Introducing the vacation blogger

April 5, 2009 • 6:59 am

This is Matthew Cobb, from the University of Manchester.  He will be posting on this website for about ten days while I’m on a trip.  Matthew is a behavioral biologist working on the neurobiology and behavior of Drosophila.  He’s published two books,  The Egg and Sperm Race, about the early history of reproduction, and a new one about the French Resistance during WW2 (!), soon to appear.  I’ve known him for twenty years, first meeting him as when he was doing a postdoctoral fellowship in France.  Matthew is married, with two daughters and two cats.  The picture below shows him with one of them, Ollie.

matthew-cobb-and-ollie

What counts as evidence for evolution?

April 4, 2009 • 7:07 am

A couple of reviewers of WEIT (and some of my friends and colleagues) have pointed out the book’s dearth of molecular evidence for evolution.  For example, why didn’t I stress that organisms thought to be related based on morphological similarities also show similar relationships in their DNA sequences?  That is, DNA phylogenies generally match morphologically-based phylogenies — doesn’t that count as evidence for evolution?  To my mind, not very strongly, and for two reasons.  First, at least for protein-coding genes, morphology and DNA are not independent: the genes are blueprints for the organism’s appearance, so the coincidence of trees is not independent evidence for evolution.

My strategy here was to use as evidence for evolution only those data that rule out the most widely-accepted alternative scenario, i.e., some form of creationism.  Similarities of molecular and morphological trees don’t necessarily rule out the action of a celestial designer.  He/She/It could have used similar genes to make similar organisms.

Well,  you ask, what about those parts of the DNA that are “neutral”?  (E.g., the third positions of codons, in which a mutation doesn’t necessarily change the structure of the protein made by that gene.)  Well, yes, those could count provided that they really are neutral.  As molecular evolutionists examine genomes more thoroughly, they often find that “neutral positions” aren’t really neutral, but could play some role in the fitness of the organism.  In such cases, their phylogenetic match to appearance-based phylogenies again fails to rule out creationism.

The one type of molecular evidence that does absolutely rule out creationism, I think, involves pseudogenes: those genes that were once active in ancestors but have become inactivated. I describe several cases in chapter 3 of WEIT; they include olfactory receptor genes in humans, many of which have become inactivated in the human lineage as we gradually lost reliance on our sense of smell and became more vision-oriented.  DNA changes in pseudogenes can hardly be subject to natural selection, so pseudogenes change in a purely time-dependent manner as those dead genes accumulate mutations over time.  Thus, the match between phylogenetic trees based on pseudogene DNA sequences (reflecting only the passage of time) with phylogenetic trees based on organisms’ appearance are expected under an evolutionary scenario but not a creationist one.  Creationists largely deny common ancestry (and don’t accept that organisms change with the passage of time). They wouldn’t, then, predict a phylogenetic match between features that simply mark the passage of time and features that independently reflect ancestry (e.g., the placenta of placental mammals that is not found in marsupials).  This is why I concentrated on pseudogenes in my book.  I’ve never seen a creationist explanation for why DNA trees based on pseudogenes match traditional trees based on morphology.

Similarly, people often cite Hox (“homeobox”) genes as evidence for evolution (these are the genes that demarcate different segments of animal bodies). It turns out that in organisms which are very dissimilar, such as humans and my beloved fruit flies, Hox genes nevertheless play similar roles in building bodies.  Why don’t I count this as evidence for evolution? Because it doesn’t rule out the alternative of a celestial designer.   Such a designer could have used the same genes in different species as His/Her/Its way of building bodies.  There’s no reason why a designer couldn’t hit on certain fundamental ways of making bodies, and then use them over and over again.

This, then, was my strategy throughout the entire book: to use only that evidence that could not easily be explained by creationism or other alternatives to evolutionary theory.  This, of course, is precisely the strategy that Darwin used in The Origin, since he had to convince readers that his theory was superior to the reigning creationist paradigm of the day.  I guess you can say that, given prevailing opinions in the US and some other countries, I adopted the same evidence-based strategy.

BBC program: “Did Darwin Kill God?”

April 4, 2009 • 5:22 am

Unsurprisingly, the answer is “of course not!””  In fact — also unsurprisingly — evolution seems to strengthen the narrator’s belief. This one-hour show was on the BBC last week, and although their website won’t play it in the US, the program has been put on YouTube in six segments.  You can access segment 1 below, and then, if you want to watch the rest of the show, go here and click on the succeeding segments that appear next to it on YouTube.

Of what value is evolutionary biology in medicine?

April 3, 2009 • 9:43 am

I have sometimes written that evolutionary biology doesn’t have much practical value in medicine or other areas impinging on humanity’s material well being.  Here is one example of what I’ve said.  However, my friend and colleague David Hillis at The University of Texas in Austin — who played a big role in trying to make the Texas State Board of Education teach real science —  has taken exception to my view.  I asked him to let me know how he thought that evolutionary biology had been of use in medicine, and he wrote me an email with his answer, which he’s given me permission to post.  He’d wants to emphasize that it’s an off-the-cuff response rather than a comprehensive reply, which of course I appreciate; but I think it’s worth posting:

OK, here are just a few examples from the thousands that are in the literature, off the top of my head:

Using positive selection to identify the pathogenic mechanisms of HIV in humans: PNAS 102:2832-2837 (one of many such studies that are now appearing and are using positive selection in pathogens to identify pathogenic mechanisms).

Using phylogenies and positive selection to predict which currently circulating strains of influenza are most likely to be closely related to future flu epidemics: Science 286: 1921-1925.

Using evolutionary analyses to track epidemics in human populations: many examples that have wider health implications, but our study of transmission in a forensic case was an interesting example with a specific legal application; PNAS 99:14292-14297.

Using evolutionary analyses to identify new disease outbreaks: new examples in every single issue of Emerging Infectious Diseases.

Using phylogenetic analyses to identify whether polio outbreaks are from native circulating viruses or from reverted, escaped vaccines (which tells health workers which vaccines to use in these areas to eradicate disease): see review in Bulletin of the World Health Organization, Vol. 82, No. 1.

Identifying changes in sodium channel genes that are under positive selection for TTX resistance, which has led to understanding the function of human diseases that are caused by the corresponding substitutions in human sodium channel genes: Mol. Biol. Evol. 25(6):1016–1024. (I included this one to show that all of the examples are not from virus work; this is the original evolutionary work from Manda Jost and Harold Zakon, with our collaboration, but there has been follow-up on the understanding of human diseases that are produced from these same mutations, now that they have been replicated by in vitro mutagenesis)

This just scratches the surface. I think there are now more papers that use evolutionary methods and analyses in the human health literature than all other areas of biology combined. I think it is crazy to not acknowledge the numerous and important human health applications of evolutionary theory and methods.

David

Well, this is good enough for me — I gladly retract my earlier opinion that evolutionary biology hasn’t been of much use in medicine.  Thanks, David.

NOTE:  In the comments to this post, one reader asks whether David’s examples aren’t just genetic, having nothing to do with evolution?  David has posted a response.

Scientists criticize The National Center for Complementary and Alternative Medicine

April 3, 2009 • 6:41 am

I’ve always been critical of the National Institute of Health’s National Center for Complementary and Alternative Medicine, thinking that it was catering to pseudoscience and feeling that most of the genuinely scientific forms of “alternative healing” could best be studied in the regular sections of the NIH, where they’d have to compete for money with every other project.  Up till now scientists have been pretty mum about the NCCAM, but now they are speaking out about it.  In a nice article in The Washington Post, David Brown talks about scientists’ growing criticism of the Center:

Although NCCAM has a comparatively minuscule budget and although it is a “center” rather than an “institute,” making it officially second-class in the NIH pantheon, the principle is what mattered. But as NIH’s budget has flattened in recent years, better use for NCCAM’s money has also become an issue.

“With a new administration and President Obama’s stated goal of moving science to the forefront, now is the time for scientists to start speaking up about issues that concern us,” Steven Salzberg, a genome researcher and computational biologist at the University of Maryland, said last week. “One of our concerns is that NIH is funding pseudoscience.”

Salzberg suggested that NCCAM be defunded on an electronic bulletin board that the Obama transition team set up to solicit ideas after November’s election. The proposal generated 218 comments, most of them in favor, before the bulletin board closed on Jan. 19.

A fuller discussion of what the NCCAM has failed to accomplish can be found on the blog Quackwatch, and a good general blog on this and similar issues is Science-Based Medicine.

(Thanks to D. J. Grothe for calling Brown’s article to my attention)

Point of Inquiry radio show

April 3, 2009 • 6:23 am

Last week I was on D. J. Grothe’s “Point of Inquiry” radio show, talking about evolution; the link is here.  I can’t bear to listen to recordings of myself, so I don’t remember what I said.  Note, however, that one listener commented that “Dr. Coyne sounded intoxicated to me.”  Let me set the record straight: I had NO titer of ethanol in my body!  Never do before 6 p.m.!

A tip of the hat to D. J. for his relentless promotion of rationality.

Green porno, but safe for work

April 2, 2009 • 7:58 am

rossellini

Isabella Rossellini has produced a group of short videos (two minutes long) for the Sundance Channel about the sex lives of animals.  She gets to dress up in all kinds of costumes and interact with bizarre creatures.  The films are actually very good, with lots of solid science and natural history behind them.  You can find the website here, with information about the series as well as five videos.  I can’t say they’re not salacious, but they’re fun.

You can read an interview with Rossellini about the series on Salon.  An excerpt:

How did you come up with the idea for the series?

Robert Redford [founder of the Sundance Film Festival] came up with the idea that the Internet might offer the opportunity to relaunch the short film series format, which had disappeared. The other thing is that Sundance is very interested in the environment. I’d just worked with them on a project called “My Dad Is 100 Years Old,” that I wrote about my father, Roberto Rossellini, and they offered me the opportunity to do these short films about the environment.