My Evolution paper officially out

May 24, 2012 • 7:30 am

My paper on the relationship between acceptance of evolution, religion, and societal health is finally available for free at Evolution (you can see the early publication section here and download my pdf here; if the second link doesn’t work, just go to the first link and download my paper directly—it’s the 9th one down). There are three typos that, I hope, will be fixed, but this is essentially the final piece. If you want the article, I’d appreciate it if you downloaded it from the Evolution site rather than asking me: Evolution keeps track of such things to assess the impact of the journal and of original articles.  If neither of those links works for you, email me and I’ll send you the pdf.

I’m grateful to Daphne Fairbairn, the indefatigable editor of the journal, for her suggestions and willingness to allow the article to be disseminated for free; to Tom Meagher (the Outlook on Evolution and Society editor) and three anonymous reviewers—yes, it was peer-reviewed—for their helpful comments; to our old friend Jason Rosenhouse for reading the whole thing and making many useful suggestions; and to Mona Albano for a wonderful (and voluntary) job of tweaking the prose.

Here’s the abstract:

American resistance to accepting evolution is uniquely high among First World countries. This is due largely to the extreme religiosity of the United States, which is much higher than that of comparably advanced nations, and to the resistance of many religious people to the facts and supposed implications of evolution. The prevalence of religious belief in the United States suggests that outreach by scientists alone will not have a huge effect in increasing the acceptance of evolution, nor will the strategy of trying to convince the faithful that evolution is compatible with their religion. Because creationism is a symptom of religion, another strategy to promote evolution involves loosening the grip of faith on America. This is easier said than done, for recent sociological surveys show that religion is highly correlated with the dysfunctionality of a society, and various measures of societal health show that the United States is one of the most socially dysfunctional First World countries. Widespread acceptance of evolution in America, then, may have to await profound social change.

The reaction in some corners of the blogosphere seems predictable, but I’ll leave you make those prognostications.  All I can say is that when you see religion as responsible for anything bad—even something as palpably obvious as creationism—or suggest that there may some incompatibility between science and religion, there will be nay-sayers alternately bawling and osculating the rump of faith.

I’ll finish with a relevant quote from p. 325 of Carl Sagan’s The Demon-Haunted World (a wonderful book; do read it). I’ve put in bold the sentence that absolutely distinguishes science from religion.

I meet many people offended by evolution, who passionately prefer to be the personal handicraft of God than to arise by blind physical and chemical forces over aeons from slime. They also tend to be less then assiduous in exposing themselves to the evidence.  Evidence has little to do with it: What they wish to be true, they believe is true. Only 9 percent of Americans accept the central finding of modern  biology that human beings (and all the other species) have slowly evolved by  natural processes from a succession of more ancient beings with no divine intervention needed along the way. (When asked merely if they accept evolution 45 percent of Americans say yes. The figure is 70 percent in China.)

Reader earlycuyler‘s cat Lynus gets educated:

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Coyne, J. A. 2012.  Science, religion, and society: the problem of evolution in America. Evolution, published online: 17 May 2012, DOI: 10.1111/j.1558-5646.2012.01664.x

An EMBO report on science blogging

October 21, 2011 • 5:16 am

In the latest EMBO Reports (EMBO = European Molecular Biology Organization) there’s a piece by Howard Wolinsky, “More than a blog,” describing the new wave of blogging by scientists.  It discusses the genre, detailing all of its benefits and perils. And it quotes, among others, Rosie Redfield (exposer of the arsenic-bacteria problems), P. Z., Bora Zivkovic, “GrrlScientist” (I wish she’d give her name, as I think science bloggers shouldn’t use pseudonyms), Sean Carroll, and Professor Ceiling Cat.  At the risk of seeming self aggrandizing, I’ll append one of my quotes:

Coyne, however, does not share his interest in blogging with other senior faculty at the University of Chicago, because he does not believe they value it as a professional activity. Still, he said that he recognizes the names of famous scientists among his blog readers and argues that scientists should consider blogging to hone their writing skills. “Blogging gives you outreach potential that you really should have if you’re grant funded, and it’s fun. It opens doors for you that wouldn’t have opened if you just were in your laboratory. So I would recommend it. It takes a certain amount of guts to put yourself out there like that, but I find it immensely rewarding,” he said. In fact, Coyne has had lecture and print publishing opportunities arise from his blogs.

True, but I don’t have a “blog”!

What I meant about being “grant funded,” of course, is that if your research is underwritten by taxpayers, you incur an obligation, I think, to either explain your work to them or do something else to help them learn about science.

I believe the article is behind a paywall, but, miscreant that I am,  if you shoot me an email I’ll send you the four-page article.

And yes, I think that more scientists should have websites, and that they should put in those websites more than just posts about science.

Science’s publication frenzy—and a solution

September 7, 2011 • 8:06 am

One of the onerous parts of being a research scientist is the pressure to publish lots of papers, which ranks second only to getting grants as a prime inducer of stress.  To obtain tenure or promotion, young scientists now must publish prolifically.  I remember that Mel Green, one of my mentors as a postdoc at The University of California at Davis, told me that in his day (he’s now in his early nineties, and still pushing flies at the bench), a mere one or two quality publications per year was considered a good output.

No longer.  Today almost nobody stands a chance of getting tenure at a major research institution without at least four or five papers per year, good or not.  Numbers are important.  When we were discussing how the administration at the University of Chicago regarded publications at tenure time, my friend Russ Lande told me, “They may count ’em, and they may weigh ’em, but they won’t readem!”  Young students are pushed to submit their papers to Science or Nature, a sure recipe for disappointment since those journals are so selective.  The pressure also leads to what I see as a destructive level of competition and ambition in young scientists.

My own output has been modest: I have 119 peer-reviewed papers since I started graduate school, which works out to about 3.1 per year.  On the other hand, I do have two books, and pride myself on not gratuitously slapping my name on my students’ papers—one reason why some scientists with big labs can have more than 600 publications in their lifetime!

In Monday’s Guardian, David Colquhoun, a well known pharmacology professor at University College London, a fellow of the Royal Society, science critic, and author of the website Improbable Science, decries the publication frenzy that characterizes modern science.  His essay, “Publish-or-perish: peer review and the corruption of science,” points out how the the publication culture has spawned a number of low-quality “peer reviewed” journals, some of such absymal standards that they’ll publish anything.

Peer review is the process that decides whether your work gets published in an academic journal. It doesn’t work very well any more, mainly as a result of the enormous number of papers that are being published (an estimated 1.3 million papers in 23,750 journals in 2006). There simply aren’t enough competent people to do the job. The overwhelming effect of the huge (and unpaid) effort that is put into reviewing papers is to maintain a status hierarchy of journals. Any paper, however bad, can now get published in a journal that claims to be peer-reviewed.

Colquhoun gives one example of an infamous paper by a group at Exeter University that studied the medical efficacy of acupuncture.  Despite the finding of at best a tiny effect of the procedure (barely a placebo effect!), the authors—and the journal (The British Journal of General Practice)—trumpeted that acupuncture “resulted in improved health status and wellbeing.”  Have a look at the figures Colquhoun presents to see how “improved” the status really was!  (note that Colquhoun’s column is followed by a response from the study’s authors as well as the journal’s editor, standing by the paper).  But clearly, there are substantial problems with the research, and the results are so unimpressive that they’re hardly an endorsement of acupuncture.

Colquhoun’s solution is self publication:

So what can be done about scientific publishing? The only service the publishers provide is to arrange for reviews and to print the journals. And for this they charge an exorbitant fee, a racket George Monbiot rightly calls “pure rentier capitalism”.

There is an alternative: publish your paper yourself on the web and open the comments. This sort of post-publication review would reduce costs enormously, and the results would be open for anyone to read without paying. It would also destroy the hegemony of half a dozen high-status journals. Everyone wants to publish in Nature, because it’s seen as a passport to promotion and funding. The Nature Publishing Group has cashed in by starting dozens of other journals with Nature in the title.

Interestingly, Colquhoun suggests Mel Green’s formula of “an average of two original papers per year” (and adds that scientists should hold only one research grant at a time, a presciption that I agree with).

An obvious problem is that junior people would be afraid, in the comments section, to criticize more established ones.  Colquhoun suggests that comments can be anonymous: after all, reviewers’ comments in regular journals are not attached to names.  As for worries of fraud because of the lack of peer review, Colquhoun responds:

Deer [Brian Deer, a journalist who exposed Andrew Wakefield’s vaccine/autism fraut] has recently backed a proposal from the House of Commons Science and Technology select committee that an official regulator should be appointed to police science. I don’t think this could work. Is the regulator going to repeat experiments, or even check original data, to make sure all is well? In all probability, a regulator would soon degenerate into yet another box-ticking quango, and end up, like the Quality Assurance Agency, doing more harm than good. The way to improve honesty is to remove official incentives to dishonesty.

By and large, the problem does not arise from outright fraud, which is rare. It arises from official pressure to publish when you have nothing to say.

The last sentence is absolutely on the mark.

Colquhoun’s proposal has substantial merit. What I see as the biggest problem is that it forces tenure and promotion committees, as well as granting agencies. to actually read and evaluate a candidate’s papers, rather than relying on secondary indicators of “quality” like journal “impact factors,” grant dollars, or numbers of publications.   The main impediment to this system is the laziness of university administrations.

h/t: Dom

The racket of academic publishing

September 1, 2011 • 9:22 am

I’ve always thought that two of the most overpriced things in the world are lattes at places like Starbucks, and the prices of some academic journals.  Most laypeople, whose taxes go to fund scientific research through institutions like the National Institutes of Health or the National Science Foundation, aren’t aware that if they want to have access to the results of their largesse—the scientific articles that emanate from that research—they have to pay huge amounts of money.  And some of those journals turn huge profits from the bloated subscription fees and prices for journal articles (the latter can reach more than $50 US to buy and read a single article online!).

In Monday’s Guardian, author George Monbiot reveals the sordid and grasping capitalism of academic publishing in a piece called “Academic publishers make Murdoch look like a socialist.

If you’re a scientist, read and weep: Elsevier, one of the most notorious offenders, turned a profit of 36% last year.  As Monbiot shows, the journals claim that these exorbitant profits reflect the value added by the journal, but that’s hogwash.  Remember that virtually all of the scientific vetting of the papers published is done for free: as a public service by other scientists!  We get nothing for our close scrutiny that decides which papers get published and which are put in the cylindrical file. 

Further, the subscription rates to libraries are often equally exorbitant (though cheaper online): Monbiot notes that a paper library subscription to Biochimica et Biophysica Acta is an astonishing $20,930 per year.  Of course, if you belong to a university that can afford such a subscription, you can get the papers for free, either in the library stacks or online, but that still leaves the layperson—and scholars at the many institutions that can’t afford these subscriptions—out of luck.

Open-access publishing, free for everyone, is a better deal, but it’s still somewhat of a scam, for in many such journals the authors have to pay thousands of dollars in “publication fees” just to get their articles to appear.  Where does that money come from? From taxpayers, for it’s simply taken out of the part of research grants devoted to “publication.” The taxpayer gets the results online free, but also unknowingly foots the bill.

Monbiot’s solution, at least the first part, is eminently sensible.

In the short term, governments should refer the academic publishers to their competition watchdogs, and insist that all papers arising from publicly funded research are placed in a free public database. In the longer term, they should work with researchers to cut out the middleman altogether, creating – along the lines proposed by Björn Brembs of Berlin’s Freie Universität – a single global archive of academic literature and data. Peer-review would be overseen by an independent body. It could be funded by the library budgets which are currently being diverted into the hands of privateers.

It outrages me as a scientist that I review papers for free (and this often takes an enormous amount of time), while the journals for which I review rake in huge gobbets of cash.  It’s unfair to scientists, and it’s unfair to the taxpayers.  I’m not sure how good a suggestion a single global “publication,” is, though—it would be nearly impossible for a scientist to winnow for good research, for we often direct our attention to those journals known to have stringent quality control and a history of publishing good papers. But at the very least, the public should have low-cost or free access to the research it funds.

Academic publishing is the Starbuck’s latte of science, and the scam has to stop.

h/t: Matthew Cobb

A strong critique of the “arsenic paper”

June 7, 2011 • 5:35 am

I’ve rarely seen a critique this strong in the reviewed scientific literature.  It’s about Wolfe-Simon et al.’s paper in Science suggesting that a bacterium could incorporate arsenic instead of phosphorus in DNA and biomolecules.  Simon Silver and and Le T. Phung take strong issue with this in a piece in the “current controversies” section of FEMS Microbiology Letters, “Novel expansion of living chemistry or just a serious mistake?”  Simon and Phung suggest that although arsenic could have been taken up by the bacteria when they were grown in vitro, there is no evidence that it was sequestered in DNA or other places save perhaps in vesicles, where the desperate bacterium was trying to remove it.

Note, this is not post-publication peer review on a blog, but a critique in the published literature.  And it’s strong from the outset. Take a look at this abstract:

The recent online report in Science (Wolfe-Simon et al., 2010; http://www.sciencexpress.org) that a newly isolated bacterial strain can apparently replace phosphate with arsenate in cellular constituents such as DNA and RNA either (1) wonderfully expands our imaginations as to how living cells might function (as the authors and the sponsoring government agency, the USA NASA, claim) or (2) is just the newest example of how scientist-authors can walk off the plank in their imaginations when interpreting their results, how peer reviewers (if there were any) simply missed their responsibilities and how a press release from the publisher of Science can result in irresponsible publicity in the New York Times and on television. We suggest the latter alternative is the case, and that this report should have been stopped at each of several stages.

Some of the meat:

The questionable conclusion of the paper appears as an established fact in the abstract (first paragraph of the report): ‘arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins.’ There are no data to support this claim, which is repeated. . . . There is no reason to conclude (as the authors have in their penultimate sentence) that they have found life ‘substituting As for P’.

And the conclusion, which tries to exculpate two authors from participating in the paper’s hype (and, I believe, lay the blame for that hype at the door of Wolfe-Simon):

One caveat: we consider two of the senior-scientist authors, R.S. Oremland and J.F. Stolz, to be microbiologists who have contributed in major ways to the understanding of the environmental microbiology of arsenic in recent years (including three reports published in Science in the last 10 years and several in FEMS journals). These caused no antihype flak. We hope our long-term relationships can survive this entirely negative and uncompromising analysis of their new report, which would have been much better handled before publication (Obama style over a bottle of beer), rather than with the excessive Internet hype that the authors initiated and the controversy that developed on newspaper and journal pages. However, this is only a current example of a report, where basically no one who can form a detailed technical opinion believes the conclusions (except the authors), based on the data shown. It is a sad story, reminiscent of the quip: déjà vu – all over again!

Ouch!

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Silver, S. and L. T. Phung. 2011. Novel expansion of living chemistry or just a serious mistake? FEMS Microbiol. Lett 315:79-80.

Neanderthals are us?

May 15, 2011 • 9:03 pm

by Greg Mayer

At least since Socrates explored the meaning of the Greek maxim “Know thyself”, and Alexander Pope added that “the proper study of Mankind is Man”, we have been interested in knowledge about ourselves. But who are we? A paper in press in the Proceedings of the National Academy of Sciences by Ron Pinhasi and colleagues raises this issue with regard to Neanderthals, an issue which Jerry considered a while back: are they us?

In several senses, they obviously are us: fellow mammals, fellow primates, fellow hominids, and fellow members of the genus Homo, and thus men in the generic sense (in both the vernacular and technical senses of generic). But are they members of the same species as us, Homo sapiens? Or members of a distinct species, Homo neanderthalensis?

Life reconstruction of a Neanderthal by John Gurche at the USNM.

The question of whether they are a different species from us is the question of whether or not we could interbreed with each other. And not just mate– but successfully produce fertile offspring. For most of the time since the first reported Neanderthal in 1856, reproductive compatibility could only be inferred based on morphological data, and opinions varied as to whether Neanderthals were a subspecies of H. sapiens or a separate species. The great Finnish paleontologist Bjorn Kurten proposed in his novel, Dance of the Tiger, that Neanderthals and modern H. sapiens could mate and produce offspring, but that the offspring, while showing somatic luxuriance (they were really smart and strong), were completely sterile (a form of post-mating reproductive isolation). Published in 1980 before there was any genetic evidence, a novel, rather than a scientific paper, was probably the right venue for Kurten’s reasoned but entirely speculative proposal.

Early genetic data from mitochondrial DNA indicated that Neanderthal mitochondria were well outside the variability of modern populations, supporting the ideas of those (such as Kurten) who supposed that Neanderthals were a separate species. More recently obtained nuclear DNA sequences, however, showed that 1-4% of the genome of modern Eurasians was derived from Neanderthals (modern Africans lack this admixture of Neanderthal DNA). Thus there was enough successful interbreeding to leave a noticeable signature in modern genomes. Even more recently, a previously unknown fossil Asian population called Denisovans, related to but distinct from Neanderthals, has been shown to have contributed about 5% of the genome of modern Melanesians. Thus, measurable interbreeding occurred between anatomically modern humans and more archaic Eurasian populations as the former spread out of Africa across the remainder of the Old World.

The paper by Pinhasi et al. revises the dating of Neanderthal fossils from the Caucasus, finding them to be older than previously thought (about 40,000 years BP). The authors also suggest that other younger dates are unreliable, and that it is unlikely that anatomically modern humans and Neanderthals coexisted for any substantial length of time. If they are correct, then the Neanderthal (and Denisovan) contribution to modern genomes speaks even more strongly of conspecficity, as the gene flow had to occur over shorter periods of time. There are, regrettably, quite a few historical instances where two peoples (both of course undoubted anatomically modern H. sapiens) met, and one quickly disappeared, with relatively little measurable gene flow having occurred, so the rapid demise of Neanderthals in the face of anatomically modern humans is no bar to their having been the same species. I would interpret the genetic evidence so far as indicating that the Neanderthals, indeed, are us.

In addition to the references below, John Hawks of the University of Wisconsin, Madison, has a fine blog in which he often comments on Neanderthals and other paleoanthropological topics. His take on the Pinhasi et al. paper, which deals more with the dating issues, is here; his view on the species question is here. [JAC: I also discussed the species problem in Neanderthals, reaching the same conclusion as Hawks.]

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Green, R.E. et al. 2010. A draft sequence of the Neandertal genome. Science 328:710-722.

Green, R.E., et al. 2008. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134:416-426.

Kurten, B. 1980. Dance of the Tiger. Reissued by University of California Press, Berkeley, 1993.

Pinhasi, R., T.F.G. Highamb, L.V. Golovanovac, and V.B. Doronichev. 2011 Revised age of late Neanderthal occupation and the end of the Middle Paleolithic in the northern Caucasus. Proceedings of the National Academy of Sciences in press.

Reich, D., et al. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053-1060.

More criticism of Nowak et al.’s attack on kin selection

April 6, 2011 • 10:03 am

For those of you keeping up with the flap on kin selection, there’s a new paper online in the Journal of Evolutionary Biology by F. Rousset and S. Lion.  It’s a critique of the Nature paper by Nowak et al. that attacked both the coherence and importance of inclusive fitness theory (“kin selection”), a theory that has been immensely productive for evolutionary biology in the last five decades.

Rousset and Leon maintain the following:

  • Nowak et al. misrepresent kin selection (inclusive fitness theory) as something different from natural selection
  • Nowak et al.’s critique of Hamilton’s “rule” (“br > c”) is misleading; many of the “criticisms” are either wrong or (as with assumptions of genetic additivity or peculiarities of population structure) became part of kin-selection theory ages ago. Nowak et al.’s assertions that these are fatal flaws in the theory are therefore wrong.
  • Nowak et al.’s own model for the origin of eusociality in insects (the presence of a queen and a sterile worker caste) is far less robust than inclusive-fitness theory, and in fact does not deal with the crucial problem of whether genetic relatedness explains eusociality since their model does not vary relatedness.
  • Nature was severely remiss in publishing such a flawed paper in the first place.

Rousset and Leon are quite critical about Nature‘s handling of the Nowak et al. manuscript.  Here are a few quotes:

We think the publication of this article in a high-profile journal, along with the large media coverage it received, is an illustration of some serious shortcomings in current scientific practice. Arguably, the impact of NTW’s paper reflects to a large extent the rhetorical ability of the authors, rather than the scientific value and novelty of the paper. . .

Stylistically, the paper often departs from the neutrality of scientific prose, using a variety of rhetorical tricks typically found in the discourses of politicians or the writings of polemists, rather than in academic articles. When they ask falsely evident rhetorical questions,1 liken inclusive fitness theory to geocentrism, or claim without justification that their approach is ‘common sense’ (their Appendix, p. 20), NTW are a long way away from what is generally expected of scientific discourse. In particular, it is troubling to see the authors turn to the argument of geocentrism and its unfalsifiable epicycles to discredit inclusive fitness (their Appendix).

The allusion to ‘Darwinian epicycles’ is indeed a typical rhetorical trick used to attack evolutionary biology. . .

. . . We think the wide impact of an article that rests on such fragile foundations calls into question the efficiency of the editorial process in the most famous scientific journals. Nature’s extravagant editorial characterization of the paper as ‘the first mathematical analysis of inclusive fitness theory’ recklessly tramples on nearly 50 years of accumulated knowledge. It is often said that science is self-correcting, but this can be so only if authors are engaged by the validity of what they are writing, if reviewers are engaged in the same way, and if science, rather than only media buzz, impact, and citations, matters to editors.

Agreed. Nature, of course, will never admit that it was remiss in handling the article.

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Rousset, F. and S. Lion (2011). Much ado about nothing: Nowak et al.’s charge against inclusive fitness theory. Journal of Evolutionary Biology, online, doi: 10.1111/j.1420-9101.2011.02251.x