Recently in Origin of new genes and new information Category

Note: I am extremely busy this summer, finishing grad school and moving to a postdoc. But when I got this book, I realized I wouldn’t be able to focus on my real work without having gotten my 2 cents in. This is a rough-and-ready piece, so typos and missing references, and missing explanations of technical terms are to be expected, although I’m sure they can all be figured out with a wee bit of googling. I am off to Evolution 2013 tomorrow and will be incognito, writing, after that. So I may not comment much. However I expect commenters to be reasonable discussants and polite and will ban people who break the spirit of this expectation. Cheers, Nick

Review of Stephen C. Meyer’s Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design

This week, a new book came out by Stephen Meyer, Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design. Having followed the ID movement and specifically its arguments on the Cambrian ‘Explosion’ for a long time, as well being somewhat up on the recent literature, and especially on phylogenetics, I feel that I have a pretty good sense of what to look for in any work purporting to be a capable commentary on the topic. As I read through Meyer’s book, though, in case after case I see misunderstandings, superficial treatment of key issues which are devastating to his thesis once understood, and complete or near-complete omission of information that any non-expert reader would need to have to make an accurate assessment of Meyer’s arguments.

There is still mostly an eerie silence from the creationists/IDists on the Springer/Cornell issue (previous PT posts: 1, 2, 3). Basically all we have in terms of official response are the comments given to Inside Higher Ed. But much of the evidence of the details of the conference that originally existed has been taken down. Here are the examples of which I am aware:

As those who have followed the comment thread on the previous post know, the link to the webpage for the forthcoming creationist/ID “Biological Information: New Perspectives” volume on the Springer website went dead yesterday, approximately 24 hours after the PT post went up. This may mean that the volume had already been identified as problematic, and the webpage was put up due to some oversight or failure to update a database.

Surprisingly for the ID movement, which normally cries “oppression” and “freedom of speech” at the first sight of criticism, there has been virtually no reaction so far. The only creationist reaction is from Todd Wood, who is a lone wolf in the creationist movement in several ways. David Klinghoffer at the Discovery Institute (DI) did put a post up at the DI Media Complaints Division soon after my post, but it was taken down before anyone saw it, except apparently for Google blog aggregators.

[Review of Shapiro, James A. Evolution: A View from the 21st Century. FT Press Science, ISBN: 0-13-278093-3, $34.99 Publisher’s site]

Over the years there have been many books that purport to “radically revise” or “supplant” Darwinian evolutionary biology; they come with predictable regularity. Usually they are of three kinds: something is wrong with natural selection, something is wrong with inheritance, or something is wrong with phylogeny. This book, by geneticist James A. Shapiro, exemplifies all three.

How to afford a big sloppy genome

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Blogging on Peer-Reviewed Research

My direct experience with prokaryotes is sadly limited — while our entire lives and environment are profoundly shaped by the activity of bacteria, we rarely actually see the little guys. The closest I've come was some years ago, when I was doing work on grasshopper embryos, and sterile technique was a pressing concern. The work was done under a hood that we regularly hosed down with 95% alcohol, we'd extract embryos from their eggs, and we'd keep them alive for hours to days in tissue culture medium — a rich soup of nutrients that was also a ripe environment for bacterial growth. I was looking at the development of neurons, so I'd put the embryo under a high-powered lens of a microscope equipped with differential interference contrast optics, and the sheet of grasshopper neurons would look like a giant's causeway, a field of tightly packed rounded boulders. I was watching processes emerging and growing from the cells, so I needed good crisp optics and a specimen that would thrive healthily for a good long period of time.

It was a bad sign when bacteria would begin to grow in the embryo. They were visible like grains of rice among the ripe watermelons of the cells I was interested in, and when I spotted them I knew my viewing time was limited: they didn't obscure much directly, but soon enough the medium would be getting cloudy and worse, grasshopper hemocytes (their immune cells) would emerge and do their amoeboid oozing all over the field, engulfing the nasty bacteria but also obscuring my view.

What was striking, though, was the disparity in size. Prokaryotic bacteria are tiny, so small they nestled in the little nooks between the hopper cells; it was like the opening to Star Wars, with the tiny little rebel corvette dwarfed by the massive eukaryotic embryonic cells that loomed vastly in the microscope, like the imperial star destroyer that just kept coming and totally overbearing the smaller targets. And the totality of the embryo itself — that's no moon. It's a multicellular organism.

Like I just said – as DI guy David Klinghoeffer posted yesterday, the origin of hundreds of new genes in Drosophila is just microevolution. This is a direct deduction from their own ID/creationist logic, where small amounts of change “within the kind” are no problem for normal evolutionary processes. Too bad for Behe, Luskin, etc. Here’s the full quote for when they realize the problem and take the post down:

Jerry Coyne reports on a new paper in Science by Manyuan Long and colleagues on the origin and history of new genes in a large group of Drosophila that have recently had their full genomes sequenced.

Having this much phylogenetic and genomic information allows researchers to estimate the phylogenetic position of the origin of a new gene (566 new genes amongst the group of 12 fully sequenced genomes, actually), and the periods of time in which directional selection, stabilizing selection, or drift were the dominant regime that the new genes were evolving under. In many cases, there is a period of high selection after the origin of the gene, which weakens later – which is just what you would expect if the well-known, standard model for the origin of new genes is correct.

Two additional points are worth mentioning: (1) in some cases (about 30%, 59 out of the 195 they targeted for knockout studies), these new genes have become essential to viability for the species in question – even though they are totally absent in other, basically similar, flies that do just fine without them! This is strong support for the notion that one way “irreducible” systems evolve is by evolving parts that are helpful at first, but later become essential as other parts coadapt to become dependent on them. (2) I’m sure Luskin, Ewert, and other DI people would like to dismiss this as just another case of evolutionists “illegitimately” inferring common ancestry from “mere” sequence similarity, and that “common design” could be the explanation. However, in any other context, these creationists, and virtually any creationists including the young-earthers, would easily say that all of these Drosophila are just different varieties of the Drosophila kind, and that whatever variety exists between them (minor, in the grand scheme of biology) is “merely” “microevolution within the kind!” (And in the Edge of Evolution, Behe clearly puts his estimated “edge” well above the genus level.)

What’s that? Standard boring microevolutionary processes can produce new genes with modified sequences and new functions, which is clearly new information on anyone’s definition, even the creationists’ and even (explicitly so) Michael Behe’s definition? Oh my goodness, someone better call the DI news blog to put out this fire and reassure the faithful!

References

Chen, S., E. Zhang, and M. Long. 2010. New genes in Drosophila quickly become essential. Science 330:1682-1685.

A previous bit of ranting on this topic by me (responding to Luskin’s ridiculous critique of another famous paper by Manyuan Long, entered into evidence in the Kitzmiller case as exhibit P-245, actually: Long et al. (2003), Nature Reviews Genetics, “The origin of new genes” (free online in many places).

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