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.

i-da53b70f97ff878afc87b689369ca148-nematostella.jpg
(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.

New York Times gives evolution a day

The NY Times has pulled out all the stops today and has dedicated their entire science section to the subject of evolution. They’ve got pieces by some of the best science journalists around, like Carl Zimmer, Cornelia Dean (although in this case, it’s a lot of nattering on about how the soul fits into evolution—not recommended), and Natalie Angier, and they’ve also drafted a few scientists. There’s a video of Sean Carroll summarizing evo-devo, and perhaps the most interesting article of them all is by Douglas Erwin, in which he speculates about whether the new ideas percolating throughout the science community (especially by those noisy developmental biologists) are precursors to a new revolution in our thinking about evolution. He’s non-committal so far, which is fair.

Does all this add up to a new modern synthesis? There is certainly no consensus among evolutionary biologists, but development, ecology, genetics and paleontology all provide new perspectives on how evolution operates, and how we should study it. None of these concerns provide a scintilla of hope for creationists, as scientific investigations are already providing new insights into these issues. The foundations for a paradigm shift may be in place, but it may be some time before we see whether a truly novel perspective develops or these tensions are accommodated within an expanded modern synthesis.

Or both! I expect that what will happen is that the deficiencies in the neo-Darwinian synthesis (which lacks any explanation for the evolution of form and pattern, for instance) will be gradually filled in with clear linkages to the evolution of genes, and despite the fact that it will be a bigger, bolder, stronger synthesis, everyone will say we knew it all along anyway. There will not be a threshold moment where everyone says “Wow! I am suddenly enlightened!” — there will just come a time when everyone acknowledges that all those papers from 40 years ago were pretty darned important, after all.

Segmentation genes evolved undesigned

Jason Rosenhouse has dug into the details of the evo-devo chapter of Behe’s The Edge of Evolution and found some clear examples of dishonest quote-mining (so what else is new, you may be thinking—it’s what creationists do). I’ve warned you all before that when you see an ellipsis in a creationist quote, you ought to just assume that there’s been something cut out that completely contradicts the point the creationist is making; Rosenhouse finds that Behe gets around that little red-flag problem by simply leaving out the ellipses.

I just want to expand a little bit on one point Behe mangles and that Jason quotes. It turns out I actually give a lecture in my developmental biology courses on this very issue, the mathematical modeling antecedents to insect segmentation, so it’s simply weird to see Behe twisting a subject around that is so well understood in the evo-devo community, and that was actually well explained in Sean Carroll’s Endless Forms Most Beautiful.

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This might be a good site for someone else…

This site has its heart in the right place, but it’s more for theistic evolutionists than my kind—all the bowing and scraping to a creator god leaves me cold (especially since it seems to substitute hearty encouragement and reconciliation over actually discussing the evidence). But if that doesn’t bother you, take a look at The Epic of Evolution. It’ll probably make somebody happy.

Everything is evolution

I can’t help it—everything I read only makes sense in the light of evolution. Here, for instance, is a story about the popularity of the AK-47 assault rifle:

The AK-47’s popularity is generally attributed to its functional characteristics; ease of operation, robustness to mistreatment and negligible failure rate. The weapon’s weaknesses — it is considerably less accurate, less safe for users, and has a smaller range than equivalently calibrated weapons — are usually overlooked, or considered to be less important than the benefits of its simplicity. But other assault rifles are approximately as simple to manage, yet they have not experienced the soaring popularity of the Kalashnikov.

The AK-47’s ubiquity could alternatively be explained as a result of a path dependent process. Economic historians recognize that an inferior product may persist when a small but early advantage becomes large over time and builds up a legacy that makes switching costly. In the case of the AK-47 that early advantage may be that as a Soviet invention it was not subject to patent and so could be freely copied.

“Path dependency”…hey, that’s another phrase for something I hammer on all the time, that you can only understand the full extent of evolution if you understand the developmental processes underlying it. Many sub-optimal solutions persist because they are part of a developmental framework that isn’t easily changed.

And speaking of suboptimal…there’s Microsoft Word, an ungainly monstrosity if ever there was one. Both Science and Nature have rejected the use of the latest version of MS Word, because it is non-standard and effectively broken.

Because of changes Microsoft has made in its recent Word release that are incompatible with our internal workflow, which was built around previous versions of the software, Science cannot at present accept any files in the new .docx format produced through Microsoft Word 2007, either for initial submission or for revision. Users of this release of Word should convert these files to a format compatible with Word 2003 or Word for Macintosh 2004 (or, for initial submission, to a PDF file) before submitting to Science.

There’s a “path dependency” for you, the ubiquity of Word. Even highly evolved, complex and otherwise necessary pathways can be replaced, though, if more effective alternative pathways acquire greater importance. If the target of selection is the production of a functional end product (a standard readable file in this case) and there are multiple paths for delivering that end product (doc or pdf), the acquisition and spread of a deleterious mutation in the dominant pathway can lead to greater importance of the alternate.

Hmm, I have to go home and start a pot of minestrone soup for dinner…somebody explain that process in evolutionary terms for me.

Evolution of direct development in echinoderms

In chapter 14 of the Origin of Species, Darwin wondered about the whole process of metamorphosis. Some species undergo radical transformations from embryo to adult, passing through larval stages that are very different from the adult, while others proceed directly to the adult form. This process of metamorphosis is of great interest to both developmental and evolutionary biologists, because what we see are major transitions in form not over long periods of time, but within a single generation.

We are so much accustomed to see a difference in structure between
the embryo and the adult, that we are tempted to look at this
difference as in some necessary manner contingent on growth. But there
is no reason why, for instance, the wing of a bat, or the fin of a
porpoise, should not have been sketched out with all their parts in
proper proportion, as soon as any part became visible. In some whole
groups of animals and in certain members of other groups this is the
case, and the embryo does not at any period differ widely from the
adult: thus Owen has remarked in regard to cuttlefish, “There is no
metamorphosis; the cephalopodic character is manifested long before
the parts of the embryo are completed.” Landshells and fresh-water
crustaceans are born having their proper forms, whilst the marine
members of the same two great classes pass through considerable and
often great changes during their development. Spiders, again, barely
undergo any metamorphosis. The larvae of most insects pass through a
worm-like stage, whether they are active and adapted to diversified
habits, or are inactive from being placed in the midst of proper
nutriment or from being fed by their parents; but in some few cases,
as in that of Aphis, if we look to the admirable drawings of the
development of this insect, by Professor Huxley, we see hardly any
trace of the vermiform stage.

Why do some lineages undergo amazing processes of morphological change over their life histories, while others quickly settle on a single form and stick with it through their entire life? In some cases, we can even find closely related species where one goes through metamorphosis, and another doesn’t; this is clearly a relatively labile character in evolution. And one of the sharpest, clearest examples of this fascinating flexibility is found in the sea urchins.

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Rah, rah, RASC

Let’s encourage this trend of scientific societies coming out with unambiguous statements of support for good science. The latest addition is the Royal Astronomical Society of Canada-Ottawa Centre statement on evolution: it’s short and to the point.

The RASC Ottawa Centre supports high standards of scientific integrity, academic freedom and the free exchange of ideas. It also respects the scientific method and recognizes that the validity of any scientific model comes only as a result of rational hypotheses, sound experimentation, and findings that can be replicated by others.

The RASC Ottawa Centre, then, is unequivocal in its support of contemporary evolutionary theory that has its roots in the seminal work of Charles Darwin and has been refined by findings accumulated over 140 years.

Some dissenters from this position are proponents of non-scientific explanations of the nature of the universe.  These may include “creation science”, “creationism”, “intelligent design” or other non-scientific “alternatives to evolution”. While we respect the dissenters’ right to express their views, these views are theirs alone and are in no way endorsed by the RASC Ottawa Centre.  It is our collective position that these explanations do not meet the characteristics and rigour of scientific empiricism.

Therefore the science agenda of the RASC Ottawa Centre and its publications will not promote any non-scientific explanations of the nature of the universe.