Fathered by the mailman? Well, not the mailman—it was the PM’s private secretary

April 10, 2016 • 9:15 am

by Greg Mayer

A lot of work in behavioral and evolutionary biology concerns the evolution of mating systems—polyandry, polygyny, monogamy, promiscuity, and the like—and elucidating the factors that lead to the evolution of one or another. Mating systems can be variable within a species, and human societies exhibit a range of mating systems, with monogamy and polygyny being perhaps the most common. But these culturally defined mating systems may exist more as aspirational norms than as universal practices. From a biological point of view, it is actual paternity and maternity that count, not what the culture deems most appropriate.

In a piece in the New York Times, Carl Zimmer takes a look at this in human societies, asking how often is it the case that the father of a family’s children is not the mother’s spouse, but rather some other male who has fathered the children through adultery.  This is a popular theme of “reality” TV, but Carl concludes it’s an old wives’ tale, citing a review by Maarten Larmuseau and colleagues in press in Trends in Ecology and Evolution. Using a variety of approaches that have become possible only since the development of DNA sequencing, including ordinary paternity testing and the clever use of Y chromosomes in concert with family genealogies and historical migration events, they show that “extra pair paternity” (EPP, i.e. cuckoldry) is actually rather rare—only 1-2%.

Carl notes that this is not as unexpected as the myth would have you believe. In species with females who frequently have multiple mates, males evolve a number of adaptations to insure the precedence of their sperm over other males—and men have none of these sorts of adaptations.

But, as luck would have it, on the very day Carl’s article appeared, a case of human EPP is also in the headlines: of all people, it turns out that the Archbishop of Canterbury’s father was not his mother’s husband! As the Independent put it “DNA test reveals Archbishop of Canterbury Justin Welby is illegitimate son of Sir Winston Churchill’s private secretary“.

The Archbishop of Canterbury, Justin Welby, is forgive me, literally a bastard. (The Sun).
The Archbishop of Canterbury, Justin Welby, is, forgive me, literally a bastard. (The Sun).

My doctoral mentor, E.E. Williams, always said that observations refuting your favorite hypothesis don’t come early in your hypothesizing; a Malevolent Nature ensures that they come only after you’re really convinced you’re right. And in the journalism version of this, the contrary example doesn’t come till you get your piece on the front page of the New York Times. In fairness to Carl, though, one example does not refute his general conclusion, and it isn’t even quite cuckoldry: the Archbishop’s mother had sex with the private secretary just before her marriage, so the birth of the Archbishop-to-be nine months after the wedding had been wrongly assumed to be the fruits of the wedding night.


Larmuseau, M.H.D., K. Matthijs, and T. Wenseleers. 2015. Cuckolded fathers rare in human populations. Trends in Ecology and Evolution in press. pdf

Darwin’s pigeons

February 5, 2013 • 8:39 am

by Greg Mayer

In today’s Science Times, Carl Zimmer has a nice article on Darwin’s favorite birds, pigeons. “Whoa”, you say, “Pigeons? Don’t you mean finches?” No, pigeons it is. While we’ve grown accustomed to associating Darwin’s name with the 15 or so finches of the Galapagos Archipelago (plus one species on Cocos Island), the term “Darwin’s finches” was coined by the British ornithologist Percy Lowe in only 1936, and popularized by David Lack in his 1947 monograph Darwin’s Finches. Darwin collected and observed finches in the Galapagos, and wrote about them, especially in the Voyage of the Beagle, but  he spent many more years studying pigeons, and learned a great deal from them.

Pigeons
Pigeon breeds by A.E. Lydon, from The Boy’s Own Paper, ca. 1892.

Darwin was greatly interested in the work of plant and animal breeders in creating and modifying domestic varieties, and the vera causa (“true cause”) of artificial selection was an important part of Darwin’s argument for the efficacy of natural selection. Darwin corresponded widely with breeders, and gleaned their magazines, collecting a wide variety of facts on the nature of variation and the response to selection. He included some of this in the Origin, but most extensively in Variation Under Domestication (1868, 2 vols.).  Darwin chose pigeons as the domestic species to study most closely, keeping them himself at Down House.

Pigeons
Pigeon skulls, showing striking variation in bill and head shape, from Variation Under Domestication (1868).

The occasion for Carl Zimmer’s piece is a paper in press by Michael Shapiro and colleagues, who have instituted a very interesting program of research on the genetic basis of evolutionary change in domestic pigeons; like Darwin, they are relying on the help of breeders. Early results indicate that all domestic pigeons arise from the wild rock dove, and that certain characteristics, such as head crests, have arisen multiple times, but on the same genetic basis. There’s a very nice set of photos online accompanying the piece.

______________________________________________________________

Darwin, C. R. 1868. The variation of animals and plants under domestication. London: John Murray. (illustrations plus link to full text)

Shapiro, M.D. et al. 2013. Genomic diversity and evolution of the head crest in the rock pigeon. Science, in press. (abstract)

Sulloway, F.J. 1982. Darwin and his finches: the evolution of a legend. Journal of the History of Biology 15:1-53. (pdf)

Evolution: Making Sense of Life

October 5, 2012 • 9:29 am

by Greg Mayer

Another book that was just published in August is a new textbook of evolution intended for biology majors, Evolution: Making Sense of Life, by Carl Zimmer and Douglas Emlen; the title evokes Theodosius Dobzhansky‘s famous 1973 paper “Nothing in Biology Makes Sense Except in the Light of Evolution” (pdf). Carl Zimmer, a science writer and journalist, should be well familiar to WEIT readers, while Douglas Emlen, a biology professor at the University of Montana who works on sexual selection, has also drawn attention here at WEIT for his marvelous photographs of beetle weapons (and I wonder if he’s related to the famous Emlen family of biologists). Many illustrations have been provided by Carl Buell, the noted scientific illustrator. (I reviewed a couple of chapters in manuscript.)

The book is an interesting collaboration between a science writer and a biologist. There have been other such collaborations, usually for large multi-author introductory textbooks, where a writer is brought on to meld together and bring unity of voice to the disparate writing styles of the many scientific authors. In this case however, Zimmer is already a noted author on evolutionary topics, having written such books as At the Water’s Edge (my favorite) and Evolution: The Triumph of an Idea (a companion to the PBS series), and had previously written The Tangled Bank: An Introduction to Evolution, intended as a non-majors text. The new majors’ text grew in part out of this earlier book.

The book is published by Roberts and Company of Greenwood Village, Colorado, a relatively new publisher that is quickly making a name for itself in academic biology publishing. In addition to textbooks, they publish important monographic works (e.g. Trevor Price’s Speciation in Birds, the perfect complement to Jerry and Allen Orr’s Speciation). We’ve noted one of their books, edited by Jonathan Losos, here at WEIT before.

Science goes to Hollywood– what are your favorites?

November 10, 2010 • 4:19 pm

by Greg Mayer

Jerry recently posted on a piece by Carl Zimmer on the depiction of science in movies. Carl doesn’t think Hollywood films have shown very realistic views of science and scientists, and is not sure Hollywood can or should do anything about it. Carl’s more jazzed by the promise and accomplishments of smaller films of the type shown at the Imagine Science Film Festival. This got me to thinking about my own favorite science-y movies, and so, in the spirit of Jerry’s recent literary selections, I thought I’d mention some of my favorite depictions of science and scientists on film. I’ll be putting one up each of the next few days.

I invite WEIT readers to tell us in the comments what are their favorite scenes or films. The ones I’m thinking of capture something I believe to be true about the scientific enterprise; let us know what you found appealing in your favorite. It might be a kernel of truth, but it might be a ‘so bad it’s good’ (a la Plan 9 From Outer Space) kind of thing. I’ll put my first one up tomorrow.

(As an aside, I note Carl wondered why the acid in Alien didn’t burn through the hull of the Nostromo; much more fantastic is how the alien managed to put on about 500 kilos and grow ten feet longer without eating anything after emerging from John Hurt’s chest. The acid, after all, would be used up in the course of reacting with the metal in the hull, but where’d all that body mass come from?)

 

Sean Carroll and Carl Zimmer quit Bloggingheads for promoting creationism

September 1, 2009 • 7:28 am

Bloggingheads.tv was founded (and still largely run) by Robert Wright, and was once funded by the Templeton Foundation.  What does that tell you?  For one thing, to expect a lot of faitheism and sympathy for religion — even on Science Saturday, where it doesn’t belong.  But what I didn’t expect was sympathy for creationism.  Although Bloggingheads, which features online discussions between pairs of writers, scientists, or scholars, has featured some really good stuff, it now seems to be tilting dangerously toward woo.

First there was a discussion on Science Saturday between historian of science Ronald Numbers and Discovery Institute young-earth creationist Paul Nelson — a discussion notable for oodles of mutual back-patting but a dearth of criticism of Nelson’s insane views on the age of the earth.  More recently, Bloggingheads featured another amiable chat between ID creationist Michael Behe and linguist John McWhorter.

Listening to the Behe/McWhorter love-fest, physicist Sean Carroll, who runs the superb blog Cosmic Variance, had enough:

I couldn’t listen to too much after that. McWhorter goes on to explain that he doesn’t see how skunks could have evolved, and what more evidence do you need than that? (Another proof that belongs in the list, as Jeff Harvey points out: “A linguist doesn’t understand skunks. Therefore, God exists.”) Those of us who have participated in Bloggingheads dialogues before have come to expect a slightly more elevated brand of discourse than this.

Various bizarre things ensued:  the LoveFest disappeared and then reappeared on the site, unconvincing reasons were given, and finally Carroll and others had a teleconference call with Robert Wright.  As Carroll tells it, things did not go well:

But, while none of the scientists involved with BH.tv was calling for the dialogue to be removed, we were a little perturbed at the appearance of an ID proponent so quickly after we thought we understood that the previous example had been judged a failed experiment. So more emails went back and forth, and this morning we had a conference call with Bob Wright, founder of BH.tv. To be honest, I went in expecting to exchange a few formalities and clear the air and we could all get on with our lives; but by the time it was over we agreed that we were disagreeing, and personally I didn’t want to be associated with the site any more. I don’t want to speak for anyone else; I know that Carl Zimmer was also very bothered by the whole thing, hopefully he will chime in. .

. . .What I objected to about the creationists was that they were not worthy opponents with whom I disagree; they’re just crackpots. Go to a biology conference, read a biology journal, spend time in a biology department; nobody is arguing about the possibility that an ill-specified supernatural “designer” is interfering at whim with the course of evolution. It’s not a serious idea. It may be out there in the public sphere as an idea that garners attention — but, as we all know, that holds true for all sorts of non-serious ideas. If I’m going to spend an hour of my life listening to two people have a discussion with each other, I want some confidence that they’re both serious people. Likewise, if I’m going to spend my own time and lend my own credibility to such an enterprise, I want to believe that serious discussions between respectable interlocutors are what the site is all about.

. . . I understand that there are considerations that go beyond high-falutin’ concerns of intellectual respectability. There is a business model to consider, and one wants to maintain the viability of the enterprise while also having some sort of standards, and that can be a very difficult compromise to negotiate. Bob suggested the analogy of a TV network — would you refuse to be interviewed by a certain network until they would guarantee to never interview a creationist? (No.) But to me, the case of BH.tv is much more analogous to a particular TV show than to an entire network — it’s NOVA, not PBS, and the different dialogues are like different episodes.

And so Carroll, in a gesture I admire immensely, said farewell to Bloggingheads.tv.

I have no doubt that BH.tv will continue to put up a lot of good stuff, and that they’ll find plenty of good scientists to take my place; meanwhile, I’ll continue to argue for increasing the emphasis on good-faith discourse between respectable opponents, and mourn the prevalence of crackpots and food fights. Keep hope alive!

Business model indeed!  It sounds as if Bloggingheads plans more injections of woo, creationism, and goddycoddling, for if Wright had promised an end to that stuff, I doubt that Carroll would have resigned.  At any rate, Carroll’s stance is personal and nuanced, so do read his piece.  He hasn’t called for anybody else to follow him in defection.

But I do. Respectable journalists like Carl Zimmer, John Horgan, and George Johnson have participated in bloggingheads.tv.  I ask them to have the courage of their convictions and resign if they don’t get assurances that Bloggingheads will stop presenting woo.

. . . Just after I wrote this, I learned that Carl Zimmer has indeed pulled out:

As you can see from Carroll’s post, he was not happy with things either. So he and I talked to Robert Wright and other Bloggingheads people today. I had expected that I’d get a clear sense of what had happened over the past month at Bloggingheads, and what sort of plan would be put in place to avoid it happening again. I imagined some kind of editorial oversight of the sort that exists at the places where I regularly write about science. I didn’t get it. . .

. . .My standard for taking part in any forum about science is pretty simple. All the participants must rely on peer-reviewed science that has direct bearing on the subject at hand, not specious arguments that may sound fancy but are scientifically empty. I believe standards like this one are crucial if we are to have productive discussions about the state of science and its effects on our lives.

This is not Blogginghead’s standard, at least as I understand it now. And so here we must part ways.

The loss of Carroll and Zimmer is a real blow to Bloggingheads.tv — and to science popularization in general.  But you can’t pin this one on Dawkins and his atheist pals; blame it instead on the accommodationist Robert Wright.

_____________________________

Note:

In a comment on Carroll’s post, Robert Wright responds:

It’s true that I didn’t give you the pledge that apparently would have kept you appearing on BhTV: No more creationists or Intelligent Design folks ever on Bloggingheads. I said that, for example, I could imagine myself interrogating ID people about their theological motivation. And I said I’d welcome a Behe-Richard Dawkins debate, since Dawkins is a rare combination of expertise and accessibility. But I also said that offhand I couldn’t imagine any other Behe pairing that would work for me (though there may be possibilities I’m overlooking).

The key thing that I tried to underscore repeatedly in our phone conversation yesterday is this: The two diavlogs in question were not reflective of BhTV editorial policy, and steps have been taken to tighten the implementation of that policy so that future content will be more reflective of it. Sean, I wish that in your post you’d conveyed this to your readers, though I realize that you had a lot of other things you wanted to say.

(Read the whole comment; it’s number 37 after Carroll’s post.)  And Wright also takes a lick at yours truly for my critique of his book.  I’m working on a response to him now, which should be up after my trip to Alabama this week.

Darwinius, the “link” and the book

July 4, 2009 • 12:50 pm

Over at the Times Literary Supplement, paleontologist Ian Tattersall reviews Colin Tudge’s new book on Darwinius, The Link.

As you may remember if you read this and other evolution-related websites (see Greg Mayer’s post on this site), Darwinius masillae is an extraordinarily complete primate fossil that was revealed to scientists and the public in May, complete with a paper in PLoS,  overheated press releases, a movie deal on the History Channel, and, of course, Tudge’s book.  What was truly remarkable about this affair was the degree of hype: a publicity explosion that has never been equaled by any evolution-related discovery (indeed, even the completion of the human genome did not receive such fanfare).  Mayor Bloomberg was there, a press release touted Darwinius (known more familarly as “Ida”) as “a revolutionary scientific find that will change everything” (everything??), and one of the authors of the Darwinius paper, Jens Franzen, proclaimed that “When we publish our results it will be like an asteroid hitting the Earth.”

Well, hardly.  Ida turned out to be a really lovely fossil that didn’t add much to our knowledge of primate evolution.  It is almost certainly an adapiform primate, member of a group that went extinct without leaving descendants, and the early reports that Ida was a “missing link” between the two branches of primates were premature and based on incomplete and sketchy analysis by the scientists who described her.  Ida probably belongs firmly in the lemur/loris group.

Several of the science bloggers realized this immediately, although most reporters swallowed the “missing link” description uncritically (to be fair, they are not primate paleontologists).   The whole sorry affair resulted from the agreement between Ida’s discoverers and the publicists to prevent any scientists other than the “dream team” (that’s what Tudge calls them) from looking at the fossil or the research before publication, and blacking out journalists’ access to the paper until after the big press conference.  In the end, it was the bloggers like Brian Switek, and a few intrepid science journalists like Ann Gibbons and Carl Zimmer, who put Ida in the correct perspective.

According to Tattersall’s review, The Link looks as hyped-up and tendentious as were the original announcements.  The book was apparently written in only a couple of months so that it would appear the day after the press conference:

Colin Tudge’s book is part of the media blitz; and, at the risk of damning it with faint praise, I have to say that it is much the best part. It is more restrained and judicious than the other coverage; and while it does strictly hew to the party line, the hyperbolic statements it makes are always carefully attributed to others. To that extent, it is a thoroughly professional job, as one would expect of a distinguished interpreter of science to the public. . .

If The Link deserves a prize of any kind, it is for the speed with which it was written. Your reviewer has it on good authority that the television producers were still trawling around the Book of Ida project as late as January of this year; and Tudge evidently found he could not meet the almost impossibly short time constraints imposed by the TV schedule without co-opting the assistance of his colleague Josh Young. In combination with deadline pressure, this co-authorship presumably helps to explain a pattern of minor and generally harmless inconsistencies and inaccuracies throughout the book that might have been resolved with more time for reflection. It was hard, for example, to credit that the same author could have written on page 13 that “dinosaurs and mammals had coexisted briefly”, and (correctly), later on, that “the oldest known mammals could be older than the first dinosaurs”. And, in a note at the end of the book, we learn that he didn’t.

In this rather unseemly rush to publication, Tudge and Young were not alone. Speed, as well as obsessive secrecy, seems to have infected the entire Ida project from its inception. As reported by Nature, a member of the Dream Team complained that “there was a TV company involved and time pressure. We’ve been pushed to finish the study; it’s not how I like to do science”. I’m sure it’s not how Colin Tudge likes to write books, either.

Let’s just say that my own opinion is along the lines of Tattersall’s, but less charitable. More about that later.

Darwinius: what’s at issue?

May 21, 2009 • 3:10 pm

by Greg Mayer

I’m leaving in a few days for Costa Rica, and Jerry is back, so this will be my last post on Darwinius, at least for awhile. At least three different issues have been debated in the blogosphere concerning “Ida“: 1) What are her phylogenetic relationships; 2) Was the media campaign excessive; and 3) Has the name been published?

Darwinius on toast1) What are her phylogenetic relationships? This is the most important one, because it is, as John Maynard Smith once put it, about the world, and not about names. Is Darwinius close to the common ancestor of monkeys, apes, and men, or is it a member of the group that includes lemurs and lorises? The question has been raised and discussed most forcefully by Brian Switek at Laelaps, who thinks the evidence presented for relationship to monkeys and apes is weak. To my mind (and I’m not a specialist in primates or even mammals), he’s got a strong point, and we can look forward to a publication by Brian (or some other critic) on this issue.

2) Was the media campaign excessive? The short answer is yes. I expressed some uneasiness over the media campaign here at WEIT, and many others have documented the extravagant claims and consequent media misunderstandings further. See especially what Carl Zimmer had at the Loom, Brian at Laelaps, and PZ Myers at Pharyngula. But by far the best (or at least funniest) take on this was Ed Yong’s satirical evisceration of the inflated media campaign at Not Exactly Rocket Science, from which I have been kindly permitted to reproduce the by now iconic “Darwinius on Toast” above. There are many unresolved questions concerning how to present science to the public, and differing views concerning how aggressive a media campaign should be, but this one was at least one step beyond.

3) Has the name been published? This is the most technical issue, and is about names (rather than the world), but it’s attracted the most attention. See the posts here at WEIT, the Loom (and here), the Lancelet, and Laelaps, including the ensuing commentary by, among others, Henry Gee, Martin Brazeau, and Larry Witmer. There are several issues, and I’ll treat them very briefly (since this is a blog post, and not a paper in the Bulletin of Zoological Nomenclature!).  For reference, The International Code is online here.

3a) Has the name Darwinius masillae been published (in the sense of the Code) in Plosone? No. Many people have noted that Art. 8.6 requires non-paper works to be deposited in 5 major libraries, and that a statement to this effect must be included in the paper. No such statement is in the paper. More importantly, although it has been noted in only one comment I’ve seen, Art. 9 goes on to specify that nothing distributed by the web counts as being published. The non-paper works envisioned in Art. 8 are things like CDs, not web postings. So, the various remedies proposed, such as reposting on Plosone with the requisite statement, would not work. To be published, a non-Web work must be made: paper, CD, DVD (the latter two requiring the fulfillment of the 5 major libraries rule), or something else which satisfies Arts. 8 and 9.

3ai) Can the name be made available by publishing a short paper (on paper) with a bibliographic reference to the Plosone posting? No, because availability by bibliographic reference must be by reference to a published work (Art. 13.1.2), and anything on the Web is not published (Art. 9.8).

3b) Has the name been published elsewhere? I hope not, but fear it may have been. I pointed out that the various newspaper articles may count as publication, because they meet the various criteria for publication (obtainability, simultaneity, etc.; Art. 8), and also contain 1) the name, and 2) are “accompanied by a description or definition that states in words characters that are purported to differentiate the taxon” (Art. 13.11), and even follow Recommendation 13A: “a summary of the characters that differentiate the new nominal taxon from related or similar taxa.” Many newspaper articles, in addition to a general description, included explicit differentia– incisors, grooming toes– from related taxa, thus providing a diagnosis.

3bi) Can newspapers provide a public and permanent scientific record? In my post, I considered that the newspaper articles might be discounted, because perhaps they had not been issued “for the purpose of providing a public and permanent scientific record” (Art. 8.1.1). Some commenters have taken the position that this is self-evidently the case, but it’s not crystal clear to me.  The Code has always been loath to mandate specific formats of publication, specifying rather general properties (availability, simultaneity, identity, etc.) that a variety of formats might fulfill.  Historically, a huge variety of things have counted as publications (although no newspaper examples come to mind). Some newspapers have science sections, some are “papers of record”; I think the spirit of the Code is to approach each case on its individual merits. That is why the Code urges authors and editors to avoid anything that might make the situation murky, but it does so through recommendations (see my previous post for the specific recommendations).

3bii) Doesn’t the Code try to avoid “accidental” publication? Yes it does, as several commentators have pointed out. It has added meeting and symposium abstracts to the list of formats that are not permissible (Art. 9.9) to help avoid what the Code calls “unintentional publication”; but newspapers, as such, are not mentioned. The Code also now requires that the intention to establish a new name be explicit (Art. 16.1). This article is intended to prevent new names, especially a replacement name (nomen novum) to be introduced without mention, en passant if you will. Unfortunately, the newspaper articles make it absolutely clear that a new nominal taxon has been discovered and is being given a new name, and that this is the intention of the authors (on which, see next paragraph).  The Daily Mail article even uses the word “christened”. The Code urges authors to use “sp. nov.” or some other appropriate indication (Rec. 16A), but, again, does not require it. The Code recommends that any appearance of a new name in a work prior to its intended publication be accompanied by a disclaimer, making the new name unavailable (Art. 8.2 and Rec. 8D). The Daily Mail article contains the phrase “a scientific study to be published”: this might be taken to be such a disclaimer, and while it’s not as clear as one might want, it’s perhaps the most straightforward way of discounting the Daily Mail article. Such phrases may (or may not) appear in the other newspaper articles.

3biii) If it has been published elsewhere, who is the author of the name? The Code provides that when it is clear from the contents of a publication that the name and the conditions that make it available other than publication (i.e. the description or diagnosis) are the work of a person(s) other than the author of the publication, then the author of the name is the other person (Art. 50.1.1). In this case, the newspaper articles make clear that the name and its description were provided by someone else, many mentioning Jorn Hurum and Phil Gingerich. They (or whoever is mentioned in the earliest article published) are thus the authors.  This is a good thing, because it gives credit to at least some of the people actually involved in the work. The newspaper reporter would not be the author of the name.

To summarize the question of publication, the name has not been published in Plosone, but it may have been published in a newspaper. I hope the latter is not the case, and perhaps the Commission could issue a clarifying opinion (following an appropriate application) on the status of names published in newspapers (the problem may be distinguishing newspapers from newsletters from cheaply printed bulletins, and so on).

There are some other issues that have been discussed– the merits of paper vs. the web, the nature of peer review– but these go well beyond the particulars of Darwinius, although it might provide a case study for some of these issues. But one of the take home lessons here is that the recommendations of the Code should be taken to heart, and authors and editors should ensure that works affecting nomenclature are “self-evidently published within the meaning of the Code“(Rec. 8B), and that new names should not appear in works prior to their intended publication, or, if they do, they should “contain a disclaimer (see Article 8.2), so that new names published for the first time therein do not enter zoological nomenclature unintentionally and pre-empt intended publication in another work” (Rec. 8D).

Update. While I was writing this, Carl Zimmer got a reply from the Executive Secretary of the ICZN. She confirms that posting on Plosone does not make a name nomenclaturally available. The issue of the newspaper publication was not addressed; I’m not sure if Carl asked about this. I’m leaning myself toward the idea that inclusion of the statement that the study is going to appear somewhere else could be construed as a disclaimer, thus avoiding newspaper publication of the name (I’m still not sure that all newspaper articles included such a statement).

Update 2. Carl Zimmer at the Loom has a nice account of the PR run-up to the press conference, which he titles “Science Held Hostage“. And, also from Carl, Plosone has today printed a 50 copy paper edition. If we can dismiss the newspaper versions (which, as I indicate in my first update, I think we can because they can be plausibly interpreted to have a disclaimer), then the name is now published with the intended authorship; the date of publication is 21 May 2009 (not 19 May, which is when it was posted to the web). Carl also succinctly explains why the nomenclatural rules are necessary:

To those not steeped in species, genera, suborders and suprafamilies, all of these bylaws and codes may trigger vertigo. But keeping the world’s biodiversity in order is not for the faint of heart. With 1.8 million species on the books, and tens of thousands of new ones being added every year, taxonomists need an intricate set of rules to keep it all straight. The fact that taxonomists share a set of rules, no matter how intricate, was one of the great advances in the history of biology.

The evolutionary biology of the swine flu virus

May 5, 2009 • 6:18 am

Carl Zimmer has a good article in today’s New York Times describing the swine flu virus (“H1N1”) as well as other pathogenic viruses, where they come from, and how they evolve.  It turns out that the swine flu virus actually derived from humans — from the strain that caused the terrible influenza epidemic of 1918 (which killed my paternal grandmother when my father was only six months old).  This virus infected swine, and then combined back with genes from humans and birds to create a more virulent strain:

. . . From time to time, a new kind of flu emerges that causes far more suffering than the typical swarm of seasonal flu viruses. In 1918, for example, the so-called Spanish flu caused an estimated 50 million deaths. In later years, some of the descendants of that strain picked up genes from bird flu viruses.

Sometimes reassortments led to new pandemics. It is possible that reassortment enables flu viruses to escape the immune system so well that they can make people sicker and spread faster to new hosts.

Reassortment also played a big role in the emergence of the current swine flu. Its genes come from several ancestors, which mainly infected pigs.

Scientists first isolated flu viruses from pigs in 1930, and their genetic sequence suggests that they descend from the Spanish flu of 1918. Once pigs picked up the flu from humans, that so-called classic strain was the only one found in pigs for decades. But in the 1970s a swine flu strain emerged in Europe that had some genes from a bird flu strain. A different pig-bird mix arose in the United States.

In the late 1990s, American scientists discovered a triple reassortant that mixed genes from classic swine flu with genes from bird viruses and human viruses. All three viruses — the triple reassortant, and the American and European pig-bird blends — contributed genes to the latest strain.

It is possible that the special biology of pigs helped foster all this mixing. Bird flu and human flu viruses can slip into pig cells, each using different receptors to gain access. “We call the pig a mixing vessel because it can replicate both avian and mammalian influenza virus at the same time,” said Juergen Richt of Kansas State University. “The mixing of these genes can happen much easier in the pig than in any other species.”

05virus1-190

H1N1 (swine flu) virus. From today’s NYT article

Fortunately, experts don’t think this virus has the stuff to cause a serious pandemic.  But they’re still worried about mutation and evolution that could increase its virulence.  As Bill Maher said in yesterday’s clip, creationists who are worried about swine flu are worried about evolution.

Good new paper on the fish-tetrapod transition

March 19, 2009 • 2:17 pm

Thanks to Carl Zimmer for pointing out a new paper by Jenny Clack in Evolution: Education and Outreach: “The Fish-Tetrapod Transition: New Fossils and Interpretations.” This is a good paper for the non-scientist who wants to know more about the documentation of this important transition. In WEIT I wrote mostly about the Tiktaalik roseae transitional form, largely because a lot of work on that fossil was done by my colleague Neil Shubin. I was criticized by some for not mentioning the other important fossils in this sequence, and Clack’s article fills this gap very well. Highly recommended.fish

Are we ready for an “extended evolutionary synthesis”?

February 16, 2009 • 3:30 pm

Over at Time magazine, Carl Zimmer has a good essay, “The Ever Evolving Theories of Darwin”, about Darwin’s contributions and what has happened in evolutionary biology since 1859. The essay was kind of spoiled for me, though, by the ending, in which Zimmer seems to buy into something he calls the “extended evolutionary synthesis”. To quote Zimmer:

In the mid-1900s, biologists succeeded in merging the newest biological developments at the time into a new vision of evolution known as the Modern Synthesis. Today a number of biologists argue that it’s time for a new understanding of evolution, one that Pigliucci has called the Extended Evolutionary Synthesis. For now, they are fiercely debating every aspect of that synthesis–how important gene-swapping is to the course of evolution, for instance, and how gene networks get rewired to produce new traits.

Some researchers argue that many patterns of nature–such as the large number of species in the tropics–cannot be reduced to the effect of natural selection on individuals. They may be following rules of their own. “Which of these ideas is going to actually survive and prove fruitful is anybody’s guess,” says Pigliucci. “I don’t see things coalescing for at least a decade or more.”

It seems to me that a science journalist should do more than simply tell their readers that something new is in the air: a journalist should EVALUATE these new claims. If all one did was say “some evolutionists think. . .”, and then describe their thoughts, any old claim could get press.

It just isn’t true to say that every aspect of the Modern Synthesis is fiercely debated. Richard Goldschmidt, the most distinguished contemporary opponent of the Modern Synthesis, was wrong about speciation, about mutation, about genetics, about the origin of higher taxa, among other things; the Synthesis got all of these pretty much right. Much of WEIT summarizes general conclusions originating in the Modern Synthesis (and the abundant evidence that supports them), about which consensus in evolutionary biology is both broad and deep (WEIT is the 250-page version; for a two-page version of the conclusions, see pp. 10 and 11 of Doug Futuyma’s Evolution, Sinauer, 2005).

And who ever said that the pattern of greater species diversity in the tropics could be completely explained by natural selection? There is the little matter of differences in climate, habitat, and geological history. We already know pretty much that gene-swapping is unlikely to be important in the evolution of many species, like vertebrates (it may play some role, but surely not a major one!), and nobody has suggested that gene networks get rewired by any means other than natural selection.

We have surely gone way beyond Darwin in our understanding of the pattern and process of evolution. But I am irritated by the constant appearance of what I call “BIS”–the Big Idea Syndrome. An evolutionist finds a new phenomenon, say transposable elements, or epigenetics, or “modularity,” and suddenly that one phenomenon becomes the centerpiece of a claim that modern evolutionary theory is ripe for a revolution. Yet when you look for the beef, it isn’t there. Where are all the examples of genetic assimilation, a phenomenon that was said to completely overturn our views?

I may sound curmudgeonly here, but it behooves all of us—especially journalists—to think twice before proclaiming that evolutionary biology is about to experience the equivalent of quantum mechanics.

Note added:  Over at his blog, Rationally Speaking, Massimo Pigliucci has taken issue with my characterization of the “extended synthesis” debate, and I recommend that people read his  case for this synthesis.  I don’t want to get into squabbling, but want to make one point. Massimo says the following:

Jerry is “irritated” by what he calls “BIS–the Big Idea Syndrome,” where any new idea that comes about, be it modularity, evolvability, evolutionary capacitors, epigenetic inheritance, phenotypic plasticity, genetic accommodation, species selection, cis-regulatory evolution, and so on and so forth, “becomes the centerpiece of a claim that modern evolutionary theory is ripe for a revolution.” Again, nobody I know is calling for a revolution, but the above mentioned ideas and empirical evidence cannot simply be filed away as “more of the same.”

Well, I beg to differ, and I think anyone who has read the literature on evo devo, genetic assimilation, modularity, and the like will realize that some of their proponents (I don’t want to name names here) are self-consciously claiming that neoDarwinism is incomplete in very important ways, and that some new viewpoints (not just new data or phenomena) are needed.  Let’s look at part of the invitation to the Altenberg 16 conference:

As you know because you have been involved in this to some extent, for some time now there have been persistent rumors that the Modern Synthesis (MS) in evolutionary biology is incomplete, and may be about to be completed. Such suggestions have been received with skepticism by a number of biologists, including some of the very originators of the MS.

The challenge seems clear to us: how do we make sense, conceptually, of the astounding advances in biology since the 1940s, when the MS was taking shape? Not only we have witnessed the molecular revolution, from the discovery of the structure of DNA to the genomic era, we are also grappling with the increasing feeling – for example as reflected by an almost comical proliferation of “-omics,” that we just don’t have the theoretical and analytical tools necessary to make sense of the bewildering diversity and complexity of living organisms.

This implies, at least to me, that we cannot grasp “the bewildering diversity and complexity of living organisms” without some new tools and insights.  I am not yet willing to sign onto this, because I think the theoretical tools–the idea of natural selection and mathematical population genetics–are already at hand, and although we may get new analytical tools (such as genomics!), the rest is just hard grinding work trying to understand speciation and natural selection in the wild.  I may be wrong, but I don’t scent revolution in the wind yet.

I close with a statement by my old mentor, Dick Lewontin, who of course as an old Marxist would be in favor of revolutions:

“The so-called evolutionary synthesis – these are all very vague terms. . . . That’s what I tried to say about Steve Gould is that scientists are always looking to find some theory or idea that they can push as something that nobody else ever thought of because that’s the way they get their prestige. . . .they have an idea which will overturn our whole view of evolution because otherwise they’re just workers in the factory, so to speak. And the factory was designed by Charles Darwin.”