Biology miscellany

July 23, 2012 • 7:35 am

I have one item to recommend and two pictures to show.

The first is Olivia Judson’s article on bacteria in an Antarctic volcano, “Life in an icy inferno,” in July’s National Geographic (you can read it for free). You may remember Judson from either her bestselling book, Aunt Tatiana’s Sex Advice to All Creation, a winsome and evolutionarily-informed look at animal reproduction (Judson has a Ph.D. in evolutionary biology from Oxford), or from her several years of writing the “Wild Side” column for The New York Times.

At any rate, the piece is excellent in three respects. It shows the immense amount of preparation it takes to even visit the Antarctic, much less do research there (she camped on the slopes of the Antarctic volcano Mt. Erebus for two weeks), but interweaves this adventure tale with a scientific discussion about why researchers  are looking for microbes in such a remote place (I’ll let you read the article to find out). Finally, it’s extremely well written.

And here are two photos sent me by pinch-blogger Matthew Cobb, who is in Vancouver this week giving a plenary talk at the 17th International Congress on Animal Reproduction. The first is from the BBC Nature News site, was communicated via Twitter by Helen Ward, and shows two northern gannets (Morus bassanus) engaged in courtship, which can apparently involves gifts of flowery necklaces.  The caption is a bit anthropomorphic, but the picture, by Steve Race, is lovely:

Adolescent northern gannets have been photographed “flirting” with flowers at Bempton Cliffs in Yorkshire, the only mainland colony of the birds in England. The birds are at their busiest in the summer; breeding, nesting and rearing young. Gannets pair for life and the adult birds will return to their cliff homes year after year, decorating it with plants, flowers and nearby debris. Wildlife photographer Steve Race has observed young birds offering feathers and flowers to potential partners during courtship at the RSPB reserve. But he described capturing this scene of a young male presenting his beau with a necklace-like sprig of red campion as “surreal”. Reserve manager Ian Kendall said, “If the pair return next year and have a family, we’ll find out whether their adolescent romancing has paid off.”

And there’s this, originally “tweeted (I hate that word!) by the estimable Ed Yong as “two handfuls of burrowing owls”.

Since many of us like owls, I’ll throw in another photo; I’m not sure who took it, but it and the one above appear on Nicholas Heitzman’s “owl” page. This snowy owl (Bubo scandiacus) is a ghostly presence in a dark wood:

Harriet Hall on Darwinian medicine: it is a useless endeavor?

July 23, 2012 • 5:49 am

In one of my very first posts on this site I questioned the value of “Darwinian medicine”—that area of inquiry that tries to explain disease and the behavior of pathogens as results of natural selection.  Cold viruses, for example, are supposed to make you sneeze to facilitate their spreading, while malaria parasites make you prostrate so that mosquitoes can transmit them to the next host without being swatted. We shouldn’t dismiss these as idle speculations, for we know from the case of the zombie ants that very simple pathogens can do complicated things to their hosts to facilitate the parasites’ transmission.

This is a popular area of evolutionary study, but I’ve sometimes questioned its value in helping us treat disease.  After all, how does knowing that we crave fats and sweets because they were valuable to our ancestors on the savanna help us deal with heart disease?  I find the value of the discipline more in raising interesting questions about the evolution of pathogens than in really dealing with the problems of human health.  Perhaps the malaria protist has indeed evolved to debilitate us as a way of spreading its genes.  But those speculations are difficult to test, and I’m not sure how, if confirmed, they’d help us deal with the disease.  But I can’t resist thinking that thinking about these things is fascinating, and could one day lead to medical payoffs. As we all know, pure science often has unexpected practical consequences.

In response to my questions about evolutionary medicine, David Hillis, an evolutionary biologist, at the University of Texas at Austin, gave a number of practical applications of evolutionary medicine (see his list at the link above). Most of David’s examples involved tracking disease epidemics by using molecular markers or using similar markers to identify, say, the strain of influenza most likely to cause future outbreaks.  And yes, these are useful contributions of evolutionary biology to medicine, though the flu method hasn’t worked all that well.

Darwinian medicine includes other fascinating speculations, like Margie Profet‘s famous theory that morning sickness is a way to protect fetuses from ingestion of damaging toxins by the mother, and therefore doctors shouldn’t try to prevent that nausea lest the alleviation cause birth defects.  I’m not sure where that’s led, though: do doctors now allow morning sickness to proceed untreated? (Profet’s personal story, by the way, is a sad one; you can read a precis here.)

Other studies have shown that fever might be adaptive: the body’s way of killing pathogens by raising its temperature to levels that kill infections. Work on lizards, who can cure themselves of infectious disease by basking in the sun, and hence raising their body temperature, show that preventing that basking allows the disease to persist. The adaptive strategy, then, would be for doctors not to try reducing non-dangerous fevers in their patients, but I’m not sure whether they do that.

So there are two ways to regard Darwinian medicine.  First, as a way to frame evolutionary hypothesis about disease that might be testable.  Second, as a way to cure disease.  But even understanding the first won’t necessarily lead to the second. We know with certainty, for example, the molecular cause of sickle-cell anemia, and are nearly certain how the gene for that disease (a form of beta-hemoglobin with a unique mutation) came to be in such high frequencies (see below), but that knowledge hasn’t lead to a cure or new advances in treatment.  But in other cases doctors simply might be unaware of the potential value of Darwinian analysis, in which case they should be educated in those aspects of evolutionary medicine that promise real benefit.

In a recent post on Science-Based Medicine, “Do we need ‘evolutionary medicine?,” Dr. Harriet Hall discusses the value of these endeavors. The impetus for her piece was reading the 1994 book Why We Get Sick: The New Science of Darwinian Medicine, by Randolph M. Nesse and George C. Williams. My own take on the book was that it was a fascinating read, and did help open up a new area of evolutionary thinking, though it’s early days to expect practical results. (Let me add here that Hall has been a tremendously important voice in the battle for scientific medicine versus quackery.)

Hall’s is a strange article in one respect: she argues both that many evolutionary speculations are untestable or untested, and thus constitute useless “just so stories,” but at the same time claims that doctors have already incorporated evolutionary principles into their practice.

As an example of Hall’s dismissal of evolutionary explanations, here’s what she says about Profet’s Darwinian theory of morning sickness:

This is a testable prediction and there is some evidence to support it; but there is no way to prove that this is the true explanation or the only one. They suggest that suppressing morning sickness might increase the risk of congenital defects. But there is no evidence for that. They recommend that women “respect their nausea” and remember that it may be beneficial. (It would likely decrease your survival prospects if you said that to your wife while she was throwing up for the umpteenth time!) They admit that relieving suffering is important too, but they recommend that any anti-nausea medicine should be carefully evaluated to make sure it doesn’t cause any harm. Of course, we already do that for all medications used during pregnancy. I fail to see how evolutionary thinking adds anything to the care of pregnant women. In fact, I can see how it might result in unnecessary worry and suffering.

But of course one could in principle test that explanation—if not in humans then in animals. (Has that been done? If not, somebody should do it.) That’s the only way to truly show that anti-nausea medication “doesn’t cause any harm.” And Hall says this about fever:

Should we treat fevers? Fever probably evolved as a defense mechanism: it may do something towards helping fight off the infection. Evolutionary thinking makes us ask why we developed this adaptation and whether it is wise to interfere. But do we need evolutionary thinking for this? Doctors have already questioned the need to lower a fever, recognizing that it is not the fever but the infection that needs to be treated, that fever itself doesn’t do much harm, and that lowering a fever might have adverse effects in some cases. I’ve read many discussions of those points, and nowhere did they mention wondering about why we evolved to have fevers. I don’t see that evolutionary thinking adds anything useful to the discussion. Fever is what it is, and we can study it and deal with it without speculating about how it came to be that way.

Yes, we do need evolutionary thinking for this, because it makes more doctors question the value of lowering fevers.  When you have a cold, treating the infection is useless, so maybe we should contemplate not taking fever-reducing medicine.  Such studies could be done (indeed, perhaps they have been—this is not my area of study!), and one would predict that colds would last longer in those individuals who didn’t try to reduce their fevers.  Low fever may not be harmful, but it’s still debilitating, and we need to know whether or not to treat it beyond wiping out the underlying infection.

But then Hall reverses her argument and says that doctors already appreciate the value of evolutionary thinking:

Evolutionary thinking is already an integral part of medicine and an essential element of all biology. E. O. Wilson’s description of medicine as “one of the last unconquered provinces” simply is not true. Doctors regularly think about evolution and study its effects. The evolution of drug resistance in bacteria is the best-known example but there are many others. For instance, we think that sickle-cell anemia has persisted because it only affects those who inherit the gene from both parents, while those with only one copy of the gene (heterozygotes) have an increased resistance to malaria.  G6PD deficiency causes hemolytic anemia but also offers protection against malaria.

But consider this: malaria is a credible explanation, but we can’t prove that it is the real one. Some other factor that we have not considered might be the true explanation, and malaria resistance might be a coincidence. And the malaria explanation is intellectually satisfying to those who ask “why” but it has had no practical impact on diagnosis or treatment.

I’m not sure that I agree with Hall’s characterization of doctors as deeply educated in evolution and its usefulness in medicine.  Certainly drug resistance in bacteria is something that most doctors know about (but many still give in to importuning patients and prescribe unneeded antibiotics), but that’s a rare example.  Beyond drug resistance, I doubt that most doctors know a lot about the application of evolution to medicine.

And Hall’s dismissal of the “malaria” hypothesis for sickle-cell anemia is unfortunate: there is lots of evidence that being a heterozygote for the sickle-cell gene helps stave off malaria.  These include studies of direct fitness of patients. “Normal” individuals carrying two copies of the nonmutant gene have about 85% of the reproductive output of heterozygotes carrying only one copy, because homozygotes are at higher risk for lethal malaria.  Individuals with two copies of the sickle-cell gene usually die before reproducing, because they have the illness, and their evolutionary fitness is zero. When carriers of a single copy have higher evolutionary fitness than either normal or mutant homozygotes, this heterozygote advantage (we geneticists call it “overdominance” or “heterosis”) keeps the disease gene at fairly high frequency in the population. This is one example of how evolution can’t produce absolute perfection, and indeed can lead to considerable suffering. (A beneficent God would have never allowed that mutation to occur).  Too, in U.S. blacks, who are not subject to the selective pressures of malaria, the frequency of the sickle-cell gene has decreased, just as evolutionary theory predicts (there’s also some reduction via intermarriage with whites.)  Finally, there is the remarkable concordance between the distribution of malaria in Africa and the distribution of the sickle-cell gene.

When Hall says that we can’t “prove” that malaria is the evolutionary cause of high frequencies of sickle-cell anemia, she’s asking for too much. Science can’t “prove” anything.  But the evidence is strong that the evolutionary theory is correct.  Of course, as I noted above, in this case it hasn’t helped us treat the disease.

Hall concludes again that evolutionary thinking is deeply ingrained in doctors, but also that that this thinking hasn’t helped us much:

I’m sorry, but I just don’t “get it.” Am I missing something? Am I just a contrary curmudgeon? Evolution is already an essential part of all science. Medical scientists already understand evolution and apply its principles appropriately. I didn’t see a single example in their book of any significant practical development in medical care that would not have occurred in the general course of medical science as it is commonly practiced, without any need for a separate discipline of “Darwinian medicine.” Evolutionary explanations, whether true or speculative, may satisfy our wish to understand “why,” but I can’t see that they have much objective usefulness.  Instead, they have produced at least one major annoyance: a movement that preaches to us how we ought to revert to the supposed diet of our ancestors (the Cave Man Diet, etc.).

The answer to Hall’s question is “yes,” she is being somewhat of a curmudgeon. She makes some good points in her piece—the most important being that understanding the evolutionary basis of disease or pathogen behavior may not help us find cures—but I think she’s wrong in believing that most doctors are deeply ingrained with principles of evolution. Many doctors haven’t taken a course in evolution in college, and certainly don’t learn about it in medical school. (Readers who are physicians may want to weigh in here.) And I’m pretty sure that some evolutionary hypotheses will lead to testable treatments that might not have arisen without an evolutionary viewpoint.  Just because an idea remains a speculation rather than graduating to a full blown theory with some empirical support does not mean that we’ll find a way to test it.  I haven’t given up on Darwinian medicine.

Alison Krauss: “Baby now that I’ve found you”

July 22, 2012 • 6:33 pm

I haven’t quite finished Female Country Singers Week. There are two to go—one American and one Canadian.

Those of a certain age will remember listening (and dancing) to the old rock song “Baby now that I’ve found you,” released in 1967 by The Foundations. It was a huge hit, and covered by several other artists, including Donnie and Marie Osmond. But the best cover by far is this one, by the awesomely talented singer and fiddler (“fiddler” doesn’t really cover it) Alison Krauss.

Born in 1971 in Decatur, Illinois, Krauss, who often records with her group Union Station, has won more Grammys than any other living artist (27); the only musician with more is the late conductor Sir George Solti (30).

I must admit that I didn’t know much about Krauss until a few months ago, but since then I’ve been entranced by her lovely voice and her talent on the fiddle.  And what she does with the Foundations song is amazing—it’s countrified a tad and made far more melancholy. And how in blazes did she even think to redo this song?

If you want to hear the original rock version, it’s here.

Rick Warren denies blaming Colorado shootings on evolution

July 22, 2012 • 4:05 pm

The other day I posted one of pastor Rick Warren’s “tweets” that appeared to blame the mass murders in Aurora, Colorado, on evolution.  That’s the way everyone interpreted it, and there was no immediate denial on Warren’s part.

Now, however, Warren has explained that his “tweet” had nothing to do with that, but was related to a parent’s question about his daughter’s sexuality.  He left this comment on the website Exploring our Matrix:

TWITTER’S limit on words allows no context for statements. A lack of contxt causes misinterpretation. So when you tweet what’s on your mind, people preassume (incorrectly) that you are talking about what’s on THEIR mind. This is a clear example. My tweet was a brief response to a question to me about SEXUAL PROMISCUITY. It had NOTHING to do with the tragedy in Colorado.! I had received this email from a dad: “Pastor Rick, my daughter told me her teacher said in class “There’s nothing wrong with sex with multiple partners! Sex is a natural, inate drive, and any attempt to limit it to one, single partner is a manmade construct.” THAT is what I was commenting on. Unfortunately, you also incorrectly presumed the context.

Assuming Warren can document that email, I have no choice but to take him at his word, and I retract my implication that he connected the Aurora shooting to evolution or science.

The lesson, I suppose, is that we lept to conclusions too fast, perhaps conditioned by other pastors’ previous actions in blaming tragedies on evolution. To be sure, I followed Warren’s Twitter feed for two days to see if he clarified his statement, and didn’t see anything. But in light of this clarification, I feel compelled to retract my accusation.

RIP John H. Willis, Jr. (1929-2012)

July 22, 2012 • 10:38 am

If you didn’t go to The College of William and Mary (W&M), as I did, or live in Williamsburg, Virginia, you probably don’t know of John H. Willis, Jr.—everyone called him “Jack”—but he was an important figure in my life as well as a regular reader of this website. He never commented here, but emailed me from time to time about how much he liked the website’s combination of literature, philosophy, biology, and theology.  And his son, John Willis III, is a close friend of mine: a former grad student in my department and now a professor of biology at Duke. (I’m grateful to John III for details and photos.)

Jack died on June 29 in Richmond, Virginia.

Jack Willis was a professor of English at W&M, specializing in 20th-century literature.  (He wrote books on William Empson and Leonard and Virginia Woolf.) I never took one of his courses, but by all accounts he was a superb teacher, and won several awards.  After he retired ten years ago, he continued teaching in W&M’s adult education program, and told me that his adult students, having experienced much more of life, were more attentive and engaged by the material than were his earlier undergraduates.  His son John told me that when he visited a cheese store in Williamsburg, the owner told John how much he had enjoyed Jack’s course on Ulysses. It takes a lot to get a purveyor of cheese interested in that dense book!

I won’t recount the details of Jack’s life, for you can read about them in the obituaries in the William and Mary News and The Virginia Gazette.  I just want to briefly describe how I knew him.

Although a former Navy man, a natty dresser, and Associate Dean and Vice-President for Academic Affairs at a conservative Southern school, Jack was at heart a liberal and a nonbeliever. That was an unimaginable combination for an administrator at W&M. I first encountered him in the summer of 1969, when I was on an NSF undergraduate fellowship, doing research on fruit fly evolution in W&M’s biology department. I was also a “hippie,” at least insofar as that term applies to someone with strong academic ambitions.

During that summer the College hosted a meeting of “Boys State,” a youth organization sponsored by the conservative American Legion.  One of the scheduled events was a presentation by military men to the kids about the awesome advantages of joining the American military.  But that was during the Vietnam war, and I was a strong opponent of that war, deploring the unnecessary killing of Americans and Vietnamese. Several students and I decided to picket the presentation.  The Virginia State Police were called in and told us we had to leave the campus.  I told the beefy state trooper that I had a right to be on campus since I was officially doing research for the Biology Department.

That didn’t matter. The cop told me not only told me I had to leave campus or face arrest, but that he wanted to see me run off campus.  He said, “Boy, I want you off this campus in two minutes, and I want to see you run.” Such were the Virginia State Police. It was purely an exercise in power: they relished seeing me run away from them in terror.

At that moment Jack Willis walked up and asked the officer what was going on. The officer, drawing himself up, said that I was on campus illegally and then demanded of Jack, “And who might you be?”

Jack replied—and I’ll never forget this—”I’m dean of this college. And who might you be?”  The officer immediately became sheepish and apologetic, and let me stay on campus.

After that I would drop in on Jack from time to time in his offices in the administration building. I was a scruffy, bearded lad in blue jeans and a tee shirt, and Jack was, as always, dressed impeccably in coat and tie, his hair cropped short as befits a former Navy man.  We talked about a lot of things, but particularly the Vietnam war, the battle for civil rights, and the troubles afflicting the college (some of us tried to boycott classes during antiwar demonstrations in Washington D.C. or engage in other unsavory left-wing activities).  Jack was always sympathetic, and it meant so much to have a big-time administrator really listen to me rather than blow me off.  He always had time for a chat and a bit of bucking-up.

When I formed my four-person examining committee for my undergraduate honors thesis, I chose three biologists—and Jack.  It was highly unusual to have an English professor on a biology committee, but he certainly pulled his weight.  Jack had a lifelong interest in biology and the outdoors (see picture below), and thoroughly read my thesis and asked penetrating questions. The biology professors were impressed. (My work was on attempts to create sexual isolation between Drosophila strains in the lab; it was later published in Genetics.)

Although I didn’t keep in touch with Jack for many years, I knew what he was up to via his son John, and, when I started this website, I heard from Jack from time to time. I knew he enjoyed the site, and I have this last email from him, dated October 18, 2011.

Dear Jerry:

I believe you might come back for your 40th Reunion this weekend for Homecoming.  If so, I’d love to hear from you if you have a minute.

I’ll be home, and probably out clearing brush and gardening on Sat., but it would be great to get a call.

Home number:  [redacted]

John and Sue [John’s spouse] are just back from an amazing ten days in China, as you may know, all expenses paid by Beijing Normal University.  Anne [Jack’s wife] and I stayed with Emma and William [John and Sue’s kids] while they were away, and had a grand time.

Congratulations on your 40th.  You make me especially proud of William and Mary.

Best wishes !    Jack

However proud I made him of William and Mary, he made me prouder of him and my college. He was an extraordinary man, a superb teacher, and an empathic friend at a time when I needed support.  My sympathies go out to his family and many friends.  A good teacher is so rare, and a good teacher who will listen to students about nonacademic problems even rarer. I’ll miss Jack a lot, and since he was an avid reader of this site, I wanted to express my appreciation here for his presence in my life. His was a life lived to the fullest, replete with family, friends, and his beloved books.

Finally, here’s a photo of Jack taken at Mountain Lake Biological Station, a University of Virginia field station in the southwest part of the state. (Butch Brodie, director of the station, is married to Jack’s daughter Susan.) It perfectly expresses both Jack’s amiability and his love of the outdoors.

Creationists vandalize a park sign for God

July 22, 2012 • 5:13 am

Reader Barry sent me two photos he took of a Park Service sign on Sheep Mountain Trail near Loveland, Colorado.  The 60-million-year age of the Rocky Mountains has been altered to something more Biblically accurate:


UPDATE: Lest you think creationist vandalism of park signs is limited to the U.S., take a gander at the email and photo sent me by reader David M. from Australia:

In relation to your WEIT post today,  this is a defaced sign in Mt Taylor Reserve, which is only 6km south of Australia’s Parliament House in Canberra. The b4stards are everywhere.  I had taken this photo last year.

Sophisticated Postmodern Theology proves a disappointment

July 22, 2012 • 5:12 am

In my latest copy of New Humanist, Jonathan Rée reviews a book by postmodernist Bruno Latour, who has written several books about the lack of objectivity of science. Latour’s new book, On the Modern Cult of the the Factish Gods, actually came out in 2010, and I didn’t know of it. But the sentences below in bold, taken from Rée’s review, piqued my interest, so I got the book from the library:

Readers with a limited appetite for paradox may quickly tire of Latour; but they should not close the book without looking at the final pages. On The Modern Cult of the Factish Gods concludes with a brief and brilliant essay entitled “How Not to Misunderstand the Science and Religion Debate”, featuring a notable act of self-outing. There is, Latour confesses, a simple crass label for the kind of thinker he has always been: “I have been raised a Catholic,” he says, and it seems his faith has never wavered, even though – “in my tradition, in my corner of the world,” as he puts it – he could never mention it without embarrassment. “I cannot even speak to my children,” Latour says, “of what I am doing at church on Sunday.”

How could I resist a demand that I read a brilliant piece on the science and religion debate? Not knowing Latour, I jumped in.  What a mistake!

Here’s Latour’s thesis as described by Rée, which I won’t belabor except to say that Latour rejects attempts to harmonize, or even compare, science and religion because of their different ways of handling “truth”:

Abjuring facetiousness for a while, Latour offers a moving comparison between religious words and words of love: their truth, he says, is a truth of transformation rather than a truth of information. Uncomprehending outsiders will assume that the transformative truths of religion are about getting yourself teleported to some other, better world, but for insiders the opposite will be the case: religious truths serve to remove distractions, enabling us to focus on what is taking place in our space and in our time – to attend to incarnation, to the flesh, to a face, a stone, a child, a fly, a tomato or a piece of wood – and to find them replete with significance, and calling for no response except gratitude, reverence and love.

. . . Religion, it seems, is far more intelligent than most philosophers give it credit for, and there is nothing in it that need offend or alarm the intelligent scientist, the intelligent humanist or the intelligent atheist. Or so Latour would have us believe.

Well, yes, some religious practices encourage introspection, but who can deny that many believers prop their faith upon the factual truth of things like the immortality of Jesus, Mohamed’s status as a prophet of Allah, and the hope of immortality?

Latour’s dissing of science is annoying, and his prose is leaden (this is characteristic of postmodernism—why do they write so dreadfully?). I offer a sample of that vaunted last chapter, which, though mercifully brief, is far from brilliant. Put on your hip boots and wade through this penultimate paragraph of postmodern piffle:

In religious talk, there is indeed a leap of faith, but this is not an acrobatic salto mortale in order to do even better than reference with more daring and risky means, it is a somersault yes, but one which aims at jumping, dancing toward the present and the close, to redirect attention away from indifference and habituation, to prepare oneself to be seized again by this presence that breaks the usual, habituated passage of time. As to knowledge, it is not a direct grasp of the plain and the visible against all beliefs in authority, but an extraordinarily daring, complex, and intricate confidence in chains of nested transformations of documents that, through many different types of proofs, lead toward new types of visions that force us to break away from the intuitions and prejudices of common sense. Belief is simply immaterial for any religious speech-act; knowledge is not an accurate way to characterize scientific activity. We might move forward a bit, if we were calling “faith” the movement that brings us to the close and to the present, and retaining the word “belief ” for this necessary mixture of confidence and diffidence with which we need to assess all the things we cannot see directly. Then the difference between science and religion would not be found in the different mental competencies brought to bear on two different realms—“belief ” applied to vague spiritual matters, “knowledge” to directly observable things—but in the same broad set of competences applied to two chains of mediators going in two different directions. The first chain leads toward what is invisible because it is simply too far and too counterintuitive to be directly grasped—namely, science; the second chain, the religious one, also leads to the invisible but what it reaches is not invisible because it would be hidden, encrypted, and far, but simply because it is difficult to renew.

Kudos to any reader who can tell me what this means. I’ve read a fair amount of postmodern lit-crit and philosophy, but it always boils down to the same conclusion: “lots of fancy words; poorly written; no content.”

All I can say is ZOMG, that I’ve done the hard work for you, and there’s no need at all to read Latour’s “brief and brilliant” last chapter.