April 29, 2007 - May 5, 2007 Archives

The American Enterprise Institute has an interesting discussion title Darwinism and conservatism: Friends and Foes? with Larry Arnhart, from the Northern Illinois University and John Derbyshire, from the National Review, and George Gilder, and John West, from the Discovery Institute.

Gilder ended with a particularly ironic comment about emergent properties

George Gilder Wrote:

When people talk about emergence, it’s a new popular way of saying “I have no clue”.

Does Gilder realize how this describes ID far better?

As a side note: West repeated the specious claim that Doug Axe’s probabilities were relevant to a working protein.

John Derbyshire’s contribution is excellent.

As you have no doubt heard by now, there was a brief exchange on evolution at last night's Republican debate. Senator John McCain was asked bluntly whether he “believed in” evolution. After a moment of hesitation he answered, simply, “Yes.” Moderator Chris Matthews then asked the ten candidates whether any of them did not believie in evolution. Representative Tom Tancredo, Senator Sam Brownback and Governor Mike Huckabee raised their hands.

I provide some further details over at EvolutionBlog. I've also assembled some reactions to the creationist hand-raisers from around the web. In this post and and this post I have discussed some other portions of the debate addressing cultural or scientific issues. Comments to all of this may be left at EvolutionBlog.

Way back in the early 19th century, Geoffroy St. Hilaire argued for a radical idea, that vertebrates and most invertebrates were inverted copies of each other. Vertebrates have a dorsal nerve cord and ventral heart, while an insect has a ventral nerve cord and dorsal heart. Could it be that there was a common plan, and that one difference is simply that one is upside down relative to the other? It was an interesting idea, but it didn't hold up at the time; critics could just enumerate the multitude of differences observable between arthropods and vertebrates and drown out an apparent similarity in a flood of documented differences. Picking out a few superficial similarities and proposing that something just looks like it ought to be so is not a persuasive argument in science.

Something has changed in the almost 200 years since Geoffroy made his suggestion, though: there has been a new flood of molecular data that shows that Geoffroy was right. We're finding that all animals seem to use the same early molecular signals to define the orientation of the body axis, and that the dorsal-ventral axis is defined by a molecule in the Bmp (Bone Morphogenetic Protein) family. In vertebrates, Bmp is high in concentration along the ventral side of the embryo, opposite the developing nervous system. In arthropods, Bmp (the homolog in insects is called decapentaplegic, or dpp) is high on the dorsal side, which is still opposite the nervous system. At this point, the question of whether the dorsal-ventral axis of the vertebrate and invertebrate body plans have a common origin and whether one is inverted relative to the other has been settled, and the answer is yes.

That raises more questions, of course. One is where the nervous system fits into this scheme.

Continue reading "We have the brains of worms" (on Pharyngula)

Lately there has been a lot of posts in the blogoshere about whether doctors need to know anything about evolutionary science. Today I got drawn into this discussion over on Uncommon Descent: I posted on a thread for another reason (see Ed Brayton’s post Sal Cordova’s Rank Dishonesty for that story), and a commenter there replied to me:

You are on record as being pro Darwinist and active in promoting Darwinism. Why don’t you take a crack at supporting Darwinism here for students in general and medical students in particular. And in the process enlighten us.

Well, I spend some time responding to this person here, and in doing so told a story that I’d been thinking about writing up for the Panda’s Thumb.

So I’m going to duplicate-post my comment there as a post here. Here’s what I wrote at Uncommon Descent:

Although many have read the transcripts of the Kitzmiller v. Dover trial (HTML version | PDF version) and found them interesting, reading the transcripts does not give the full sense of what it was like to be in the Kitzmiller courtroom. In real life, in addition to the witness answering questions, the lawyers and witnesses were constantly referring to exhibits that were digitally projected onto a large screen on the right wall of the courtroom. Usually the exhibits were just documents, but when the science witnesses testified, their powerpoint presentations contain fossils, flagella, and everything else in between. I think it is safe to say that the testimony is much easier to understand when read with the demonstrative exhibits available (the exhibit lists and a few exhibits are available online).

However, it takes a lot of work to convert the slides to web format, add captions, embed them in HTML, etc. But as a first step, I and others at NCSE have done this for Kevin Padian’s testimony (testimony+slides | just slides).

I’d like to direct you all over to Red State Rabble to read Pat Hayes’ post this morning entitled “Discovery’s Disturbing Legacy.”

The ID movement has failed scientifically (never having got off the ground), in the courts, and at the ballot box in school Board elections at the state and local level. This has not fazed the Discovery Institute, which is now concentrating on the culture war tactic of associating science (“Darwinism”) with Nazism, eugenics and other cultural evils.

I have just read the latest post of young-earth creationist/Discovery Institute fellow/Biola professor/blogger John Mark Reynolds. I think I am just going to have to occasionally serve the role of his guilty conscience in matters scientific. He has apparently thrown his own scientific conscience down a well somewhere, or he wouldn’t be able to say the wildly hypocritical things he does.

I know we’re all used to seeing creationists dishonestly quoting something written by scientists, but folks I’m about to show you one of the most egregious examples you will ever see of it. This is as bad as Morris and Whitcomb’s famous distortion of Ross and Rezak’s paper on the Lewis overthrust, where they literally quoted a paragraph and stopped just before the sentence that began, “However…..”, to give the impression that the authors were saying the exact opposite of what they actually said. Go read this post by Sal at UD and you will see the following quote:

Continue Reading at Dispatches from the Culture Wars. Comments may be left there.

by Bora Zivkovic

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As the 2007 Science Blogging Conference was such a great success, we are already in full swing in organizing the 2008 conference and hoping to make it even bigger and better than the first one.

Our beta-version wiki is up—check out the homepage and the first, rough outlines of the program (feel free to edit the page and add your idea at the bottom or in the comments). At this point we are trying to get more sponsors so if you and your organization/company/magazine is interested, let us know soon.

Check out out blog for updates.

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Last time, almost in time for the conference, we edited and published the first-ever science blogging anthology, the Open Laboratory 2006, which was an instant hit. Thus, we are already collecting nominations for the next years’ edition. Send us your best posts (or best posts written by others) of the year by using this submission form and help us spread the news by adding this code to your blog or website.

There has been a spate of interest in the blogosphere recently in the matter of protein evolution, and in particular the proposition that new protein function can evolve. Nick Matzke summarized a review (reference 1) on the subject here. Briefly, the various mechanisms discussed in the review include exon shuffling, gene duplication, retroposition, recruitment of mobile element sequences, lateral gene transfer, gene fusion, and de novo origination. Of all of these, the mechanism that received the least attention was the last – the de novo appearance of new protein-coding genes basically “from scratch”. A few examples are mentioned (such as antifreeze proteins, or AFGPs), and long-time followers of ev/cre discussions will recognize the players. However, what I would argue is the most impressive of such examples is not mentioned by Long et al. (1). Below the fold, I will describe an example of de novo appearance of a new protein-coding gene that should open one’s eyes as to the reach of evolutionary processes. To get readers to actually read below the fold, I’ll summarize – what we will learn of is a protein that is not merely a “simple” binding protein, or one with some novel physicochemical properties (like the AFGPs), but rather a gated ion channel. Specifically, a multimeric complex that: 1. permits passage of ions through membranes; 2. and binds a “trigger” that causes the gate to open (from what is otherwise a “closed” state). Recalling that Behe, in Darwin’s Black Box, explicitly calls gated ion channels IC systems, what the following amounts to is an example of the de novo appearance of a multifunctional, IC system.

I'm sure you've already heard about it, so I'm a little redundant to bring it up — Carl Zimmer has a spiffy article in the NY Times about duck phalluses. No, that's not quite right; the most interesting part of the story was the bit about duck oviducts. Female ducks have been evolving increasingly convoluted oviducts to baffle the efforts of duck rapists to inseminate them, and male ducks have been evolving concomitantly long phalluses to thread the maze and deliver sperm to the ovaries.

I'd heard about these huge intromittent organs in ducks before, but this is another fascinating revelation: it took a woman scientist to suggest that maybe, just maybe, they also ought to look at what's going on in the female ducks, and then the whole wonderful story of coevolution of these structures emerged. It's actually a rather embarrassing instance of a scientific blind spot, where the biases of the investigators led them to overlook an important component of the story.

A few weeks back during the whole Egnor kerfuffle, I mentioned how important an understanding of evolutionary biology was to many areas of epidemiology, and specifically, for vaccine development and implementation. As one example, I brought up the phenomenon of serotype replacement, which can occur due to the use of what are called “multi-valent vaccines.” Essentially, these vaccines include strains of pathogens which are either the most common, or the most likely to cause disease–thereby protecting individuals from infection with these specific serotypes, but not making the recipient immune to infection with other strains that aren’t included in the vaccine formulation. The concern is, then, that once those types are reduced in the population via vaccination, other serotypes can come along and fill the niche that they’ve vacated. A recent story by Helen Branswell notes that this is exactly what’s happening with pneumococci:

(Continued at Aetiology)

After having dinner with Dr. Irene Pepperberg, Prof. Steve Steve was pandanapped by a man in a top hat. Perhaps one of those intelligent-design activists at Telic Thoughts, who recently accused the professor of being a panda puppet. They seem to be more familiar with him than they should be.

I know it would mean a lot to Prof. Steve Steve if you friended him on Myspace or joined his fan club on Facebook.

It is spring and dandelion season. I am performing an interesting experiment in artificial selection. Every day, I go outside and pick dandelion flowers. Dandelion flowers are practically the only vegetable waste that I do not compost.

I usually take a bucket and pop the flowers off, as well as the buds. I am more likely to miss the shorter-stemmed flowers, because they are hidden below the grass, which normally needs mowing. I am therefore selecting for dandelions whose flowers mature and go to seed in less than 1 day or whose flowers grow shorter than the grass. It remains to be seen whether growing too short a stem is adaptive; possibly the grass will then prevent the dispersal of seeds by the wind. If so, we can expect to see a period of stasis.

Even after a few days I find that I am picking shorter-stemmed dandelions. Clearly, the later-maturing dandelions are acquiring the characteristics of those I have just picked – even though they are not descended from the previous generation. More surprisingly, the previous generation was not short-stemmed but only aspired to shortness before I nipped it in the bud. The effect depends on distance: there appears to be an inverse-square law, with more-distant dandelions less likely to inherit the shortness of their neighbors.

Dandelions undergo spontaneous generation. More surprisingly, they sometimes appear in their fully mature, adult form within less than 30 minutes: I can scour my backyard, find not a single dandelion, and then come back 30 minutes later and easily find more than one.

I have developed a quantitative theory that explains how the dandelions can appear spontaneously and bring with them characteristics that their neighbors only wished they had: Goddidit.

I anticipate green dandelion flowers any day now.

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