The Evolving World

Feeling pragmatic? Is your focus entirely practical, on what works and what will get the job done? Are you one of those fighters for evolutionary biology who waves away all the theory and the abstractions and the strange experimental manipulations, and thinks the best argument for evolution is the fact that it works and is important? This book, The Evolving World: Evolution in Everyday Life(amzn/b&n/abe/pwll) by David Mindell, does make you sit down and learn a little history and philosophy to start off, but the focus throughout is on the application of evolution to the real world. It does a fine job of it, too.

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The ladies already knew about our lack, of course

A correspondent just reminded me of this classic paper from the literature—it’s the only contemporary scientific work I know of that managed to combine a discussion of the induction of a tissue by TGF-β and BMP proteins with a discussion of the Hebrew noun tzela to suggest that the book of Genesis wasn’t talking about thoracic ribs at all. All us sneering atheist professors who’ve had to exhibit human skeletons to show the creationists in our classrooms that men are not missing a rib apparently should have been pointing a little lower — where humans are missing a bone.

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This comment on the Panda’s Thumb leads to a very interesting entry on OMIM, the database of human genetic characters. We’re missing something.

OS PENIS, CONGENITAL ABSENCE OF

Deletion of the gulonolactone oxidase gene on 8p21 is a genetic disease that affects 100% of humans. Lack of the enzyme causes severe connective tissue disease and makes humans dependent upon dietary supplements of ascorbic acid; see 240400. Gilbert and Zevit (2001) pointed out that another genetic condition, affecting 100% of human males, is congenital lack of a baculum (os priapi; os penis). Whereas most mammals (including common species such as dogs and mice) and most other primates (except spider monkeys) have a penile bone, human males lack this bone and must rely on fluid hydraulics to maintain erections. The size of the rodent baculum is regulated by the posterior members of the HOXD (142987) set of transcription factors. Gilbert and Zevit (2001) suggested that it was not a costal rib but rather the penile ‘rib’ or baculum that God removed from Adam to create Eve (Genesis 2:21-23). Genesis also states that ‘the Lord God closed up the flesh.’ Gilbert and Zevit (2001) suggested that the raphe on the penis and scrotum was thought to be the surgical scar.

I’m a deformed mutant, a pathetic shadow of my bold, upright ancestors. My only consolation is that all you other guys are, too.

A general predilection for delusion

The first review of my talk yesterday is in! Too bad it is from somebody who wasn’t there and who is a world-class fool. Yes, it’s Michael Egnor again, and he’s got a lengthy post up with the pretext of giving me advice on future talks, but is really an attempt to preempt my arguments and chide me for my crazy materialist position. He doesn’t even come close to any of my arguments, and he makes false assumptions all over the place about what I and the audience think. I’m used to straw men from creationists, but this is ridiculous.

Here’s what I actually said at the talk.

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Thank God for Evolution!

Why me, O Lord, why me?

One of the more recent books sent to me is Thank God for Evolution!: How the Marriage of Science and Religion Will Transform Your Life and Our World(amzn/b&n/abe/pwll) by Michael Dowd. I have read it, and I’m feeling biblical.

My God, my God, why hast thou forsaken me? why art thou so far from helping me, and from the words of my roaring?
Psalm 22:1

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Evolution of a sex ratio observed

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If you’ve been reading that fascinating graphic novel, Y: The Last Man(amzn/b&n/abe/pwll), you know the premise: a mysterious disease has swept over the planet and bloodily killed every male mammal except two, a human named Yorick and a monkey named Ampersand. Substantial parts of it are biologically nearly impossible: the wide cross-species susceptibility, the near instantaneous lethality, and the simultaneity of its effect everywhere (there are also all kinds of weird correlations with other sort of magical putative causes, which may be red herrings). On the other hand, the sociological part of the story seems very plausible. There is no feminist utopia, the world goes on in a traumatized and rather complicated way, and the reactions everywhere vary from crazed euphoria to a more common despair. One thing that isn’t at all implausible, and actually has been observed, is a plague that selectively exterminates males.

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Reinventing the worm

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Sometimes, I confess, this whole common descent thing gets in the way and is really annoying. What we’ve learned over the years is that the evolution of life on earth is constrained by historical factors at every turn; every animal bears this wonderfully powerful toolbox of common developmental genes, inherited from pre-Cambrian ancestors, and it’s getting rather predictable that every time you open up some fundamental aspect of developmental pattern formation in a zebrafish, for instance, it is a modified echo of something we also see in a fruit fly. Sometimes you just want to see what evolution would do with a completely different starting point — if you could, as SJ Gould suggested, rewind the tape of life and let it play forward again, and see what novelties arose.

Take the worm. We take the generic worm for granted in biology: it’s a bilaterally symmetric muscular tube with a hydrostatic skeleton which propels itself through a medium with sinuous undulations, and with most of its sense organs concentrated in the forward end. The last common ancestor of all bilaterian animals was a worm, and we can see that ancestry in the organization of most animals today, even when it is obscured by odd little geegaws, like limbs and armor and regional specializations and various dangly spiky jointed bits. You’ll even see the argument made that that worm is the best of all possible simple forms, so it isn’t just an accident of history, it’s a morphological optimum.

But what if we could rewind the tape of life a little bit, to the first worms? Is it possible there are other ways such an animal could have been built? It seems nature may have carried out this little experiment for us, and we have an example of a reinvented worm, one not constructed by common descent from that initial triumphal exemplar in the pre-Cambrian — an alternative worm.

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Gay roundup

This is a nice, short summary of some of the explanations for the evolution of homosexuality. It could be shorter; there are really just two classes of explanation, the adaptationist strategy of trying to find a necessary enhancement to fitness, and the correct strategy of recognizing that not all attributes of an individual organism are going to be optimal for that individual’s reproduction, so don’t even try. Love isn’t hardwired by biology, and it can go in all kinds of different directions.

So I’m saying the best answer in the list is #5. I wouldn’t be biased by the fact that the author is quoting me, no, not at all.

Common elements of eumetazoan gene organization in an anemone

We now have a draft of the sea anemone genome, and it is revealing tantalizing details of metazoan evolution. The subject is the starlet anemone, Nematostella vectensis, a beautiful little animal that is also an up-and-coming star of developmental biology research.

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(click for larger image)
Nematostella development. a. unfertilized egg (~200 micron diameter) with sperm head; b. early cleavage stage; c. blastula; d. gastrula; e. planula; f. juvenile polyp; g. adult stained with DAPI to show nematocysts with a zoom in on the tentacle in the inset; h, i. confocal images of a tentacle bud stage and a gastrula respectively showing nuclei (red) and actin (green); j. a gastrula showing snail mRNA(purple) in the endoderm and forkhead mRNA (red) in the pharynx and endoderm; k. a gastrula showing Anthox8 mRNA expression; l. an adult Nematostella.

A most important reason for this work is that the anemone Nematostella is a distant relative of many of the animals that have already been sequenced, and so provides an essential perspective on the evolutionary changes that we observe in those other organisms. Comparison of its genome with that of other metazoans is helping us decipher the likely genetic organization of the last common ancestor of all animals.

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Artificial evolution looks an awful lot like the natural kind

What properties should we expect from an evolved system rather than a designed one? Complexity is one, another is surprises. We should see features that baffle us and that don’t make sense from a simply functional and logical standpoint.

That’s also exactly what we see in systems designed by processes of artificial evolution. Adrian Thompson used randomized binary data on Field-Programmable Gate Arrays, followed by selection for FPGAs that could recognize tones input into them. After several thousand generations, he had FPGAs that would discriminate between two tones, or respond to the words “stop” and “go”, by producing 0 or 5 volts. Then came the fun part: trying to figure out how the best performing chip worked:

Dr. Thompson peered inside his perfect offspring to gain insight into its methods, but what he found inside was baffling. The plucky chip was utilizing only thirty-seven of its one hundred logic gates, and most of them were arranged in a curious collection of feedback loops. Five individual logic cells were functionally disconnected from the rest — with no pathways that would allow them to influence the output — yet when the researcher disabled any one of them the chip lost its ability to discriminate the tones. Furthermore, the final program did not work reliably when it was loaded onto other FPGAs of the same type.

That looks a lot like what we see in developmental networks in living organisms — unpredictable results when pieces are “disconnected”, or mutated, lots and lots of odd feedback loops everywhere, and sensitivity to specific conditions (although we also see selection for fidelity from generation to generation, more so than occurred in this exercise, I think). This is exactly what evolution does, producing a functional complexity from random input.

I suppose it’s possible, though, that Michael Behe’s God also tinkers with electronics as a hobby, and applied his ineffably l33t hacks to the chips when Thompson wasn’t looking.