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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IEDG2008: Model systems are dead, long live model systems

I’ve discovered a couple of important things at this meeting.

One, late night sessions at west coast meetings are deadly for any of us coming from more eastern time zones. At least the morning sessions are low stress.

Two, I haven’t heard one Drosophila talk yet, and the message is clear: we’re now in the stage of evo-devo in which everyone is diversifying and chasing down a wide array of species. There was a bit of model-system bashing, but at the same time, everyone is acknowledging the crucial role of those traditional, but weird and derived, lab critters in providing a point of comparison and being the source of many of the tools being used to explore phylogeny now. I thought, though, that the smartest comment of the evening was that now everything is a model system.

I’ve got some dense piles of notes on the evening session, but I’m going to give you the short version of everything, with an emphasis on the novel twists.

Michael Akam talked about segmentation genes, which every developmental zoologist now knows inside and out — trust me, this is a familiar topic with over 25 years of detailed research … in Drosophila. Akam made the point that now it’s looking clear that three of the major segmented phyla, the arthropods, annelids, and chordates, may be using related genes to accomplish segmentation, but they seem to be using different mechanisms — so he considers the question of whether segmentation in these three is homologous is still an open question. He also discussed recent work on the centipede Strigamia (definitely not a lab animal: they can’t breed them in the lab yet, so all the work is done by collecting embryos in the field, in Scotland). They have a dynamic pattern of segment addition that is very different from what you find in flies, and more similar in some ways to chodate segmentation.

Chelsea Specht talked about floral evolution in the Zingiberales. I’m an animal guy, so even the most basic stuff in this talk was entirely new to me. I know the general rules of the spatial development of in the fruit fly of the plant world, Arabidopsis, and she gave us a bit of context there, reminding us of the concentric development of sepals, petals, stamens, and carpels. The Zingiberales are a large and diverse group of plants that includes bananas and ginger, and one characteristic is an extravagant modification of the canonical pattern, with extra stamens, a loss of select stamens, and a fusion of stamens to form a novel structure, the labellum, which in these plants functionally replaces the petals. So of course they’re looking into the genes involved in the patterns, which turn out to be the familiar Arabidopsis genes redeployed in new patterns.

Paul Sereno had a talk that took a very different tack, and was unfortunately giving it at the equivalent of 11:00pm Minnesota time, so I’m sorry to say I didn’t follow it carefully. He was discussing the analysis of morphology, and was advocating the development of tools and techniques to compare data sets in addition to the usual output, phylogenetic trees. He was making the case that a lot of morphological studies are actually very poor (a creationist in the audience would have loved it, largely because he wouldn’t have understood the context) because the input data sets of different studies are not comparable.

And now I have to get back to work and listen to the next set of talks.

Gerobatrachus hottoni

Blogging on Peer-Reviewed Research

It’s another transitional form, this time an amphibian from the Permian that shares characteristics of both frogs and salamanders — in life, it would have looked like a short-tailed, wide-headed salamander with frog-like ears, which is why it’s being called a “frogamander”.

i-3085796f01e5d09425d897b5cd6092e2-gerobatrachus.jpg
Complete specimen in ventral view, photograph (left) and interpretive outline drawing (right). Abbreviations: bc, basale commune; cl, cleithrum; cv, clavicle; dm, digital elements of the manus; dt3, distal tarsal 3; fe, femur; h, humerus; ic, intercentrum; il, ilium; is, ischium; op, olecranon process of ulna; pc, pleurocentrum; r, radius; sr, sacral rib.

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Bat wings and mouse feet

You may recall that a while back I mentioned how Jerry Coyne praised some work on bat evo-devo. I also said that I was going to have to write that paper up sometime. The bad news: I haven’t written it up for the blog. The good news: I did write it up for a future Seed column. The better news: Stephen Matheson has a summary right now, so you don’t have to wait for my column to come out.

You should still subscribe anyway. It’s pretty on shiny paper.

The platypus genome

Blogging on Peer-Reviewed Research

Finals week is upon me, and I should be working on piles of paper work right now, but I need a break … and I have to vent some frustration with the popular press coverage of an important scientific event this week, the publication of a draft of the platypus genome. Over and over again, the newspaper lead is that the platypus is “weird” or “odd” or worse, they imply that the animal is a chimera — “the egg-laying critter is a genetic potpourri — part bird, part reptile and part lactating mammal”. No, no, no, a thousand times no; this is the wrong message. The platypus is not part bird, as birds are an independent and (directly) unrelated lineage; you can say it is part reptile, but that is because it is a member of a great reptilian clade that includes prototherians, marsupials, birds, lizards and snakes, dinosaurs, and us eutherian mammals. We can say with equal justification that we are part reptile, too. What’s interesting about the platypus is that it belongs to a lineage that separated from ours approximately 166 million years ago, deep in the Mesozoic, and it has independently lost different elements of our last common ancestor, and by comparing bits, we can get a clearer picture of what the Jurassic mammals were like, and what we contemporary mammals have gained and lost genetically over the course of evolution.

We can see that the journalistic convention of emphasizing the platypus as an odd duck of a composite creature is missing the whole point if we just look at the title of the paper: “Genome analysis of the platypus reveals unique signatures of evolution.” This is work that is describing the evidence for evolution in a comparative analysis of the genomes of multiple organisms, with emphasis on the newly revealed data from the platypus.

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Evolution, with teeth

My last Seed column is online, which reminds me (as if I weren’t uncomfortably aware already) that I have to finish up the next one today, which actually isn’t the next one, which is already done and submitted, but the one after that. These long leading deadlines force one to live a few months in the future…

You know, if you subscribed to the print magazine, you’d be halfway to my future already instead of living in my distant past.