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.


A Sea Biscuit’s Life from Bruno Vellutini on Vimeo.

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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Entropy and evolution

Blogging on Peer-Reviewed Research

One of the oldest canards in the creationists’ book is the claim that evolution must be false because it violates the second law of thermodynamics, or the principle that, as they put it, everything must go from order to disorder. One of the more persistent perpetrators of this kind of sloppy thinking is Henry Morris, and few creationists today seem able to get beyond this error.

Remember this tendency from order to disorder applies to all real processes. Real processes include, of course, biological and geological processes, as well as chemical and physical processes. The interesting question is: “How does a real biological process, which goes from order to disorder, result in evolution. which goes from disorder to order?” Perhaps the evolutionist can ultimately find an answer to this question, but he at least should not ignore it, as most evolutionists do.

Especially is such a question vital, when we are thinking of evolution as a growth process on the grand scale from atom to Adam and from particle to people. This represents in absolutely gigantic increase in order and complexity, and is clearly out of place altogether in the context of the Second Law.

As most biologists get a fair amount of training in chemistry, I’m afraid he’s wrong on one bit of slander there: we do not ignore entropy, and are in fact better informed on it than most creationists, as is clearly shown by their continued use of this bad argument. I usually rebut this claim about the second law in a qualitative way, and by example — it’s obvious that the second law does not state that nothing can ever increase in order, but only that an decrease in one part must be accompanied by a greater increase in entropy in another. Two gametes, for instance, can fuse and begin a complicated process in development that represents a long-term local decrease in entropy, but at the same time that embryo is pumping heat out into its environment and increasing the entropy of the surrounding bit of the world.

It’s a very bad argument they are making, but let’s consider just the last sentence of the quote above.

This represents in absolutely gigantic increase in order and complexity, and is clearly out of place altogether in the context of the Second Law.

A “gigantic increase in order and complexity” … how interesting. How much of an increase? Can we get some numbers for that?

Daniel Styer has published an eminently useful article on “Entropy and Evolution” that does exactly that — he makes some quantitative estimates of how much entropy might be decreased by the process of evolution. I knew we kept physicists around for something; they are so useful for filling in the tricky details.

The article nicely summarizes the general problems with the creationist claim. They confuse the metaphor of ‘disorder’ for the actual phenomenon of entropy; they seem to have an absolutist notion that the second law prohibits all decreases in entropy; and they generally lack any quantitative notion of how entropy actually works. The cool part of this particular article, though, is that he makes an estimate of exactly how much entropy is decreased by the process of evolution.

First he estimates, very generously, how much entropy is decreased per individual. If we assume each individual is 1000 times “more improbable” than its ancestor one century ago, that is, that we are specified a thousand times more precisely than our great-grandparents (obviously a ludicrously high over-estimate, but he’s trying to give every advantage to the creationists here), then we can describe the reduction in the number of microstates in the modern organism as:

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Now I’m strolling into dangerous ground for us poor biologists, since this is a mathematical argument, but really, this is simple enough for me to understand. We know the statistical definition of entropy:

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In the formula above, kB is the Boltzmann constant. We can just plug in our estimated (grossly overestimated!) value for Ω, have fun with a little algebra, and presto, a measure of the change in entropy per individual per century emerges.

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Centuries are awkward units, so Styer converts that to something more conventional: the entropy change per second is -3.02 x 10-30 J/K. There are, of course, a lot of individual organisms on the planet, so that number needs to be multiplied by the total number of evolving organism, which, again, we charitably overestimate at 1032, most of which are prokaryotes, of course. The final result is a number that tells us the total change in entropy of the planet caused by evolution each second:

-302 J/K

What does that number mean? We need a context. Styer also estimates the Earth’s total entropy throughput per second, that is, the total flux involved from absorption of the sun’s energy and re-radiation of heat out into space. It’s a slightly bigger number:

420 x 1012 J/K

To spell it out, there’s about a trillion times more entropy flux available than is required for evolution. The degree by which earth’s entropy is reduced by the action of evolutionary processes is miniscule relative to the amount that the entropy of the cosmic microwave background is increased.

This is very cool and very clear. I’m folding up my copy of Styer’s paper and tucking it into my copy of The Counter-Creationism Handbook, where it will come in handy.

Styer DF (2008) Entropy and evolution. Am J Phys 76(11):1031-1033.

Oxygen has eyelashes!

It’s cute: this exercise in molecular visualization has been all dolled up with anthropomorphized atoms to sneak it into kids’ attention spans.

I can’t be entirely dismissive, though. There’s some cool stuff lurking in the backgrounds of these scenes, it’s just unfortunate that the goofy cartoon stuff is always being placed front and center.

I am kind of hoping that the creationists, with all their talk of cars and buses and traffic lights in the cell, steal this video. I can almost imagine Michael Behe exclaiming that the sophisticated facial expressions of atoms are evidence of intent and design.

The Mason’s Apprentice

My latest Seed column slipped quietly onto the interwebs last week — it’s an overview of how the glues that hold multicellular organisms together first evolved in single celled creatures, represented today by the choanoflagellates.

Just as a teaser, the next print edition that should be coming out soon will continue the focus on enlightening organisms of remarkable simplicity with a description of the results of the Trichoplax genome. Get it! You will also be rewarded with a great issue focusing on science policy.

Epidexipteryx

The Mesozoic was inhabited by some strange-looking critters, and here’s another example: a Jurassic dinosaur called Epidexipteryx, which has spiky teeth, big claws, fluffy feathers all over its body, and four long decorative feathers coming off a stumpy tail. It resembles a particularly ugly bird with a nasty bite, but it couldn’t fly — none of the feathers covering its forelimbs are pennaceous, but are more like an insulating fur. Or, alternatively, its feathers were all about display, a possibility suggested by the odd long feathers of the tail. Here are the bones; as you can see, the integument is remarkably well preserved, with a scruffy ruff of short, non-shafted feathers over the body and limbs, and a surprising spray of just four very long feathers coming off the tail.

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(Click for larger image)
a, Main slab; b, c, skull in main slab (b) and counterslab (c); d, four elongate ribbon-like tail feathers; b’, c’, line drawings of b and c, respectively. Abbreviations: l1, l2 and l7, 1st, 2nd and 7th left teeth of upper jaw; l1′, r1′ and r5′, 1st left, 1st right and 5th right teeth of lower jaw; l2 and r2, 2nd left and right teeth of upper jaw.

And here’s what it would have looked like in life (only the colors are imaginary). It would have been about the size of a pigeon — I think a pack of these scurrying about New York’s Times Square would be both scenic and would quickly clean up the pigeon problem there.

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For all the details, read the write-up on Tetrapod Zoology.

Zhang F, Zhou Z, Xu X, Wang X, Sullivan C (2008) A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers. Nature 455:1105-1108.

Here’s something else Darwin didn’t have

Tracking of the HMS Beagle by a manned space station. I don’t know why; maybe those pre-Victorian Space Engineers had their steam-powered space-stations all tied up trying to find the source of the Nile or plotting invasion routes into Afghanistan, or something. This time around our 21st century panjandrums of outer space have their priorities a bit more in focus, and NASA has committed to using the ISS to watch the new Voyage of the Beagle. Read the Beagle Project for more details.

I’m just relieved that finally we’ve found something useful for these space nuts to do — providing supplemental assistance to a biological and historical project, instead of noodling around staring at space rocks, space debris, and space vapor.