darwin 200


In which a load is lifted

I think I’ve mentioned before that I keep a copy of Burkhardt’s Selected Letters of Charles Darwin handy in the smallest room (“for fun“). In this letter to Asa Gray in November 1857, a load is lifted from Chaz’s mind…

By the way I must tell you what I heard yesterday, though not in your line, but on subject of the crossing of individuals. Barnacles (Balanus) are hermaphrodite & with their well shut up shell offer as great a difficulty to crossing as can well be conceived: I found an individual with a monstrous & imperforate penis, but yet with fertilised ova; but I did not know whether it might not be case of parthogenesis or a strange accident of some floating spermatozoa. Well yesterday I had an account by a man who, watching some shells, saw one protrude its long probosciformed penis, & insert it in the shell of an adjoining individual! So here is a load off my mind.


Origin Ch.15: Polemic

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

There are those who declare Darwin’s literary brilliance, and those who proudly announce that The Origin is beyond their wit and attention span. Occasionally, the truth may be found between extremes: reading The Origin has been frequently fascinating, occasionally a joy, and not infrequently tedious. Chapter 15, however, is nothing but a delight.

Darwin recapitulates his “one long argument”, putting together a brilliant persuasive case. He starts with the objections to common descent and natural selection, admitting that he has “felt these difficulties far too heavily over many years”, before reminding us where the objections fail. Throughout the book, Darwin has made few references to the alternative ideas on the origin of species that had been proposed during his time, but in chapter 15, he openly mocks them: “how inexplicable on the theory of special creation is X, Y, and Z;” “do they really believe that at certain innumerable periods in the earth’s history certain elemental atoms have been commanded suddenly to flash into living tissues?;” “mammals: were they created bearing the false marks of nourishment from the mother’s womb?”

Meanwhile, he constantly reminds us of the power of evolution: “how simply explained X, Y, and Z are on the theory of common descent;” “innumerable other facts at once explain themselves;” “we may cease marveling, and understand on this view…”. He reminds us of some of the many otherwise inexplicable quirks of biology that he can shed light on: his “specific characters”; the honey-bee’s comb; the neuter insects and their social structure; the geographic distribution of species; the structure of different genera; the homologous bone structures of the human hand, bat wing, and porpoise fin; the identical number of vertebrae in elephant and giraffe necks; the branchial slits of mammalian embryos. “It can hardly be supposed that a false theory would explain in so satisfactory a manner as does the theory of natural selection, the several large classes of facts above specified.”

This is the sixth edition of The Origin, and by now Darwin can allow himself a moment to bask in some glory. By the time he got to the sixth, “almost every naturalist now accepts the great principle of evolution,” with only a few old dissenters stuck in their ways. And, knowing how powerful the theory is in explaining the items on his list of quirks, he knows that it will revolutionise biology — “a grand and almost untrodden field will open up” — and even notes how it applies to neighbouring fields like psychology. “Much light will be thrown on the origin of man and his history.” And, in the knowledge that he has made a contribution to science as great as that of Newton, he goes out with the famous bang.

“There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”


Origin Ch.14: Explanatory power

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

It’s getting late in the book, and for a while now Darwin has not so much been explaining and testing his theories, as sitting back and letting his theories do some explaining and testing of their own. It seems to require constant repeating that a scientific “theory” is not a “guess”. A “theory” is a general principle which is supported by a significant and diverse body of data and observations, which stands up to testing, which makes predictions which can be shown to be true, and which has explanatory power. The explanatory power of evolution permeates all branches of biology.

The classic line is that evolution turned biology from a “stamp collecting” science into a modern and productive field. Nevertheless, taxonomists have not been dissuaded from their stamp collecting. In chapter 14, though, Darwin did give meaning to many of their practices and trends. Linnaeus, father of the taxonomic system, was found that there were intuitive ways to place species in groups, and that the relationship between those species was somehow something more than just their shared traits. Darwin showed that this was because taxonomy had intuitively developed into grouping species roughly by how closely they are related by descent, and that evolution, by explaining the patterns of descent, thereby explained many of the quirks of taxonomy. “Community of descent is the hidden bond that naturalists have been unconsciously seeking.”

Evolution explains why we see great variation on the same fundamental body plans, and how those slight morphological variations underpin classification. And so evolution explains why, to the naturalist, it feels right to classify a marsupial mouse amongst its fellow marsupials, even though it superficially resembles the placental mouse. And evolution explains large scale trends, such as why some groups contain so many more species or sub-groups than others.

And evolution explains why, even though there are real distinct groups of species and real distinct groups of those groups, the system of calling those groups orders, sub-orders, families, sub-families, and genera is all so arbitrary — the observable divergence of characteristics and the diversification of groups is highly variable depending on the nature of those groups and their situation, and the non-uniform nature of extinction further complicates things. He uses an analogy to the evolution of language, and it is often claimed (though I am not sure whether it is true or a myth) that English has changed and diversified much more rapidly and extensively than French. (And molecular biologists and genomicists will be pleased that this analogy can also incorporate horizontal transfer.)

And evolution explains mimicry: why two butterflies which, based on the finer details of their anatomy and life cycle, should be placed in very distant groups, even though they look so similar that one can not tell them apart while they swarm. These mimics occur when one species has evolved a defense against predation — foul taste, poison, or a sting — and another takes advantage of the predator’s fear of that species, or rather, any individual which looks like it belongs to that species. And evolution explains why the mimic is always the less dominant species in terms of population than the mimicked. And evolution explains why mimicry is so much more common in insects than in other major animal groups.

And evolution explains why such diverse species as the vertebrates share such similar patterns of early development, and why vertebrate body plans are not entirely different from those of other animals. Today we can take this last principle even further: the field of genomics combines evolution with molecular biology to further explain quirks of classification, such as why bacteria are so hard to classify, why traits can stick together, and how we can be sure that all of the groups of life on earth can, ultimately, be classified into one group, related by descent.


Origin Ch.13: Darwin the experimentalist

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

Two pages into chapter thirteen we get a fantastic image of Darwin pottering in his conservatory, dipping his duck in various fish tanks. Later on the same page he’s keeping a mug of mud on his desk, pulling out the weeds as they come up. At other points in the book we find him cutting out pictures and counting the plants in his lawn. The Origin is not just Darwin writing down his thoughts after 25 years of thinking about the Galapagos. Darwin made sure his argument was solid, and in science, you find the solid ideas by giving them all a good shake, and seeing which ones fall down under the stress. Darwin made hypotheses about how the world might look if his theory is true, and then took a look to see whether the world cooperates.

Darwin’s theory dictated that all individuals within a species are related by descent; species within a genus similarly related, but more distantly; and so on for all life. Darwin observed that there are many fresh-water aquatic species whose individuals occupy many different ponds or streams. He reasoned that if all individuals of a species are related, there must be some mechanism by which individuals from those fresh-water aquatic species have spread from one pond to another. He made a hypothesis: that eggs from these species might stick to the feet of ducks, and thus spread. And so he found himself dipping ducks feet in tanks, and seeing how long the duck’s feet could remain dry while maintaining their ability to seed a sterile tank with pond life. Nowadays he would probably need institutional ethics review board approval for the use of fowl in laboratory research.

Other great practical work from Darwin includes determining the relative areas of igneous, metamorphic, and sedimentary rocks in the United States by cutting up a geological map and weighing the parts; and the time he spent several weeks observing slugs eating weeds (described here by Mike Dunford). And there is one more great experiment that I have heard attributed to Darwin, but for which I can sadly find no credible evidence, and not even at hint in Voyage. The story, told by m’colleague, who in turn has attributed it to a friendly archivist at the Grant Museum of Zoology (UCL), features a young Darwin in the Galapagos spending an afternoon tossing land and marine iguanas into the sea to see how long each could survive in the water. The naive iguanas would inevitably swim straight back to their spot on the shore, never learning to avoid the bastard with the mean overarm who kept throwing them back in. It would be a good experiment to show whether both species could have immigrated to the islands, or only the marine variety.

It’s probably not true. But Darwin was still an ingenious experimentalist.


Origin Ch.12: Noah’s Ark

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

Oh dear, the topic seems to have taken a distinct veer into creationism, around here, and I fear that will not change with chapter twelve of The Origin. This chapter deals with biogeography: the distribution of species and and groups of species across the Earth. Darwin discusses what he has learnt about mechanisms of migration and dispersal of species, and he describes the patterns of geographical occurrence of species.

We take it for granted that Australia has Kangaroos and Koalas, South Africa has lions and giraffes, and Uruguay has Capybaras and Armadillos. But it’s an observation that demonstrates the explanatory power of evolution as the overarching theory in biology. When you know that species arise by descent with modification, the geographic isolation of species, and of groups of species, makes sense. Marsupials evolved from a common ancestor on an isolated continent, and so they remain largely restricted to Australia. Similarly the Xenarthra (sloths, anteaters, armadillos) and the Cavies (Patagonia hares, Guinea pigs, and capybaras) are restricted to the Americas.

Other historical hypotheses for the generation of species did not have any such explanatory power. Spontaneous generation could not explain why three countries with relatively similar climate and conditions, but divided by continent, should have such vastly different flora and fauna. Nor would it explain why the marsupial mammals should all spontaneously generate in Australia, and none of the placental mammals do so. But there is one alternative hypothesis which epically fails when it comes to biogeography: the book of Genesis.

The book of Genesis describes a great flood sent by God in the 3rd millennium BC to destroy all life. Noah, a sprightly middle-aged six-hundred year old, thought God’s genocidal plans a great lark, and dutifully built a big boat for his family and a couple from any animal species which happened to be within seven days walking distance. After forty days of flooding, the water receded, presumably revealing great plains of dead animals and vegetation, killed by their drowning in the salty water. The boat then grounded in a mountainous region of eastern Turkey as the waters receded.

At this point, the Kangaroo bounced off back to Australia. The Capybara waddled home to South America, and the polar bear sweated his way up to the arctic. Apparently the rancid decaying victims of God’s temper were sufficient to sustain the individuals on their journey, as we can know from the fact that they survived to repopulate their species. And the geographical features which now prove insurmountable for the migration of species — such as the Atlantic Ocean — were no challenge for the three-toed sloth.

M’colleague put this to Answers In Genesis’ Paul Taylor at Skeptics in the Pub one time. I think Taylor’s response went something along the lines of, “oh, er,uhm, well, the water wouldn’t have been that salty.”


Origin Ch.11: Where the fossil record went right

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

The creationist site that I briefly reviewed yesterday repeated the claim that the fossil record does not support descent with modification, and that Darwin could only handwave about the imperfection of the fossil record. Clearly the author got to chapter ten of The Origin but had difficulty getting any further, because chapter eleven is exactly where Darwin addresses this question: “that the extinct forms of life help to fill up the intervals between existing genera, families, and orders, is certainly true; but as this statement has often been ignored or even denied, it may be well to make some remarks on the subject, and to give some instances.” Far from desperately covering up an embarrassment, Darwin is embracing the rich evidence provided by the fossil record.

In a few cases, history shows that Darwin made some relatively minor mistakes. In his response to geological catastrophism, for example, Darwin could perhaps be charged with going too far the other way, and denying that mass extinctions occur (though such events present no problem for the theory). But generally, Darwin presents a good introduction to why the fossil record is firmly on his side, listing for several pages groups for which interesting ancestral and “intermediate” fossils were already known. More importantly, in chapters 10 and 11 he turns the fossil-record burden back on his detractors. For their objection to hold, the creationists must believe either in the absurd proposition that our knowledge of the fossil-record is already complete, or must constantly divide their God over ever smaller gaps of incredulity.

Darwin is not the prophet of evolution. Attacking his character is irrelevant, and pointing out that he could not answer every objection in The Origin does not mean that those objections hold up today. And yet, reading The Origin one is struck repeatedly by how relevant the book remains in the context of creationism — not just because the creationists still attack it, but because Darwin had already answered so many of their objections in the book. The fossil record objection is as old as the theory of evolution, and is still parroted by the unimaginative, yet even with the limited resources of 150 years ago, Darwin was able to pretty conclusively trash this and so many of the other familiar canards that creationists just won’t allow to die.


Having a BLAST with Darwin

-or- “(One of many reasons) Why genomics matters”

This is an archival repost which was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

In chapter 14 of The Origin Darwin discussed embryological stages and their utility in classification. This utility derives from the fact that in animals phenotypic variation between species is less complicated at earlier developmental stages, and less influenced by what Darwin calls “special habits”. In some cases, this principle can be taken to extremes. Today, we refine species classification using the gold-standard method of comparative genomics. Comparative genomics involves matching up the As, Cs, Gs, and Ts of orthologous sequences (that is, sequences related by descent in now separate species) and highlighting where the genes have diverged. But sometimes, the most interesting finding is where the genes have not diverged.

The genomes of animals are stuffed full of sequences which have no obvious purpose, and in which mutation seems to be able to run free without consequence. Over evolutionary time, these sequences are buffeted by random processes, and as species diverge, so these sections of their genomes drift apart. Buried in amongst all of this nonsense, though, are functional sequences, including genes. In these functional sequences, mutations and variation might have all sorts of phenotypic consequences, and genomic variations which have consequences can be subject to selection. There is a tendency, therefore, for such sequences to show very different patterns of variation between species to that of the “junk” sequences. These patterns can reveal important principles in biology, and the patterns themselves are discovered by comparative genomics.

One of the most notorious finds is the homeobox motif.[1] This motif is a gene-subsection found in a set of genes called Hox genes, and it has the rare distinction of being found in such distant groups as vertebrates and insects with an almost identical sequence – it is therefore said to be highly “conserved”. The sequences vary only in that they contain “silent mutations”. Due to the redundancy of the “genetic code”, which maps the 64 possible triplets of nucleotides – gene letters – to the twenty commonly used amino acids – protein letters – many mutations within genes will make absolutely no difference to their carrier’s phenotype, and thus go unnoticed by selection. Such mutations are said to be “silent”. Darwin may have been interested to learn that the Hox genes, which contain this famously conserved motif, happen to be key in determining the layout of the body early in development. There is genetic conformity to match the phenotypic conformity in early development.

But the sequences encoding proteins are not the only important functional sequences in the genome. There are plenty of sequences associated with genes – regulators of gene expression, for instance – and a few interesting things that are not associated with genes at all. “Cis-regulatory regions”, for example, are found beside genes, and contain sequences which enable enzymes to attach themselves to the DNA and initiate gene expression. During the past decade, interesting patterns of conservation have been discovered in the cis-regulatory regions associated with many genes, and especially with key developmental genes. These cis-regulatory sequences do not directly map to protein sequences, and so they can not contain “silent mutations” in the sense that protein coding regions can. But these sequences can be conserved. They can be very highly conserved. They can be ultraconserved![2][3] Sanderlin, et al found in 2004, for example, “ultraconserved” cis-regulatory sequences over 1000 bases in length which were identical in human, mouse, and pufferfish, and over 3,500 perfectly identical regulatory regions of 50 bases or more.[4] Those numbers might mean nothing to you, but the bottom line is that if genomes were essays, somebody would be in front of a plagiarism tribunal right now.

In BMC Evolutionary Biology, last year, Lin et al[5] described a novel collection of ultraconserved regions (UCRs) that they stumbled upon in the Hox genes of placental mammals. These particular UCRs were not found in the cis-regulatory regions, but are the first to be found in the protein-coding sections of genes. The URCs are at least 125 bases in length, and are identical in humans, dogs, and mice – indeed, they actually show a greater degree of identity in these species than does the famously conserved homeobox. Lin et al can not yet explain the importance of the UCRs that they have found, but it is reasonable to assume that important they must be. The thing I find particularly interesting about their story, however, is how the UCRs were found and investigated. Lin et al stumbled upon the conserved regions while looking at a different question – the divergence of Hox genes in mammals. They had retrieved the sequences of orthologous Hox genes for mammalian species such as human, chimp, cow, dog, duck-billed platypus, macaque, mouse, opossum, and rat, along with chicken, pufferfish, and zebrafish for comparison. These are all species whose genomes have been sequenced and made publicly available in government funded databases. Lin et al used a clever search engine called BLAST to find all of the Hox genes of these species, and then used a classic piece of bioinformatics software, ClustalX, to “align” all of the genes and point out where they do and do not vary between the species.

Why do I get excited by BLAST and ClustalX, the workhorses of computational biology? Because it’s little studies like this which serve to remind us of why genomics and computational biology are important. Genomics it seems has still not recovered from accusations of being overhyped after the biotech bubble burst a decade ago; and computational biology gets all kinds of slander thrown at it – a discipline churning out unreliable results to be dismissed, or a field to turn to in desperation as laboratory studies refuse to give you the answer you want. Perhaps, when you’ve slaved for years as a student and had to fight for the funding to maintain a laboratory, there is something a little frightening about research that requires just a PC, an internet connection, and a clever idea. But Lin et al discovered a whole new category of ultraconserved genomic regions right under the noses of the hundreds of molecular and developmental “wet” biologists who work on these hugely important Hox genes, using just some everyday software, the bulk raw data of genome projects, and the wit to spot an interesting pattern.

BLAST and ClustalX are exciting because with just a sequence alignment, you can demonstrate again and again, in an almost endless variety of ways, just how right and how powerful the theory of evolution is.

References

  1. ^ Woltering J, and Duboule D: Conserved elements within open reading frames of mammalian Hox genes. J. Biol. 2009 8:17. doi.
  2. ^ Dermitzakis ET, Reymond A, Antonarakis SE: Conserved non-genic sequences – an unexpected feature of mammalian genomes. Nat Rev Genet 2005, 6:151-157.
  3. ^ Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D: Ultraconserved elements in the human genome. Science 2004, 304:1321-1325.
  4. ^ Sandelin A, Bailey P, Bruce S, Engström PG, Klos JM, Wasserman WW, Ericson J, Lenhard B: Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 2004, 5:99. doi
  5. ^ Zhenguo Lin, Hong Ma, Masatoshi Nei (2008). Ultraconserved coding regions outside the homeobox of mammalian Hox genes BMC Evolutionary Biology, 8 (1) DOI: 10.1186/1471-2148-8-260

Disclosure: I work for the publisher of three of the journals cited, and handled one of the papers (Lin, 2008). All opinions are my own, this post was written on the train, not in the course of duties, no privileged detail that can’t be found in the paper was disclosed, etc, etc.


Origin Ch.10: Darwin the geologist 1

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

Chapter ten is supposed to be a response to the objection that if evolution were true, one ought surely to be able to reconstruct its historical course with our fossils. It’s an objection that can very easily be addressed, on two fronts — firstly, that we can reconstruct much evolution with fossils (though this is a lot more true today than it was when The Origin was written), and secondly that the fossil record is a long way from perfection. Even when Darwin was writing, it was well established that only a tiny fraction of individuals will ever present themselves for fossilisation; that some species will never — can never — end up represented in the fossil record; that fossils have been and are being destroyed without ever being recorded by science; and that the overwhelming majority of fossils will remain hidden in the ground forever.

So if it’s so easy to rebut the objection, why does Darwin devote a whole chapter to it? Probably because he’s a geology nerd. The imperfection of the geology record isn’t the real point of the chapter, Darwin just wants an excuse to chat about rocks. And rocks are important in the story of Darwin and evolution for reasons other than the fossil record. You can find these reasons in reading Voyage of the Beagle or the letters he sends back to mentor John StevensHenslow from the ship. Darwin isn’t just looking at the botany and zoology of South America on the voyage, he is spending at least as much time documenting the geology. And why shouldn’t he? Why do mere stamp collecting — or beetle collecting — when you can work in a field that has the beginnings of explanatory theories? Why look at isolated cases when you can look at processes and events?

Geology had taken those first steps to maturity. Rather than being the unaltered creation of the almighty, the Earth had become an unimaginably ancient planet whose stasis could not be relied upon, and ideas like these did seem to impress the young Darwin. And Darwin went on to take the stamp collecting field of biology and turn it into a modern science with a core overarching theory. And yet it would be nearly another half century before a core theory — plate tectonics — would complete the transformation for geology.


Origin Ch.9: Recombination

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

In chapter nine, Darwin takes a long look at hybrids. And I mean a long look: he can really go off on one when he’s enthusiastic about a subject. After all of those chapters on natural selection, I could not at first understand why the topic of hybridisation came up — thirty pages just to explain why hybrid sterility can not be an adaptation? — before I remembered that Darwin’s remit is to explain the origin of species, not just the process of natural selection.

A major point of the chapter is to explore the proposed idea, which Darwin had once found attractive, that the sterility of hybrid species is an adaptation. It was proposed that the sterility of hybrids was beneficial as it prevents different varieties blending together, diluting incipient species. Darwin puts across the evidence for hybrid fertility being a much more complicated situation, and one not suggestive of sterility being an adaptation. But he could have skipped the dry details and gone straight to the bit where he points out that, since evolution requires reproduction, deliberately reducing one’s legacy is not likely to be adaptive: “… now, what is there that could favour those individuals which happened to be endowed in a slightly higher degree with mutual infertility?” The argument for hybrid sterility being adaptive is a group- or species-selectionist one. (Actually, it might be possible to imagine that, under certain very restricted ranges of conditions, kin selection could favour hybrid sterility — nevertheless, in general Darwin’s argument stands.)

More interestingly, Darwin goes on to hint at the actual mechanism of and “reason” for hybrid infertility. It is not adaptive, but, as we now know, it is merely a constraint of the way that genomes are organised and development progresses. As Darwin notes, first (F1) generation hybrids are quite capable of producing gametes (egg and sperm), but the second (F2) generation produced from F1 gametes tend to fail somewhen during development. We now know that the process of recombination, which occurs during the production of gametes is one key to understanding this.

Our genomes consist of one set of chromosomes inherited from each of our parents. When gametes are produced, these need to be cut down to a single set that we pass on (otherwise the genome would double in each generation!). In recombination, the chromosome you inherited from your mother is lined up with its counterpart inherited from your father. The two contain pretty much the same genes in the same order, though there may be some within-gene variation between them. Sections of the chromosomes are then “crossed over” and shuffled between them, and the result is a new chromosome containing the same genes, in the same order, but in a novel combination of varieties.

Recombination causes a problem in hybrids, because the chromosomes of, say, a horse and a donkey, may have diverged, and might no longer contain the same genes in the same order. The F1 mule develops fine — it has a complete copy of both genomes — but a chromosome produced during the production of gametes in that mule might be missing genes crucial for development, or contain too many copies of some genes. Development is achieved through complex and sensitive systems of gene expression, and when genes go missing, or their numbers get upset, these systems are liable to fail, and, in the case of animals, the developing F2 embryo will miscarry.


Origin Ch.8: Instincts

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

In chapter eight, Darwin looks at instincts. Instincts are subject to the same processes of variation and heredity as everything else in life, so obviously they are subject to evolution. Rather than catalogue lots of examples of instincts as adaptations, Darwin focuses on three case studies which represent especially complicated or problematic instincts, but which Darwin sets out to show are clear examples of adaptation by natural selection. These are the cuckoo’s exploitation other birds in the fostering of young; the honey-bee’s skills in constructing perfect wax cells; and the complex habits of ants, particularly their symbiotic relationships with other species.

When it comes to instinct and behaviour, it’s difficult to keep one’s communications clear, concise, and objective: it’s almost impossible to avoid connotations of purpose, forethought, and consciousness in the language that we use to describe animal instincts and their evolution. Darwin is soft on and forgiving of the cuckoo: the poor dear can’t help being a parasite on bird society, she has to dump her kids on other birds because she’s just popping them out all over the place, and could never take care of them all herself. And, sure the offspring, before they can even open their eyes, push their foster siblings out of their foster nest, in order to get the undivided attention of their poor foster parents. But what you don’t realise is that this is a beneficent arrangement, because the cuckoo is kind enough to butcher his foster brothers and foster sisters while they’re still young to suffer greatly while they die.

But Mr Darwin is no softie on ants. The accepted terminology for the sort of relationship where one species of ant exploits the labour of another species of ant in the nest was that this is a “master” and “slave” relationship. Darwin does his best to make a disinterested study into the ants’ “remarkable” instincts, but can not help passing a few judgements. After some big ants get into a fight with some little ants, the “tyrants” run off with the little ants’ pupae. Meanwhile some masters go on expeditions to “ravage” the homes of other ants, searching for potential slaves. And the poor slave species run around in “despair”. I don’t believe the claims that Darwin was motivated in his work by his hatred of slavery. His motivation, I would hope, was to seek the truth. But I think he let his political leanings show in the half-hidden asides.


Origin Ch.7: Adaptation

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

In chapter seven, Darwin responds to some more objections to his theory of natural selection. One such objection is that “many characters appear to be of no service whatever to their possessors, and therefore cannot have been influenced through natural selection.” Darwin acknowledges that there may be other processes at play in evolution — he believes that “spontaneous variability” has been under-rated, for example — but he says, “it is impossible to attribute to this cause the innumerable structures which are so well adapted to the habits of life of each species.” The illusion of design can be explained only with the aid of natural selection.

Darwin goes on to explore specific versions of this objection in more detail, and provide explanations for how they can have arisen by natural selection — not mere “just-so stories”, but explanations that can stand up to testing. One such case-study is the apparently random variation in ear and tail size between species of mice: how could natural selection be bothered with these trivial details? These organs turn out to be well endowed with nerves which allow them to act as tactile organs, and the differences in size may therefore be explained as adaptations to the different situations that different species of mice find themselves in.

The life sciences were torn over questions of natural selection and adaptation throughout the second half of the twentieth century, and there are still bitter feelings amongst the veterans. In the 1960s, the likes of George C Williams further developed the principle that natural selection is the only process that can account for the creation of complex traits which appear designed, and introduced methods for identifying adaptations and investigating them. These ideas, and the power of natural selection to explain the design illusion, were popularised by Richard Dawkins, who passionately promoted natural selection at the level of the gene, and argued against other ideas and proposed evolutionary processes which were then popular, such as a group selection.

Since then, other scientists and writers, interested in a variety of other questions in the life sciences, have championed many other processes that are important in evolution. Stephen Jay Gould, for example, was a prominent champion of the role of chance events and accident in the history of life — like the extinction of the dinosaurs allowing the rise of mammals. And there have been huge advances in fields from population genetics to molecular biology and genomics, which have identified new features and processes, most notably genetic drift — random drifting of gene frequencies in populations, unaffected by selection. Gould and geneticist Richard Lewontin also identified a genuine reason why the illusion of design might not always represent adaptation — the famous case of the spandrels, an analogy to an architectural feature that serves no purpose, but simply has to exist as a result of the surrounding features.

I have the benefit of having arrived on the scene after the so-called “Darwin wars” over these issues had died down, and each side had mostly conceded the other’s points. The battles often appear more about ego than substance, and seem to have arisen due to the fact that evolutionary biology is not concerned with just one question, but several. Chance events have become firmly established as important in describing how evolution unfolds over time — in the question of the origin of species. But, with only minor concessions for the likes of spandrels, Darwin’s greatest idea, natural selection, remains the solution to the other great problem: the illusion of design. He was right to defend it so in chapter seven.


Origin Ch.6: Down the quote mines

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

Chapter six is where Darwin humbly acknowledges that his work is not entirely watertight, explains some of the problems that have been noticed and objections raised, and then goes on to demonstrate why the objections are all wrong. It’s particularly notable for the passage explaining the evolution of the eye, in which Darwin explains just how moronic the still pervasive creationist argument from apparent design is. That’s why it’s so shocking that some creationists are so pathologically dishonest and tragically incompetent that they quote one line from this anti-creationist passage — “to suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.” — as being Darwin’s admittance of defeat in explaining the origin of complex traits.

But as several people have noted, even those readers of The Origin who have a grounding in reality are just getting out of the book whatever they want to get from it. The book was written 150 years ago, in the style of its time, and in a different intellectual context, after all. We are not quote mining, but neither are we really stating the facts as Darwin saw them. We think that we spot ideas that look very prescient of major principles in biology which weren’t developed until after Darwin’s time — but can we be sure that’s not just an invention of our modern informed selves? And, primed with myths from many varied sources, surprise surprise, our reading of the book conforms to those myths. Like my opening remark: Darwin was a humble man?

Simon Conway Morris and Larry Moran suggest that the “doubts” that Darwin raises are a rhetorical trick: he is sarcastically agreeing with his detractors in order to demolish them. Darwin knows very well that his argument is a strong one, and his opponents’ demonstrably flawed. He has no need to lack confidence, and indeed he does not. I can fully believe this theory.

But this does not mean that Darwin was not a humble man. Whether the man knew he was right, and whether he was humble about it, are two very different questions. Darwin did allow himself a rare moment of glory in the closing passage of the book, acknowledging that he had discovered some of the most important principles in science. But he was no Craig Venter.


Chas bloody well deserves his party

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

What’s all this backlash nonsense about? We’re getting essays telling us to forget about Darwin (ironic coming from Steve Jones, who has probably occupied more column inches and more airwave hours on the topic of Darwin than everyone else put together other the past month or two); people telling us to stop worshiping Charlie; and then this on FriendFeed this morning. It’s cool to be contrarian, apparently.

Well bugger the party poopers. They might be worried about a simple celebration of the life of a great and good man being painted as a the atheist religious holiday, or as being at the expense of everyday scientists, or whatever other perceived consequence they have invented, but those are no excuses to spoil the party. If it were Newton, Galileo, or Einstein’s 200th, there wouldn’t be this issue — indeed, it isn’t an issue for the Gelileo-Keplerists over at International Year of Astronomy — but for some reason it is a different story for Darwin and evolution. We have to be careful not to do anything that might feed the creationists; not to make Darwin our secular god and evolution our secular religion.

Well bugger that. Didn’t you know that when you start changing your habits just because of the creationists, they’ve already won? (Or is that terrorists? I forget.) I for one will be raising a glass this evening to biology legend, international roaming geologist, fourth-place runner-up greatest Briton of all time and winner of best facial hair in class, south-east region, 1860, 1869, and 1877, Chas Darwin.


Origin Ch.5: Drift

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

It has been noted enough times now that Darwin knew nothing of genetics, and I already described Darwin’s bizarre Lamarckian hypothesis for why some domestic animals have droopy ears (they don’t need to prick them up to listen out for predators or prey, so they are lazy and let the muscles waste). But in chapter five, Darwin goes into a little more detail about the loss of previously evolved traits. “Natural selection is continually trying to economise every part of the organisation,” he says. And, “natural selection will tend in the long run to reduce any part of the organisation, as soon as it becomes, through changed habits, superfluous.”

This might be — indeed, almost certainly is, to some extent — true. But we don’t need to posit active selection to explain dereliction of traits. If you take out the Lamarckian tones of the ear-disuse hypothesis, there might actually be something in the idea. Indeed, from our modern understanding of biology, the most parsimonious explanation for the droopy ears of some domesticated animals may well be that strong and structured upright ears became superfluous for survival. The mechanism would not be laziness causing heritable muscle wastage, though. Rather, it is random mutation, coupled with that oft neglected evolutionary process, genetic drift.

Random mutations are appearing all the time, and, silent mutations aside, probability is more on the side of such mutations destroying complex traits than developing them. In the absence of any stabilising selection to maintain that complex trait, the new variant alleles will be randomly buffeted around the gene pool, perhaps dying out, or perhaps spreading. This is one of the many reasons why we can be confident that humans are still evolving: if it true that advances in agriculture, technology, medicine, and culture, have lifted selection pressures on some traits, it follows that genetic drift will have been unleashed in their place. We are rightly celebrating Darwin’s great discovery of natural selection, but don’t forget that there are other important evolutionary processes.


Darwin, desperate for a cure

This post is part of a series on The Origin Of Species.  It was originally posted on the old blog in feb 2009, during the Darwin 200 celebrations.

I’ve not been up to writing anything new and insightful today. I’ve not been feeling so good or thinking so efficiently, after standing around in the cold and wet, and crowded trains full of bugs. Nothing big — nothing like the chronic illness that plagued Darwin, and interrupted his work, as evidenced in this fantastic letter from Darwin to his sister, as reproduced in Burkhardt’s marvelous collection Origins.

For three and a half months in the spring of 1849, Darwin packed off to the spa town of Malvern for some relief from his illness. In Malvern he received a couple of quack treatments: hydrotherapy and homeopathy. The former has died out, but the latter remains popular, despite the ridiculousness of it being perfectly apparent 160 years ago. In the letter, Darwin describes his disdain for the “remedy”, and notes the homeopath’s hypothesis that Darwin’s mysterious ailment may have its origins in his upper spine. I immediately wondered whether there was an element of another form of quackery here — chiropractic — before it occurred to me that it would be another fifty years before that particular brand of nonsense was created.

Darwin, incidentally, believed that he received a great amount of benefit from the cold water cure. Of course, he would not have been familiar with the placebo effect.

Malvern

Monday

My dear Susan.

As you say you want my hydropathical diary, I will give it you—though tomorrow it is to change to a certain extent:

1⁄4 before 7. get up, & am scrubbed with rough towel in cold water for 2 or 3 minutes, which after the few first days, made & makes me very like a lobster— I have a washerman , a very nice person, & he scrubs behind, whilst I scrub in front. Drink a tumbler of water & get my clothes on as quick as possible & walk for 20 minutes—I could walk further, but I find it tires me afterward— I like all this very much.— At same time I put on a compress, which is a broad wet folded linen covered by mackintosh & which is “refreshed”—i.e. dipt in cold water every 2 hours & I wear it all day, except for about 2 hours after midday dinner; I don’t perceive much effect from this of any kind. After my walk, shave & wash & get my breakfast, which was to have been exclusively toast with meat or egg, but he has allowed me a little milk to sop the stale toast in. At no time must I take any sugar, butter, spices tea bacon or anything good. At 12 o’clock I put my feet for 10 minutes in cold water with a little mustard & they are violently rubbed by my man; the coldness makes my feet ache much, but upon the whole my feet are certainly less cold than formerly. Walk for 20 minutes & dine at one. He has relaxed a little about my dinner & says I may try plain pudding, if I am sure it lessens sickness.

After dinner lie down & try to go to sleep for one hour. At 5 o’clock feet in cold water, drink cold water & walk as before. Supper same as breakfast at 6 o’clock. I have had much sickness this week, but certainly I have felt much stronger & the sickness has depressed me much less. Tomorrow I am to be packed at 6 o’clock a.m. for 1 & 1⁄2 hour in blanket, with hot bottle to my feet & then rubbed with cold dripping sheet; but I do not know anything about this. I grieve to say that Dr Gully gives me homoeopathic medicines three times a day, which I take obediently without an atom of faith. I like Dr Gully much—he is certainly an able man: I have been struck with how many remarks he has made similar to those of my Father.

He is very kind & attentive; but seems puzzled with my case—thinks my head or top of spinal chord cause of mischief. He has generously allowed me 6 pinches of snuff for all this week, which is my chief comfort except thinking all day of myself & prosing to Emma, who bless her old soul, thinks as much about me as I do even myself. I am become perfectly indolent which I feel the oddest change of all to myself & this letter is the greatest mental effort done by me since coming here. My dearest sisters I wish I could see you here. I saw absolutely nothing of you at Down & never talked about my dear Father about whom it is now to me the sweetest pleasure to think, which I fear cannot be your case as yet.

My dears | Yours affectionly | C.D.