Altenberg meeting next week: expect evolution to simply evolve slightly

Remember Suzan Mazur, the credulous reporter hyping a revolution in evolution? She’s at it again, publishing an e-book chapter by chapter on the “Altenberg 16”, this meeting that she thinks is all about radically revising evolutionary biology.

I can tell that Massimo Pigliucci — one of the 16 — is feeling a little exasperation at this nonsense, especially since some of the IDists have seized on it as vindication of their delusions about the “weakness” of evolutionary theory. He’s got an excellent post summarizing some of the motivation behind this meeting, which is actually part of a fairly routine process of occasional get-togethers by scientists with similar ideas to hash out the concepts. Here’s the actual subject of discussion at the Altenberg meeting.

The basic idea is that there have been some interesting empirical discoveries, as well as the articulation of some new concepts, subsequently to the Modern Synthesis, that one needs to explicitly integrate with the standard ideas about natural selection, common descent, population genetics and statistical genetics (nowadays known as evolutionary quantitative genetics). Some of these empirical discoveries include (but are not limited to) the existence of molecular buffering systems (like the so-called “heat shock response”) that may act as “capacitors” (i.e., facilitators) of bursts of phenotypic evolution, and the increasing evidence of the role of epigenetic (i.e., non-genetic) inheritance systems (this has nothing to do with Lamarckism, by the way). Some of the new concepts that have arisen since the MS include (but again are not limited to) the idea of “evolvability” (that different lineages have different propensities to evolve novel structures or functions), complexity theory (which opens the possibility of natural sources of organic complexity other than natural selection), and “accommodation” (a developmental process that may facilitate the coordinated appearance of complex traits in short evolutionary periods).

Now, did you see anything in the above that suggests that evolution is “a theory in crisis”? Did I say anything about intelligent designers, or the rejection of Darwinism, or any of the other nonsense that has filled the various uninformed and sometimes downright ridiculous commentaries that have appeared on the web about the Altenberg meeting? Didn’t think so. If next week’s workshop succeeds, what we will achieve is taking one more step in an ongoing discussion among scientists about how our theories account for biological phenomena, and how the discovery of new phenomena is to be matched by the elaboration of new theoretical constructs. This is how science works, folks, not a sign of “crisis.”

You cannot imagine how pleased I was to see this — not because I was at all concerned about this meeting, but because I’ve been scribbling down notes for the last few weeks on the subjects I want to discuss in my keynote at GECCO 2008, and that’s practically an outline of my plans. I was going to go over some of these concepts and define them and give examples; I didn’t have molecular buffers on my list (maybe I’ll have to add it), and I was going to say a bit about conservation/canalization vs. plasticity, but at least I’m reassured that I’m on the right track.

Origin of life

Nick Matzke has a fine summary of progress in research into abiogenesis. He chastises those people who try to argue that abiogenesis is independent of evolution, or that you can get out of trying to answer the question of where life came from by simply saying that that isn’t evolution. It is! I’ve said it myself, and I really wish people would stop trying weasel out of that question by punting it off to some other discipline.

Evolving proteins in snakes

Blogging on Peer-Reviewed Research

We’ve heard the arguments about the relative importance of mutations in cis regulatory regions vs. coding sequences in evolution before — it’s the idea that major transitions in evolution were accomplished more by changes in the timing and pattern of gene expression than by significant changes in the genes themselves. We developmental biologists tend to side with the cis-sies, because timing and pattern are what we’re most interested in. But I have to admit that there are plenty of accounts of functional adaptation in populations that are well-founded in molecular evidence, and the cis regulatory element story is weaker in the practical sense that counts most in science (In large part, I think that’s an artifact of the tools — we have better techniques for examining expressed sequences, while regulatory elements are hidden away in unexpressed regions of the genome. Give it time, the cis proponents will catch up!)

This morning, I was sent a nice paper that describes a pattern of functional change in an important molecule — there is absolutely no development in it. It’s a classic example of an evolutionary arms race, though, so it’s good that I mention this important and dominant side of the discipline of evolutionary biology — I know I leave the impression that all the cool stuff is in evo-devo, but there’s even more exciting biology outside the scope of my tunnel vision. Also, this paper describes a situation and animals with which I am very familiar, and wondered about years ago.

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Ventastega

Blogging on Peer-Reviewed Research

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The paleontologists are going too far. This is getting ridiculous. They keep digging up these collections of bones that illuminate tetrapod origins, and they keep making finer and finer distinctions. On one earlier side we have a bunch of tetrapod-like fish — Tiktaalik and Panderichthys, for instance — and on the later side we have fish-like tetrapods, such as Acanthostega and Ichthyostega. Now they’re talking about shades of fishiness or tetrapodiness within those groups! You’d almost think they were documenting a pattern of gradual evolutionary change.

The latest addition is a description of Ventastega curonica, a creature that falls within the domain of the fish-like tetrapods, but is a bit fishier than other forms, so it actually bridges the gap between something like Tiktaalik and Acanthostega. We look forward to the imminent discovery of yet more fossils that bridge the gap between Ventastega and Tiktaalik, and between Ventastega and Acanthostega, and all the intermediates between them.

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Amphioxus and the evolution of the chordate genome

Blogging on Peer-Reviewed Research

This is an amphioxus, a cephalochordate or lancelet. It’s been stained to increase contrast; in life, they are pale, almost transparent.

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It looks rather fish-like, or rather, much like a larval fish, with it’s repeated blocks of muscle arranged along a stream-lined form, and a notochord, or elastic rod that forms a central axis for efficient lateral motion of the tail…and it has a true tail that extends beyond the anus. Look closely at the front end, though: this is no vertebrate.

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It’s not much of a head. The notochord extends all the way to the front of the animal (in us vertebrates, it only reaches up as far as the base of the hindbrain); there’s no obvious brain, only the continuation of the spinal cord; there isn’t even a face, just an open hole fringed with tentacles. This animal collects small microorganisms in coastal waters, gulping them down and passing them back to the gill slits, which aren’t actually part of gills, but are components of a branchial net that allows water to filter through while trapping food particles. It’s a good living — they lounge about in large numbers on tropical beaches, sucking down liquids and any passing food, much like American tourists.

These animals have fascinated biologists for well over a century. They seem so primitive, with a mixture of features that are clearly similar to those of modern vertebrates, yet at the same time lacking significant elements. Could they be relics of the ancestral chordate condition? A new paper is out that discusses in detail the structure of the amphioxus genome, which reveals unifying elements that tell us much about the last common ancestor of all chordates.

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Basics: Synteny

Let’s play the most boring card game in the universe!

Here are the rules. We start with a fully sorted deck of 52 cards, and we deal out four hands. We don’t deal in the ordinary way, either: we give the top 13 cards to the first player, then the next 13 to the second, and so forth. (We could also do the usual deal, but it makes the illustration and logic a little more difficult to see. We’ll keep it simple for now.)

This is what the table will look like.

Hand 1 Ai-233f23e2a2ca8059264849e39e1760d2-heart.gif Ki-233f23e2a2ca8059264849e39e1760d2-heart.gif Qi-233f23e2a2ca8059264849e39e1760d2-heart.gif Ji-233f23e2a2ca8059264849e39e1760d2-heart.gif 10i-233f23e2a2ca8059264849e39e1760d2-heart.gif 9i-233f23e2a2ca8059264849e39e1760d2-heart.gif 8i-233f23e2a2ca8059264849e39e1760d2-heart.gif 7i-233f23e2a2ca8059264849e39e1760d2-heart.gif 6i-233f23e2a2ca8059264849e39e1760d2-heart.gif 5i-233f23e2a2ca8059264849e39e1760d2-heart.gif 4i-233f23e2a2ca8059264849e39e1760d2-heart.gif 3i-233f23e2a2ca8059264849e39e1760d2-heart.gif 2i-233f23e2a2ca8059264849e39e1760d2-heart.gif
Hand 2 Ai-94f8cf214b78029e2cd1e9398229dda0-club.gif Ki-94f8cf214b78029e2cd1e9398229dda0-club.gif Qi-94f8cf214b78029e2cd1e9398229dda0-club.gif Ji-94f8cf214b78029e2cd1e9398229dda0-club.gif 10i-94f8cf214b78029e2cd1e9398229dda0-club.gif 9i-94f8cf214b78029e2cd1e9398229dda0-club.gif 8i-94f8cf214b78029e2cd1e9398229dda0-club.gif 7i-94f8cf214b78029e2cd1e9398229dda0-club.gif 6i-94f8cf214b78029e2cd1e9398229dda0-club.gif 5i-94f8cf214b78029e2cd1e9398229dda0-club.gif 4i-94f8cf214b78029e2cd1e9398229dda0-club.gif 3i-94f8cf214b78029e2cd1e9398229dda0-club.gif 2i-94f8cf214b78029e2cd1e9398229dda0-club.gif
Hand 3 Ai-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif Ki-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif Qi-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif Ji-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 10i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 9i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 8i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 7i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 6i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 5i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 4i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 3i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif 2i-2b47b78b9878c3d3b29bd4f7d2d03e19-diamond.gif
Hand 4 Ai-37cc42c4042ea4372806e327e67b2e42-spade.gif Ki-37cc42c4042ea4372806e327e67b2e42-spade.gif Qi-37cc42c4042ea4372806e327e67b2e42-spade.gif Ji-37cc42c4042ea4372806e327e67b2e42-spade.gif 10i-37cc42c4042ea4372806e327e67b2e42-spade.gif 9i-37cc42c4042ea4372806e327e67b2e42-spade.gif 8i-37cc42c4042ea4372806e327e67b2e42-spade.gif 7i-37cc42c4042ea4372806e327e67b2e42-spade.gif 6i-37cc42c4042ea4372806e327e67b2e42-spade.gif 5i-37cc42c4042ea4372806e327e67b2e42-spade.gif 4i-37cc42c4042ea4372806e327e67b2e42-spade.gif 3i-37cc42c4042ea4372806e327e67b2e42-spade.gif 2i-37cc42c4042ea4372806e327e67b2e42-spade.gif

Next, we play the game, whatever it is. It really doesn’t matter, since we know exactly what hand everyone has, right? So don’t worry about the rules for that. What’s important is that next the dealer carefully picks up each hand in reverse order and stacks them, restoring the original arrangement of the deck.

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Lenski gives Conservapædia a lesson

Once again, Richard Lenski has replied to the goons and fools at Conservapædia, and boy, does he ever outclass them. For a quick outline of the saga, read this summary at A Candid World; basically, Andy Schlafly has been demanding every bit of data from Richard Lenski’s work on the evolution of E. coli, despite the fact that Schlafly doesn’t have the background to understand it and doesn’t have any plan for what he would do with it if he got it. Lenski has been polite and helpful in his replies; his first response is a model for how to explain difficult science to a bullying ideologue. Now his second response is available, and while he has clearly lost some patience and is unequivocal in denouncing their bad faith efforts to discredit good science, he still gives an awfully good and instructional discussion.

I’ve put the whole thing below the fold, in case you’d rather not click through to that wretched hive of pretentious villainy at Conservapædia.

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The wisdom of the cephalopod

That smart guy, Carl Zimmer, has written an article on those smart molluscs, the octopus. I like that his conclusion is that we can’t really judge their intelligence, because it is different than our own.

That’s the same answer I give to questions about the existence of intelligent life in the universe. I suspect that it’s there (but rarer than most astronomers seem to think — intelligence is an extremely uncommon adaptive strategy here on Earth, as is probably likewise elsewhere), but that it will be radically different in intent and action than our own, as different as we are from a squid, or a dolphin, or an elephant, to name a few forms that have evolved large brains. Often, the question of alien intelligence is more like, “Are there people like us out there?”, and I think the answer to that one is clearly no, almost certainly not. There are too many alternative pathways.

Historical contingency in the evolution of E. coli

Blogging on Peer-Reviewed Research

While I was traveling last week, an important paper came out on evolution in E. coli, describing the work of Blount, Borland, and Lenski on the appearance of novel traits in an experimental population of bacteria. I thought everyone would have covered this story by the time I got back, but there hasn’t been a lot of information in the blogosphere yet. Some of the stories get the emphasis wrong, claiming that this is all about the rapid acquisition of complex traits, while the creationists are making a complete hash of the story. Carl Zimmer gets it right, of course, and he has the advantage of having just published a book(amzn/b&n/abe/pwll) on the subject, with some excellent discussion of Lenski’s work.

The key phrase is right there at the beginning of the title: historical contingency. This paper is all about how accidents in the genetics of a population can shape its future evolutionary trajectory. It is describing how a new capability that requires some complex novelties can evolve, and it is saying plainly that in this case it is not by the fortuitous simultaneous appearance of a set of mutations, but is conditional on the genetic background of the population. That is, two populations may be roughly equivalent in fitness and phenotype, but the presence of (probably) neutral mutations in one may enable other changes that predispose it to particular patterns of change.

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