Tag: Carl Zimmer

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.”

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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.”