BioSec: Evolution

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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 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 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 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.

“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.”

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.

“… 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.”

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.

"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."

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.

"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?"

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

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

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CHAPTER XI. ON THE GEOLOGICAL SUCCESSION OF ORGANIC BEINGS

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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

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CHAPTER XIV. MUTUAL AFFINITIES OF ORGANIC BEINGS

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CHAPTER XV. RECAPITULATION AND CONCLUSION

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