Ladders and cranes everywhere!

There is a painful assumption of progress in many interpretations of evolution — and sometimes it’s by people who ought to know better. T. Ryan Gregory finds a ghastly example of a figure that, by cherry-picking the data and doing a little suggestive ordering of the presentation, makes it look like there’s a correlation between the amount of non-coding DNA and organismal complexity. Fortunately, he counters it with a much more useful chart (that I’m definitely stealing for the next time I teach genetics) with no such bias.

And then Larry Moran tops Gregory with an even worse figure. I don’t quite understand it; maybe this distortion of the evidence to support progress, increasing molecular complexity, and the superiority of humans has roots in misunderstandings before my time, because my genetics and cell biology instructors in the 1970s sure didn’t promote this nonsense then. We were told even in those ancient days that the C-value paradox wasn’t a problem if you didn’t try to shoehorn mammals into a position at the pinnacle of evolution.

Maybe I just had really good professors. Thanks, Arthur Whiteley and Larry Sandler!

Transitions

Whenever I spot some old thread suddenly getting a surge of new comments, I can guess what has happened: a creationist or two has come to visit. That’s happening right now on this very short article that mentions the peppered moths; we’re up above 200 comments now, and it seems to have very little to do with moths anymore. Instead, we’ve got a creationist complaining about the absence of transitional species and the Cambrian ‘explosion’, with a little quote-mining of Richard Dawkins. You commenters are taking care of him ably, but there are just a few things I want to mention, and a few questions I want to ask of the creationists.

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FunGenEvoDevo

I got some email today with lots of constructive suggestions (See? Not all my email is evil!) for how we ought to change the education of biology students — such as by giving them a foundation in the history and philosophy of our science, using creationist arguments as bad examples so the students can see the errors for themselves, etc. — and it was absolutely brilliant, even the parts where he disagreed with some things I’d written before. Best email ever!

Of course, what helped is that I spent my summer “vacation” putting together a new freshman first semester course for biology majors that I’m teaching for the first time right now, and it’s exactly the course he described. It was eerie, like one of my future students had invented a time machine and come back into the past to tell me what to do. A lot of the course content is locked up behind a password-protected firewall, I’m afraid, but just to show you what I’m talking about, I’ll put the course schedule below the fold.

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Evolution of the cichlid mandible

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When we look at the face of another person, we can recognize specific features that have familial resemblances. In my family, for instance, I can recognize a “Myers nose” that my grandmother and my father and some of my siblings and kids have, and it’s different than my wife’s or my mother’s nose. These are subtle differences in shape—a bit of a curve, a knob, a seam—and their inheritance suggests that these differences are specified somehow in the DNA. If you think about it, though…how can whether the profile of a nose is straight or curved be encoded in a linear stretch of nucleotides? The complicated answer is that it isn’t—morphology is a consequence of epigenetic interactions during development—but we know that the alleles present in the genome do contribute in some significant way to three-dimensional form. How?

We don’t know all the details. This is one of those huge research problems that has gaping holes, full of promise and interest, where we don’t understand exactly how all the pieces fit together. However, here’s an important point that is relevant to other, larger issues in evolution: even where we lack full information about mechanisms, we can roughly perceive the shape of the answer, and that helps us rule out many alternative explanations and guides us in the general direction of a more complete understanding.

People’s noses are a difficult subject for research; we don’t get to define human crosses, people tend to be a little snippy about telling them who to breed with and taking their genes apart, and humans are awfully slow to breed. Fish are better experimental animals, much more pliable and faster and more prolific in their breeding. Some fish, such as the African cichlids, also have highly diverse populations and species with easily recognized and often quite dramatic morphological differences—and we can explore how those differences are generated by genetic and molecular differences in development. In particular, we can start to figure out how fish jaws are shaped by developmental processes.

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Two horrible new diseases

Scott Lanyon, director of the Bell Museum, has an article on two disease we should worry about, VHSv and EAS.

Personally, I think VHSv is the worst. It’s a virus that causes hemorrhagic septicemia in fish; just from the name you know it’s bad, involving blood and sepsis. My most horrible experience raising zebrafish was the time hemorrhagic septicemia swept through my colony and I had to euthanize every animal and bleach every last bit of plumbing to eradicate it. This disease has been detected in waters of Wisconsin, and it’s definitely not good.

EAS may not be as dramatically gory and lethal in its effects, but it strikes humans directly. It’s Evolution Avoidance Syndrome, and it causes the brains of scientists and journalists to seize up when circumstances are appropriate to discuss evolution in public. Apparently, we want local fish populations to develop, acquire, improve or have arise resistance to the hemorrhagic septicemia virus; we can’t possibly suggest that evolution might be at work.

Battling giants

Want to see Freeman Dyson and Richard Dawkins butt heads? It begins with a talk Dyson gave to an Edge conference in which Dyson (watch the whole talk) made these comments:

“By Darwinian evolution he [Woese] means evolution as Darwin understood it, based on the competition for survival of noninterbreeding species.”

“With rare exceptions, Darwinian evolution requires established species to become extinct so that new species can replace them.”

Dawkins rightly objects. Those are weird claims: the first is, I think, a misreading of Darwin. Darwin says something very different.

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Lucy’s legacy

As I’ve mentioned before, Lucy is going to be in Houston at the end of this week for an extended stay. This is not entirely a joyous occasion in the scientific community: many people, including Richard Leakey, are not happy that such a precious specimen has been subjected to the risks of travel. I sympathize. The bones of Lucy must be treated with the utmost care and regard, and any loss or damage would be an awful tragedy. However, there’s more to it than preserving an important fossil: Lucy is a touchstone to our past and is a symbol of the importance of our long history. We need to bring the ancient world to life for our citizens, and for not entirely rational reasons, people will want to see the real thing. I see that someone else shares my sentiment:

There is a wanton arrogance alive and kicking within the general scientific community. An arrogance that clings stubbornly to fact while at the same time stridently denying reality. And it pisses me the hell off. The facts in this case are clear: Lucy is one of the oldest hominid fossils ever discovered, and is very valuable for researchers. The reality of the situation is equally clear-cut, if a bit harder for the critics to swallow: Nobody gives a shit about replicas. Does it look the same? Sure. Can 99.9 percent of the population not tell the difference? You betcha. Does that matter? Not one iota. You see, for all the cranial capacity human beings have developed since little Lucy made do with a glob of gray matter the size of a key lime, we are not rational thinkers. Homo sapiens are, first and foremost, irrational and emotional.

I wouldn’t go so far as to call it arrogance, but there is a little selfishness to it, and most importantly, there’s a deep appreciation of the importance of that long-dead individual and a greater fear of its loss. What balances that fear, though, should be the recognition that other people could also stand to learn to love that tiny scrap of our long-past ancestry — the Lucy exhibit is an opportunity to teach.

Shouldn’t that be part of our mission? In addition to our own intimate learning of science, the task of sharing it with everyone else?

Nope, no aquatic apes found in Morris

How come you people never come visit? I’m only an hour from the freeway by way of a two-lane county road, roughly equidistant from Fargo, Sioux Falls, and Minneapolis, yet somehow no one ever happens to be passing through this remote rural town … until today. Jim Moore took a little detour from his road trip from Victoria, BC to Oklahoma to pop by lovely Morris, Minnesota and say hello. Now we expect the rest of you to come on by.

In case you don’t know who Jim Moor is, he maintains this web page, a critique of the Aquatic Ape “Theory”. This “theory” (really, it doesn’t deserve the promotion) is often taken as quite reasonable at first glance — hey, whales have reduced body hair and are aquatic, humans have reduced body hair so maybe they also went through an aquatic stage in their evolution — but once you dig just a tiny bit deeper, the inconsistencies within the hypothesis and the contradictions with reality loom larger and larger, and you really should realize that it’s utter nonsense. But weirdly, there are a number of people who have gotten quite obsessed with the idea and who have written reams of papers to rationalize the baloney. Back in the 20th century wrangles over the Aquatic Ape nonsense would spontaneously emerge on usenet all the time (here’s one example) because its proponents had to be completely refractory to contradicting evidence. Good times.

One interesting twist to it all is that it’s an odd variant of denialism. These people aren’t rejecting an established scientific conclusion, such as that HIV causes AIDS or that human activities contribute to global warming — they are pushing beyond reason for a conclusion that science denies. I suppose you could say they’re denying the evidence that shoots down their favored beliefs, but at least they actually have a positive (but bogus!) hypothesis that they aren’t afraid to recite at you, which puts them several notches above the Intelligent Design creationists.

Anyway, Moore has a tremendous amount of useful information rebutting the Aquatic Ape Speculation — it’s well worth a browse, and also amusing to read some of the crackpot defenses (one of my favorites is the claim that Neandertals had large noses that they used as snorkels). And I’m not just saying that because he was nice enough to stop by Morris!

Axis formation in spider embryos

Blogging on Peer-Reviewed Research

Some of you may have never seen an arthropod embryo (or any embryo, for that matter). You’re missing something: embryos are gorgeous and dynamic and just all around wonderful, so let’s correct that lack. Here are two photographs of an insect and a spider embryo. The one on the left is a grasshopper, Schistocerca nitens at about a third of the way through development; the one on the right is Achaearanea tepidariorum. Both are lying on their backs, or dorsal side, with their legs wiggling up towards you.

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There are differences in the photographic technique — one is an SEM, the other is a DAPI-stained fluorescence photograph — and the spider embryo has had yolk removed and been flattened (it’s usually curled backward to wrap around a ball of yolk), and you can probably see the expected difference in limb number, but the cool thing is that they look so much alike. The affinities in the body plans just leap out at you. (You may also notice that it doesn’t seem to resemble a certain other rendition of spider development).

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Clearly, bloggers need to take over science journalism

Aaargh. When will the media learn? National Geographic is running this ridiculous headline right now: New Fossil Ape May Shatter Human Evolution Theory, in which the reporter claims a discovery of some teeth could “demolish a working theory of human evolution.” It’s not true. Where is this nonsense coming from?

I read the article. It’s titled “A new species of great ape from the late Miocene epoch in Ethiopia.” The exciting news is that the “combined evidence suggests that Chororapithecus may be a basal member of the gorilla clade, and that the latter exhibited some amount of adaptive and phyletic diversity at around 10-11 Myr ago.” It concludes with a suggestion that we need to do more research in sediments appropriate to Miocene apes. There aren’t an exploding paradigms or revolutions suggested.

I read the associated news article in Nature. It’s titled “Oldest gorilla ages our joint ancestor.” It says that this discovery pushes back the time of divergence of the gorilla lineage from our own. This is just ordinary science.

Now read the blogs — they’re doing a much better job of evaluating this work than the traditional media. For one thing, they’re actually looking at it critically. Afarensis points out that these are only a few teeth, and it’s awfully thin grounds for a substantial revision of the timeline. John Hawks makes a similar point, but also highlights the fact that there is an unresolved problem — we need to reconcile paleontological and molecular dates. Even John Wilkins, a “mere” philosopher, weighs in sensibly that teeth are plastic characters in phylogeny, and deplores this peculiar media habit of taking a recalibration of a historical detail as a major reformulation of theory. All these discussions are sober and interested and most important of all, accurate.

The lesson is clear: when you see some wild and crazy claim of scientific revolutions and the demolition of long-held theories, go immediately to the science blogs for some clear-eyed sanity and informed evaluation from experts.