Opisthokont

Craig Venter's Synthetic Bacterium

2010-05-24T08:35:00.000-07:00

Wow, it's been a while since I posted. I have been getting occasional prods to write something, and everything seems to have fit into place for it to happen now, so here we go.

Much has been said over the announcement last week of the creation of a "synthetic life form" by the J. Craig Venter Institute. Much of that has been woefully uninformed, which is probably the topic of another post. The news is impressive, to be sure, but it is not really that groundbreaking. The actual procedure is the bacterial equivalent to the procedure that produced Dolly the cloned sheep, technology that, while remarkable, is hardly news (although I would imagine that it might be more difficult to do with a bacterial cell than a mammalian one). The big advance in this project was the fact that the genome that was introduced into the cell was completely synthetic -- its sequence designed on a computer, and its chemistry produced in a laboratory. In fact these tasks are both routine in biology and biochemistry laboratories. The difference here is the application: specifically, the combining of the synthetic-DNA and cloning procedures. The fact that we have a functioning cell with a completely synthetic genome is a remarkable outcome, to be sure, but the principle has been an obvious one for a couple of decades now. If one were to compare this to a society-changing invention, it would be to Henry Ford's adoption of the assembly line to produce the same cars he had been making for several years, rather than the Wright Brothers' first powered flights.

Another aspect that gets sometimes mentioned but (I suspect) overlooked is the nature of this new organism's genome. True, it did not exist in any chemical state before its synthesis by human researchers, which is to say that it was not spliced together from fragments of preëxisting genomes taken from extant viable organisms. However, that is true only in the chemical sense. The actual sequences for the genes used for this genome were taken from extant viable organisms, and if one were to do a phylogenetic analysis of any of those genes, the new organism would be a sister lineage for the source of whichever gene was used, not a completely separate branch from any other life form. In fact, as far as I understand it, there is nothing to distinguish the actual organism from a hypothetical one made from spliced bits of the same source genomes -- in other words, a clone in the more traditional (Dolly-the-sheep) sense. This work, important though it unquestionably is, is not the creation of a completely new life-form, but a proof-of-concept that such a creation is possible.

There are one minor and two major hurdles that need to be overcome before we actually do have the sort of unprecedentedly novel life-form that many in the press and the public think this is. The minor one is that the new organism that Venter and his team have created is based mostly on genes from an obligate parasite with highly specific environmental requirements: it is not what we would unreservedly call "free-living". Parasites can be tricky to grow in the lab, and parasites potentially missing parts of various biochemical pathways (which this one is likely to be) can be a nightmare to keep alive, even if they start off growing vigorously. Venter's new organism has a synthetic genome, yes, but it has been injected into another cell whose genome had been removed, leaving all the rest of the life-giving biochemical machinery intact. While it is estimated that the new organism should replace all of that in about twenty generations, it is still possible that (for instance) some important and overlooked protein is also long-lived enough to keep the cell and much of its progeny alive for quite a while before finally giving out and causing the population to crash.

In fact this points to one of the most important applications of this research. In spite of all of the attention given of late to genomics, proteomics, transcriptomics, interactomics, and a number of other "omicses", we really have only an inkling of what is actually required to keep a cell functional. One obvious future direction of this research is to produce organisms with various subsets of the current genome, to determine exactly what the minimal set of genes is to keep something alive. I hasten to add that the subset that would eventually be arrived at would be specific to the starting set of genes in the genome; other starting points will almost certainly result in other final genomes. In other words, what might be the smallest number of genes needed to keep a Mycoplasma-derived organism alive might still be more than the smallest number of genes required for (say) a Rickettsia-derived organism, even if the original genome is larger. Nevertheless, given that the Mycoplasma genome is the smallest known, this is a good starting point.

So the minor hurdle that I mentioned earlier is that, while the genome is supposed to be functional from a minimal standpoint, there is no guarantee at this stage that it is in fact indefinitely viable; Venter may already have stripped the genome past its minimal complement of genes, and omitted some critical component to the genome without which the cell can eke by for several generations. Time will tell whether this is in fact the case, of course, and if it is, the remedy is obvious. Venter and his team have proven that they can generate a synthetic bacterium once; if this one fails, they need only do it again with a different genome, and repeat as necessary until they have something that works.

That leads to one of the major hurdles. This is a new genome, yes, but as I said already, it was taken from bits of other organisms' genomes. Probably the greatest milestone in synthetic biology will be when we are able to design completely new genes. This would amount to deciding what chemical reaction we want the gene's product to perform, how we want it regulated in the cell (specifically, what other genes and gene products it must interact with), and with that information alone coming up with a previously unknown string of A's, C's, G's and T's that can be inserted into a genome to do exactly what we ask of the new gene product. A fully synthetic life-form would have all of its genes so constructed, and none taken from already-extant organisms. This is precisely opposite to Venter's new organism, and its advent is probably decades away still, barring some major and sudden advance in our understanding of protein function and generation.

Meanwhile, the fact that this technique requires that the new genome be injected into a "recipient" cell -- a previously viable organism that has left all of its life-sustaining machinery for its new genome to use -- is itself the other major hurdle to making a completely novel organism. While a truly and completely synthetic organism would need entirely novel genes, it would also need to be made without using any pre-existing cellular materials. This, and this alone, would be the actual creation of new life, similar to what happened naturally in Earth's primordial oceans some four billion years ago. We can already make coacervates, lipid vesicles similar to cell membranes, in the laboratory -- in fact, it was an exercise in my high school biology class! Putting those vesicles into the proper context for a living cell is probably not so easy, but also not impossible. Generating life in this sense will also probably require a rather different biochemistry from what Venter's techniques require. It may not be possible (or if so, prohibitively difficult) to make it work with the DNA-and-protein biochemistry used by all currently extant life. It may instead be necessary to replicate the "RNA World" that is thought to have preceded it, and probably in a progenotic sense, meaning that while all functions necessary for life would be carried out by the complete population of protocells, no individual cells would carry the full complement of genes required for those functions.

What all this amounts to is that Venter's procedure is a top-down approach: taking pre-existing components and combining them to create a new combination. The further steps down this road amount to trying to figure out which components can be removed without causing the system to collapse, and which can be simplified. This is a laudable goal, and I congratulate Venter and his team for making the advances that they have. But the truly groundbreaking work, based on the bottom-up approach, generating new life from whole cloth, has yet to be accomplished, and will not come soon.

Heckling

2009-10-10T05:57:00.000-07:00

Earlier in the week, on my way home from a long day, I passed a group of protesters outside one of the hospitals here. The professional-looking signs and banners that they were displaying said "Pray to End Abortion". My immediate and cynical reaction, as both a supporter of abortion rights and an atheist, was one of approval: these people are using as ineffective a means as possible to support a cause with which I disagree entirely. Two of them had big pieces of cardboard with handwritten signs as well. One said "Today? Abortion - Tomorrow? Godless Anarchy", and that almost made me stop. I am a big fan of civilisation (see my previous post for more thoughts on that) and, Ursula K. LeGuin notwithstanding, I suspect anarchy to be its antithesis. I do not see the connection between abortion and anarchy, but was not tempted to ask the protester for details. Rather, I was more than a little incenced at the use of the word "godless" as a negative modifier. "What's wrong with being godless?" I wanted to ask. The obvious connection that the religiously deluded seem not to get over is that it is impossible to be moral without a belief in God, and I feel that this should be challenged vigorously and often.

But I had had a long day, which began with swimming for the first time in six months and at a time far earlier than I am usually out of bed, a surprisingly busy and productive time in the lab, and just now a soccer game, and I just wanted to get home. I passed the protesters without comment, but I thought about the possible consequences of heckling on the way. Would it be possible for me to make a difference that way? I would not attempt to argue for abortion rights, or make any snide comments about the efficacy of prayer: just challenge the notion that "godless" is a bad thing. Perhaps I might make the person think a little. Perhaps I might at the very least make him aware that equating "godless" with "immoral" ranges from annoying to offensive for a substantial number of people. Keep the topic focussed and the discussion civil, and maybe some good would come of it. That would be worth the effort. But I figured that the effort would have to be spent another day.

A couple of days later, as I got on the bus to go home, I was heckled myself -- by the bus driver! It was late, and it was windy, and I was cold. For those of you who have not lived here, Halifax can get impressively windy. It would not actually have been unpleasant except for the wind-chill factor. The bus pulled up, and I stepped in, grateful to start warming up, and the fellow that was heading out pushed by me. I flashed my U-Pass and headed back, and the bus driver barked at me to come back and "take those things out of your ears" (meaning my earhones). I figured that maybe he needed a second look at my U-Pass, but no, he asked me, "Why did you charge in here without letting that guy off first?" I told him that it was cold outside, and I wanted to get out of it, and he went on that I was supposed to let people off the bus before I got on myself, and that "you can't just push people around like that." I have no idea what made him think that I got some sort of satisfaction from bullying people, but there were people behind me waiting to get on the bus as well, and I did not want to keep them out in the cold, so I tried to shrug it off. But the bus driver was not going to accept that. He kept at it, insisting that I change my attitude to those around me. The fellow that I had bumped into was long gone, and did not seem to have made any issue of the matter: why was the driver so offended? Eventually I expressed enough flustered apology for him and he let me go.

I would have fumed had I not recently contemplated heckling people myself. But I think there are definite differences between the two situations. The bus driver was acting on an event that took only a few seconds, and did not consider the possibility of extenuating circumstances. The protester was, after a fashion, asking for a response. I was not about to give the protester the response that he was expecting -- and in fact I had made up my mind when I fist saw the sign not to address the issue that he was protesting. In retrospect, "What's wrong with being godless?" is a rather confrontational approach, but there are worse ways of addressing the topic, especially if one maintains a calm demeanour while doing so. Perhaps I am deluding myself, but the more I think of the two events, the less similarity I see between them, aside from a spontaneous interaction between strangers. Still, it had me thinking, and that is always a good thing.

Health and Taxes

2009-08-30T15:07:00.001-07:00

Civilisation is an agreement. It is an unspoken acknowledgement to behave in particular ways towards strangers, and an acceptance that others have many of the same needs and rights as ourselves. We agree not to kill, hurt, or steal from others, and they agree not to kill, hurt, or steal from us. Furthermore, we agree that there are limits to our individual capacities, and that a division of labour allows us to live beyond those limits. We agree that we cannot afford some things individually, such as protection from rogue elements within and hostile groups without our own. Thus, we willingly constrain our actions in such a way as not to impede the well-being of others, and we (often not as willingly) pay in part for those services that we cannot afford by ourselves. Enlightened civilisations have further recognised that we are better off individually if we are all well-educated, and if we are all healthy.

This, fundamentally, is the rationale behind universal healthcare. We live in a time when the US, long the only developed nation without it, is finally facing that reality, and considering correcting it. The more intelligent objections to this focus on the notion that it would require individuals to pay for a system for which they might not approve, and which might not function as well as what the better-off citizens have come to expect. But these arguments tend to focus upon the failings, perceived or real, of individual systems. There are legitimate observations here, but these are not reasons to abandon the principle. Rather, they are examples to us, datapoints to be analysed, challenges to overcome. They can be overcome. It is entirely possible that America will wind up with a respelling of the same expensive, exploitive, and unjust system that it has now. I hope that this does not happen. The principle is worth struggling for, to get it right. We gain nothing, and lose much, by allowing those in less fortunate circumstances to suffer. Civilisation has its price: most of us pay taxes to fund it, but we must also remember that it also requires compassion.

The Origin, Chapter Fourteen

2009-04-11T04:56:00.000-07:00

This chapter comprises two very distinct sections. It is titled appropriately ("Recapitulation and Conclusion") although we might expect there to be less of a distinction between the two than Darwin gives us. Even then, the first part is not a proper recounting of the entire book, but a somewhat ricocheting run through most of its major concepts. Here more than before he emphasises the distinctions between common descent and special creation, finding for all cases the former to fit far better than the latter. He rightly identifies that the introduction of the supernatural into science has a tendency only to perpetuate ignorance: "But it deserves especial notice that the more important objections relate to questions on which we are confessedly ignorant; nor do we know how ignorant we are." Of the latter, he points out the identification of species as an example made far more contentious because of an assumption of independent creation. The Victorian view of diversity was that each species was separately created, while varieties (including subspecies) had arisen afterward, "by secondary causes", meaning by natural ones. Such arguments are meaningless if, as Darwin says, "species are only well-marked varieties"; indeed all controversies (and Darwin suggests that there were several) over the boundaries of extant species are meaningless.

Darwin spends most of his time here on his strengths, and especially on biogeography, but does not ignore his other evidence. The origin of modern diversity through adaptation of existing structures is evident throughout: "We can plainly see why nature is prodigal in variety, though niggard in innovation." His pioneering of ecology gets a brief mention, amounding to emphasis on the primary importance of the biotic environment to the success or failure of any species. He brings up again the "Red-Queen" nature of invasiveness: "As natural selection acts by competition, it adapts the inhabitants of each country only in relation to the degree of perfection of their associates; so that we need feel no surprise at the inhabitants of any one country, although on the ordinary view supposed to have been specially created and adapted for that country, being beaten and supplanted by the naturalised productions from another land." It is unsurprising that we should see in this concluding chapter Darwin's least ambiguous writing, but the assertions are nevertheless uncharacteristically forceful: "The real affinities of all organic beings are due to inheritance or community of descent. The natural system is a genealogical arrangement, in which we have to discover the lines of descent by the most permanent characters, however slight their vital importance may be." There is no room for doubt here.

The conclusion section is more of a meta-study of evolution, looking at the contemporary state as well as the history and probable future of biology. It starts with an assertion that Darwin and his theory will face opposition. Some few naturalists will be persuaded by his work, he speculates, and certainly, given that the idea of common descent was much discussed, many more would already have been looking for proof, and might have their minds made up. But the most important recruits to Darwin's cause, he expects, will be the next generation. Modern creationists would actually find a friend in Darwin, had they lived then, as he suggests that we should (in their words) "teach the controversy": "I look with confidence to the future, to young and rising naturalists, who will be able to view both sides of the question with impartiality." But in our modern persective, we must bear in mind that this controversy raged some 150 years ago! Science has settled on an answer, and has moved on. On the other hand, Darwin is not content to allow his opponents to continue unchallenged, and asks them to answer some of his own questions. How did the Creator go about creating? How many forms were originally created? Were they adults, or juveniles, or seeds or eggs? If they were adults, did mammals have signs of having been gestated (in other words, did they have navels)? This section is a startling contrast to Darwin's usual demeanour. He is almost mocking in his requests, but he does not ask them without full knowledge that they are, after all, questions about the natural world, which follow logically from the theory of special creation, and which are therefore not unfair.

He then moves onto questions of his own theory. How far, he asks, can common descent be taken? Owen's work on homology makes it clear to Darwin (indeed, to the modern reader as well) that all phyla (plant and animal) have had each their own common ancestor. Darwin speculates that this can be taken further, that all animals and all plants had each a single ancestor, and probably all life, although he doubts that this can go far beyond speculation in his own time. On the finer end of the scale, he comes very close to proposing his own species concept: "Hereafter we shall be compelled to acknowledge that the only distinction between species and well-marked varieties is, that the latter are known, or believed, to be connected at the present day by intermediate gradations, whereas species were formerly thus connected." This, consistent with most modern species concepts, covers many of the points of its competitors, but places each in a different light. Extant species, says Darwin, are discontinuous from other extant species, while genealogically intermingling groups are necessarily the same species. This combines aspects of the biological and phylogenetic species concepts; whatever its utility today, it must be recognised as one of the first attempts (if not the first) to define "species", and indeed an early (although implicit) assertion that such a need exists in the first place.

It is difficult to convey how exactly Darwin can retain his customary modesty while predicting that his theory will revolutionise biology, but somehow he manages it. He sees its subjects as being "ennobled" by common descent, and that in that light, "how far more interesting ... will the study of natural history become!" Geology will be influenced as well: "The noble science of Geology loses glory from the extreme imperfection of the [fossil] record. The crust of the earth with its embedded remains must not be looked at as a well-filled museum, but as a poor collection made at hazard and at rare intervals." In other words, what biologists knew all along to be a highly imperfect understanding of the world is not dissimilar to what geologists must come to grips with. The fossil record's scantiness nevertheless does not hide an emphasis on change over time, and although he only at most implies this, living things becomeall the more precious by their transiency: "Judging from the past, we may safely infer that not one living species will transmit its unaltered likeness to a distant futurity."

There is a great deal of eloquence in these final pages, which I will not reproduce here; it is readily enough looked up. This amplifying rhetoric almost hides the fact that Darwin recognises this work to be a turning point in the history of science, a change in its world-view, a paradigm shift. Very, very few people can do more than try to imagine what that realisation must have felt like. I have not pursued the matter far enough to read Darwin's notes on the subject, but by all accounts he knew what he was about to do when he wrote this book. He does so with admirable humility, presents his arguments as humbly as is possible, but does not back down from its implications. Not only in how the world works, but in how to present one's understanding of it, we all have a lot to learn from him.

The Origin, Chapter Thirteen

2009-04-05T14:24:00.000-07:00

This chapter of the Origin, the last before its conclusion, is something of a grab-bag of miscellaneous points. As is typically the case for such chapters, its author is clearly wrapping things up, drawing them together for the big conclusion to come. At the same time, it presents some of Darwin's stronger points, albeit more in favour of the principle of common descent (what we now refer to as "the fact of evolution") than of that of his mechanism behind evolution (natural selection). This is not to say that the latter goes unsupported (indeed Darwin makes some cogent arguments for it); rather it is that it is simply not the point of this chapter to make the case for natural selection. Here, as in the last chapter, Darwin contrasts his view of the living world against that of what was then "the ordinary view of special creation", and finds the latter wanting. And here, as in the last chapter, I am somewhat surprised that he has chosen to make these arguments so late in his work. This is essentially opposite to how I (and, I like to think, most other modern biologists) would present their case: first show the data, and then explain how the theory fits it. The "data" here is the genealogical organisation and common ancestry of all life, which itself is not necessarily obvious, and in Darwin's time required some hefty arguments in order to be taken seriously, arguments which he has provided in these latter parts of his book. But he has not provided them in such a way that they require an understanding of his theory in order to make sense. He refers to his theory here, but any other theory involving common descent (Lamarck's being the one most often presented to beginning students in biology) would be as apt. Once again, I am somewhat perplexed at the organisation of this book, although I will not deny that it works as presented.

The first topic brought up in this chapter is of classification. Darwin's view on this head is entirely modern: Classification should be genealogical. Einstein once said that "the most incomprehensible thing about the world is that it is comprehensible." Darwin notes a similar point in biology: the hierarchical classification that we all take for granted (even those of us who are not biologists are familiar with it on an intuitive level) should be remarkable, if we were honestly to assume that every living thing was made independently of every other. That this is not the case is a compelling argument in favour of common descent; at the very least it should be a noteworthy puzzle. The universe, as far as biological classification is concerned, is eminently comprehensible. And yet, Darwin's lengthy discussion of the topic gives no imminent indication that this was regarded as particularly revelatory. The idea of evolution had been in the air for over half a century by the time that Darwin wrote publicly about it; it could well be said that, like Galileo's popularisation of the heliocentric model of the Solar System, the world was ready to hear about it when Darwin wrote about it, even if it required to be convinced.

This is not to say that there were not contemporary alternatives to the principle of genealogically based classification (which requires common descent). Darwin lists a couple: similarity of form in closely-related organisms either "gives some unknown plan of creation" or is "simply a scheme for enunciating general propositions and of placing together the forms most like each other". Neither of these is satisfactory; for either to be true would require a tremendous amount of coincidence that looks very much like common descent. In contrast, common descent does not provide any substantial difficulties that are eased by assuming either of these alternatives.

Darwin quotes Linnaeus a few times in this chapter: "The characters do not make the genus, but the genus gives the characters." Most of this chapter regards character evolution, so this is an apt point. There is still debate as to how best to define taxa, whether it should be by some suite of characters unique to the group in question or by some limits to its genealogical makeup. The latter is harder to overturn, assuming that the phylogeny used to define the group is accurate, but the former is more satisfying. The risk there is that, after the group is defined according to its shared ancestral character states, some critical character will be found to have been misinterpreted, or some member with an abnormal character state will be discovered or found to be basal, calling into question the basis for the group's identity. Certainly, when starting work on a new group, it can be easier and more intuitive to start with the assemblage of organisms and to try to figure out what they have in common, and with modern molecular phylogeny this is exactly what happens. However, a genuinely objective system would require a completely consistent set of diagnostic features which would definitively place an organism within or without a group, rather than requiring its genealogy to be known (which in any event is often difficult to determine). Personally, I prefer the character-based definition, but this requires frequent updating as our understanding of the evolutionary history of the group is improved. Ultimately, what we take for significant characters in a group is dictated by our understanding of the group's evolutionary history, which in turn is based on a number of sources. So ultimately, Linnaeus is right, but not in quite the way that we (or I, at least) first read him: rather than the genus indicating which character states are significant (here meaning that they are constant within the genus in question), the genus indicates which characters -- variable within the containing group, and constant within the genus under discussion -- are important to use as diagnostic markers.

Darwin elaborates: important characters are prone to vary. Things that are critical to an organism's way of life can easily converge, and so we have fish and dolphins superficially resembling one another when in fact they are very different animals. The phylogenetically important characters do not vary, and are not affected (at least, not within the more primitive members of the group in question) by natural selection. (Here, incidentally, is the one point in this chapter where an understanding of Darwin's theory is actually important to his arguments in favour of common descent. Even still, it could as well be brought up later in the book, had he chosen to present common descent first and natural selection later.) This is not to say that such characters never vary; indeed, characters that are highly conserved in one group (and so are reliable indicators of membership in that group) can be highly variable in another, related group; furthermore, these characters may have ample and even equal value to members of each group. On the face of it, things that unite a group may be of trifling importance, but consistent: Darwin gives the example of an inflection in the jaws of marsupials, which is indeed diagnostic, but probably not significant to the animals' physiology. Another example that Darwin gives, which betrays his lack of understanding of biochemistry, is the colour of algae: this is known (and has been for a long time) to be related to the biochemistry of the pigments used in collecting light, and of great physiological as well as phylogenetic significance. In any event, this is what Darwin means in his invocation of Linnaeus: we cannot guess what aspect of an organism's anatomy is significant to determining its classification without reference to other organisms, both similar and dissimilar. "Hence, as has often been remarked, a species may depart from its allies in several characters, both of high physiological importance and of almost universal prevalence, and yet leave us in no doubt where it should be ranked. Hence, also, it has been found, that a classification founded on any single character, however important that may be, has always failed; for no part of the organisation is universally constant."

Darwin returns to his prior point with remarkable pithiness: "all true classification is genealogical." He addresses this now from the other angle: the question of descent itself implies the existence of ancestors. We classify the descendents of a single genus in several, but those little changed from the common ancestor may be placed in the same genus as that ancestor. Does this make sense? To some extent, perhaps; and yet, all members of the lineage will have undergone some amount of adaptation. It would be true to say that they have all evolved for the same period of time, but this is not necessarily relevant. Did they all proceed through the same number of generations in that time? If not, the amount of evolutionary pressure that could be brought to bear on any one descendent lineage is not necessarily comparable to that of any other. Even if they have, the number of cell cycles undergone by one individual (each of which, on a smaller scale, presents its own opportunity for mutation and selection) may not be the same as another, and once again the lineages may not be comparable. So we may reasonably ask whether it is proper to put any living organisms in the same genera as their far-removed ancestors. But this is a question that is itself far removed from Darwin's discussion, and one which is still discussed today.

Returning to Darwin's observations, he notes that relatedness in character states follows certain patterns. Specifically, a member of one group resembling members of another will do so only in generalities; the first will not resemble any one member of the second group more than any other -- unless some members of that group are obviously less derived, in which case they will be the ones to which the member of the first group will bear a resemblance. This is a very important point, and one which requires us again to return to Linnaeus's dictum: what we regard as important in defining a group requires that we look around to related groups. Darwin concludes his discussion of classification with another nice quote: "We shall never, probably, disentangle the inextricable web of affinities between the members of any one class; but when we have a distinct object in view, and do not look to some unknown plan of creation, we may hope to make sure but slow progress."

The next section is ostensibly about Morphology, but is actually more about Homology. It should be mentioned here that Darwin uses the modern terminology in distinguishing actual homology (a term defined in its modern form some ten years earlier by Richard Owen) from analogy (a term not used in Owen's treatise) -- I do not know when the term first eneterd into use, but it is unlikely that Darwin introduced it here, as he does not define it. Much of Darwin's attention in this section focusses on serial homology, the phenomenon in which structures within the same organism can be seen to have developed from similar primordia. Thus our arms and legs have similar skeletal structures, and our vertebrae are all fundamentally similar, based on the same essential pattern. Owen went further, to suppose that the bones of the skull were themselves highly modified vertebrae, an idea that has since fallen from favour. (One of the hallmarks of any type of homology is that homologous structures arise through similar processes, but the plates of the skull have a very different embryonic origin from the components of the vertebrae, thus ruling out the possibility of homology.) Darwin also cites Owen's observation that more highly advanced forms (by which he means organisms more removed than their contemporaries from their common ancestor) have fewer similarities in their serially repeating body parts. Thus, to give a modern example, insects have only three pairs of functional legs, while their ancestors, the crustaceans, have several. Darwin cites Huxley as well, who says that serially homologous structures are not formed one from another, but all from some primitive precursor. Darwin corrects this view, though, pointing out that that precursor could well be, and usually is, present in even highly-derived modern forms.

From this discussion of the origins of serially homologous body parts, it is only natural that Darwin should turn to the subject of embryology in general. This is a topic that has recently exploded in evolutionary utility, the subject of evolutionary developmental biology, or "evo-devo". Here, Darwin's understanding of the topic is strikingly modern. Over and again he emphasises that "[t]he question is not, at what period of life any variation has been caused, but at what period it is fully displayed." Again: "at whatever age any variation first appears in the parent, it tends to reappear at a corresponding age in the offspring." In other words, not just an organism's form, but the regulation of development that produces that form, is heritable. We often think of there being "a gene for" a given trait, but in reality this is rarely the case: many, perhaps most, of our genes are for fairly standard things, like digestive enzymes or structural proteins. What varies amongst multicellular organisms like ourselves is more the patterns in which those genes are expressed than the genes themselves. For example, all of my genes for actin (a structural protein used, among other things, to make muscles contract) could be replaced by those from a chimpanzee, and nobody would be able to tell the difference unless they actually sequenced my genes. However, if the regulatory regions of my genome were to have been replaced with those of a chimpanzee's while I was growing up, I would have some distinctly chimpanzee-like characteristics, assuming that such replacements did not sabotage some essential bodily functions. To put it another way, the components are the same in most organisms; what changes is the way in which they are assembled.

Another point in which Darwin sounds strikingly modern is his view of the relationship of embryonic morphology to evolution. Haeckel famously said that "ontogeny recapitulates phylogeny" (a saying I find remarkable in its concentration of both syllables and jargon), meaning that an embryonic mammal was in fact a fish. Darwin, while not making a point of the matter, disagrees: rather, the embryo of a mammal resembles the embryo of a fish. Fishes may not develop much beyond that embryonic state in many ways (for instance, they retain the gill pouches that mammals lose) but in others they do depart from the common form (as in, for example, the development of fin rays). I am not well-read in Darwin's views of the matter, but in the first edition of the Origin he gives a very modern account of this relationship, even if he does not contrast it against Haeckel's view.

This is not to say that Darwin gets everything right here. He regards holometaboly in insects (the process in which individuals undergo a radical metamorphosis from larva through pupa to adult) as ancestral, and incomplete metamorphosis (a blanket term covering various alternatives now understood to be primitive amongst insects) to be derived. He gives no explanation for this, and supposes that incomplete metamorphosis arose from the juvenile insects being under the same ecological pressures as their adult counterparts. Certainly something like this has occurred in cephalopods, which lack the larval stages common to other mollusks, but in the case of insects we know this to be the wrong way around. Interestingly, this bears on a fundamental question in animal evolution, one of which Darwin either was unaware or chose to ignore: that of the point at which planktonic larvae arose. Darwin points out that he was amongst the first to have recognised barnacles as crustaceans, based on their obviously crustacean larval stage; obviously he regards crustacean larvae to have been ancestral, and the adult crustaceans to have adapted from that. But whether the larvae of other animals represent their ancestral state, from which the current adult form is a later development, or the adults were the original forms, and the larvae arose later to fill different ecological or life-history roles, is not a topic that Darwin broaches.

The remaining original section of this chapter is on vestigial organs. Darwin has already discussed this topic, and brings little new to it here. He is again impressively modern in his understanding of the matter, and I have little to add to his discussion. Likewise, his summary of the chapter is short and (almost) sweet, beginning with another impressively colossal Victorian sentence, enumerating his main points, and bringing little new by way of synthesis to the matter. This is not terribly surprising in a chapter devoted to the miscellaneous ideas that have not received discussion earlier, of course. All that remains now is his final summary, the capstone on the entire project.

The Origin, Chapter Twelve

2009-03-28T05:56:00.000-07:00

This chapter is very clearly a continuation of the previous, and very much a climax of the ideas outlined therein. Darwin starts it by plunging right into the question of how freshwater species are distributed, and applies the same arguments as before to eggs and seeds. He then returns to oceanic islands, and reiterates his pivotal observation: they have a small number of species, but a high proportion of those species are found nowhere else in the world. Furthermore, these species are often easily outcompeted by invasive species brought in by humans. Here Darwin implies the Red Queen hypothesis again: living things need only be good enough to survive in their present circumstances. The more species present in a given environment, the more variables must be accounted for by each (a point that Darwin has made before and emphasises repeatedly in this chapter), and so the more likely it will be ready to conquer those species which have had to adapt to fewer such variables. In his discussion of island species, Darwin brings up what would become known as Wallace's Line, although he mentions it here as described by Windsor Earl but to be reported further on by Wallace. And finally, some four hundred pages into the book, we get to the Galápagos Islands! Darwin mentions his famed finches here but spends less time on them than one might expect; all the same, he makes his points clear.

Moreso than in the previous chapter, and in fact moreso than in most of the book so far, Darwin regards the findings of natural historians (what biologists were called in his time) in the context of his theory of evolution and of that of special creation. In all cases, the latter is found completely unsatisfying, while the former answers most questions and suggests useful avenues for addressing the remainder. It must be remembered that, while we today regard fossils as an important line of evidence for the theory of evolution, they were more of a puzzle to be explained in Darwin's time. Comparative anatomy was and remains a powerful source for evidence in favour of common descent as well, but this evidence was also interpreted -- somewhat unsatisfyingly, but nevertheless not unreasonably, and by very highly regarded authorities -- to support special creation. One of the most convincing lines of evidence, that of molecular and genetic data, was not even imagined in Darwin's time. Accordingly, it was biogeography, the subject of this and the previous chapter, that provided Darwin's strongest case for common descent -- what has been called elsewhere "the fact of evolution". Natural selection was a critical insight, providing the mechanism by which dissimilar things could have had a common ancestor, but convincing though the theory was, the Victorian audience needed as well to be convinced of the facts which that theory was meant to explain. That is the purpose of this and the previous chapter (although of course Darwin makes his case that natural selection is right at home in this context here as well as previously), and Darwin's descriptions and explanations are nothing if not sound.

Really, I find myself having little to critique here. This is perhaps not Darwin's finest work: it is not his most eloquent, nor his most revolutionary, but it fulfills a very necessary function, and it does so with a rigour not often seen elsewhere. Darwin is very careful not to insist that everything has been explained in his examples, but rather (and more importantly) that everything is explainable. It is somewhat odd that, after first explaining the theory so well, Darwin should then move on to describe the facts that the theory is meant to explain; certainly if I were writing this work I would have done so in the opposite order. But for all that, this chapter is satisfying: it addresses all manner of issues and shies away from none of them. Before the Origin, natural historians had ample argument against evolution; afterward, such arguments' days were numbered, and in no small part these chapters on biogeography were the pivotal development that changed that.

The Origin, Chapter Eleven

2009-03-21T07:57:00.000-07:00

In this chapter Darwin returns to a favourite subject, that of biogeography. This is one of the topics that led him to start thinking about evolution in the first place, and it is here that we can expect to find some of his strongest arguments. Oddly, he is not very forceful; while he does argue here and there that special creation cannot account for the data that he describes, he does so almost in passing. Mostly he gives his by-now-familiar "long lists of facts", albeit tempered with some actual experimentation! -- and a thorough analysis of how these data concord with the principle of common descent.

He starts out with the fundamental observations of biogeography: regions similar in climate but remote from one another have very different organisms living therein, while regions different in climate but adjacent have similar organisms. This is an argument for common descent, the principle wherein related but distinct species diverged from a single ancestral species. Such observations have little to say about the mechanism by which related forms come to differ, and Darwin accordingly spills little ink on the topic here. What he does say is emphatic that natural selection is more important than other mechanisms: change, he says, is always adaptive! This is (at least to my recollection) at odds with what he has said earlier in the book. Then again, this is pretty much a footnote observation, and (as I have already said) largely irrelevant to the topic at hand.

Another point that Darwin emphasises is quite familiar by now: the organisms living in an environment are far more important than the physical conditions when determining what pressures will be faced by anything living there. Another, less familiar, point, more genetic than ecological, and made with admirable emphasis, is that the lineages that we trace through evolutionary history are not those of individuals, but of populations. Although Darwin did not imbue upon it as much import, this is nevertheless a very important point. Here as elsewhere he hints, prehaps unconsciously, at what would become productive avenues of research.

An interesting fact of this chapter is its complete neglect (at least by name) of the Galapagos Islands. We refer today to some of the birds living there as "Darwin's finches" and we know that observations of them were incendiary to Darwin's thoughts on evolution, and yet Darwin at best coyly alludes to them in this chapter, where he could easily be using them as a powerful example. I can only suppose that he mentioned this in his notes and correspondence, and that his reasons are more clear there; or perhaps he discusses them in the next chapter.

Returning to his main observations, Darwin notes that biogeography indicates the closeness of existing species across geographical barriers, and infers that such barriers had to have arisen before the species diverged. Such barriers can be greater than is obvious, as oceanic islands are often volcanic and therefore not geologically related to the closest land, which in turn indicates that they were not connected at any point in history recently enough to be populated by the species that now reside there. Dispersal therefore must be proven to have occurred through the water or the air, and to demonstrate that this is possible Darwin resorts (again!) to experimentation. In a modern work, the results would have been presented in a table, allowing for easy comparison and confirmation, but Darwin gives us a few lengthy paragraphs with more of his "long lists of facts". Happily, he interprets things for those of us whose eyes glaze over. One of his experiments involves feeding different species of bird prey that had previously ingested seeds, and looking for the seeds in their excrement. One might well wonder how he did this, given that the birds whose digestion he was tracking included "fishing-eagles, storks, and pelicans"! (Naturally, he concludes that birds are effective agents of dispersal.) Overall, the middle part of this chapter amounts to another of Darwin's set-up-and-take-down of his opponents, although much more drawn-out than previously: dispersal is not inconceivable, and over time inevitable. At the same time, at least for the time-scales involved with this chapter, actual naturalisation of species as they move through different regions is not discussed, and neither is the possibility of populations remaining in a region and adapting as the climate changes. In all likelihood, it is more probable that they would be outcompeted by invading organisms already adapted to the new climate, but the possibility remains that they might adapt quickly and well enough to fend the invaders off is not even addressed by Darwin.

The remainder of the chapter concerns the exchange of flora (Darwin here concentrates on plants) through the course of recent geological history -- namely, glaciation, and the immediately preceding epoch during which Darwin understands global temperatures to have been warmer than now. Darwin's arguments, at least at first, apply best to immutable species. He brings up natural selection and local adaptation every so often, but he recognises (without specifying) that he is discussing changes in the history of life on Earth on a timescale insufficient for much evolution to have occurred. Interestingly, he considers the intermingling of related forms resulting from mass emigration to be of great import, colouring the descendants in both regions after the climate changes and their accompanying emigrations have reversed themselves. This (unbeknownst to Darwin) mirrors the relative importance of mechanisms of change in eukaryotic reproduction: recombination is more likely to cause change in the short term than is mutation.

Darwin gives a great deal of attention to species that are remarkably similar in extremely disparate regions: plants in England that are obviously related moreso to those in New Zealand than to those in any intervening region. On the face of things, this would be a powerful objection against Darwin's models of dispersal. Here Darwin seems almost meek, in that he does not address this argument at all. Rather he slowly builds up examples and then explains how they provide a reasonable exception to his theory rather than a major challenge to it. On a less extreme scale, he notes the point made famous by Jared Diamond, that species in northern regions tend to expand their ranges southwards, but the converse is rare. Darwin draws the same conclusions, too, that the larger areas of the northern regions allow for a larger population, which will have had to have undergone more intraspecies pressure to survive (competition being, as Darwin supposes, fiercest between individuals of the same species), and therefore will be better competitors against species not so challenged.

Darwin's grasp of geology is occasionally frustrating. Continental drift is an extremely powerful theory, one which makes a lot of phenomena perplexing in Darwin's time transparently obvious. And yet, Darwin explicitly denies its possibility, for reasons not at all obvious (and in any event not given in this chapter). Certainly the amount of continental drift that occurred during the last few epochs has been insufficient to have impacted the emigrations with which Darwin concerns himself here, so the modern mind is not terribly assaulted by this plesiological notion. But another supposition does rankle: Darwin expects sea levels to have lowered as temperatures rose! I do not know whence this idea comes. More satisfactorily, Darwin extends his observations beyond islands, with the attractively terse observation that "A mountain is an island on the land;" and here, he leaves us, to discuss further details on the same topic in the next chapter.

The Origin, Chapter Ten

2009-03-14T06:35:00.000-07:00

This chapter is very much a follow-up on the previous. In it Darwin draws connections between his theory of evolution and his observations in the previous chapter, which was quite removed from the former topic. Specifically, he brings in a favourite subject, that of biogeography, and outlines how it intersects with palaeontology. He also emphasises a point made in the previous chapter, on the paucity of fossils: "Each formation, on this view, does not mark a new and complete act of creation, but only an occasional scene, taken almost at hazard, in a slowly changing drama." It is worth remarking how gentle his argument is in this chapter against special creation; he is clearly opposed to it, but (as in the chapter on hybridism) only rarely addresses the matter directly. More often he does not connect all the dots, rather presenting them to his reader with an understated nudge in the direction of the pencil.

The chapter opens with the observation, which Darwin repeats throughout, that not everything evolves at the same rate. Indeed, he alludes to what we often call "living fossils": organisms that have not changed significantly from earlier forms. He also touches again on the Red Queen hypothesis, stating that organisms must always be striving to catch up with their surroundings, to outdo their competitors' advancements, and that those forms that have remained static over long periods of time have simply acquired traits early on that have kept their edge against their their competitors. Another point repeated throughout (and taken from previous chapters as well) is that fossils are not necessarily -- indeed only rarely -- intermediates between extant allied forms: rather they are intermediates only between their own predecessors and extant forms. This is exemplified in his reaction to those who mockingly asked whether the notable Pleistocene fauna of South America (glyptodonts, ground sloths, and the like) were supposed to be ancestral to their much-smaller extant counterparts (anteaters, armadillos, and such). Of course not, says Darwin; the large animals from the Pleistocene had common ancestors with the extant ones, but there is no necessary ancestor-descendant relationship between the two. In his words: "The species extreme in character are not the oldest, or the most recent; nor are those which are intermediate in character, intermediate in age."

Upon first exposure, one of Darwin's pithier maxims seems laughably understated: "rarity precedes extinction". But what he means here is not merely that things tend to become scarce before they disappear entirely but that they dwindle before they go: extinction is, he avers, a lengthy process. He goes further, saying that it is considerably slower than is its opposite, speciation. Personally, I think that he has it the wrong way around, but then, non-palaeontologist that I am, I am more familiar with the famous but rare catastrophic mass extinctions than I am with the periods in between, and Darwin could well be right for those periods. Actually, I do not think that it matters much, but Darwin seems to be intent upon pressing the point.

While reading this book, it is impossible not to be aware that it was a product of its time. Darwin was a Victorian, not just in style but in outlook. Part of this is displayed by his continual use of the words "higher" and "lower". This is taken to mean several things: it could refer to complexity, specialisation, or degree of divergence from a common ancestor (in which case, for example, birds are "higher" than lizards); it could refer to geological succession (in which case the terms take on a literal meaning as well as the connotation of more-evolved being superior); or as Darwin defines it here, it could refer to the capacity for one species to outcompete another. This is another indication of Darwin's ecological thinking, and his placement of the terms on objective grounds demonstrates a remarkable degree of egalitarianism. If something outcompetes something else, it is "higher" than its competitor. We would of course use the term "more successful", and I am not sure that adding further ambiguity to a term already much used and little specified is a good idea, but the concept itself is important and groundbreaking.

Oddly, Darwin drops the ball in his discussion of ecological priority. He addresses the question of species being transplanted from one region to another, and competing against their native equivalents, judging the victor the "higher" of the two. Here he seems to have forgotten his earlier point about environments containing a biotic component: what makes one species thrive in one region might be another species (a symbiont, prey, something that takes out principal predators, etc.), and if both species are transplanted, the outcome might well be very different. More likely the connections are subtler and manifold. Furthermore, he assumes that competitive relationships are mathematically transitive: if A outcompetes B, and B outcompetes C, A must then outcompete C. But there is no reason why this must always be the case. This is not a point that was brought up earlier in the book, but it is not out of line with Darwin's thinking; in any event, his failure to consider multiple-species relationships is quite puzzling.

Darwin gives us a taste of things to come in his discussion of the putative resemblance of ancient organisms to the embryos of their modern counterparts. This principle has been pithily but polysyllabically presented as "Ontogeny recapitulates phylogeny"; while it is true that embryology is important in studying the evolution of morphology, the actual principle, in which embryos for all intents and purposes are their ancestors, is incorrect. Darwin points out that it was at the time unproven, but thinks it likely true, and that it will soon be proven. However, he phrases his arguments conditionally: if true, it would be supportive of his theory. (Incidentally, he mentions the concept as being proposed by Agassiz, who was one of the few biologists to hold out against evolution even to the end of the century. This flies in the face of its criticism by modern creationists!)

There are many points in this book (many in this chapter) where I kept thinking how much Darwin would have benefitted from a modern understanding of plate tectonics. Much like genetics, however, he does not allow his (in each case flawed) understanding of the matter get in the way of his theory. Here, he does not attempt to explain biogeography, just to describe it, and that is sufficient to help his theory. Oddly, in the summary, he explicitly denies the possibility of continental drift (on what basis he does not even hint at) during the Phanerozoic, but speculates on its possibility earlier. He is free to do so, of course, in that fossils even from the early Phanerozoic were unknown in his time, and so Precambrian biogeography was entirely speculative.

The summary begins with one of those sentences so long that only a Victorian could have written it. It is not Victorian in its structure, though: it is more of a list, and in fact a comprehensive and succinct summary of the two chapters on palaeontology. Darwin got a lot of things wrong, but it is refreshing to see how many he got right.

The Origin, Chapter Nine

2009-03-09T06:48:00.000-07:00

Chapter Nine addresses the lack of transitional forms found in the geological record, another issue that creationists like to bring up today. Of course, things have changed significantly since then: we have an incredible amount of transitional fossils now (not that that, or indeed anything, will satisfy the creationists), but we still do not have, and probably will never have, transitional forms for everything. The reasons for that may be more subtle than Darwin supposes, but he has it essentially right.

One important point that he makes early on in this chapter: "I have found it difficult, when looking at any two species, to avoid picturing to myself, forms directly intermediate between them. But this is a wholly false view; we should always look for forms intermediate between each species and a common but unknown progenitor; and the progenitor will generally have differed in some respects from all its modified descendants." In other words, identifying transitional forms is confounded by the fact that they are more properly transitional between their ancestors and their descendents than between any two of their descendents, and so we may have a faulty search image for the latter. As an exaggerated example, to say that crocodiles and ducks had a common ancestor does not mean that we must find a "crocoduck" in the geological record. Rather, we will find something with some ducklike features and some crocodilelike features, but it will also have features found in neither, while others will be found in all three. (In the mathematical jargon that inexplicably imposes itself upon me, the two sets are not necessarily mutually exclusive, nor will their union be isomorphic to the common ancestor.)

An important point that Darwin makes in passing is that our classification system for living things should properly be based on their patterns of descent from common ancestors. In perhaps most cases this can be taken backwards as a rule of thumb: common ancestors can be inferred for members of most of our heirarchical groups that are exclusive of all other groups at the same level. That this is the case was and is one of Darwin's more compelling but also more subtle arguments. He has made this point before, and will make it again.

One of the larger issues that many had in Darwin's day was that the amount of time required for the diversification of life into its myriad extant forms is huge. This is something that Darwin freely admits, and of course modern science says no different. The age of the earth was something of a hot topic at the time of the publication of the Origin. He mentions "Sir Charles Lyell's grand work on the Principles of Geology, which the future historian will recognise as having produced a revolution in natural science…" and in our day (Darwin's future) these words have borne out. Charles Lyell had made a compelling argument for an ancient Earth just before Darwin set out on his voyage on the Beagle in the 1830s, but many still argued against it. Lyell's view was ultimately to persevere, just as Darwin's, but it was sufficiently controversial that Darwin needed to defend it himself in his work. Darwin's arguments centre on rates of sedimentation and erosion, and while we now have many other forms of corroborating evidence, his arguments are sound at least in principle (I am not geologist enough to say how far off he may be on the particulars). One noteworthy point is his conclusion of an age of 300 million years for the earliest "secondary" (which is to say, Mesozoic) strata, which is actually not too far off.

Having shown that great spans of time will have passed between the deposition of successive strata, Darwin moves on to the fact that those ages have not resulted in abundant fossils. It is somewhat comical how easily some of these chapters' points can be collapsed into one pithy sentence. In this chapter's case, it is simply "Fossilisation is uncommon." This, again, is still quite accepted today, but Darwin takes the principle further. Specifically, he feels the optimal conditions for fossilisation and for speciation are opposite to one another, so that those organisms that do get fossilised will most likely be from long periods of morphological stasis. In his words, "Nature may almost be said to have guarded against the frequent discovery of her transitional or linking forms." Darwin's argument betrays a bias toward land-based life: when sea level falls, new habitat is exposed, and extant land-based life-forms have all sorts of opportunities to take advantage of otherwise virgin territory in adaptive radiations, but of course sea-based life-forms must retreat to formerly deeper regions. Meanwhile, Darwin supposes that only the sedimentation occurring at the floors of bodies of water is capable of initiating the process of fossilisation, rather than (say) mudslides or river runoff. Again, I do not know enough geology to say whether this is in fact accurate.

Another essential observation is that stratigraphic range is almost always smaller than actual historical range. In other words, the earliest fossil found of a given organism is unlikely to be from its point of speciation, and the latest fossil found is unlikely to be the point of its extinction (or diversification into other forms). Fossils can only establish minimum expectations, and unless compelling evidence exists otherwise, we should always assume conservatively. Meanwhile, linked to this argument (found at the end of page 298 in the original, and reprised on page 301) is a surprising (although unemphasised) precursor to the theory of punctuated equilibria! Specifically: evolution is likely slow and gradual everywhere, but slower in some places than others, and should a more-quickly-evolving form reinvade and conquer territory held by their slower-evolving cousins, the appearance in the fossil record will be of one form suddenly giving way to another. Should the rapidly-evolving form have done its evolving in a climate noncondusive to fossilisation, this sudden transition may represent as much of a record as we may be able to acquire, but it does not indicate that the transitional forms existed only for a very brief moment of time, or not at all.

In summary, Darwin dismantles fairly comprehensively the arguments against his theory that his critics were likely to make (and, in the case of modern creationists, continue to make) based on the fossil record. It is possible that he is being merely rhetorical when he says that "I do not pretend that I should ever have suspected how poor a record of the mutations of life, the best preserved geological section presented" until he started to examine the problem in detail, but it is certainly true that science is full of surprises, and in the course of finding a simple and elegant explanation for a phenomenon one first finds that the data to be explained are far fuzzier, fuller of exceptions and borderline cases, than previously imagined. Evolutionary history is full of these sorts of things. I will let Darwin have the last word here: "I look at the natural geological record, as a history of the world imperfectly kept, and written in a changing dialect…."

The Origin, Chapter Eight

2009-02-28T15:32:00.000-08:00

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.

The Origin, Chapter Seven

2009-02-22T09:09:00.000-08:00

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.

The Origin, Chapter Six

2009-02-15T09:12:00.000-08:00

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.

The Origin, Chapter Five, Part Two

2009-02-10T12:50:00.001-08:00

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.

The Origin, Chapter Five, Part One

2009-02-09T16:02:00.000-08:00

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.

The Origin, Chapter Four, Part Two

2009-02-03T15:51:00.001-08:00

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.

The Origin, Chapter Four, Part One

2009-02-02T16:13:00.000-08:00

Darwin begins this chapter by stating the obvious conclusions from even the most casual synthesis of the previous three. The logic is simple:

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.
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.
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

The Origin, Chapter Three

2009-01-29T16:16:00.000-08:00

Chapter Three is, in many ways, the beginning of ecology. One of the ecologists in our reading group said that very little in modern community ecology was not laid out there. The concept of organisms interacting with both their environment, other species, and other members of the same species, and indeed the word "competition" in its ecological sense, are if not Darwin's pioneering work alone at least popularised by him (I do not know enough of the history of biology to say which). This chapter was inspired primarily by the work of the economist Thomas Malthus, who analysed the relative birth and death rates in human populations. Darwin's genius was to take this to a mechanical level, without the action of individual intentions. It was one of those ideas which seems obvious in retrospect but which was groundbreaking when first presented. As I read it I kept thinking that this chapter would be an ideal assignment to an introductory ecology class: it really is that comprehensive, that modern. The majority of the work that followed (at least in community ecology) has been merely refinement, primarily through the application of mathematics.

The chapter focuses on what Darwin called the "struggle for existence". The language was meant only partly to be taken literally: while animals must in fact frequently struggle to avoid being eaten, or to subdue rivals, the concept can also be applied to plants (as Darwin did). Those organisms that are able to leave offspring have succeeded in that struggle: they have had to survive long enough to reach reproductive maturity. The struggle goes further for those organisms that must mate in order to reproduce, and still further for those that must nurture their offspring -- but again, the struggle can be metaphorical. Plants which release more pollen, for instance, might win their struggle against others of the same species, in that they would leave more offspring. The struggle to produce viable offspring is implicit in the amount of energy that must be expended to build another organism: pregnant and nursing mothers, for instance, "eat for two", and this intensifies the daily efforts of finding food.

The struggle for existence has its place in the theory of evolution by making explicit the fact that more offspring are produced in each generation than can survive to replace their parents. In a stable population, this means that some offspring will die without having themselves reproduced: they will have lost in Darwin's struggle. Meanwhile, organisms are also individuals, and as such they vary, as was discussed in the previous chapter. Some individuals succeed in the struggle by virtue of inherited characteristics that give them an advantage over their less-endowed kin, and will pass those characteristics on to their own offspring. These advantages may help adapt the organism to its physical environment, or they may help the organism find food or avoid becoming food, or they may help the organism increase its likelihood of reproducing, or the number or health of its offspring.

This leads to the concept of natural selection, which is the topic of the next chapter, but not without offering what must be one of the most obvious attempts at softening the blow in scientific history. Darwin's depiction of Nature is as a brutal and ultimately losing struggle to stay alive, wherein the best that any living thing can hope for is to leave successful offspring before it succumbs to the myriad and overwhelming forces arrayed against it. This must have been appalling to Victorian sensibilities, which Darwin attempts to soothe: "When we reflect on this struggle, we may console ourselves with the full belief, that the war of nature is not incessant, that no fear is felt, that death is generally prompt, and that the vigorous, the healthy, and the happy survive and multiply." I will not deny that there is much joy in life, but fear, sorrow, anger, and pain are also unavoidable. Darwin's empathy for living things is here curiously selective: what of the weak, the sickly, the despondent? Do they really feel no fear? Do they never suffer for long? Of course, the question must here be addressed as to whether other forms of life are capable of feeling fear or suffering pain. It is not my intention to debate that here, except to say that it was this same work of Darwin's that made this question scientifically viable.

But while such a passage fails in any way to support its implication that (in this context) ecological and (ultimately) evolutionary success leads to a more enjoyable life, its greatest failing lies in its assertion that the "struggle for existence" is not constant. Perhaps it is not constant in every aspect of life, but the interactions between living things are so complex that it cannot be assumed that, at one level or another, one is never at loggerheads with something. In finding shelter, we must displace others looking for that same resource. The very act of eating implies that something else had to die: how is that not part of the struggle? Our immune systems are continually fighting off infections -- and doing so the more militantly when we are not aware of it! In winning the hand of one's mate, another must lose the same; what is (one hopes) a happy union for some is necessarily a source of frustration and feelings of loss for others. Nature may not always be red in tooth and claw, but our interactions with one another and with other living things are rarely benign for all.

The Origin, Chapter Two

2009-01-25T15:05:00.000-08:00

Chapters Two and Three will be discussed this week together. They lay the foundation for the principle of Natural Selection, covering respectively variation in nature and the "struggle for existence", the principle wherein with each generation many more offspring are generated than can survive.

Chapter Two is only twenty pages long in the online facsimile, and alludes to Darwin's never-written follow-up to the Origin, in which he planned on expanding on the Origin to his satisfaction. As it happened, the degree of detail provided in this work proved sufficient, and the "long catalogue of dry facts" that would have constituted much of the successor unnecessary.

The question of variation within species brings up the question of what constitutes a species, which is a contentious issue today. Back in Darwin's day, the question was just as open, although the candidate answers were very different. One of the more popular notions was that each species was created independently, and that "varieties" (sub-species and so on, a term used here with some scientific force, and somewhat interchangeable with "race") had obviously descended from and were members of the same species. At the same time, then as now, "every naturalist knows vaguely what he means when he speaks of a species." It is odd how some things never change!

Again anticipating the study of ecology, Darwin notes that features found to be useful in one individual of a species may not be so useful in another. He alludes to thickness of coat as an example: this is a more important feature to an animal in an extreme environment than to one in a more temperate locale, although the capacity to vary its thickness seasonally may be more important to the resident of the temperate zone. What varies in a species has traditionally not been considered important, but Darwin notes the circularity of the argument in which "important organs never vary", thereby removing such variation from consideration by using it to divide organisms into different species. Yet, substantial variation in unambiguously important organs can be found within otherwise-defined species: what we now know to be developmental variation in insects is noted by Darwin to produce very different morphologies in the paths taken by individual nerves.

The problem is most severe in what Darwin calls "protean" or "polymorphic" species. Such species (or indeed genera), claims Darwin, tend to be highly variable everywhere that they have been found, and in the case of fossils, in every period. This suggests that plasticity in development is itself an inheritable trait, at least inasmuch as that the corrective forces keeping development on a particular path are stronger in less-variable species, and weaker in more-variable ones. Darwin notes that the parts of organisms that vary are likely of less value to their survival than are the parts that do not, which is a necessary observation of any system in which natural selection is in operation.

Darwin next delves into the question of terminology, addressing the question of how much variation can be tolerated within a given species. Essentially, he says, the question cannot easily be settled; every specialist has a different list of valid species. He brushes by the distinction between allopatric and sympatric species, which would become important to evolutionary theorists in years to come. Here he merely notes that geography can be as characteristic as is form to determining species boundaries. Ultimately, the question of dividing individual species must be done using objective criteria, something that still has not been settled today; to do otherwise is "vainly to beat the air." Darwin briefly mentions what are now called "ring species", in which neighbouring forms are obviously continuous species, but members of the extremes of the range are distinct and do not easily interbreed.

The degree of known variation within a group of organisms is in no small part a function of the degree to which it has been studied. This is, of course, obvious, but it has important implications to the distinction of individual species, and Darwin goes from there to point out that it is much easier to learn a new group of organisms by taking their representatives from a particular locale in isolation; to consider initially those from other locations as well tends to confuse things. Once familiarity with a particular flora or fauna is attained, though, extending one's range of observations will challange one's sense of "species", both usefully and otherwise, as what could be diagnostic for a species in one region may ultimately prove highly variable between regions.

Having shown how variable individual species may be, and having suggested almost in passing that varieties within a species may in fact be incipient species, Darwin makes the important point that such varieties need not ultimately become different species. He goes on to point out that larger genera (those with more species) are both more widely distributed and more dominant than smaller genera, a point which I am not sure holds today. There are, at the very least, certainly exceptions, and Darwin points to a few of them himself. In particular, those species adapted to unusual environments (aquatic plants, for instance), tend to be more uniform. The other case that he gives, "plants low in the scale of organisation" being more widely distributed than their "higher" counterparts, I find definitely doubtful, on a similar principle to Darwin's own above. While individual knowledge of variation increases (at the very least) one's capacity to erect species distinctions, the features which vary in "lowly" organisms do so less markedly, and so the important distinctions are all the more subtle. To make a modern point of this, while they may not have evolved as far from the common ancestor as "higher" forms, they have nevertheless been evolving for the same length of time, and often for the same number of generations, and have had every opportunity to vary in ways that we may not appreciate.

An unwritten generalisation follows: Darwin believes nature to be essentially uniformitarian. This was a controversial geological principle when Darwin left on the Beagle, stating that the processes which shaped the Earth in the past are still in effect today. There are too many known exceptions for this to be considered strictly true today, and many of the processes which we now understand to be in effect (plate tectonics, for instance) were unsuspected in the early nineteenth century, but the essential notion is correct. Darwin's application of this to biology is a cornerstone to the science. In other words, evolution has happened, and it is continuing to happen today: it can be made an experimental science. These notions are not explicit in the Origin (at least not at this point in the work), but they are very much implied.

In summary, this chapter appears to make two important main points. First, the larger genera (by which is meant the more speciose genera), the more varieties can be found within each of its species. A related though distinct point is that the threshold of variation characterising each of those species and varieties is lower than that for the smaller genera, within which species and varieties tend to be more distinct from one another. As I said above, I am not sure that this is actually the case, and in any event, I do not see how it is critical to Darwin's argument. Far more important is this chapter's other point, that variation is a continuum: the more closely one looks, the more similarities one finds between different groups, and the more individual differences one sees within individual groups. Species are artificial constructs, conveniences for human classification, and are not always unambiguously delineated. Furthermore, "little groups of species are generally clustered like satellites around certain other species", by which Darwin means that genera may be divided into subgenera, the species of which resemble one another to a greater degree than they do members of other subgenera, and which tend to be found in closer proximity to one another geographically as well as morphologically. This is not an unimportant point: the continuity between species is not evenly distributed, and the fuzziness of the species definition can be extended to higher levels as well.

The Origin, Chapter One

2009-01-20T15:58:00.000-08:00

A couple of weeks ago, a friend asked whether there was a group in place to read Darwin's Origin of Species this year, on the 150th anniversary of its initial publication. I replied that I was not aware of any such group, and somehow wound up helping to found one. I had read the sixth and final edition before, and have decided to read the first edition for this group. (All editions are available for free online at Darwin Online.) We are having our initial meeting tomorrow, but I have had enough thoughts about the work that I felt it appropriate to record them here, before being shaped too much by others' interpretations.

The Introduction begins abruptly, so much so that I almost wondered whether there was a page missing in the submitted manuscript. It is written in a comparatively casual tone, almost as a letter to the reader, and nothing like one would expect of one of the most significant works of science ever published. It starts with a summary of the genesis of the work, in what would be a brief account in modern terms, and nothing short of astonishingly so in Darwin's Victorian terms. I should mention that, though I am tempted to cover this history here, it is not my point to summarise the book, so much as to critique it, from both a modern and (so far as I can succeed in placing myself into it) a contemporary context. My prior experience with it was positive enough that I would encourage others to read it for themselves; I flatter myself to think that this account might help in understanding Darwin's work, but I have no intention of replacing it. At the same time, Darwin regarded this 450-page book as an abstract, which only a Victorian could do. He apologises for not citing the work of others (although he does refer to such work frequently, and attributes it accordingly, he does not indicate where one might find it published), appealing to a lack of space -- again, a charmingly (some might say irritatingly) Victorian conceit in so large a work. I think it more reasonable to consider that Darwin was under considerable pressure to get his work published, since he had almost been scooped by Wallace. He gives an acknowledgement to his peers and mentors that (again) would be concise in modern terms, mentioning nobody by name aside from Hooker.

Then the Introduction begins as one might expect it to, setting the stage for the work to follow. Darwin first addresses the complexity not only of living things in and of themselves but as well that of their interactions with their environment and with other living things, which he supposes makes the proposition all the more marvellous that they arrived at their present state exclusively through natural processes. All this, he says, will be explained; and he feels it best to start with a discussion of a process analogous to his favoured mechanism, and so begins an outline of the book itself. The first part of the book (comprising five chapters) takes off from this point to discuss artificial selection, and moves on from there to cover variation in nature; the overproduction and differential survival of members of each successive variation; and the central principle of natural selection. He rounds this part of the book off with a discussion of the laws of variation and of correlation (of which I have more to say shortly). The second part of the book (the next four chapters) discusses possible objections to his theory: the complexity of any living thing and its constituent parts; the matter of instinct and other behavioural traits; the erection of biologically relevant boundaries between species; and the paucity of data from the fossil record. The third part of the book (another four chapters) picks up on this last theme, but move from addressing possible flaws in the theory to demonstrating its strengths: the continuity of living things from one form to another through time; two chapters on biogeography; and finally one on classification and comparative biology. Finally, he summarises the whole work in the last chapter.

Darwin finishes his Introduction with more uncharacteristic brevity, remarking with model honesty that the theory is far from finished, and while it is capable of explaining much, it does not cover everything. His last sentence is worthy of repetition: "Furthermore, I am convinced that Natural Selection has been the main but not exclusive means of modification." This is remarkable especially in that Darwin is often assumed to have been a strict adaptationist -- to have held that everything in life can be explained solely through natural selection acting on existing variation. This misconception has gone to the point of modern scientists claiming exactly that being called "Darwinians". Darwin was ahead of his time in many ways, and one of them was this very conviction.

Chapter One of the book (as mentioned) covers artificial selection. I have comparatively less to say on this; it is at this point that the Victorian locks are opened and the flood of words rushes through. Stylistic considerations aside, the fact that the meat of the book begins here means that the pace must necessarily slow somewhat. My earlier impression is not contradicted, though: Darwin remains quite readable, for all his verbosity.

The first chapter is divided into several sections in the table of contents, but these are lumped together by headings in the text itself, and by the running titles at the top of the page. The first such section deals with what Darwin knew of genetics, which is almost embarrassingly incorrect. It is truly impressive how much he got wrong -- not just wrong, but at times fantastically so -- and yet he managed to draw the right conclusions from such faulty premises. Much has been said of the irony of Darwin and Mendel being contemporaries unaware of one another's work, and of how the combination of their work led to a paradigm shift in biology almost as significant as that generated by each body of work taken by itself. Darwin assumed that inheritance was an analogue matter, that traits from each parent blended together rather than existed as isolatable units, and had no explanation for such phenomena as recessive traits or chromosomal linkage. At the same time, he was quite aware that some traits did seem to be connected, and suggests something suspiciously close to pleiotropy, in which a single gene affects multiple traits -- a situation which can explain the evolution of many seemingly neutral or even deleterious traits, assuming them to be so linked to beneficial traits. Darwin is similarly aware of reversions as significant, but has no appreciation for any mechanisms behind such phenomena. Then again, he is not concerned with the mechanisms of genetics, which is perhaps why is able to be so right in his conclusions while being so wrong in his premises. Another angle that Darwin plays a fair bit on is the origin of domestic animals and plants, on which he speculates somewhat unrestrainedly, but rarely far from what has become accepted today.

The second section of this chapter deals with one particular example of domestication. Having spent five years at sea, Darwin proceeded to invest himself in studies of individual groups of living things -- beetles, barnacles, earthworms, and pigeons. The latter provide the subject of this section. Here he is on much firmer footing. Darwin impresses, perhaps ostentatiously so, with his encyclopaedic knowledge of breeds and characteristics of pigeons, and gives examples of how some of the more extravagant breeds could have come about. This blends into the third section, which expands the discussion to cover other species, and from there to the fourth, which covers the mechanisms of selection -- but from an ecological rather than a genetic point of view. The fifth and sixth sections take this further, positing that much artificial selection is unconscious. There are thus two types of artificial selection at work, one planned and rapid, the other a slow and organic extension of the collective preference of those charged with keeping living things. Throughout these sections, this is where Darwin truly shines (I have read -- though I forget where -- of Darwin being regarded as a pioneer in ecology as well as evolution); he looks best at the big picture, even while supplying a torrent of fine details. At the same time, his arguments here are obvious, which is perhaps why his work made such an impression at the time. It is impossible not to agree with him.

A seventh section concerns the "circumstances of man's selection", in which Darwin refutes the notion that many domesticated varieties arose recently because their variability manifested itself only recently. Not so, claims Darwin: rather, it is only recently that human meticulousness and record-keeping rose to the level of being able to pick out such subtle differences as were always present but insufficiently selected before. At the same time, he falters a little here, in his assessment of the degrees of variability amongst different domesticated plants and animals. It is true that (as he suggests) individual species' behavioural attributes contribute (and this is an important factor which I am not sure others had noted beforehand), but there are many more dimensions to consider. Among other things, some species simply do have a greater tendency toward morphological variation than others. Time is a factor as well: something that has been bred for thousands of years will have had the chance to diverge much further from its original form than something that has only been bred for hundreds of years. Dogs and cats illustrate both of these points: dogs are not merely more tractable animals than cats -- they are in fact more plastic as a species, and they have been domesticated for far longer than cats (or, for that matter, anything else), giving far more time in which to exaggerate that plasticity.

Finally, Darwin gives us a single-page summary of the chapter, and a pithy ending: "Over all these causes of Change I am convinced that the accumulative action of Selection, whether applied methodically and more quickly, or unconsciously and more slowly, but more efficiently, is by far the predominant Power." Thus begins the book that changed biology.

One Reason Why We Need Government

2009-01-08T15:05:00.000-08:00

The always-excellent Slacktivist has a long but very readable post about the evils of big monopolies. Go read it.

I continue to maintain that any Libertarian whingeing about "big government" fails to take into consideration the fact that, in theory at least, the government is accountable to the people, while international corporations (and especially monopolies) can and will do anything that they can get away with. It is only the government that is capable of defining what they can get away with. The government may not presently be as accountable as it should be, but that is the fault of the voters. So, when the opportunity arises, vote, and vote responsibly. Only that way will we get both fair government and fair businesses.

Ethics and Aesthetics

2008-12-27T19:01:00.000-08:00

I had an amazing discussion with a devoutly Christian friend this week. We have discussed religion before, and one of the things that we agreed was not at issue was a question of morality: we agreed that it was inherent, that living a moral life requires no external dictum (such as the Ten Commandments). Our trains of thought departed on the origin of this moral sense (the product of evolution acting on social animals versus a gift of God), but it was refreshing not to have to defend my ability to make moral decisions without God.

This week we returned to the topic, and expanded it to include other things that are (at least commonly considered to be) uniquely human, which he and others have thought evidence of a divine hand. Among those things was ethics, the ability of humans to act in a fair and just manner even to our detriment. But, I contended, we are social animals; experiments with other social animals have shown at the very least a rudimentary sense of justice or of fair play. Our consciences are a safety mechanism that allows us to live together, to rely on one another. I contend that the conscience has its root in the ability to empathise, to imagine ourselves in the place of others. "How would I feel if someone treated me the way that I am thinking of treating this other person?" is perhaps one of the most fundamental questions that we can ask ourselves on a day-to-day basis, and it guides our behaviour in ways too varied and subtle to describe.

Our conversation moved on, and my friend appealed as well to a sense of the spiritual that most people have, the ability to be awed by nature, as well as by great works of humankind. This is something that neither of us had thought much about: where does that sense of awe come from? What would its predecessor be in our pre-human forebears? Again, he thought this to hint at the divine: God gave it to us, a gift with which to appreciate our world. At one point my friend described the feeling that he got admiring a beautiful sunset as "hollow".

Another friend, who was sitting in on the whole conversation, did not quite get what he meant, but think that I did. This is not the bad sort of hollow that we equate with guilt or loss or failure. It is a feeling of inadequacy, of humility, that we can appreciate something so much vaster and more beautiful than ourselves. But, I said, we also feel a sense of gratefulness: we know how much talent and hard work goes into making something beautiful, and we appreciate the sacrifice of those who invest such skill and energy in making beautiful things. It is our ability to empathise with others that gives us this ability -- we put ourselves in the place of the artist, and see how poorly we would do in creating work of such power, and we thank them for having done that for us.

To give an example, there has been and will forever remain, for instance, only one Johann Sebastian Bach, and nobody will ever be able to write what he did. The level of brilliance in his music is so far beyond that of anyone most of us will ever meet that to contemplate it being played -- to contemplate it being written -- for us is to imagine ourselves indebted beyond any hope of repayment. It was not written for us, and unless we are very priveleged we will not ever even experience it being played for us, but we can still appreciate it, and we are grateful beyond words for it. (Of course, one can replace Bach with any icon of artistic brilliance if this example does not stir one's own emotions. I could argue that this would be evidence of a deficiency in taste or exposure, but I will leave that for another argument.)

But what of our ability to appreciate nature? Scientists have possibly the highest proportion of atheists amongst the professions, and yet what drives one to be a successful scientist is exactly this sense of wonder. How can one feel indebted to the Universe? And yet, how can one not? We exist, we experience things. As scientists we appreciate (I cannot honestly say "understand") just how complicated and contingent everything is: how fragile is that existence, how precious is that experience. We empathise with the Universe, knowing at the same time just how impossible it would be for one of us to create the thing being appreciated, and we feel indebted to the Universe for having made it for us. There is a sense of guilt at not being able to repay it -- ever -- and a sense of duty to appreciate it. But more than that, there is a sense of gratefulness, that it is there to be appreciated, and that we are here to appreciate it.

All of this springs from our conscience. It is not the primary function of our conscience, but it is hardly a bad side-effect. It is also not something that I would have connected before this conversation: ethics and aesthetics are not things that I would guess were intertwined, but I am drawn to the simplicity and elegence of this idea. I have no clue how original it is, but I think that I rather like it.

Rejected!

2008-06-02T16:59:00.000-07:00

This morning I received one of the least-welcome messages it is possible for a scientist to receive: my manuscript was rejected for publication. I was assured by the professor for whom I had originally written the paper that it would sail through peer review, but apparently it did not: both reviewers were negative.

This was my first real introduction to the receiving end of peer review. I have always been in favour of the process: it is a sort of quality control for science. It has its flaws, to be sure, but they are far less significant than some of the other problems with science.* I always figured that I could take a rejection gracefully, that I would grow from it and make my work into something better when I resubmitted it. It took this experience to show that I was really not prepared for dealing with it. I managed to pull myself together, though, and thought about it on my way into campus.

For one thing, my paper is not on a topic in which I am actually doing research. It is a review of work done in a distantly related field, written for a class and coached into publication by the class's professor. I suppose that I had started to feel somewhat overconfident of my talents in the latter stages of submission. Getting a paper published outside of my field would be something of a coup, proof of my versatility. But at the same time, there is nothing halfway about this. Publishing a paper is not playing in a sandbox: submitting something for publication is tantamount to saying that one is ready to play with the big kids. One is asking for the roughest treatment that one's work could possibly merit. Like the saying goes, "what doesn't kill you makes you stronger," and that is certainly true here. If a paper survives the peer-review process, it was either exemplary to begin with, or (more likely) was considerably improved through its criticism. I was asking to be taken seriously as an expert in a field in which I have in fact had little formal training (none at all, in the case of palaeontology, of which I had much to say in this paper), and I should have expected a thorough smacking in any way that could be delivered.

However, things are not as negative as that implies. One of the reviewers provided about four pages of commentary, which I take to mean that s/he thought my work of sufficient merit to indicate at the very least that I was thinking along the right lines. If nothing else, s/he has helped me learn more about the field, pointing out where I was making false assumptions or missing critical papers. Although there was nothing explicit by way of encouragement in what s/he wrote, it is not reading between the lines too much to see that, at the very least, the reviewer respected my effort.

The other review was quite different. For one thing, it was well under half a page. It began with explicit praise for my writing, and regards the paper's principal flaw as a lack of novel ideas (which, being a review paper, is not a particularly hurtful observation). However, the second paragraph reads almost as if it were describing a different paper entirely. It deplores my lack of expertise and experience, and concludes by calling my work "poor". I am not sure what to make of the conflicting messages in this review, but I will continue to ruminate on the matter, and both the professor for whom I originally wrote the paper and my supervisor have promised advice and encouragement. I may take the first reviewer's suggestions to heart, rework the manuscript, and resubmit it. I may get my coup after all. But overall, this is a side project, and not a critical one to my career, and if it fails to produce anything that can go on my CV, so be it.

In any event, I have made it through the day with my dignity largely intact -- challenged, to be sure, but not broken. This is part of the process. I would expect nothing less: I have asked for my work to be taken seriously, and it was, even if that amounted to being told that it was not an effort worthy of being taken seriously. This is a sign that science is working. If I am to make anything of my effort, it will be all the better for having weathered such a challenge. In short, things are not so bad.

* This is worthy of another post in and of itself. The principal problems with science that concern me are research priorities, funding, job availability, and regard for educational talent -- but those are all problems within science. More significant still is the general public ignorance of what science is, how it works, and what scientists do, running from general lack of exposure all the way to the mistruths spread by Creationists. But I will restrain myself: I will post about that another time.

Perils of Electron Microscopy

2008-02-25T17:46:00.000-08:00

I do a lot of work with electron microscopes. This is amazingly neat stuff, every bit as fun as I imagined it would be, and perhaps the closest thing that biologists have to being astronauts. I get to play with exotic, highly expensive equipment, and I get to see alien things that nobody has ever seen (or, in some cases, dreamed of) before. Twice in the last six months my lab has had a visiting scientist come to do work that is right up my alley, and since I am checked out on the microscope and she is not, I got to "drive" (the term that we seem to use for operating the 'scope) with her giving me instructions. It was very illuminating, seeing what is pertinent to our study and what can be skipped over, and at the same time there were several moments of both of us sitting and gaping and asking each other, "What on earth is that?!" It is fantastic stuff.

There are several kinds of electron microscope. The one that my lab uses most is the transmission electron microscope (or TEM), which operates in a very intuitive way: it works just like a regular light microscope, except that instead of shining a beam of light through the specimen, it shines a beam of electrons. The electrons are focussed using lenses, and (just as with the more expensive light microscopes) the images are captured by a camera. Of course, there are other significant differences as well: the lenses are in fact magnetic fields, and because electrons do not travel very far through air, the inside of the microscope is pumped down to a high vacuum.

Specimens for a light microscope are generally mounted on slides. This means that the specimen, usually aqueous in nature, is dropped onto a glass slide, over which is placed a coverslip. If the specimen is important enough, and stable enough not to degrade on its own, the slide may be sealed using Vaseline or fingernail polish, which can preserve the specimen indefinitely, but otherwise, that tends to be it. Of course, there are often also specific ways of preparing specimens, but I will not get into that right now.

Specimens for a TEM are analagous. The specimens are mounted not on slides but "grids", which are little (3 mm diameter) copper circles with a slot-shaped hole in the middle. (Yes, they are not actually gridlike: this is a historical term, used because other grids actually do have mesh gridwork in the holes. Many labs use those kinds as well, but my lab has so far used only the other kind, called slot grids.) The specimen is actually mounted on a very thin plastic film, on the order of 40-100 nm thick, which is suspended in the middle of the grid. Like a well-preserved slide, the specimen will last indefinitely.

There are of course other differences, many of which are obvious upon contemplation, and some of which require further explanation (which I may get to in other posts). However, one difference that is significant here is that electron microscopes (all of them, but particularly TEMs) are not just sending a beam of light through the specimen: they are shooting charged particles, which can and often do interact with the specimens. Electrons can be really harsh! In the case of my recent work, for which I was using very thin films (40 nm or so), the electrons can rip right through the specimen. This means that -- often right after discovering the perfect example of a cell amongst dozens of unusable contenders -- one can watch one's precious work tear apart, wrinkle, and wither away before one's eyes. No amount of preparation can prevent this: it just happens. Thicker films are less prone to this sort of damage, but they also impede the electron beam more, and so lose resolution. Resolution is the reason why we use electron microscopes in the first place, so we tend to use the thinnest films that we can. Obviously, I need to experiment more with this, to find a better film thickness that will not break apart in the electron beam, without losing too much resolution.

There are numerous other ways in which TEM specimens can be irreparably lost. One of the most frustrating is tweezering -- putting a hole in the film with clumsily handled forceps while moving the grid around. I have had much hapless experience with that. Another is that some of the stages (the devices that hold the specimens inside the microscope) hold the specimens in place with spring clips, which can and often do tear through the films when removed (or, on occasion, when put in). There are ways of minimising this, which I have only recently become competent at.

Unfortunately, "recently" means that I had lost several specimens while learning how to handle, mount, and dismount them. Up until last Friday, I had only one pristine specimen left, undamaged by my apprentice clumsiness. That specimen, last Friday, self-destructed in the 'scope, as the film gave way spontaneously. This is a setback, of course, but I can always make more specimens. This is of course how science works. Only now, I will try thicker films!

God, Morality, and Progress

2007-12-17T15:40:00.000-08:00

I recently finished reading Richard Dawkins's The God Delusion. Partially this has been because I admire Dawkins but have read comparatively little of his work, and partially this is because I have gotten rather annoyed with people that criticise the book without having read it (which seems to amount to most published reviews and many book-length rebuttals). Mostly, however, I read it because the Evolution Studies Group at Dalhousie chose it for their most recent reading.

Although one might think that it comprises mostly biologists, this group is actually made up mostly of people from the social sciences: philosophers, mainly, with some historians and sociologists for good measure, and I believe a stray psychologist or two as well. This makes for some interesting discussions, usually in directions that I cannot predict. In the case of Dawkins, though, I am right at home: a biologist wandering through theology, generally in agreement with the philosophers, but somewhat out of place all the same.

Much of the criticism of Dawkins is levelled at his lack of philosophical sophistication. I had heard this myself, but did not appreciate it until the philosophers explained things. Indeed, as it turns out, there are far better versions of the historical proofs for God's existence than are addressed by Dawkins. They are just as flawed, only in a more sophisticated fashion, and take far more verbiage to refute. I would argue that a proper refutation would require the book to be twice as long as it is, and probably nowhere near as witty. More than that, Dawkins's intent is not to provide the final word in the question of God's existence (something that talented philosophers and theologians have attempted for millennia) but to demonstrate that his dismissal of said entity's existence is not without consideration of the more famous arguments. Still, I would be a little less embarrassed by proxy if Dawkins had at least acknowledged that he was not dealing with the best versions of the arguments, that he had considered them but found them to be just as lacking. Instead he seems to think that any one version is as good as any other, and tackles at best mediocre and at worst laughable takes on the matter.

His argument against the existence of God is oddly one-dimensional: he merely refutes the argument from design (which as a biologist I know to be complete poppycock, although an understanding of that may take some considerable education to acquire fully). He does so very well, but I am not certain that he has made his case merely through the inversion of a popular (if fallacious) argument. He does take it to be illustrative of a far more powerful concept, though, one which I feel is the most important aspect of the matter: there is really no reason to support the notion of God in the first place. The argument from design purports not only the existence of God but that God created, designed, or guided the development of the material universe. As Dawkins succinctly puts it, a universe with such a God is demonstrably different from a universe without one, and every prediction made by the creator/designer/intervener-God hypothesis can be shown to be contradicted. There is thus no evidence for God, and Occam's Razor suggests strongly that such a fantastic entity must therefore be very unlikely. As Carl Sagan put it, extraordinary claims require extraordinary evidence, and here we have one of the most extraordinary claims ever put forth, with no evidence whatsoever. Still, this is not a demonstration of non-existence, and it leaves the reader somewhat unfulfilled.

It is a tremendous stretch from the purely philosophical discussion of the existence of a creator God to assertions of God's nature and desires, and of God's past actions, as are made in the Bible. The number of a priori assumptions that must be made to require that God fit the character of the Bible is stupendous: one must specify God's positions on a vast number of completely arbitrary issues (positions that are themselves often impossible to justify without a holy text to dictate them). However, it is exactly this version of a God that is used by the faithful to argue for a religious foundation of morality. This is implied in every offhanded assertion that atheists are immoral, or less moral than the religious: God dictates morality, and without God, one's morality is arbitrary.

This is an assertion that has repulsed me for as long as I have been aware of it. It is demonstrably false, both from a philosophical perspective and from empirical evidence. I would argue that the opposite is in fact true: I (as an atheist) try to do good because it is good, not out of fear of punishment or hope for reward. I identify what is good through reflection and compassion, and while my complete set of "good acts" may differ in small ways from that of another, I have enough confidence in the goodness of human nature to expect that it will not differ substantially. We each have our own moral compass, and each points in more or less the same direction. (I make exceptions, of course, for psychopathic individuals such as Hitler, Stalin, and more recently, Saddam Hussein. Of course, while the religious like to attribute their evils to atheism -- a demonstrable falsehood in Hitler's case, at least: he outlawed atheist groups, and ranted against the evils of atheism -- the fact of the matter is that these were twisted, evil people, and fortunately such are very rare in society.) Dawkins makes a compelling point on the matter: the Bible is full of contradictions on what is ethically correct, and so one must choose which one agrees with. What one agrees with is guided, either by one's own moral compass or by edicts from one's church, but ultimately, it is and must be guided.

My view of atheist ethics goes further than this. I pity the religious people who do what they identify as good exclusively through hope for reward or fear of punishment. Such a view of morality must result in little short of paranoia. Life is far more than what one understands as a toddler, when every interaction with the wider world revolves around pleasing one's parents. I suspect (and others in the group agreed) that in fact the deeply religious operate more by their own moral compasses than by constant comparison against some Biblical standard of behaviour. They may calibrate their compasses by Biblical standards, but ultimately they operate, to all intents and purposes, autonomously. The religious fear that atheism leads to chaos overlooks the fact that they themselves operate using the same equipment as the atheists, with more or less the same effects. Many aspects of our morality are, I am fairly certain, so deeply ingrained as to be universal: the edict that one must do unto others as one would have them do unto you is one such aspect. Other things, such as conservative sexual standards, are functions of culture: how one calibrates one's moral compass is not ingrained. The only difference is that the religious have an external and absolute set of standards, while atheists must come to their own conclusions.

This leads to the real argument behind religiously-guided morality: that without that external set of standards, people will have differing moral compasses. The religious do not trust that moral compasses will all point in more or less the same direction (aside from the psychopaths, who will not be improved through religious influence). One might say that atheists such as I have faith in humanity, but I would not go so far. Humans are social animals, and all social animals have internal mechanisms to help them to get along with others of their kind. Our moral compass is a manifestation of those mechanisms, and all the more wondrous for it. That it varies, and that it is influenced by others, allows it to evolve.

This brings up another point made by Dawkins: that morality evolves. Darwin was, by the standards of his day, liberal and progressive, and yet he held attitudes toward race that would make modern-day conservatives cringe. As Dawkins put it, the moral Zeitgeist has changed. We see this as a good thing: racial bias (to take just the one example) has proven to be founded in error and has been perpetuated to the detriment of all. The fact that European culture and those derived from it is more liberal than it was a hundred years ago can be argued to be a good thing from any number of perspectives. I would certainly make those arguments myself, but I would also point out that, having been brought up in a liberal environment, I would see any change in the moral Zeitgeist towards the direction of the values that I hold myself as a good one, regardless of the direction of that change. If I were taught from an early age that (say) people of Asian descent were constitutionally untrustworthy, and this was a common belief in the culture in which I grew up, a history of cultural change towards distrust of Asians would be seen as a good thing. The fact that I can attribute such differences to differences and misunderstandings between cultures leads me to believe that, by objective standards (if they can be said to exist at all), modern European morality has improved from its past state, but I must still be cautious of the very real possibility that a perception of positive progress in other values is merely a reflection of them having become more like my own, which may in turn be entirely arbitrary from an objective standpoint.

So, is the prospect of objective morality actually viable? I would like to think that it is, at least for the major issues: respect for the persons and property of others. The Golden Rule ("do unto others as you would have them do unto you") is key here, applied to all humanity. There are many less critical issues, in which I may disagree with others, but my (and most liberals') compass is calibrated by another, relativistic, edict: "live and let live." In other words, I allow others to decide what is right and wrong for them, so long as it does not affect me. I believe that the core of objective morality follows from these two edicts (although I will grant the possibility that I have not -- yet -- identified some further guideline for morality that further refines matters). There are of course situations in which my application of these guidelines differs from another's; further refinement of each compass may be necessary, but I do not believe that objective morality need cover all possible situations. Personal moralities are, I am fairly certain, tied up with personalities, and so cannot be the same for all people; at this point, they are perhaps not properly called "moralities" in the first place. But the fundamentals are the same, for the religious and the atheist alike: we all want to live in a safe place, where we will not be assaulted or robbed or otherwise abused, and that has nothing at all to do with religion. Making the world a safe and secure place is not a mandate of religion: it is a mandate of humanitarianism, something that we all share.

More Thoughts on Immigration

2007-11-10T18:45:00.000-08:00

This is another publication that my father e-mailed me. I have found it online here, and it is another, more direct, screed against immigration across the southern US border. Again, because it is not my work, I will only link to it, but again, I recommend reading it before reading my response.

To begin with, I certainly sympathise with the wish that these people change their own country for the better; I would in fact dearly love to see that happen. However, their situation is far removed from that of the Revolutionary War era colonists. In many ways, ours is the heel from under which these people are trying to escape. America is the idyllic land of plenty, after all, and our patriotic posturing does nothing to diminish that image. We project exactly the image that draws them to us, and we do little to ease their misery where they come from.

I have had my own Mexican border experience. I drove through Tijuana to get to my partner's sister's wedding, and saw from a distance but nevertheless firsthand the abject poverty and desperation that has unfortunately come to characterise that city. That people would want to get away from it is more than understandable; it would be surprising to find anyone wanting otherwise. There is most certainly a problem here, and elsewhere along the border, but the solution to the problem is not merely to make it harder for desperate people to escape their predicament. (I would emphasise as well that I acknowledge that even legal immigration will not necessarily allow them to escape their predicament. This is a deeper and more complex
issue than the right wing is usually willing to acknowledge, one which requires a concerted effort on many fronts to resolve.)

The article implies that all illegal immigrants are drug smugglers, burglars, and vandals. Many may be, but I would be surprised if all or even most were. Mostly, they just want a better life for themselves and their families, and I would not deny them that. These people, as the article freely admits, are desperate. Fencing them out will not alleviate that. Treating them like human beings will. In fact, I am amazed at the lack of empathy expressed in this piece. The allusion to the Boston Tea Party in the last paragraph reminds me more of Marie Antoinette's "let them eat cake": the Americans here simply have no comprehension of what life is like for the Mexicans. Honestly, I may not have a clue as to what life is like for Americans
on the border, and I certainly wouldn't want to live there. But I can tell pretty clearly that the Americans on the border do not know or care what life is like for the Mexicans on the border. I can say with certainly that, however desperate the Americans may think their lot is, that of the Mexicans is considerably worse.

Actually, rereading this article, I find myself appalled at the writer's lack of empathy. "The first time Kennedy saw 30 illegals
dashing across his property, he'd trip over his Guatemalan lawn guy rushing to the Senate floor to demand enforcement"? I would hope not. I would not. I am not "confused", or without logic, or "all emotion." I want for these immigrants no more than they want for themselves: a reasonable chance at making an honest, sustainable living. You want emotion? My emotional reaction to this is that Americans tend to act as though they are a different and superior species from all other
humans on the planet, and this article does nothing to persuade me otherwise. These are *people* that we're talking about here, human beings, not "just Mexicans". I find that this attitude puts the lie to the supposedly superior moral sense that the Christian right likes to pat itself on the back for.

So, how should we fix things? Honestly, this is not a matter to which I have given enough thought to feel competent to suggest solutions. I am not familiar with the legislation in question, and as such will not speculate on its effectiveness. Amnesty and guest-worker programmes are one step, perhaps in the right direction; I am not sure. I would emphasise that I deplore the Gastarbeiter situation in Germany as you have described it to me. Ultimately, the solution there is to make
things in the Middle East better for the Gastarbeiter, and here to improve the lot of Mexico. More than that, we need to recognise the worth of each of these places, to help their natives acknowledge that they need not leave to improve their lots in life. That cannot happen, of course, unless they genuinely can improve their lots in life in their own countries, and we must acknowledge that, to some extent at least, their inability to do so is our own fault. I think that unrestrained capitalism, combined with an almost religious patriotism, is ultimately at the root of the problem. I do not advocate abandoning capitalism (at least not as regards international competition) but it must be regulated far more, with an eye to the living condition that it fosters amongst other countries, if it is to be fair.

The article's bias is likewise apparent in its disparagement of the ACLU and its approval of the Minutemen. I do not doubt that the latter organisation has many good people with genuine concern for their country amongst it, but the fact remains that it is at its heart a vigilante organisation. Yes, we need to patrol our borders more effectively, but we need to do so with accountability, a principle inherently lacking in vigilante organisations. As for the ACLU, I am not sure what that particular organisation's role in this affair is, and this article does not give the impression that its author attempted to find out. I doubt that the ACLU is "confused": human rights are human rights, and are not limited by nationality or legal status, and with the high emotions, low opinion of immigrants, and lack of accountability here, I would be suspicious as well of how people were treated.

To summarise, I think this article is a prime example of how conservativism is anything but compassionate.

The Next Big Question

2007-10-06T13:40:00.000-07:00

Last week I attended the Canadian Institute for Advanced Research's Next Big Question event. It was an interesting idea, one which has fallen more out of fashion than I would have liked: a public lecture on scientific topics. Importantly, attendance was free, and although I recognised a substantial fraction of people in the audience (CIfAR is a funding body, from which many of my colleagues, including both my former and current graduate supervisors, have benefitted), there were a number of people from the community at large, and that was good to see. It was also interesting to hear their questions, which were good but which belied a general lack of understanding about the subjects at hand. This is a problem, of course, but it is exactly this sort of problem that public science lectures are meant to address.

The idea behind the event was to have representatives from different CIfAR programmes answer a (presumably CIfAR-chosen) "Big Question" pertinent to their research. Although there are around a dozen such "Big Questions", only three are posed at each event; the event "tours" major Canadian cities, with a different subset of "Big Questions" asked at each. All are available at the site, and there is much good food for thought there. The three "Big Questions" asked at this event (the first of the series -- so if you have the opportunity, you can still go to future events, and I would recommend it) were: "How do we build a quantum computer?", "What makes societies succeed?", and "How to microbes change the oceans?"

That the questions were chosen my CIfAR and not the speakers was obvious from the first talk, which was not so much about how to build a quantum computer (although that was covered) but why. It is an interesting topic, one about which I am now motivated to learn more, but still one very much in its infancy. A number of strategies proposed for building such computers was presented; the unit of measurement for quantum-computer memory is the quantum bit (or "qubit"), of which the most advanced design has twelve. The most promising technology currently has only managed to produce four. Considering that eight regular bits corresponds to one letter, that is not much, especially considering the scale of problems that these machines are hoped to tackle. Those problems are, of course, the (partial!) answer to the presenter's preferred question: why to build a quantum computer. These included applications in quantum mechanical models and in large-scale simulations, but perhaps the most compelling case was made for cryptography. A quantum computer can crack pretty much any code set up by a regular electronic computer, and it can set up codes that are completely uncrackable by the same technology (I do not recall whether they might be crackable by other quantum computers, though). Impressive stuff, indeed!

The next talk, on successful societies, was unusual even for this event. Not only was the question posed by CIfAR, but the group tasked to answer it was itself the result of CIfAR's own initiative, rather than (as is the more common case) some independent researcher putting together a proposal for the group. This group is impressively heterogeneous, comprising historians, psychologists, sociologists, economists, and even a biologist or two, and its focus is the same as the Big Question that its representative addressed: "What makes societies succeed?" Of course, such a question is impossible to answer without a definition of "success", and so far the group has spent much of its four years addressing just that, and how to identify it in any given society. I was pleased that the definition was not simply GDP or per-capita income: it had to do with education levels, access to health care, lifespan, and so on. Contrasts were drawn between different countries with similar historical and geographical circumstances but which have had different levels of success, and the reasons for the differences are the focus of this group. The talk brought strongly to mind the work of Jared Diamond and Ronald Wright (the latter's book, A Short History of Progress, I cannot recommend highly enough), as well as more quantitative work by Dalhousie's own Hal Whitehead, all of which carries with it the cautionary message that we must change much about our own society if we do not want it to fail spectacularly.

The final talk, by a professor that I had met but had not gotten to know well at UBC, was about microbial biodiversity. The emphasis here was on the sheer volume of unknown species in existence on Earth, a topic very close to my own heart. Furthermore, although we can characterise the processes that occur on our planet on a global scale, much of the details (such as which organisms do what, how effectively, and what happens when they are perturbed) are a complete mystery. Changes in the oceans' microbial life could have drastic impacts on the world's climate, which we cannot now predict because we have only an inkling of how diverse that life is. At the same time, I did not find the talk very well executed; the speaker was very good, but his understanding of some topics was a little light (he is a virologist, and the sorts of errors that he made about eukaryotes were things that only specialists would catch), and some of his more sweeping statements I thought more dramatic than necessary.

At the end of the three presentations, the audience was asked to vote for what they thought was the "Next Big Question". Given my field of inquiry, I was not at all surprised to be in the midst of a show of hands for the microbe talk; I was surprised, however, at how obvious was the majority of hands from the rest of the auditorium for the same topic. The speaker evidently had impressed his audience, and I did feel some pride in a topic so close to my own being appreciated. I felt a bit of a traitor for it, but I did not vote for that myself. Make no mistake: I am in the right field for me. What I study is more interesting to me than anything else in the world, and I enjoy my labwork immensely. However, my vote went to the societal research, because whatever I might discover or establish will not count for anything if there is not a society around to appreciate it in the future. We as a culture are rapidly approaching the point at which we must change drastically or collapse, and how we must change is a compelling question. What probably clinched the matter for me was that the UN has come to this research group, to ask for recommendations to give to some of those less-successful nations that ask why their neighbours do so much better than they. If there is any chance of this group having any influence, it will be inestimably more important than my own field of study.

That having been said, the vote was all in fun: no decisions were made on its basis, and the funding was guaranteed for each group long before these events were even planned. My personal suspicion was that it was a ploy to keep the audience's attention, although I would prefer to think something less cynical. In any event, it was a good experience, and a nice exposure to a generally good idea -- that of making science more accessible, and more compelling, to the general public.

The Commandments of Science

2007-09-09T04:31:00.000-07:00

I have been reading blogs more than is good for me (and I must admit that writing one is not something that I have time for, either), but every so often I come across something that reminds me that, however much time I may spend on them, I am not (entirely) wasting my time by reading blogs. This example was not a post on a blog: it was a comment. The comments section of a blog post is often more enlightening than the post itself, something not realised by people who only read what shows up on their RSS reader. This particular example was on a post on EvolutionBlog on an interview on Fox News discussing Ken Ham's new Creation Museum. The interview itself was somewhat predictable, and not very noteworthy; the post was mainly there to allow those of us unable or unwilling to watch Fox News see how each side presented itself (a service which is in itself much appreciated!). A commenter called Hoary Puccoon, however, wrote a truly remarkable piece. Since I suspect that this is a pseudonym, and since no Web site or blog was given, I fear that this will fall into undeserved obscurity. (I recognise that my own blog is not likely even more obscure than the comments section of a far better established blog, but at the very least this renders it more prominent to me, and any further dissemination that it can achieve is good.) This is the complete comment, with nothing changed except the formatting.

The whole is-there-a-god thing bores me. But why doesn't anyone emphasize how ethical science is-- and how unethical the creationists look to scientists?
 The Six (and counting) Commandments of Science 
Thou shalt not lie. Fudging data is a mortal sin, enough to terminate one's career.
 
Honor thy fathers. You must give credit to the previously-published work of other scientists.
 
Thou shalt not bear false witness against thy neighbor. Misrepresenting another scientist's work merits public exposure and condemnation. (The creationists never understand just how immoral their quote-mining seems to scientists.)
 
Love thy neighbor. Ad hominem arguments are not acceptable in scientific discourse.
 
By their works ye shall know them. If Linus Pauling is a legend and Watson and Crick are complete unknowns, whose model of DNA is accepted? W&C's-- because theirs is right and Pauling's was wrong.
 
Let your yeas be yeas, and your nays, nays. Scientists must define their variables explicitly, and not fudge and say, 'oh, I really meant something else' if their hypothesis is disproven. (This is actually why theism versus atheism doesn't much matter in practicing science. God, whether he/she/it exists or not, is too fuzzy a variable to produce clear results.)
 This could probably be worked up to ten commandments, but the point is, scientists, whether theists or atheists, do have strict rules of ethics-- which the creationists constantly violate. This point needs to be hammered into the public discourse. The creationists aren't just getting a few dry facts wrong-- they are undermining the entire ethical basis of science. Letting the fundies get away with claiming they represent morality is, in my opinion, morally wrong.

While obviously aimed towards the creation/evolution controversy rampant in the USA, and something that the creationists would do very well to read and understand, it is also absolutely right about how science works. The only change that I would make is one of ordering; some of the more important issues in discussing creationism are almost trivial (or taken for granted) in discussions of science. Each of these points deserves further elaboration, here in an order that makes more sense outside of the creation/evolution discussion.

"Thou shalt not lie." This is absolutely binding in science. There is in science, as anywhere, room for cynicism, but never when one reports data. This is one of the reasons -- the main reason -- why most papers have separate "results" and "discussion" sections. The "discussion" section is interpretation, and there the scientist may be dead wrong (although s/he must support every significant assertion with data, either hir own or someone else's through citation), but the "results" section is pure fact. It is for this reason that scientific data are never published without an accounting of how the data were acquired. Should the data in fact be wrong, repeating the experiments or observations that produced those data will show that. Scientists demand transparency and accountability. Anything worthy of inclusion in the scientific canon must pass through editorial and peer review before publication, the latter process being undertaken by specialists, often the reporting scientists' competitors. Because of this, it is very hard to get away with a deliberate tampering of data (although it does -- very occasionally -- happen). Incorrect data resulting from a misreading of experimental results, or from the application of an incorrect analysis to such results, are generally dealt with graciously by both the discoverer and the scientists reporting those incorrect data. Should something -- anything -- in the "results" section prove to be a conscious fabrication, however, sooner or later, someone will find out, and their perpetrators' careers are over: nobody will take them seriously again. Scientists are unforgiving of frauds.

It is worth noting here that faked-data scandals (including the creationists' favourite, "Piltdown Man") are invariably brought to light by scientists. It is for this reason that science is called "self-correcting".

"By their works ye shall know them." There is a status system in science. This is based, among other things, on credentials, networking, position, seniority, and awards. Status in science is never inherited or bought or bestowed. Everyone in science must work for their status, producing and interpreting data and hypotheses that withstand the most exacting scrutiny. Status ultimately comes from one's ability to do that work. Since anybody -- even a high-school dropout -- can challenge any piece of work (assuming that they have novel interpretations or data, that these make sense, and that they are articulated intelligibly), science is in a sense the ultimate classless society. In other words, one must prove oneself, but anyone and everyone is given the opportunity to do so. If proving oneself means showing that a highly-regarded scientist is wrong, so be it. Science values truth* more than status.
"Thou shalt not bear false witness against thy neighbor." This actually follows from the first two points. One must be honest, and one must acknowledge one's sources honestly. Scientists take a dim view to having words put in their mouths. Intentionally misrepresenting others' work is not as bad as making up one's own, but it is still a grievous breach of ethics. For the most part, it does not happen in science, but when it does, it is quickly established as such, and is thereafter ignored.

Unfortunately, this is not how mass media operates. Non-scientifically-trained writers and editors tend to take things out of context, or to reword things in manners that they may think are paraphases but actually have significantly different meanings scientifically. Corrections in the popular literature often go unregarded, so that a single misinterpretation may plague a scientist for the rest of their career. (The classic example of this is the tendency for creationists to use quotes by the prominent evolutionary biologist Stephen Jay Gould out of context to suggest that he did not believe that evolution was a real thing.) Given the complex and often-conditional nature of their work, many scientists simply refuse to discuss their work with the media. The irony of this is that scientists in general value communication -- which is why they tend to be eager to publish and to teach.
"Let your yeas be yeas, and your nays, nays." Although it may not seem that way to the uninitiated, science demands clarity and simplicity. Much of scientific jargon is essential because it is unambiguous; new terms are always carefully defined before they are used. Of course, words do get redefined, or used in different ways by different scientists; but in such cases, the scientists are always careful to indicate the meanings that they employ.

Scientists are expected to stand by, and to defend, what they present to the scientific community. They may, and often do, change their minds, but they lose respect if they say that they really meant something that they did not say. To use a metaphor often mentioned in the creation/evolution debate, the goalposts may not be moved. Once terms are agreed upon, they may not be changed, and if an explanation fails to account for any given phenomenon under those terms, it must be discarded. The only exception to this is when additional data can be produced to account for the phenomenon under question.

"Honor thy fathers." Citing others' work goes beyond courtesy. If one did not acquire a given datum, one should acknowledge its source. This allows for the data supporting original ideas to be investigated, to determine whether or not they actually apply to the new idea. If one is arguing for or against an idea already articulated in the scientific literature, one should indicate whose idea it is, which allows for arguments both for and against older ideas to be interpreted in the context of the ideas' original construction. It also allows for those whose ideas have been misunderstood or misinterpreted to present their arguments explaining that.

All of this pertains to an aspect of science not commonly appreciated amongst the lay: it is a social enterprise. Many scientists are intensely competitive, but all acknowledge that, ultimately, science is a collaborative process. Everybody has access to, and can use and interpret, everybody else's published data. Progress cannot be made otherwise.
"Love thy neighbor." This is actually not that important in science itself; it is more a question of style than anything else. The expectation actually goes further than this, though. In the scientific literature, one never refers to others except through their publications. All that matters in science is science; the personal lives of individual scientists are irrelevant. Scientists have friends, but friendships are acknowledged at most in the (invariably brief) "acknowledgements" section of scientific papers. Everything else in a scientific publication is regarded as timeless, outside the scope of personal activities and allegiances, and anything that does not directly affect the work being published is omitted. Such matters impede papers' being relevant and understandable indefinitely, which is as close to immortal as any scientist can hope their work to be.

I am fairly certain that I will want to re-order these, probably soon after I hit the "post" button. (Arguments about this order will be gratefully accepted!) I make exceptions for the first and last points, which will always be first and last. But overall, it is a good list (and much tidier than mine in its original presentation). I will be happy to see it get more widespread dissemination. 

* "Truth" is a somewhat dangerous word to use in descriptions of science for the layperson. In science, "truth" is always provisional, "proof" always conditional. This is not to say that scientists are necessarily postmodernists; indeed, I would argue that science is inherently opposed to postmodernism. Rather, scientists accept that the world around them is a real place, and that it operates in a consistent fashion. What scientists regard as "true" is their best understanding of how independently verifiable observations and/or experimental results fit with one another. New observations or experiments may require the re-evaluation, and sometimes indeed the replacement, of established understandings, but such understandings did not become established without having already proven themselves consistent many times over.

Some Thoughts on Immigration

2007-09-01T10:08:00.000-07:00

A while ago, my father and I started to send each other links to political opinion pieces. My responses to his posts quickly grew in length, and I flatter myself to believe that others might find them of interest as well. So, given that I plan on discussing politics on this blog as well as science, I will repost my responses to my father's findings here.

This first article is one about immigration into the USA. This has been a popular rallying point for American conservatives of late; both sides of the issue are certainly prone to agree that there is in fact an issue, that illegal immigration is a problem. The article sent to me by my father, though, presents another angle. Since it is not my work, I will only link to it here; should that link not work, a quick search is likely to turn the article up. It regards the "immigration crisis" in the USA, and compares it to the situation in South Africa. The author, however, seems to think that SA was better off under apartheid, and has a surprisingly negative view of Nelson Mandela. I encourage my readers to read the whole thing first. My response to it follows.

I find this article interesting, in many less-than-complimentary senses of the term. Certainly, there is a germ of truth, but come on: Nelson Mandela is about as evil a man as Ghandi or MLK. Granted, neither of those men resorted to armed conflict, but Mandela has been a paragon of civility, thoughtfulness, and humility after he was released from prison. He has gone so far as to stop his own ANC from censoring references to their violent history. His days of inciting "revolution in the streets, strikes, civil unrest and... sheer terror and murder" are long over, copiously apologised for, and in all likelihood necessary. In the years since apartheid fell, South Africa has continued to be one of the saner places in Africa. Granted, it still has a long way to go, but if I were to settle in Africa, SA springs right to the top of the list of places to check out.

There is a substanatial difference between the USA's "immigration crisis" and SA's apartheid. Most prominently, apartheid was an appalling oppression of native peoples by a colonially-derived minority. The USA, on the other hand, is a nation of immigrants (save for a tiny few natives, hanging on to what shreds of land, culture, and respect have been left them by our colonially-derived majority), and the discrimination of immigrants from anywhere but the places from which the original colonists came has gone on for as long as those original colonists (and their descendants) have been on this continent. We no longer denigrate the Irish, Italians, or Jews, for instance, while Latin Americans were not an issue until recently. The
discrimination has persisted, although its targets have changed. The USA, and its particular flavour of Western culture, did not collapse as a result of a lessening of vigilance against cultural encroachment by any of those groups, and has arguably been strengthened by it.

That having been said, there is a substantial difference between the current and previous "immigration crises", in that Latin Americans come from the same continent, and so are able to arrive under their own power, often illegally. I do not question that this is a problem. However, I also do not see that allowing Latin Americans to immigrate legally will hurt things. We have been very bullish on free trade, generally without consideration of its consequences in other countries. Free trade has resulted in a widening of the gulf between the developed and developing countries, and an inevitable consequence of that is that people in the developing countries will want to move to the developed ones. The only way that free trade can also be made fair for all is if people are also allowed to move freely over borders; until we allow that, we are asking for those whose livelihoods we have rendered harder and harder to want to come here all the more desperately. If we are not to change our trade policies, we will have to deal with these unwanted immigrants one way or another. Like distributing condoms to teenagers or clean needles to drug addicts, I believe that it is better to deal with our problems in a conciliatory but humane and (most importantly) effective manner, rather than repress or deny them.

Do I worry about them changing our culture? Not terribly. One of the things that I have grown to appreciate from living in Canada is the extent to which the USA is truly a "melting pot", in which cultural differences do not persist beyond a generation. Maybe the average skin tone will become a little darker in the USA, maybe Spanish will be a more common language, maybe the percentage of Catholics will rise, but not so much as to overwhelm the current culture. I would go
so far as to say that America's cultural strength comes in large part from its assimilation of other cultures. There will always be those that resist the most prominent group being assimilated at any one time, but what they regard as "normal" contains a good deal of what their parents were resisting before them.

Meanwhile, I found much in this article to reveal more than was perhaps intended. Its author is obviously a social conservative (she puts gay rights in the same basket as pornography, for instance, two "problems" of very different nature). She has a shockingly dim view of non-Whites, implying that they do not share with us a desire to live peacefully and safely. Yes, there are many "primitive" aspects of indigenous African cultures, many of which really should be abolished (female genital mutilation, for instance, or some of the superstitions about health). There are also positive aspects of those cultures; the fact that I may not be able to name them does not mean that they do not exist (I am not an anthropologist, after all!), but I would be very surprised if they were not there. South Africa has many problems, but it is not as "broken" as this author implies, unless one is a white supremacist, as she appears to be.

I did a little bit of Internet research on "Gemma Meyer". This is the only piece of writing available attributed to her, and what is included here is the only bit of biography. She has no entry on Wikipedia. I suspect that "Gemma" is in fact an invention to lend credibility to this piece's reactionary stance. (The reactionary nature is emphasised by its being republished on a neo-Nazi site as well.) The only thing that implies otherwise is the article's lack of American optimism, but I am sufficiently cynical as to suspect this to be an attempt both to give the piece added realism and to spur American conservatives to more concerted action. I may well be wrong, but in any event I do not believe that this author is a reliable source.

Comments are welcomed!

The Meaning of the Word "Opisthokont"

2007-08-26T07:58:00.000-07:00

The name that I have chosen for this blog is bound to be an unfamiliar term for most people. It probably represents an unfamiliar concept as well, so I will start gently. It is a term that denotes a specific, large, and (to humans) very important group of organisms. The importance of the group is probably understandable once one understands that humans are opisthokonts. So, however, are all other animals. So are all fungi! Rounding out the group are a number of single-celled organisms known to be related to either animals or fungi or both. Notably absent from this group are plants, algae, and quite a few other organisms, including all bacteria.

What can animals and fungi have in common that plants do not? Well, think of a sperm cell. This is a tadpole-like thing, with a roughly spherical cell body and a single, tail-like flagellum trailing behind. The cell swims by wiggling its flagellum, again much like a tadpole swims by wiggling its tail. As it happens, this is a very unusual cell type. Most other flagellated organisms swim with their flagella in front, pulling themselves through the surroinding medium. Only the flagellated cells found in animals, fungi, and related microbes swim with their flagella behind. This gives rise to the name: "opistho-" means "behind", and "-kont" refers to the flagellum.

One could easily be forgiven for finding this a minor difference, given everyday experience. To most of us, animals are things that move around and eat things, and plants and fungi are rooted in the ground. However, there are animals that are rooted to the ground as well (including sponges, corals, and sea squirts), and animals that do not eat (such as some of the worms living near deep sea hydrothermal vents). There are fungi that do not grow in the ground (yeasts are fungi, for instance, and do not root themselves in anything). Everyday experience, it turns out, is insufficient to categorise life; science has moved well beyond that.

Science has taken its time to get to where it is today, though. Decades ago, fungi were classed amongst the "lower plants" because their cells are surrounded by rigid cell walls, a characteristic then thought to define a "plant". However, it has since been shown that the materials that make up those cell walls are completely unrelated (they are derived from sugars in plants and from proteins in fungi, for instance). More importantly, the organisms indisputably most closely related to each, which look like single-celled versions of their better-known counterparts, lack any vestige of the cell wall. In other words, the common ancestor of plants and fungi did not have a cell wall; this character is a homoplasy, something that evolved more than once in the history of life.

Genetic analysis confirms this. Most hypotheses of evolutionary history (of extant organisms, anyway) are now made by having computers analyse the DNA of comparable genes from different organisms, and these tend to connect animals to fungi, to the exclusion of plants. (There are exceptions -- there are always exceptions -- but those are from genes with a lot of evolutionary "noise". In other words, such genes are either not large enough or evolve too quickly to retain enough information to resolve the animal/plant/fungus relationship with any reliability. There are statistical tests that indicate the trustworthiness of these computer analyses, and those which are judged acceptable almost always support the close relationship between animals and fungi.)

Analysis of genes goes beyond using them to reconstruct evolutionary history directly. For instance, there is an insertion into one of the genes used in the replication of DNA, an extra stretch of about fifty nucleotides (the "letters" of DNA's "alphabet"), which is found in animals, fungi, and their close relatives, and nothing else. This might not seem particularly important, but the gene in question is important enough that it is not prone to change easily (in scientific parlance, it is "evolutionarily conserved"), and perhaps more importantly, the insertion is itself conserved. In other words, the same nucleotides (or some obvious derivation of them) are present in the same place in all opisthokonts.

Non-genetic data helps link the two groups as well. The architecture of individual cells in the single-celled relatives of animals and fungi is strikingly similar, both inside and out. This was not apparent until the advent of electron microscopy; many of the features that link the two groups are either too small to be seen with a light microscope (the "regular" kind) or are easily overlooked in favour of other, more striking features, many of which (like the cell walls already mentioned) can be taken to imply connections that do not hold up when investigated through other techniques.

These features include the arrangements of the components of the cytoskeleton, a set of protein-based rods and tubes that gives a cell its shape. The arrangement and replication of the flagella is also thought to be a conserved trait. A substantial part of my graduate work is investigating these things; while the coherence of the opisthokonts as a group is nowadays almost beyond question, the uniqueness of some of its defining characteristics is simply not known. Electron microscopy has not been around long enough for much data to have been generated, and most of what has been observed focuses on a few well-known organisms. Those organisms that can tell us the most about the relationships of living things are often obscure and poorly studied, a situation that holds perhaps nowhere more strongly than in this case.

But there is one feature that is readily observed and consistent, and that is the number and position of flagella. Like I mentioned, most organisms have flagella at the front ends of their cells, and pull themselves through their surroundings with them; opisthokonts are unusual in pushing their cells through their surroundings. Furthermore, most non-opisthokont cells have flagella that appear in twos, or are obviously derived from ancestors that had flagella in twos, while all opisthokonts' flagella appear without any others associated with them. These may not seem like significant things, but one must bear in mind that, when discussing the divergence of animals and plants and fungi, we are discussing the evolution of single-celled organisms. In that context, seemingly unimportant things like the position and number of flagella can be highly significant.

So, classifying something as an opisthokont is not a natural thing for most people. It may seem like an obscure and unimportant distinction. Classifying animals and fungi as each others' closest multicellular relatives has (so far) no known consequences to medicine or agriculture or anything else that most people would notice. But the opisthokont hypothesis is, as far as we can tell, an accurate description of the relationships of living things: it is our best understanding of the relevant facts, and the closest that science can come to the truth.

Who I Am

2007-06-24T17:04:00.000-07:00

There is a tradition amongst computer programmers that the first program written in a new language simply displays, "Hello world!" Unsurprisingly, it is referred to as a "hello world" program. In the spirit of pioneering computer geekiness, then, this is my "hello world!"

At the same time, this is not quite my introduction to the blogosphere. I am a long-time lurker at Pharyngula, and I have a LiveJournal account as well, but this is my first foray into the realm of serious blogging. As such, I should introduce myself to the blogosphere as well.

I am an American atheist living in Canada. My political leanings are so far to the left that they do not fit on the American spectrum (in other words, roughly in the middle of the European spectrum). As such, I expect to comment a fair bit on the inanities of the American right wing. Presently I am studying for my Ph.D. in biology, investigating the evolutionary relationships of microbes (for more details, see my posts). I get to play with electron microscopes and sequence genes. It is as much fun as one might imagine!

In fact, I may have quite a lot to comment on very soon. Today is the first day of the big annual conference of the Society for Molecular Biology and Evolution, followed by another two conferences, which will keep me interested and involved for the whole week. I have already attended a fascinating talk on human migration, and chatted with some of the luminaries of my field about my thesis project, and expect much more excitement to come. Stay tuned!