to provide stimuli.

“An optically refined eye is no good unless the brain of the organism improves at the same time, allowing for more advanced neural processing of the information being sent by the optic nerve.”

This makes me think of the case for an older camera driver for a newer model of video camera which is 1080 p enabled technically, but due to the old driver it can only process a lower resolution.

What can computer scientists learn from certain biological processes – don't throw out the old to replace with the new (as generally this type of thing doesn't work). Change can happen a lot but it doesn't completely waste what has already been created.

== Light can Damage Biological Molecules ==

Light is a form of energy that has the potential to damage biological molecules both directly and indirectly. All organisms have developed mechanisms to help prevent or repair damage once it occurs.
Carotenoids are accessory pigments that protect the photosynthetic apparatus from high light levels by absorbing extra light and converting the energy to heat.

Question: Plants unable to synthesize carotenoids turn white when exposed to light because the chlorophyll becomes oxidized and the light harvesting capabilities destroyed – (what about mushrooms – is this the same for fungus (plant or animal)?)

Melanin is a pigment that absorbs UV radiation. Melanin in cells prevents light from damaging the DNA in skin cells that is linked with cancer by preventing the destruction of B vitamin folate. Melanin cannot completely filter out all light rays because vitamin d is necessary for proper bone development.

Melanin is the “firewall” of light entering our bodies. A firewall being a device or set of devices designed to permit or deny network transmissions based on a set of rules used to protect networks from unauthorized access while permitting legitimate traffic. /ref{http://en.wikipedia.org/wiki/Firewall_%28computing%29}

== Role of Light in Ecology and Behaviour ==

circadian rythyms
nightly backups
nightly software updates / system upgrades
controlled by an internal clock – there are a lot of computational processes controlled by internal clock devices
normal operational behaviour – versus abnormal operational behaviour – logins that occur in the middle of the night to specific accounts

DNA replication only occurs at night. <- highly sensitive processing occurs nightly in order to avoid serious damaging errors.

Hormone – melatonin – secreted from the brain in order to control sleep wake cycles as it's synthesis is active at night.

Camouflage – works when an animal is indistinguishable to another in its current environment.

Separating the message from the noise. Microdots. Cryptography. (Ideas that come to mind within this context.)

Story of the industrial revolution moths – reminded me of the mac laptops in the classroom – one university professor noted that a certain year, there were many different types of laptops and one or two macs, and the following year it was all macs. (can't find the reference right now) now due to the emergence of better security (ahem - supposidely) on Windows 7, will the variety go back to the way that it was?

Using Color as signals – warnings / error messages – The effective ones are different colors or make different sounds when they occur. So many high tech security companies focus their marketing also around these stark contrast colors – Symantec Yellow / Black – Black / White / Red – McAfee – Avast Orange / Black – Norton Orange / Yellow / Black

== Life in the Dark ==

Even blind animals need to set their biological clocks to a circadian rythym. (Blind mole rat / Mexican cavefish)

== Organisms Making their own Light: Bioluminescence ==

This is a process by which the pigment transfers energy from an electron to a photon to assume a grounded state. This reaction in nature is highly efficient in order to ensure less heat production within an organism.

Most bioluminescence is found under the sea, and less on land animals – most often found at great depths, but also in algae / bacterial blooms near the surface. One great mystery surrounding this phenomenon is bioluminescent mushrooms.

= Origins of Life =

== What is Life? ==

The types of atoms and molecules found in living things is the same as those found in non living forms of matter. Living cells also obey the same fundamental laws of chemistry and physics as does the non living particles. Biochemical reactions that take place although complex are only modifications of reactions that take place by non living materials.

All forms of life share a set of attributes:

display order (cell fundamental unit – arranged in a highly ordered pattern)
harness and utilize energy (acquire energy and use it to maintain state)
reproduce (make more copies)
respond to stimuli (adjust structure, function or behaviour according to environment)
exhibit homeostasis (functions to maintain constant internal conditions)
growth and development (increase their size)
evolve (change over the course of generations to adapt to their environment)

Viruses are not alive because the lack the mechanisms required to produce proteins, and instead rely on highjacking the processes of a living cell to accomplish their replication.

3 Tenets of Cell Theory
1. Organisms are composed of one or more cells.

Single celled organisms are capable of carrying out all living activities. Multi-cellular organisms compartmentalize – that is, the activities are divided among groups of specialized cells.

2. The cell is the smallest unit that has the properties of life.
3. Cells arise only from growth and division of pre-existing cells.

== The Chemical Origins of Life ==

The key building blocks of life – nucleic acids and proteins – are not individually synthesized molecules called monomers – they are macromolecules built up from large numbers of subunit monomers coming together to produce polymers.
The synthesis of proteins and nucleic acids require protein-based catalysts (enzymes).

Clay – consists of very thin layers of minerals separated by thin layers of water. Present in evaporating tidal pools. The layered structure absorbs ions and organic molecules and promotes interactions (example: condensation).

Protobionts – first cells – abiotically produced organic molecules surrounded by a membrane.

== The Origins of Information and Metabolism ==

Critical events necessary for life development: one to store, replicate and translate information for protein synthesis and the other to develop metabolic pathways to capture and harness energy for life functions (metabolism).

Deoxyribonucleic acid (DNA) is a large double stranded, helical molecule that contains a unique alphabet that provides the instructions necessary for assembling many components of a cell organism from simpler molecules. DNA is copied onto molecules of a related substance (RNA) which is used to direct the production of proteins. Any changes to DNA are what contribute to evolutionary change over generations.

Group of RNA molecules called ribozymes can catalyze reactions on precursor RNA molecules that lead to their own synthesis and on related RNA molecules. (single stranded molecules that can bend into specialized shapes) A single type of molecule could serve as both a carrier of information and a catalyst.

Selection may have favored DNA for the following advantages over RNA:
Each strand is chemically more stable – due to the presence of the sugar deoxyribose instead of ribose.
Base uracil found in RNA was replaced by thymine which allows for the detection of a damaged cytosine
DNA is double stranded – in the case of a mutation / error – the complementary strand can be used to repair the damaged strand.

== Early Life ==

The earliest conclusive evidence of life are fossilized remains of structures called stromatolites – a type of layered rock that is formed when microorganisms bind particles of sediment together to form thin sheets.

Panspermia – hypothesis that forms of life are present in outer space and may have seeded early Earth.
Although life is complex it arose very quickly after the formation of the Earth. (The window for the development of life is very narrow)
life is more resilient than previously thought, and could survive for years in space. (Extremophiles which are mostly prokaryotes can thrive under harsh conditions of temperature, pressure and nutrients and might be able to survive in a dormant state in interstellar space.)

prokaryotic and eukaryotic cells are the two fundamental cell types all forms of life are based from.
Prokaryotic organsims exist in two domains: bacteria and Archaea.

Prokaryotic cells lack a nucleus (eukaryotic cells have a nucleus). All cells share fundamental features: - permeable plasma membrane (to separate external environment from cytoplasm (consisting of cytosol – mostly water, salts and various organic molecules, and structural features within the cell, including organelles)) – the membrane contains protein complexes that allow controlled transport of materials into and out of the cell.
In photosynthetic prokaryotic cells the plasma membrane is the site of photosynthetic electron transport chains which harvest light energy for the synthesis of energy rich molecules.
In eukaryotes mitochondria and chloroplasts perform energy transduction.

Prokaryotic cells have a nucleiod (central region) instead of a nucleus which is where the DNA of this organism is stored. They are 10 times smaller than a eukaryotic cell. They appear deceptively simple, as they are metabolically flexible which means they are able to use a variety of substances as energy and carbon sources to synthesize almost all of their required organic molecules from simple inorganic raw materials.

Where did oxygen come from? - Cyanobacteria could harness the electrons from water and when it split the water, Oxygen was a byproduct. The rise in oxygen in the atmosphere led to the evolution of prokaryotic cells. These cells were able to undergo aerobic respiration where energy is extracted from food molecules where oxygen acts as the final electron acceptor. Aerobic respiration enabled organisms to extract larger amounts of energy from food molecules than respiration that does not include oxygen. This was a key factor in the development of eukaryotic cells.

== Eukaryotic Cells ==

Distinguished characteristics that separate eukaryotic cells from prokaryotic cells:
separation of DNA and cytoplasm by nuclear envelope
membrane bound compartments with specialized functions (mitochondria, chloroplasts, endoplasmic reticulum, Golgi complex, etc)
highly specialized motor proteins that move cells and internal cell parts.

Membranes are connected directly or indirectly by vesicles – small membrane bound compartments that transfer substances between parts of the system. ER and Golgi complex serve the following functions:
synthesis and modification of proteins
protein transport into membranes or outside of the cell
synthesis of lipids
detoxification of harmful compounds
Endoplasmic Reticulum – ER – extensive interconnected network of membranous channels and vesicles – each vesicle is formed by a single membrane that surrounds an enclosed space called the lumen.
Rough er – ribosomes stud outer surface – destined for plasma membrane or release outside the cell
smooth er – lipid production

Golgi complex – stack of flattened membranous sacs located between the rough er and the plasma membrane that recieves and chemically modifies proteins made in the ER transported to the complex by vesicles.

Secretory vesicles release their contents to the exterior of the cell by exocitosis. Vesicles may also absorb molecules from outside the cell using endocitosis.

Established theory of endosymbiosis states that prokaryotic ancestors of modern mitochondria and chloroplasts were engulfed by larger prokaryotic cells forming a mutually advantageous relationship called symbiosis.
Mitochondria carry out aerobic respiration. Chloroplasts are thought to derive from endosymbiotic events involving cyanobacteria. Since cyanobacteria perform oxygenic photosynthesis – the host cell can easily supply the H20 necessary to drive photosynthesis. Only plants and algae have both mitochondria and chloroplasts.

The shape and internal organization of each type of cell are maintained by it's cytoskeleton (an interconnected system of protein fibers and tubes that extend throughout the cytoplasm). Three structural elements: microtubules (microscopic hollow tubes), intermediate filaments (fibres that occur singly, in parallel bundles and in interlinked networks) and microfilaments (thin fibres that consist of two rows of protein subunits wound around each other in a long spiral).

Flagella are long hairlike structures that project from the cell surface and function in cell movement.

“The internet is a series of Tubes” - unknown origin -

Structures that perform the same function but do not share a common evolutionary history are said to be analogous. If they do share history, they are homologous.

Division of labour – some cells specialize in harnessing energy – others for the motility of the organism. Cells no longer needed to be independent.

= Selection, Biodiversity, and Biosphere =

Air travel can affect the spread of viruses such as influenza A which kills 500000 people a year.
Since H3N2 was first reported in 1968 – it has undergone periods of relative stasis lasting 3 to 8 years followed by rapid changes. WHO has the opportunity to monitor the situation in East and SE Asia allowing vaccines to be developed against the most threatening strains.

== Biodiversity ==

Measured as the number of species of organisms, and reflects the reality that life exists from the ocean floor to the atmosphere. Other than taxonomic categories organisms are grouped based on how they obtain carbon.

Autotroph – self nourishing – synthesize organic carbon molecules using inorganic carbon (C02)
heterotrophs – they obtain carbon from organic molecules, either from living hosts or from organic molecules in the products, wastes or remains of dead organisms.
Chemotrophs – chemical nourishment – obtain energy by oxidizing inorganic or organic substances
phototrophs – obtain energy from light

chemoautotrophs – bacteria and archeans; not found in eukaryotes
chemoheterotrophs – found in some bacteria and archeans, also in proteins, fungi, animals, and plants
photoautotrophs – photosynthetic bacteria – in some proteins and some plants
photoheterotrophs – found in some photosynthetic bacteria

== Selection ==

Occurs when some force or phenomenon affects the survival of individual organisms, when a large population is exposed to a lethal factor and only resistant individuals survive to reproduce. If resistance is inherited, then the offspring of survivors will be resistant. If the resistant population is able to reproduce quickly, there is the potential for explosive growth of a population of individuals immune to the lethal factor.
Key factors – selective force and capacity for explosive population growth.

User interface adoption and product availability. (Economic comparison?)

== Evolution ==

Defined as a gradual change in the characteristics of a population of organisms over time, and can be a result of selection. Explains both the unity and diversity of life: all organisms alive today descended from a common ancestor – why all organisms share features such as the use of ATP (adenosine triphosphate) as a cellular energy source, DNA (deoxyribonucleic acid) as genetic material, and plasma membranes composed of lipid bilayers.
Darwin's central ideas to the theory of evolution by natural selection:
individual organisms in a population vary in many heritable traits.
Any population has the potential to produce far more offspring than the environment can support. Competition for limited resources means that only some individuals can survive.
Individuals may have traits that give them an advantage in their local environment; these are more likely to survive and reproduce.
These individuals pass on favorable traits to their offspring

Adaptive Radiation – these occur when an evolutionary breakthrough allows diversification of life.

The appearance of oxygenetic photosynthesis increased the concentrations of oxygen which led to aerobic respiration and the ozone layer, which allowed organisms to colonize terrestrial environments by blocking harmful (UV) rays. Changes caused by an increase in atmospheric oxygen triggered an extraordinary diversification of life.

Islands are seen as showcases of evolution – Hawaii, New Zealand, Madagascar, Mauritius, Galapagos Islands – also island populations of animals and plants can be vulnerable to extinction. (negative impact of humans on biodiversity)

Terrestrial animals used nontoxic excretory products (urea, uric acid), whereas aquatic ones still relied heavily on ammonia.

== The Biosphere ==

The area occupied by life on Earth. The various physical environments and their different abiotic factors (sunlight, temperature, humidity, wind speed, cloud cover and rainfall) influence the evolution and diversity of organisms.

Climate – weather conditions prevailing over an extended period of time.

== Biotic Factors ==
== Cumulative Impact on Biotic and Abiotic Factors ==

= Energy and Enzymes =
== Energy and the Laws of Thermodynamics ==
== Free Energy and Spontaneous Reactions ==
== The Energy Currency of the Cell: ATP ==
== The Role of Enzymes in Biological Reactions ==
== Conditions and Factors that Affect Enzyme Activity ==

(Mohamed)

Energy and Enzymes:

Catalyst called enzymes speed up the rates of reaction without the need for an increase in temperature.

Phosphatases: A group of enzymes catalyze the removal of phosphates groups from a range of molecules.

Energy: The capacity to do work e.g build a protein from a group of amino acids or pump sucrose across a cell membrane.

First law of thermodynamics: Energy can be transformed from one place to another, but it cannot be created or destroyed.

Second law of thermodynamics: The total disorder (entropy) of a system and its surroundings always increases.

It takes energy to maintain low entropy or the “orderness” of things.

Cells are always breaking down and new ones are always being created by the synthesis of a huge array of proteins, carbohydrates and lipid molecules.

Free energy: The portion of a system’s energy that is available to do work.

Spontaneous reactions:

1- Reactions tend to be spontaneous if the products have less potential energy than the reactants.

2- Reactions tend to be spontaneous when the products are less ordered than the reactants.

3- Change in free energy indicated whether a reaction is spontaneous. The free energy change as the system goes from initial to final states is the sum of the changes in the energy content and entropy.

Point of chemical equilibrium: a state in which reaction does not stop but rather a state in which the rate of the forward reaction equals the rate of the backward reactions.

The change in free energy of life is always negative as organisms constantly take in energy-rich molecules and use them to do work. Organisms reach equilibrium only when they die.

Exergonic reaction: A reaction that releases free energy. Products contain less free energy than the reactants

Endergonic reaction: The products contain more free energy than the reactants.The reactants involved in the reaction need to gain free energy from the surroundings to form products of the reaction.
Catabolic pathway: Energy is released by the breakdown of complex molecules to simpler compounds e.g. cellular respiration

Anabolic pathway: Energy is consumed to build complex molecules from more simple ones. e.g. photosynthesis.

Cells supplies energy to drive endergonic reactions using ATP (adenosine triphosphate)

ATP contains free enegry from high energy phosphate bonds.

Removal of one or two of the three phosphate groups is a spontaneous reaction that relieves the repulsion of the negatively charged phosphate groups and releases large amounts of free energy.

The breakdown of ATP is a hydrolysis reaction and results in the formation of ADP (adenosine diphosphate) and a molecule of inorganic phosphate.

Hydrolysis of ATP produces free energy (heat).

How do living cells link the hydrolysis of ATP to an endergonic reaction such that the energy is not wasted as heat?: Energy coupling: An enzyme brings ATP and the reactant molecule into close association.

Energy in carbohydrates, fats and proteins consumed in food is used in the energy requiring endergonic process that combines ADP and Pi.

The continued breakdown and resynthesis of ATP is called the ATP cycle.

A spontaneous reaction does not mean that it proceeds rapidly.

Activation Energy: initial energy required to start a reaction and tranform molecules into transition state where bonds are stable and are ready to be broken.

Enzymes act as a catalyst by lowering the activation energy required by molecules in reactants to start a reaction.

Enzymes speed-up the rate of spontaneous exergonic reactions.

Enzymes do not supply free energy to the reaction.

Three main mechanisms in which an Enzyme lowers activation Energy:

1- Bringing the reacting molecules together

2- Exposing the reactant molecule to altered charge environments that promote catalysis

3- Changing the shape of a substrate molecule

Temperature and pH levels have a significant effect on enzyme activity and thus the reaction rates. The optimum pH level for an enzyme depends on the pH level of its environment. If Temperature becomes too high the enzyme of denatured.

As the enzyme concentration increases the rate of catalysis increases.

Competitive Enzyme inhibition: enzyme inhibitors bind to the enzyme’s active site

Non-competitive inhibitors: enzyme inhibitors bind to a location on the enzyme other than the active site.

Enzyme inhibition is important to the cell since it controls the presence of multiple active enzymes at the same time. (allosteric regulation).

Feedback inhibition provides a mechanism to prevent the wasting of cell’s energy. If the concentration of the inhibitor increases the enzyme action is inhibited, if the concentration of the inhibitor decreases, the enzyme is activated.

= Membranes and Transport =
== An overview of the Structure of Membranes ==
== The Lipid Fabric of a Membrane ==
== Membrane Proteins ==
== Passive Membrane Transport ==
== Active Membrane Transport ==
== Exocytosis and Endocytosis ==

= Cellular Respiration =
== The Chemical Basis of Cellular Respiration ==
Cellular respiration allows organism to uses energy that is stored in chemical bonds of glucose (transferring electrons). This energy is then used to create ATP.

Redox reactions are a set of reactions that partially or completely transfer electrons. The reason they are called redox reactions is because they always occur in pairs – one oxidation and one reduction. The oxidation reaction is the reaction that releases an electron (increases in oxidation state). While the reduction reaction is the reaction that accepts this electron (decreases in oxidation state).

== Cellular Respiration: An Overview ==
== Glycolysis ==
== Pyruvate Oxidation and the Citric Acid Cycle ==
== Electron Transport and Chemiosmosis ==
== The Efficiency and Regulation of Cellular Respiration ==
== Oxygen and Cellular Respiration ==

BioSec: Evolution

2012-01-16T15:18:14Z

Dsouza3190: /* Origin of Domestic Varieties from one or more Species */

BioSec: Evolution

2012-01-16T15:18:06Z

Dsouza3190: /* Origin of Domestic Varieties from one or more Species */

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2012-01-16T14:17:55Z

Dsouza3190: /* Inheritance */

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2012-01-16T14:16:35Z

Dsouza3190: /* Inheritance */

BioSec: Evolution

2012-01-15T22:46:12Z

Dsouza3190: /* Inheritance */

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2012-01-15T22:31:27Z

Dsouza3190: /* Inheritance */