Saturday, 28 February 2009

The Origin, Chapter Eight

This chapter, on hybridism, actually deals primarily with an issue that is still contentious today: species concepts. There are over a dozen of these in common use today, all formalised and clear and intuitive and very, very wrong in certain applications. Darwin does not here discuss various individual definitions of "species", although he hints at an acceptance of an unspoken predecessor to the biological species concepts: a species is a closed genetically continuous community, which does not interbreed with other such communities in nature. Darwin ably emphasises the nature of the problem in his discussion of the distinction between varieties (or subspecies) and species, as recognised by his contemporaries. They disagree, he points out, on whether two plants represent different species or merely varieties of the same species; furthermore, when presented with evidence that two individuals can (or cannot) interbreed, they will describe them as (or as not) different species! The circularity of their arguments proves Darwin's point: even experts cannot agree on the threshold between species on a case-by-case basis.

Even in the case where the experts agree on two individuals being of different species, this does not mean that one cannot interbreed with the other; such crosses have occsionally been artificially attempted, and the offspring are often viable -- but also often sterile. This is the crux of this chapter. The facts that Darwin lays out amount to a long list of exceptions to our intuitive notions of clearly defined species. Rather than a simple distinction, in which all hybrids are inviable or sterile and the results of all intraspecies matings are fertile, there is a continuum. Sometimes hybrids are fertile, but are not readily obtained, usually (in Darwin's examples and estimation) by the anatomy of the parents' reproductive systems being incompatible. More importantly, hybrid sterility is not always mathematically transitive, which is to say that while species A and B might produce fertile hybrids when crossed, and species B and C might do likewise, species A and C might not. Furthermore, as Darwin points out, a male of A mating with a female of B might have more success producing fertile or viable offspring than the other way around.

Darwin's attempts at explaining these phenomena use a fair bit of Victorian phrasing, and appear antique, quaint, and occasionally clueless to the well-educated modern mind. After using the concept of homology in its modern sense, after getting so much right and pioneering so much else, Darwin's discussion of "systematic affinity" seems a giant leap backward. In using this latter term he seems to understand that he is groping about for a mechanism that he knows he will not find. It seems to encompass both homology and recent common ancestry, but in no particularly consistent combination. Indeed, he admits that, even when two species have it, that is still no guarantee that their offspring will be fertile or even viable. But in all of this discussion, here as elsewhere, the actual mechanism is not so important as its consequences, and it is to those that Darwin gives most of his attention.

Those consequences are the most important insight in this chapter, and are clearly stated in the last clause of its last sentence: "there is no fundamental distinction between species and varieties." This is an important point, to be sure, but I must wonder why it is made here, after the arguments in favour of Darwin's theory of evolution have already been laid out. Darwin introduced hybridism two chapters earlier as a potential challenge to his theory, but he does not discuss it in that context here. Indeed, he mentions this difficulty earlier in the book, but does not there develop it; doing so here seems almost an afterthought. I have no explanation for this, and it is possible (even likely) that I am missing something, but this chapter strikes me as out of place, and perhaps even ultimately unnecessary.

Sunday, 22 February 2009

The Origin, Chapter Seven

This chapter, on the evolution of instinct and behaviour in animals, begins with an important distinction, one which has shown up before: Darwin is not interested here in its origin, rather in how and why it changes over time. This partitioning of a subject into different problems is standard fare in science today; we spend a lot of time in science learning how to judge which aspects of a topic are dependent upon others, which are addressable given the current state of the art (and our ability to access the state of the art!), which are likely to fit into our current research programme (the sorts of things that a grad student can propose to do being very different from those that a post-doc, faculty member, or researcher at an institute or in the private sector), which are likely to be attractive enough to others to be likely to get funding, and so on. For all his wordiness, Darwin is very clear: he will not so much as speculate about the origin of variation, even though that is a critical component of his model of evolution. It is a fantastically interesting question, for which there was no known mechanism in the 19th century; indeed, it was not until well into the 20th century that the first tiny steps were to be taken that would elucidate this problem. Meanwhile, Darwin assumes a model of inheritance which is now known to be completely wrong, but he does not propose to test it: while this was possible in the 19th century (and Gregor Mendel investigated just that at the same time as Darwin was working on natural selection), it involved a great deal of time and effort, and Darwin recognised this (consciously or otherwise) and steered clear of it. Darwin's insight is actually very specific, dealing with a comparatively small aspect of life, and yet he recognised that it was a powerful and flexible concept in spite of the mechanisms for its implementation being (in his time) unknowable or uninvestigated. This is a sign of a remarkable mind, and the best that one can hope for in science: to recognise one's limits, to make the most of what one has available, to minimise the liabilities inherent in one's deficits, and to combine one's own data with that of one's forebears and contemporaries to produce a greater understanding of the world than existed before.

The delineations continue throughout the chapter. The "habit"/"instinct" dichotomy is an exact parallel to the "nature"/"nurture" dualism in humans, but Darwin does not pick sides here; he takes a more balanced approach, judging that each plays a role in every situation, but to varying extents. At the same time, he is careful to separate instinct from reason, and (as most scientists do today) to avoid seeing human capacities in non-human animals. Many of his arguments seem to the modern reader worryingly anecdotal, but much of the study of behaviour in animals is necessarily so. Ethology, like ecology and evolution, had yet to become its own field; Darwin was treading upon virgin territory. He was right to be circumspect. But for all his appeals to folksy common sense, his distinctions are fundamentally sound. He moves the discussion quickly away from the dichotomy between instinct and reason to that between instinct and habit, a much more neutrally approachable topic. Habits are flexible and learned; instincts are stereotyped and inherited. Darwin's latent Lamarckianism does surface here and there, offering the notion that what one organism learns can be passed on to its offspring without being taught, but he does not make so much of this that it drives his theory.

The most important insight in this chapter is Darwin's recognition of instinct as varying and heritable, and thus evolvable -- fundamentally no different from any other character subject to the forces of evolution. He uses this rightly to extend his corollaries on evolution to instinct as well, specifically to the concept that natural selection will act in favour only of the organism possessing the trait being acted upon. Like in earlier chapters, he discusses examples from domesticated animals, arguing that the processes by which humans produced various breeds from a single ancestral stock are the same as those at work in nature. As with much in the Origin, the arguments seem "soft": superficial, suppositional, anecdotal. But to find fault with this is to pursue the wrong problem. Darwin deals with several examples, around which he can occasionally justifiably be accused of spinning "just-so" stories, but his intention is not to show how things happened so much as how they could reasonably be supposed to have happened. His burden of proof, in other words, is very low. "Just-so" stories are completely acceptable, so long as he can demonstrate that his naturalistic examples are more plausible than the creationist alternative.

In fact, the details of his "just-so" stories are largely irrelevant. His supposition of brood-parasitism as initially a habit which became ingrained is mostly wrong, and his examples involving ants demonstrate a complete ignorance of the action of pheremones. He misses an obvious "just-so" story involving ant slaves: the pupae of the future "slave" ants could have been taken in a raid for food, matured and emerged while in storage, and the resulting workers put to use in their "adoptive" colony. But the strength of Darwin's theory is such that these details do not need to be correct. Rather, the principle behind them is the important thing: so long as some aspect of life varies, so long as those variations are inherited, so long as those variations affect the differential survival of individuals expressing them, so long as more individuals are present than can survive and reproduce, the population in question will evolve. How those traits come to vary, be inherited, or affect the survival of their possessors does not matter. What is important is Darwin's awareness of the existence and import of a spectrum of graded states from putatively ancestral ("primitive") through highly derived ("advanced"); from incipient through fully developed, from occasionally useful (facultative) through absolutely necessary (obligate). This argument from homology is one of the most powerful in favour of evolution even today, and this easily makes up for all Darwin's use of anecdotes and supposition. His application of this process to non-material traits such as behaviour is all the more remarkable.

Sunday, 15 February 2009

The Origin, Chapter Six

Having rounded out the basis of his theory, Darwin now proceeds on possible objections to it. He begins this chapter, on "Difficulties on [the] Theory", with a list of four main topics: the nature of transitional forms, and the fact that we do not observe them now; the massive degree of transformation that occured (to give Darwin's example) between the forelimb of the ancestral mammal (much like a modern shrew or opossum) and the wing of the bat, as well as the capacity of natural selection to produce both seemingly inconsequential and highly developed body parts; instinct, and how natural selection might affect behaviour; and what we now call the reproductive barrier between species, which is not apparent when subspecific crosses are made. The latter two points he plans on treating in later chapters.

On the question of transitional forms, Darwin first mentions the trivial case of completely separated populations of the same species adapting to local conditions and thereby forming new species. This he judges to be trivial and worthy of no further discussion, although he does not deny that it can be and has been a potent force for speciation. Rather, he is concerned with the fact that many obviously related species occur with overlapping ranges. He notes that it is possible and even likely that these ranges did not always overlap; changes in sea level may create islands or join them to the mainland, for instance, isolating populations temporarily but long enough to speciate, and then rejoining them with their now-non-conspecific relatives. Again, however, he is not interested in pursuing this line of reasoning; he does not expect us to believe (nor does he believe himself) that something like this has been the case with all closely-related species. Instead he brings up the topics central to ecology: species must relate not just to their physical environments but also to one another; they may eat or be eaten by other species, and they almost certainly will compete with other species for resources. The assemblage of species itself is a stabilising influence, and will tend to limit the amount of acceptable variation within any one component. Also, Darwin posits that for any two populations connected by an intermediate form, the intermediate form's range will be small, and its population size likewise. I am not sure that this is in fact the case, but certainly species specialised for a given area (the extreme populations) will do better in those areas than generalists (the intermediate form); each form will be able to compete (at a disadvantage, but nevertheless) for resources in the adjacent zone, which means that the intermediate form will be dealing with competition from both extreme forms.

Next Darwin comes to a very important insight: evolution does not produce perfection. However miraculously ideal something might look, it only needs to be good enough to work. There is always something better possible, and when it comes along (as it tends to), it will displace the good-enough equivalent of its now-transitional parent. Another point, which I am not sure of myself but which makes sense to me, is that newly adapted features do not lend themselves to an adaptive radiation until they have diverged considerably from their parent type. To put it another way, adaptive radiations do not occur until the transition has completed. This explains the rarity of transitional forms: there will be only one or a few species of a transitional type in existence, compared with countless more already-adapted forms, so the number of individuals available to be preserved is correspondingly smaller. A final point about transitional features is that they may not appear transitional at first. They may lose their function (or, to anticipate another point that Darwin gets to later, change their function) without changing their structure, and thereby be indistinguishable from their predecessors when in fact considerable adaptation is happening elsewhere in the organism.

Now Darwin reaches one of the most famous parts of the Origin: "Organs of Extreme Perfection and Complication". This section focuses primarily on the evolution of the eye, and begins with a line to set the stage that Creationists are fond of quoting to claim that Darwin himself did not believe evolution capable of producing such an organ. Creationists fail to mention the very next sentence, wherein Darwin explains how this only seems to be the case, and sets forth a series of transitions -- with corresponding forms still extant -- through which evolution might arrive at the present state! As he develops his refutation of this objection, he makes a statement in passing that explicitly states what natural selection cannot do: "How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated…." This is an important distinction between the source of a feature and its subsequent evolution. The comparison to the origin of life is an apt one: much research is presently being done on it, but the processes involved, although called evolution, are very different from those at play once life has become established. Beck to the eye, Darwin notes that transitional forms between primitive light sensors and image-forming eyes are abundant. He even proposes research into evolving an eye, a simulation which has actually been done! The project in question* concluded that, even with very conservative parameters, such a transition could take place in about half a million years, which is considerably less than the "millions and millions" proposed by Darwin! Along the way, such transitional forms will be considerably generalised compared to their extant equivalents, and Darwin astutely notes that such generalised organs often have multiple functions. Darwin's example is a crustacean that respires using its digestive system; I do not know whether this is physiologically accurate, but the point is a reasonable one, and several other organisms have similarly multifunctional systems. Such principles inevitably bring up a concept articulated in its modern form a decade earlier by Richard Owen: that of homology (or, to use the Victorian equivalent that even he used little, "ideal similarity"). Darwin here argues that homologous structures in different species look similar because they descend from a common ancestor, an important point, although perhaps not obviously so. A more radical point is that many organisms have features which sometimes strongly resemble those of others to which they are not closely related. The evolutionary process leading to this is now called "convergence", and the resemblance itself "homoplasy"; and here Darwin correctly points out that it is always, at some level, fundamentally distinct from homology, and detectable as such. He makes reference to a Latin saying that he claims is current: "natura non facit saltum" ("nature does not make leaps"), to indicate not so much that he is a committed gradualist (although he is) so much as to say that everything has a transitional form, however fleeting.

The next major topic deals with the opposite of highly specialised and adapted features: "Organs of Small Importance". Although this sounds like typical Victorian hyperbole, Darwin claims that this is as big an issue to him as the prior topic. He has dealt with this subject before: such features are possibly vestigial, developing from well-developed functional forms, or they may be correlated with important organs which have driven them to a reduced or less-functional state. Importantly, he notes the possibility of misidentification, in which case functionally important features can appear structurally reduced. He also cautions against what Stephen Jay Gould called "the Panglossian Paradigm", the point that because we see something useful in one context does not mean that it origiinally appeared in that context. In many cases this leads to what is now called preadaptation (or, in an effort to make evolution sound less deterministic, exaptation). One good example that Darwin gives is that of the skull plates of mammals, which in the young are not fused, and thereby impart some flexibility to the head which facilitates the passage of soon-to-be-newborns through their mother's reproductive tract. Such features, although invaluable now, may arise from some unknown state of little or no function. Another, out of which he gets more mileage, is the tail in most mammals, which is in most cases nowhere near as critically important an organ as it is to a fish, in which it generally provides the primary force for propulsion. A similarly unknown solution (to Darwin, anyway) often lies behind "chicken-and-egg" problems, such as (in Darwin's day) the origin of feathers and flight in birds. Darwin brings the point up but has little to say on it. Other features which may seem of little importance in an organism's "struggle for existence" are judged striking by humans, the opinion being that "very many structures have been created for beauty in the eyes of man, or for mere variety." If true, this would be a perfect counterexample to natural selection. Darwin supplies a litany of possible explanations how this is nowhere the case, but ultimately stresses that inheritance is the most important factor. Organisms are the way they are because they inherit their features from their parents, who may or may not have used their bodies in the same way. This leads to a reiteration of a critical principle: features are of utility to the possessing species alone. This is actually a restatement and generalisation of the earlier point, and like it any proven exceptions would be fatal (to use Darwin's term) to the theory, but in reality nonexistant. However, he goes on, one species can take advantage of traits in another, giving the appearance of those traits having evolved for the one taking advantage. In all cases, that trait was originally of more use to its possessor than anything else. This is a foreshadowing of Leigh van Valen's Red Queen hypothesis, and leads to a reiteration of the important point that natural selection only makes things "good enough"; except that here the point is made in the context of other species likewise evolving. If one species takes advantage of a trait of another, that other species (if it is to survive and the advantage taken is sufficiently negative to it) will develop some feature to prevent the first from taking such advantage, and the first will develop some means of getting around that feature, and so on. This is the evolutionary equivalent of an arms race, and can lead to spectacular coadaptations. Meanwhile, to close the point on things having been made for humanity's (or anyone else's) enjoyment, Darwin emphasises the mechanistic aspects of the theory. This is to say that all of this happens without any guidance or predetermined outcome: God is not necessary.

The summary offers a surprisingly concise reiteration of the major points of the chapter, and offers nothing new until the last paragraph. Here Darwin deals with two contemporary terms: "Unity of Type" and "Conditions of Existence". The former he sees to encapsulate homology (and I expect that this was uncontroversial; homology was a new but established idea), and is explained by common descent. The latter Darwin believes to be equivalent to natural selection, although from his brief (and possibly inadequate) description it sounds more properly like what we now call autecology, or an organism's natural history (definitely not what Darwin would have called it, "natural history" being the contemporary term for all of biology!). Whatever one calls it, it is obvious that it influences natural selection.

Next up is an in-depth discussion of another objection to the theory, concerning instinct, or specifically the evolution of animal behaviour.

* Nilsson, D.-E.; Pelger, S. (1994): "A Pessimistic Estimate of the Time Required for an Eye to Evolve". Proceedings: Biological Sciences, 256(1435):53-58.

Tuesday, 10 February 2009

The Origin, Chapter Five, Part Two

In the second half of Chapter Five, Darwin discusses the differing degrees of variability found in related organisms. He claims that features exaggerated in one species compared to others of the same genera are more likely to vary within that species, than the same features found in entire genera for which none have the features in question exaggerated. In other words, he says (albeit in a great many more words) that evolution has not yet stopped playing with highly characteristic features: the effects of evolution are still visible after speciation. The features in question will eventually stabilise, but only after enough time has passed to allow the new species to have become new genera. This is an interesting idea, but I am not sure how well supported it is by modern data, and I have yet to look. It would be interesting to have this confirmed.

A related idea is that secondary sexual characteristics -- generally those characteristics visibly distinguishing male from female, but properly those characteristics not directly linked with reproduction (and represented as such by Darwin) -- vary within species more than those characteristics common to both sexes. Again, I am not familiar with the details here, but taking Darwin at his word, one might find some sense in this which Darwin himself seems not to have noted. Here I mean the fact that secondary sexual characteristics include those which individuals (typically but not always females) use in choosing from multiple suitors (typically but not always males) are in fact often species identifiers as well. A bird's song, for instance, carries many messages, which could include that the singer is male, well-fed, and looking for a mate -- but also, and always (at least when signalling specifically to members of the same species), that the singer is of a given species. While aspects of the song might vary from one individual to another (and they invariably will), any significant departures from the cues used to identify species will result in that individual failing to attract the attention of either mates or rivals. What features of a call characterise a species differs from one species to the next; and in the process of speciation, a consensus might form around a particular variant of some feature which previously had no species-descriptive function, and over time this consensus might result in that variant of that feature becoming "fixed" for the population. Ultimately, if the population becomes a distinct species, that feature would become a descriptor of the new species. In other words, the variation of secondary sexual characteristics (of which a bird's mating song is one) is itself one possible engine driving the generation of new species.

The remainder of the chapter features Darwin blindly groping about to connect his theory to his (mis)understanding of genetics. Specifically, he spends a good bit of it discussing reversions, which he rightly supposes to be preserved somehow in the makeup of individuals far removed from their ancestors displaying the features to which they have reverted. There really is not very much to say about this from a modern perspective, or even from a classical-genetics perspective: one may continue to remain completely ignorant of DNA and still be able to follow Mendel's and his successors' explanations. What Darwin does do well here, however, is point out how unrealistic the explanations for his examples must be in the context of what he calls special creation, the notion that each species was created separately. This was, of course, a major purpose to his work -- to establish evolution as a unifying principle in biology, and to show the uselessness of the competing theory of special creation. Much of his work is overkill here, but then the theory of evolution required a great deal of support to replace what had been asserted as truth for literally millennia before.

Monday, 9 February 2009

The Origin, Chapter Five, Part One

This chapter is entitled "Laws of Variation", which implies that it will discuss genetics, the subject which Darwin famously got wrong. That having been said, Darwin is also very forthright in admitting his ignorance, that his understanding of genetics is in effect a hunch. Surprisingly, he actually noticed the proportions expected of dominant allele inheritance that Mendel pursued further to propose the first viable model of particulate inheritance. Had he only investigated that further himself! But he did not; and it is a testament to his model of evolution that it did not matter to his main point. Darwin assumed a "blending" model of inheritance, in which -- on average -- the character states of any set of offspring will represent the mean between their parents. This does not happen with particulate inheritance, in which a state is either present or not, and can persist for many generations in spite of individuals having it mating with those having its corresponding opposite state. How could Darwin's model work to preserve useful mutations? Remember that I said that the character states of individuals were on average the mean between those of their parents: variation will always occur in Darwin's model, and may offset the tendency for extreme characters to "average out" into the less remarkable norm.

To put it another way, suppose that a natural amount of variation exists in a population, such that some trait can be measured as being anywhere from x to -x, and all values have an even distribution. The average value of the trait across the entire population will then be 0. Now, suppose that we remove all individuals with a negative value of that trait (we could suppose that environmental circumstances changed such that positive values of the trait were extremely advantageous). The range of the trait is now x to 0, and its average value is x/2. Now, if we suppose that this trait arose by a process of variation that tends to extend the extremes of the range of values by an additional degree that we will call y. Even if no further selection acts upon this population, so long as y is large enough to counter the blending of a trait towards the average, the extreme values will persist; if y is greater than that, the range of variation will increase, and when y=x, we will have the full range of variation that existed in the original population, except in our selected sample with a mean at x/2 rather than at 0. Obviously, further selection can drive the average value ot this trait further in the same direction. Thus, Darwin's model of blending inheritance can be made to work.

Now, of course, this is all ultimately irrelevant: inheritance does not work that way. But I feel it important to spell out how it could have worked were it true, so as to illustrate how Darwin's theory was not significantly threatened by his defective model of genetics. I do not know whether Darwin himself thought things through this far, or whether any of his contemporaries did -- or indeed whether anyone has -- but I believe this to be a reasonable model.

That having been discussed, on with the chapter! Darwin starts out with observations on the effect of environment on the adult form, which he correctly infers to influence succeeding generations only when it affects the gametes (produced by what he calls the "generative organs" or gonads, and upon which he focuses his attention). It is in fact known that an individual's development can be altered, sometimes significantly, by the environmental conditions under which it was brought up: the resulting differences delineate what are called ecotypes. It is important to note that the capacity to produce all of the forms present in the population is still (potentially, at least) inherited, even if it is not displayed in the population. To give an example, a high-altitude ecotype of a plant might have leaves of a different size or shape than those of a low-altitude ecotype, but seeds from either ecotype will produce plants that match their environment rather than their parents in those features characteristic of the ecotype. Confusingly, the capacity to adapt in the course of development (necessary to produce different ecotypes) can itself be subject to genetic variation, such that one population might have a more extreme range of ecotypes than another. Darwin is aware of this distinction, although the terminology had not yet been invented, and correctly dismisses it in his discussion, since it only confuses matters. Evolution can only act upon heritable traits, and if a trait can be shown to be influenced by its environment, it becomes overly complicated for use as a model of evolution.

The next section of this chapter covers another aspect of biology that Darwin got wrong: he assumed that the effects of use or disuse were heritable. This is similar to Lamarck's concept of evolution, in which an individual improving some faculty or structure in the course of its life passes on such improvements to its offspring. (The famous example of this is the giraffe, which Lamarck supposed originally had a neck no longer than that of any other hoofed mammal, but which over successive generations kept straining to reach ever higher leaves, and thereby managed to lengthen its neck.) However, Darwin does not long dwell upon this, and does not suppose it to be as important an evolutionary force as natural selection. He supposes the reduction of eyes in subterranean animals, and the wings of island birds and beetles, to be due to the continued effects of disuse, and yet if one looks at the level of the population rather than of the individual, this is not an unreasonable shorthand. In discussing such examples, interestingly, this section deals less with the inheritance of acquired characteristics (to use the proper terminology for Lamarckian evolution) than it does with biogeography: the tendency of organisms in a given region to be related to one another, rather than to their counterparts from similar ecosystems in more distant regions.

The next section, on acclimatisation, touches on these ideas as well, but quickly returns to the concept of the ecotype. Darwin was astute to discern the difference between these phenomena, even as he was ignorant of the facts behind them. He even goes so far as to propose experiments to test the limits of acclimatisation, in order to suggest that the boundaries between ecotype and inherited variation were not yet then known.

Darwin next addresses "Correlation of Growth", which he ties quickly to Richard Owen's concept of serial homology, developed more or less to its present form about a decade previously. Perhaps the most significant aspect of this, understated by just about everybody, is the homology inherent in symmetry. In other words, the structures on the left side of the body are homologous to their counterparts on the right; and the developmental processes that influence one side will also influence the other. Similarly, processes that affect an animal's forelimbs will tend as well to affect its hind limbs. This is not absolute, of course; the dissimilarly sized claws of fiddler crabs are one clear example of symmetry being broken, and one of the most striking differences between humans and our closest relatives is the much greater length of our legs and of their arms. In any event, the importance of development to evolution is immense, and Darwin had clearly grasped this. He also pointed out that correlation between structures need not involve any developmental linkage: closely related species will tend to have traits in common due to simple inheritance, and developmental correlation need not be invoked.

Darwin proceeds from there to speculate upon an idea popular in his time, of a sort of balance across all parts of the developing body, such that overdevelopment in one part draws resources from elsewhere and results in underdevelopment in another part. He is circumspect about this, though, and unwilling to draw any lines between this effect and that of a combination of natural selection and inherited reduction of unusued body parts. He streamlines this further, with the adage that "natural selection is continually trying to economise in every part of the organisation." This is not a bad personification of the process of evolution, although now we would see developmental correlation and genetic drift as more significant players in the reduction of unused characters. As a result, less-derived organisms (or, as Darwin would put it, "those lower on the scale") show a greater degree of similarity in serially homologous parts: they have had less evolutionary pressure to specialise individual organs, which renders all of them more similar to one another. He concludes this section by pointing out that unused structures are prone to vary more. In other words, if there is no natural selection on a trait, it is free to vary. All that remains to bring this to the modern concept of genetic drift is the notion of fixation, that in a sufficiently small population some nonselected character states will be lost simply by chance.

This brings us to the halfway point in this chapter; I shall tackle the remaining half tomorrow.

Tuesday, 3 February 2009

The Origin, Chapter Four, Part Two

In the beginning of the section on extinction we find an amusingly extreme understatement: "Rarity, as geology tells us, is the precursor to extinction." But this is followed by a comment to the effect that the fluctuations in population size will make smaller populations are more likely to go extinct than larger ones: and the same could be said of allele frequencies in genes, which is a respelling of the concept of genetic drift. Darwin could have gone so much farther with that idea, but it is impressive that he got as far as he did. Darwin's point here appears primarily to be a reminder that extinction is a real phenomenon, and to reiterate and emphasise his earlier point, that competition between very similar species is the most severe. I am not sure whether this is in fact the case, but if so, it gives a nice mechanism for the quick and clean separation into different species of differently constituted but overlapping populations of the same species.

The next section, on "Divergence of Character", is an effort to explain how the slight differences between populations can become the stronger differences between species. He strikes analogy again with artificial selection: breeders, when selecting from amongst their charges, will choose those individuals most characteristic of the breed in question, which will tend to be the more extreme in those traits when compared to the wild stock. The point here is that selection acts continually over a long period in the same direction, and exaggerates those traits which it selects. Because of this, local populations become specialised. This results in another phenomenon that he notes next, that invasive species (to use the modern term) tend to come from different genera from those of the native populations: they have evolved from dissimilar species to fit similar niches. He draws an analogy between different species in an ecosystem to different systems in a single organism, thereby anticipating the Gaia hypothesis! On a more respectable front, however, looking at the analogy from the opposite direction offers a description of the evolution of multicellularity, in which early organisms were largely homogeneous, and easily outcompeted by those organisms whose cells started to specialise.

At this point Darwin introduces us to the only diagram in his book, which is also almost an early cladogram. Darwin takes some trouble to explain it; to those of us used to reading cladograms, it offers nothing new, but he offers more than cladograms do here as well. In this diagram, unlike in cladograms, the horizontal axis has meaning. It is well-designed for his purpose, as it simultaneously demonstrates diversification, extinction, and the varying genetic relationships between descendants that we now call phylogeny. He also touches on an important point made by Stephen Jay Gould in Wonderful Life, that the history of life is not one of increasing diversity from a small group of ancestors, but one of pruning of radically different branches of the tree and their subsequent replacement by radically different descendents of the few survivors. Darwin posits that life becomes more varied over time, but here he is not necessarily correct: in some ways (as Gould points out) the variety of life diminishes as time goes on and fundamentally different lineages are wiped out. While the surviving lineages may diversify, even into niches unoccupied by the previous assemblage, they are built on fewer platforms than at one time existed.

Darwin concludes the chapter with a summary, which offers nothing new, aside from an explicit description of a concept that is still current, that of the Tree of Life. While this has come under attack of late (endosymbiosis and gene transfer between unrelated groups providing two significant challenges), it is still a useful metaphor -- especially so in macroscopic organisms. Darwin also employs some very nice language. To give an example: "It is a truly wonderful fact -- the wonder of which we are apt to overlook from familiarity -- that all animals and all plants throughout all time and space should be related to each other in group subordinate to group…." And another: "As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications." Darwin is not done yet with the fundamentals of this theory, but he has still managed to encapsulate its essence admirably.

Monday, 2 February 2009

The Origin, Chapter Four, Part One

Darwin begins this chapter by stating the obvious conclusions from even the most casual synthesis of the previous three. The logic is simple:
  1. Individuals amongst a population differ from one another. Some differences are useful in one's daily life, and confer an advantage to their possessors. Importantly, some of these differences are heritable: having a feature means that one's offspring will also have that feature.
  2. More individuals are produced in each generation than represent the previous generation, meaning that (if the population is stable) more are produced than can survive.
  3. Putting these together, those individuals with differences that help them in their lives will have a better chance at surviving than those without. Those differences that are heritable will be more prevalent in the succeeding generations (assuming that they continue to confer an advantage over their alternatives), and so the average individual from one generation will differ from the average individual from the next.
That really is all that there is to natural selection.

Darwin was right to regard this as a significant force in evolution, but even here, immediately after his formal introduction of the topic, he hastens to add that it is not the only force: "Variations neither useful nor injurious would not be affected by natural selection, and would be left a fluctuating element". Were he to have elaborated on this more fully, he would have developed the theory of genetic drift; as it is, he has hinted at it strongly. He then moves onto another force in the evolution of populations, that of immigration. In other words, the influx or efflux of individuals can affect the course of a community's development, and can assist or hamper the force of selection on those that stay. As with drift, this is an important alternative to natural selection. Students of evolution who are counting along will note that the only major evolutionary force that has not been accounted for here (variation comprising at least in part the force of mutation) is sexual selection, which is another topic that Darwin explicitly developed. In other words, barely two paragraphs into the chapter, we have already been introduced to the gamut of evolutionary thinking, albeit in a preliminary and decidedly non-quantitative way. Darwin's view of evolution was impressively comprehensive. The whirlwind tour through modern evolutionary concepts is complemented by a modern ecological concept, that of invasive species, although not by that term. These, Darwin explains, alter the dynamic of their new environment and thus the nature of the features of its native inhabitants most useful to increasing their numbers.

Now he ties in the first chapter, comparing natural with artificial selection. There are of course differences: one is that natural selection has had a much greater length of time in which to work to produce extant organisms. But perhaps more importantly, "nature cares nothing for appearances, except in so far as they may be useful to any being. She can act on every internal organ, on every shade of constitutional difference, on the whole machinery of life." In other words, natural selection can influence changes too complex and subtle for human breeders to understand, and such changes are always useful to their possessors, rather than to the occasionally arbitrary preferences of human masters. "How fleeting are the wishes and efforts of man! how short his time!" -- and so what nature can do to life is immeasurably greater than what humanity has been able to accomplish (although of course genetic manipulation rather changes that picture!).

Darwin then goes on with more concepts that extend the theory of evolution into modern concepts. For one, he gives another passing mention of correlation of traits, which includes both what would become known as pleiotropy (wherein one gene controls more than one trait) and genetic linkage (in which multiple genes are inherited together). For another, he makes an even more passing comment in the direction of kin selection: "In social animals [natural selection] will adapt the structure of each individual for the benefit of the community; if each in consequence profits by the selected change." This smacks as well of a related but far more contentious topic, that of group selection; at least in this passage it is not clear how far and in which direction Darwin thought this sort of process could be taken. The principal point that Darwin is driving at here, though, is what he already touched on: natural selection acts for the benefit of each species in question, and for no-one else. Every adaptation brought about through natural selection is an adaptation to help the species possessing it in its environment, and no harmful change will persist. This is of course not necessarily the case, given the complexity of environment and inheritance: a classic case is that in which a mutation that provides resistance to malaria can also cause sickle-cell anemia, depending on how many copies of that gene an individual has. But even here, there is a trade-off that benefits the individual: so long as the probability that one will be exposed to malaria is higher than the probability that one will have the sickle-cell trait, the mutation in question will persist.

At this point, Darwin gives us a section heading, and introduces already his other major contribution to the theory of evolution: sexual selection. He would have much more to say on this in later work (particularly in The Descent of Man), but here brushes by the subject's two main factors: competition between members of the same sex for access to members of the opposite sex (exemplified by fights for dominance), and the tendency for members of one sex to prefer some and not other individuals of the opposite sex (exemplified by the bright plumage of many male birds). The subtleties between these two types of sexual selection are here unexplored, but they are at least mentioned.

Darwin proceeds with two illustrations of the principle of natural selection. The first focuses on wolves; several possibilities are presented in which a population might change over time, driven by environmental biasses. Importantly, the traits that Darwin supposes to be heritable and significant include behavioural ones. His second example is a compound one, showing how flowers and pollinating insects must co-evolve as each adapts to changes in the other. It is in this process that a species might exhibit traits that appear to benefit another species -- but if that other species provides some essential service to the first, then those traits that benefit the other are indirectly benefitting the first as well. He concludes this section with a reminder that natural selection acts on small differences over vast periods of time, much like Lyell's uniformitarian geology -- a significant comparison, one which continues to be made.

The next section is entitled "On the Advantage of Intercrossing", but it could as easily been called "On the Disadvantages of Hermaphroditism", which is at least to the modern reader a somewhat clearer description of its topic. Ignorant though Darwin was of even classical genetics, he was still quite cognisant of (and states explicitly) the fact that nothing can persist indefinitely without at least occasional genetic interchange with other members of the same species. One can almost feel the perplexed wonder in this section. The topic is brought up in prelude to the next section, "Circumstances Favourable to Natural Selection": here, he posits that self-fertilising hermaphrodites (and by extension asexual organisms) are more likely to adapt to smaller-scale differences in their environments. In other words, the genetic interchange in obligately sexual organisms (like birds) will tend to even out differences over a wide area, making local adaptation unlikely unless the circumstances are widespread across many locales. (Darwin alludes to an ill-defined lack of vigour and fertility of self-crossers when compared to outcrossers which is explained by, though does not imply, inbreeding depression; the vagueness borne of his lack of understanding of genetics is dismissable, though, in his recognition of the importance of genetic interchange to the spread of favourable adaptations. One factor missing in this analysis is the possibility of different adaptations recombining in new ways that render the offspring carrying those combinations even better adapted -- a puzzling omission.) The discussion of range size continues, to compare the benefits bestowed upon a species living for a long time in small and isolated region with those incurred by a species living in a large and varied region. Darwin argues that the latter will produce a species more capable of fending off intruders from other regions, and alludes to the plights of species endemic to isolated areas, including oceanic islands and the continent of Australia. Natural selection is supposed to lead to such generalised species by, among other things, the possibilities of range fractionation allowing for local adaptations to arise which are then spread across the larger range when the environmental factors enforcing the fractionation are lifted. In other words, Darwin is supposing the larger region to allow for a genetic reservoir of local adaptations, a library of useful traits that can be called upon to