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July 19, 2013

Weed evolution in the New York Times

Carl Zimmer, author of several evolution-themed books and an interesting blog, published an article on weed evolution in Tuesday's New York Times. He used one of my favorite examples of rapid evolution of complex traits (flooding tolerance and crop mimicry in Echinochloa barnyardgrass/watergrass in <1000 years) to make the point that evolution of herbicide resistance (a much-simpler trait) in only a few years shouldn't have been a surprise.
Barrett1983.jpg
(Left) Under selection pressure imposed by farmers with hoes, Echinochloa watergrass evolved to resemble rice more than it resembles its own recent ancestor, barnyardgrass (Barrett, 1983). I discussed this example near the end of this lecture at the International Rice Research Institute.

Glyphosate-resistant weeds are becoming increasingly common, just before the expiration of Monsanto's patent on Roundup-Ready soybeans. What does the US Constitution say about patents?

"The Congress shall have Power To...promote the Progress of Science and useful Arts, by securing for limited Times to Authors and Inventors the exclusive Right to their respective Writings and Discoveries...."
If the original intent was to give inventors short-term monopolies, in exchange for long-term benefits to society, should the duration of patent protection be shorter for inventions whose useful life is likely to be limited by evolution? For example, 17 years with a really good resistance-management plan, 5 years with no resistance-management plan.... Of course, the Patent Office might need to hire an evolutionary biologist or two.

I agree with the statement from David Mortensen that adding another resistance gene to glyphosate-resistant crops, and spraying with both herbicides, will be only "a short-lived solution," although it might last long enough to be worth patenting. If they had put two different herbicide-resistant genes into soybean from the start, and if evolution of resistance requires two or more independent mutations -- this isn't always true -- and if farmers growing that herbicide-resistant crop were somehow required to use both herbicides (so that mutants resistant to just one of the herbicides wouldn't have increased in frequency), evolution of resistance might have taken much longer.

Zimnmer quoted me and mentioned my book on Darwinian Agriculture, depleting Amazon's stock, though they still have a few copies left. You could try your favorite independent bookstore or library.

July 12, 2013

Snowden for President?

I doubt that he has the breadth of experience. But Napolitano is retiring as Homeland Security Chief. Snowden might be a good replacement. We certainly need someone willing to put reasonable limits on government surveillance, and especially on how the data they collect are used.

I hope I don't have to worry about being sent to rot in Guantanamo without trial (like the Count of Monte Cristo), but recording everything we do on the internet, and giving some unknown number of analysts access to that information, as Snowden claims in this interview, puts most of us at risk for identity theft. We need to defend ourselves from terrorists, but we also need to defend ourselves from analysts with gambling debts or expensive habits, selling our mutual-fund passwords. Or, for that matter, selling identity information Al Queda could use to get onto airplanes.

This week's picks

Oxytocin blunts social vigilance in the rhesus macaque "reduced species typical social vigilance for unfamiliar, dominant, and emotional faces"

Evolutionary lag times and recent origin of the biota of an ancient desert (Atacama-Sechura) "Chaetanthera and Malesherbia (plants) and Liolaemus (animal) invaded arid regions of the Atacama-Sechura Desert in the last 10 million years, some 20 million years after the initial onset of aridity in the region... many lineages may require very long time scales to adapt to modern desertification and climatic change. "

Diversification through multitrait evolution in a coevolving interaction "more than a thousand plant species are pollinated exclusively by insects specialized to lay their eggs in the flowers they pollinate.... The lack of known intermediate stages in most of these mutualisms, however, makes it difficult to understand whether these interactions could have begun to diversify even before they became reciprocally obligate. Experimental studies of the incompletely obligate interactions between woodland star (Lithophragma; Saxifragaceae) plants and their pollinating floral parasites in the moth genus Greya (Prodoxidae) show that, as these lineages have diversified, the moths and plants have evolved in ways that maintain effective oviposition and pollination."

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato "footprints of positive selection in over 50 genes... thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure... commonly associated with environmental response and stress tolerance."

Fossil Musculature of the Most Primitive Jawed Vertebrates "placoderm data suggest that neck musculature evolved together with a dermal joint between skull and shoulder girdle, not as part of a broadly flexible neck as in sharks"

July 10, 2013

Fake scientific journals: a boon to "intelligent design"?

Over the years, intelligent-design advocates have only published "12 peer-reviewed articles from scientific journals that are claimed to support intelligent design," none which stands up to critical analysis. That analysis is more important than mere numbers, although it's worth noting that there are more than 12 papers on evolution published every day. However, the recent proliferation of fake "scientific journals," which will publish anything for money, may lead to a big increase in fake intelligent-design publications. We'll see.

For example, Scientific Research Publishing just invited me to join the editorial board for its open-access journal, Advances in Reproductive Sciences. Looks like an invitation sent at random, since I have no expertise in that field and since the email (from Editorial Assistant "Christine") was totally generic. One way to assess journals is by the qualifications of people on their editorial board, but that breaks down if journals lie about who's on their board. For example, I found this discussion of Scientific Research Publishing on the James Randi Educational Foundation web site:

"Oddly, I've been searching through the editorial board on the JBSE and haven't seen anyone listed there actually have it on thier own CV. ETA: Alright. It's getting a bit more strange. I saw they had listed a Dr. Sridharan Devarajan, from stanford. on the editorial board. however, this person is currently a PhD student. Further, he has listed on his cv that he is an "ad hoc" reviewer. hmmm.... "

I can't vouch for the accuracy of the comment, of course. This article in The Hindu quotes a professor listed as "editor-in-chief" of a journal published by the OMICS group, denying that he ever accepted that position. The article links to this lengthy list of suspect publishers, which includes both OMICS Group and Scientific Research Publishing.

There's more on fake scientific journals and fake scientific meetings in the New York Times and Nature.

The Scientific Research Publishing web site says they publish 200 journals and it looks like most of them were started this year. I guess it's too much work to look for qualified board members when you're starting that many journals all at once. Interestingly, the email I got didn't mention reviewing manuscripts as one of the responsibilities, but did mention "a valuable credential for tenure and promotion." They charge $600 to "process" a manuscript. I wonder if they charge for this "valuable credential."

Committees responsible for hiring, tenure, and promotion are supposed to evaluate publications, not just count them, although busy people aren't always as thorough as we should be. I can't imagine anyone getting hired at a major university based solely on publication in fake journals (or low-quality journals, even if they're not deliberate scams) and invited talks at fake conferences. But, when I was a research scientist for USDA, we were expected to publish at least one paper every year. This wasn't a problem for colleagues publishing low-quality research in journals whose "peer review" process overlooked even obvious errors (like including the same citation twice in a five-paper bibliography). But one of my best (and most-cited) colleagues was put on probation when he missed a year, despite publishing in top journals right before and right after the period in question. Years ago, a postdoc from another country told me that US Immigration uses citations, not mere publication, to evaluate scientific credentials of visa applicants. Citation analysis has limits, but it's an improvement over just counting publications.

See "Recent Comments" for reader reactions to my previous posts on fake scientific meetings and similar science scams, including two claiming these conferences are legit. One commenter used a pseudonym and the other is worth Googling.

July 1, 2013

Carnival of Evolution

This month's host is the Teaching Biology blog. Marc Srour uses the post to promote crustaceans, including my new favorite model, Daphnia, which he suggests could be used to test hypotheses about group selection. Good idea, but I'm busy using them to test hypotheses about the evolution of aging.