Copy Number Variants are not evidence of design

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The Institute for Creation Research has a charming little magazine called “Acts & Facts” that prints examples of their “research” — which usually means misreading some scientific paper and distorting it to make a fallacious case for a literal interpretation of the bible. Here’s a classic example: Chimps and People Show ‘Architectural’ Genetic Design, by Brian Thomas, M.S. (Note: this is not the peer-reviewed research paper implied by the logo to the left — that comes later.) The paper is a weird gloss on recent work on CNVs, or copy number variants. Mr Thomas makes a standard creationist inference that I have to hold up for public ridicule.

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A Natural History of Seeing: The Art and Science of Vision

Simon Ings has written a wonderful survey of the eye, called A Natural History of Seeing: The Art and Science of Vision(amzn/b&n/abe/pwll), and it’s another of those books you ought to be sticking on your Christmas lists right now. The title give you an idea of its content. It’s a “natural history”, so don’t expect some dry exposition on deep details, but instead look forward to a light and readable exploration of the many facets of vision.

There is a discussion of the evolution of eyes, of course, but the topics are wide-ranging — Ings covers optics, chemistry, physiology, optical illusions, decapitated heads, Edgar Rice Burroughs’ many-legged, compound-eyed apts, pointillisme, cephalopods (how could he not?), scurvy, phacopids, Purkinje shifts…you get the idea. It’s a hodge-podge, a little bit of everything, a fascinating cabinet of curiousities where every door opened reveals some peculiar variant of an eye.

Don’t think it’s lacking in science, though, or is entirely superficial. This is a book that asks the good questions: how do we know what we know? Each topic is addressed by digging deep to see how scientists came to their conclusion, and often that means we get an entertaining story from history or philosophy or the lab. Explaining the evolution of our theories of vision, for example, leads to the story of Abu’Ali al-Hasan ibn al-Hasan ibn al-Haythem, who pretended to be mad to avoid the cruelty of a despotic Caliph, and who spent 12 years in a darkened house doing experiments in optics (perhaps calling him “mad” really wasn’t much of a stretch), and emerged at the death of the tyrant with an understanding of refraction and a good theory of optics that involved light, instead of mysterious vision rays emerging from an eye. Ings is also a novelist, and it shows — these are stories that inform and lead to a deeper understanding.

If the book has any shortcoming, though, it is that some subjects are barely touched upon. Signal transduction and molecular evolution are given short shrift, for example, but then, if every sub-discipline were given the depth given to basic optics, this book would be unmanageably immense. Enjoy it for what it is: a literate exploration of the major questions people have asked about eyes and vision for the last few thousand years.

The radiation of deep sea octopuses

Last week’s Friday Cephalopod actually has an interesting story behind it. It was taken from a paper that describes the evolutionary radiation of deep-sea cephalopods.

First, a little background in geological history. Antarctica is a special case, in which a major shift in its climate occurred in the last 50 million years. If you look at a map, you’ll notice that Antarctica comes very close to the southern tip of South America; 50 million years ago, they were fully connected, and they only separated relatively recently due to continental drift.

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An audio advent calendar

The New Humanist blog is running an advent calendar podcast, in which various people are asked what scientist they’d like to have a Christmas-style celebration around, and what invention from scientific history they’d most like to receive for Christmas.

First up is Stephen Fry, who made the interesting choice of Robert Hooke — I approve, he’s an interesting character — and all he wants for Christmas is an orrery.

You’ll have to listen every day. I’m going to be in there somewhere, and Richard Dawkins gets to be the Christmas eve fairy.

Interpretive dance, really?

Whoa. It’s kind of a standing joke that when our presentation tools fail us, we’ll have to fall back on interpretive dance to make our points. We never mean it seriously, though. Until now. Science magazine challenged researchers to actually illustrate their work with dance, and people did! There are four youtube videos at that link that show the winners. I liked the graduate student entry best, but I’ll include this one because a) it was most comprehensible to me, and b) Laurie Anderson is wonderful.

You will never catch me doing this, though — I can’t dance, and I’m too ungainly anyway.

Odontochelys, a transitional turtle

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Now this is an interesting beast. It’s a 220 million year old fossil from China of an animal that is distinctly turtle-like. Here’s a look at its dorsal side:

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a, Skeleton in dorsal view. b, Skull in dorsal view. c, Skull in ventral view. d, Body in dorsal view. Teeth on the upper jaw and palatal elements were scratched out during excavation. Abbreviations: ar, articular; as, astragalus; ca, calcaneum; d, dentary; dep, dorsal process of epiplastron; dsc, dorsal process of scapula; ep, epiplastron; fe, femur; fi, fibula; gpep, gular projection of epiplastron; hu, humerus; hyo, hyoplastron; hyp, hypoplastron; il, ilium; ipt, interpterygoid vacuity; j, jugal; ldv, last dorsal vertebra; m, maxilla; n, nasal; na, naris; op, opisthotic; p, parietal; phyis, posterolateral process of hypoischium; pm, premaxilla; po, postorbital; prf, prefrontal; q, quadrate; sq, squamosal; st, supratemporal; sv1, 1st sacral vertebra; ti, tibia; ul, ulna; vot, vomerine teeth; I, V, 1st and 5th metatarsals.

Notice in the skull: it’s got teeth, not just a beak like modern turtles. The back is also odd, for a turtle. The ribs are flattened and broadened, but…no shell! It’s a turtle without a shell!

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Understanding Darwin: The legacy of evolution

As I’ve already mentioned, I was off in Philadelphia this past weekend, participating in a symposium entitled “Understanding Darwin: The legacy of evolution”. I was a bit amazed to be there, since this was primarily a history and philosophy event with several big names in those fields, and I’m an itty-bitty biologist with more of a popular following than an academic one, but I was also glad to be involved and learned quite a bit, hob-nobbing with the big shots. Here’s a short summary of the content of the talks.

John Beatty talked about Natural Selection of & Versus Chance Variation. He began with a discussion of Gould’s classic metaphor of ‘rewinding life’s tape’ and asking what would happen on replay. Recently, everyone thinks of Lenski’s experiments with bacteria in this context, and Beatty discussed those, but he also pointed out that Darwin’s studies of orchid morphology are also beautiful examples of developmental contingencies, of diversity by chance. That stuff is going to end up in one of my Seed columns soon, I think.

Rasmus Winther gave an overview of systems thinking in a talk titled Systemic Darwinism. He made the case that there are three different kinds of evolutionary thinking: evolutionary genetics, where we’re concerned with gene frequencies over time, cladistics, which is all about changes in character state distributions over time, and self-organization, or change in the organization of parts over time (that last, I thought, was a rather peculiar definition). Darwin, while lacking the specifics of modern fields like genetics, seems to have been a good systems thinker, who tried to address different modes of thought in his own work.

This guy PZ Myers rambled on about Haeckel, embryos, and the phylotypic stage. He tried to make the self-evident case that there are some simple facts, observations of embryo similarities, and that there are interpretations of those facts, which ranged from Haeckel’s recapitulation to von Baer’s differentiation from the general to the specific to more modern models of global gene regulation, and that we have to be careful not to let models overwhelm the data (Winther phrased it succinctly: watch out for the reification of abstractions). I contrasted the errors and excess of zeal of someone like Haeckel with modern creationist mangling, which is malicious and unscholarly, and tries to deny the observations.

Jane Maienschein discussed Embryos in Evolution and History. I had already run roughshod over a chunk of her talk—we both talked a fair bit about Ernst Haeckel—but she had much more breadth to her story, since she also brought in Entwicklungsmechanik and 20th century embryologists and developmental biologists. Rather than railing against the affront of creationism in contemporary science, she focused on stem cell research, and how it is changing earlier preconceptions about the nature of differentiation.

And now for something completely different — Janet Browne talked about Charles Darwin and the Natural Economy of Households. She has this wealth of information about Darwin, one of the best documented figures in modern history, and she was intrigued by one peculiar observation. Francis Galton had sent out a questionnaire to many prominent people, surveying attitudes and backgrounds, and one question asked the respondents to list their special talents. Darwin’s answer was surprising. He said he had none, except for business! He regarded himself as an extremely successful businessman, first of all. It actually was true: all of Darwin’s account books are extant, and he was a guy who wrote down everything, from the purchase of a toothbrush to major railroad investments, and it’s all there.

At his wedding, the Darwin family financial seed was £10,000 granted to Charles and £10,000 to Emma. From this grew a fortune that, in the year before his death, was about £282,000. That’s a lot of money: Darwin’s expedition on the Beagle cost his father about £5,000, which was enough to buy a very nice house in those days, so Darwin was the equivalent of a modern multi-millionaire.

Browne argued that this talent was put to good use in his science. Like his accounts, he was a meticulous observer, noting everything. Further, accountancy taught him important principles of organization and abstraction. He kept day-to-day books of all expenses, which he then transcribed to books organized by category of expenses, which were further abstracted into yearly account books that summarized the totals. This is the same kind of methodology he used in tracking observations in natural history. She also noted that his diligence also reflected a common Malthusian sentiment of the times, that virtue was found in the proper management of money and resources.

I wondered whether this gradual and seemingly inevitable accumulation of wealth might also have colored Darwin’s perception of how evolution might work, but Browne was careful to say that she was only focusing on the application of Darwin’s business skills to his scientific methodology, and wasn’t saying anything about it’s application to his theory.

It was a great and stimulating meeting, and special appreciation has to go to Michael Weisberg of the University of Pennsylvania, who organized it all. At least 4 of the 5 talks were excellent. And really, people, tune in to your local universities — these kinds of events are going on all the time, and they’re often open to the public — you can get a marvelous education for free just by watching for the public seminars that university departments put on. We’re the opposite of elitist, we welcome everyone who wants to learn.

The heartbreaking beauty of development

This is a spectacular video of the development of Clypeaster subdepressus, also called a sand dollar or sea biscuit. These are stunningly beautiful creatures (as are we all, of course), and it is so cool to see them changing here. The video starts with a little echinoderm porn — these animals are profligate with their gametes — and then we see early divisions, gastrulation, the formation of the pluteus larva, metamorphosis into Aristotle’s lantern (one of the more charming names for a developmental stage), and into an ungainly spiky juvenile.

This is why some of us are developmental biologists: it’s all about the exotic weirdness and delicate loveliness of transformation.

Charismatic cephalofauna

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Christine Huffard sent me a note alerting me to the publication of her latest paper, and she thought I might be interested because I “seem to like cephalopods”. Hah. Well. I’ve noticed that Dr Huffard seems to have some small affection for the tentacled beasties herself.

The paper follows on an old tradition and an old problem. While people have no problem distinguishing human individuals, we have a tough time telling one individual animal from another. This perceptual difficulty complicates problems of studying variations in behavior or physiology, or monitoring numbers and behavior, in natural populations. One solution is tagging or marking the animals in some way, but that always has the risk of changing or harming the disturbed animals — non-invasive procedures are much preferred. This is an especially difficult problem with small animals, like zebrafish or small octopus; I’ve struggled myself with trying to track individual fish in experiments.

I came up with one solution, and Huffard et al. have come up with something similar: humans can be trained to recognize distinctive individual variations, and learn to identify single animals. In this paper, they describe a pattern of white pigmented regions that are consistent within single animals of the species Wunderpus photogenicus…and as you might guess, that is a great excuse to put together a collection of photographs of these aptly named animals.

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