Soma-notes - User contributions [en]

BioSec: DNMar23

2012-03-27T23:26:27Z

Daniel: /* List of individual detectors */

== Design Exercise: Phishing ==

How can we design an anti-phishing strategy that uses a biological approach?

Our theoretical phishing scenario involves:
* banking
* want credentials
* using email
* send an email that looks like it comes from the bank
* link goes to malicious site that looks arbitrarily like the bank
** what does it mean to look like the bank?
* user types in credentials, potentially gets transparently redirected to real bank site

Some of the problems that arise in phishing are related to:
* faked email
* link to site that looks like the bank but isn't the bank
* url that looks like the bank's url, but isn't the bank's url
* credentials being entered in wrong domain, wrong page
* misappropriated text and images (both in email, and on the faked website)
* bad/missing/suspect certificate
** certificate/credential combination is suspect

Human algorithm:
* is the domain the same for the one where credentials are normally sent?
* not normally in response to email request
* certificate is the same

Think of individual detectors as autonomous:
* how would they be useful?
* how would they work? to detect?
* how should they change system state in the normal case?

Possible anti-phishing system characteristics:
* language checks
** phishing attacks often have poor grammar and spelling
** system could check the spelling and grammar to look for changes
* URLs
** phishing URLs are often designed to look like those of the legitimate site (e.g., www.paypa1.com)
** system could check for unusual url characteristics, such as numbers, non-printing characters, characters like "|"
* past behaviour
** has the user entered this username/password at this domain before?
** does the user normally follow a link from an email before entering these credentials?
** does the certificate match the one where the user normally enters these credentials?

How would the system react to information gathered?
* the system should holistically assess all kinds of information gathered
* gather a rich picture of the email's characteristics, the website characteristics, and the user's behaviour
* there should be a sort of saturation point where enough characteristics point to phishing that the system reacts in such a way as to prevent loss of information
** what should the system do?
* should some system characteristics have more weight than others?
** should elements like certificate validity be considered more important and have more effect on the decision?
* the system should base this decision on many small indicators

= List of individual detectors =

* '''Image filename/content sensor'''
** A fuzzy hash/fingerprinting technique of the images would be another idea.
*** Could hook into something like [http://www.tineye.com/commercial_api TinEye]

* '''Cascading Stylesheet sensor''' -- a sort of visual appearance sensor.
** Might give an indication that a page is visually masquerading as another page.
** Are the elements of this page styled identically to the elements on my banking website?
** Is the CSS file a hash-identical version of the CSS on my banking website?

* context / semantic word descriptions --> semantic integrity - verifying message / content integrity based on the content itself - even if it is digitally signed. ''(huh? Could the original author of this fragment add more?)''

* '''Content depth sensor'''
** Is the page a facade with no content except that which is visible and the login form meant to capture credentials?
** Many phishing pages will jack the front/login page of a bank and then link all other content back to the original bank.
*** A detector that scored a page based on the structure/depth of the content it offers, stopping on any cross-server boundaries (i.e. not following links back to the 'real' bank if the phisher has emulated depth of content that way).

* '''Spellcheck sensor'''

* '''Domain / ip address sensor'''
** Could use more advanced metrics. Is the domain name within a certain [http://en.wikipedia.org/wiki/Levenshtein_distance Levenshtein distance] of a known financial institution?
*** Of one of the financial institutions that I frequent?
** Is the whois lookup of the domain I'm connecting to sensible?
*** I.e. is it associated to the company I expect. Does it have proper contact information? Do e-mails to this information bounce?

*''' GeoIP lookup sensor'''
** Is the IP address I'm connecting to in the same country as my financial institution?

* '''Certificate sensor'''
** issuer name, domain name, client name, date of issue, date of expiry

* '''HTTP Header sensor'''
** Does the server reply with the same HTTP headers as were returned in previous visits to my bank?
** Does it employ any of the X-headers for things such as content security policy, http-only cookies, etc.? Security features are likely not common to fake websites.

* '''Web Search sensor'''
** If I do a Google, Yahoo, Bing and DuckDuckGo search for the name of the company I'm connecting to does the URL I'm visiting appear in the results?
** Does it appear in the top 10 results?

*''' Load time sensor'''
** How long does it take the website to load?
** Does it match the ballpark of how long it took me to load the website on prior visits?

* '''Traceroute sensor'''
** What hops do my packets take along the way to the site I'm connecting to?
** Is it absurdly different than usual?
** Probably a more hair-brained idea. Prone to drift/uncertainty in normal cases...

* '''Safe browsing sensor'''
** Does the URL get flagged when submitted to the [http://code.google.com/apis/safebrowsing/ Google Safebrowsing API]?

BioSec 2012: Daniel

2012-02-15T04:13:13Z

Daniel: Adding some brief thoughts from chapter 10.

== Daniel's BioSec Notes ==

These are just some general thoughts... Overall I feel I have a pretty shaky handle on a lot of the minute details of these systems. I'm having increasing trouble making analogies to computer security (or computer science in general) as things progress. I've approached this page as a summary of my 'take-aways' from the course so far.

If I could have any influence in the progression of the course from here on out it would be more structured and have a little bit more guidance in terms of what to focus on, and how to frame it in a familiar way. I feel that reading the biology and then trying to form abstractions that relate it to computer science isn't straightforward for someone with my background. It would be easier to start with the security analogies or some abstractions and then try to read the biology to fill in the gaps or appreciate the merit of the comparison.

Food (ATP?) for thought.

=== Core Dump ===

If there is a way to do something, biology does it that way in some cases. Optimization occurs only when it's required, imperfect solutions are not always imperfect. Even when they are there might not be an evolutionary gain to be had by improving it. There seems to be common patterns similar to a design pattern language that are used in several different areas and systems. A good example of this is the idea of a feedback loop, when too much of something is produced it feeds back into the production subsystem to limit further production. This is seen in photosynthesis as well as other metabolic pathways.

I notice that there is a strong emphasis on the decentralization of things. I see parallels between the ''Unix philosophy'' of having small components tailored for doing one specific thing really well, and chaining them together to achieve complex tasks or to wring out all possible energy. A good example of this (from my perspective) was cellular respiration. The three stages of cellular respiration (glycolysis, the citric acid cycle and chemiosmosis) each wring out a little bit more ATP that was missed by earlier stages.

The ''pattern matching'' approach taken by biology seems to recur frequently. I think of cellular communications and the challenges it faces as similar to those found in distributed systems. Dealing with highly concurrent processes it is very difficult to maintain and transfer state or to synchronise very complex communications between parties. Biology seems to have taken a ''spray and pray'' approach that is coupled with feedback mechanisms to deal with overloading of signals.

The ''broadcast'' nature of cellular communication makes it difficult for us to develop a drug highly tailored to a specific receptor or cellular subsystem that does not affect other receptors/cells. This property is fundamental to how the immune system is able to recognise threats quickly by a sort of aggregate sensing ability. This comes back to the difference between the way we engineer systems by adding pieces one by one to accomplish a goal and the way that biology/nature seems to have ''connected everything and removed connections that were superfluous or harmful''.

The theory about eukaryotic cells having developed through the absorption of smaller prokaryotic emphasises the component based approach to the development of complex systems. I think about it in terms of the modular development of operating systems, you may start with a unified memory and then later add a component that presents that sort of model to individual processes through virtual memory but in reality has a highly complex individual purpose (isolating processes).

=== Chapter 10 — Genetic Recombination ===

* Diversity of protocol implementations
** Similar to genetic diversity?
** Minor differences in spec implementation that eventually accrue into entirely separate instances?
** Genetic diversity arises from minor copying errors shuffled into different combinations

* Bacterial Conjugation
** need to bring together the DNA of two cells into close proximity
** Using a ‘sex pilus’ one cell sends a copy of part of it’s DNA across a cytoplasmic bridge
*** Is this like a .patch diff being sent from one person to another?

* Conjugation is one means to transfer DNA/achieve recombination in bacteria
** Two other ways: transformation and transduction
*** Biology doing things different ways, again…

* In transformation, bits of DNA from dead cells gets ‘picked up’
* In transduction, bacteriophage (viruses that infect bacteria) inject DNA
** Viruses end up transferring bacterial DNA from hosts they killed to newly infected bacteria
** These bacteria don’t die because they are injected with bacterial DNA not viral DNA

* Meiosis - reduces chromosome count in half
** otherwise reproduction would be doubling # of chromosomes in each generation

* Handled by specialized machinery - producing gametes and spores (depending on animal/plant/etc)
** Not meant to produce “sameness” that helps contribute to the body/mechanisms that make them

* The ‘halving’ process achieves compression in the sense that each zygote/spore has half the required chromosomes
** Chromosome ‘values’ differ -> alleles?

* Sexual reproduction as an ‘optimal’ strategy
** In that it increases genetic variability
** Offspring have better chances of having combinations of alleles that will be successful

BioSec 2012: Daniel

2012-02-07T23:07:43Z

Daniel: Adding some initial thoughts/opinions/junk? :(

BioSec: Evolution

2012-01-18T01:10:55Z

Daniel: Not sure if adding attribution to my username is needed for each chapter section when we're dividing things up by chapter, but I figure it's worth maintaining the page convention.

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)

=== 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)
=== 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)

== 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)

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

== CHAPTER VIII. INSTINCT ==
(???)

== CHAPTER IX. HYBRIDISM ==
(???)

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

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

== CHAPTER XII. GEOGRAPHICAL DISTRIBUTION ==
(???)

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

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

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

BioSec: Evolution

2012-01-18T01:09:52Z

Daniel: Chapter IV summary completed. Needs more "comp sci" perspective.

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)

=== 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)
=== 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)

== 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 ===

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. ===

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. ===

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. ===

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. ===

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. ===

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. ===

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. ===

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. ===

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)

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

== CHAPTER VIII. INSTINCT ==
(???)

== CHAPTER IX. HYBRIDISM ==
(???)

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

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

== CHAPTER XII. GEOGRAPHICAL DISTRIBUTION ==
(???)

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

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

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

User:Daniel

2012-01-18T00:19:00Z

Daniel: Adding a quick user page

== Daniel McCarney ==

Computer Science Masters Student
Supervisor: Dr. Paul Van Oorschot

WWW: [https://www.ccsl.carleton.ca/~dmccarney/ https://www.ccsl.carleton.ca/~dmccarney/]
E-mail: dmccarney@ccsl.carleton.ca

BioSec: Evolution

2012-01-17T23:59:57Z

Daniel: Adding the other chapters and who was assigned the summary (as many as I can remember anyway, add your name where appropriate)

BioSec: Evolution

2012-01-17T23:56:57Z

Daniel: Restructuring to allow for more than Chapter 1 to be put on this page. Maybe we should have separate pages per-chapter? Worth discussing?

BioSec: Evolution

2012-01-13T04:13:06Z

Daniel: Pigeons. I think they are hellish, winged poo-beasts. Darwin thought they were pretty cool. Adding my summary.

== 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 ==

== Effects of Habit and the use or disuse of Parts ==
== Correlated Variation ==
(Annie)
== Inheritance ==
== Character of Domestic Varieties ==
(Annie)
== Difficulty of distinguishing between Varieties and Species ==
(Annie)
== Origin of Domestic Varieties from one or more Species ==
== 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 ==
== 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.

BioSec: Evolution

2012-01-13T03:38:53Z

Daniel: /* Domestic Pigeons, their Differences and Origin */

BioSec: Evolution

2012-01-13T03:38:41Z

Daniel: dmccarne

BioSec: Evolution

2012-01-13T03:38:04Z

Daniel: Staking a claim.