Category Archives: science

Science online, roller derby to tenure edition

Posted on by
coconut You’re not hydrated—you’ve got two empty halves of coconuts and you’re banging them together. Photo by Minette Layne.
  • This week at Nothing in Biology Makes Sense! Sarah Hird reports on a workshop, The Ecology and Evolution of Host-Associated Microbiota.
  • And at The Molecular Ecologist: Making maps with R.
  • Applying sports psychology to an academic career, part I and part II—and further thoughts on that theme.
  • Prepare for a whole week of Friday Weird Science. Scicurious gets ready to blog the Ig-Nobels.
  • Endangered species, catfish, and—gasp—American ginseng. What a DNA barcoding study found in dietary supplements.
  • Bird brains. The only thing that drives Creationists crazier than fossils is fossils of feathered dinosaurs.
  • The stuff from the tap still wins. Running the nutritional—and hydrational—numbers on coconut water.
  • Maybe if they drink enough coconut water? Could humans become photosynthetic?
  • Splitters v lumpers, round eight thousand. The arguments, pro and con, on whether to split genus Anolis.
  • Convenient. Turns out that many of the most-sustainable and least-mercury-laden fish species are also better for you.

◼

Science online, grafted glitter-berries edition

Posted on by
Swimming with Dolphins These two mammalian species evolved bigger brains via changes in the same gene. Photo by Sagolla.

◼

Give the NSF a piece of your mind

Posted on by

This last year, the Biological Sciences Directorate at the National Science Foundation—one of the biggest single funders of ecology and evolutionary biology research in the U.S.—introduced a new process for reviewing grant proposals.

Lots of other folks with better first-hand knowledge have written about the new process. The key change is that, where formerly NSF offered two opportunities per year to submit a proposal for funds, the new procedures introduced a “pre-proposal” stage in which biologists write a much shorter pre-proposal first. If this mini-proposal is judged worthy, the applicant is then invited to submit a full proposal several months later.

This effectively reduced the workload (in terms of full proposals) for NSF reviewers, and it makes the funding rate for “full” proposals look much better—as long as you don’t look too closely at the triage (i.e., rejection) rate for preproposals, which, eek. But it also cut the “real” opportunities to submit a grant proposal in half. If you’re trying to land NSF funding in the few short years before a tenure review, that might make you a bit … concerned.

So a bunch of biologists wrote to NSF about this [PDF], pointing out that the new process

  • Creates a much longer “lag time” between submitting a new idea as a proposal and recieving money to pursue the idea, effectively slowing down the pace of basic science;
  • Reduces the scope and complexity of ideas that can be proposed; and
  • Provides less feedback for applicants, which makes it difficult to improve rejected proposals for the next round of applications.

That letter, and followup discussions, got NSF thinking about (or maybe thinking about thinking about) some changes to the new process. I’ve just learned via an e-mail from the Society for the Study of Evolution that there’s a very short survey that interested parties (i.e., those of us who study ecology and evolutionary biology, and might like the NSF to pay for some of our work) should fill out by next Tuesday, the 18th. It took me about a minute. So maybe go do it now?◼

The Molecular Ecologist: ABC, quick as A-B-C

Posted on by
If I said you had a nice posterior Reverend Bayes, would you take offense? Photo via WikiMedia Commons.

Over at The Molecular Ecologist, new contributor Peter Fields—a Ph.D. student studying plant-pathogen coevolution at the University of Virginia—writes about approximate Bayesian computation and a new approach to this still-developing method of statistical inference that can make it quite a bit faster.

ABC functions upon the rationale that the likelihood might be approximated through the use of simulation and simulation summary statistics2, and that the evaluation of model fit to a dataset can be identified through a comparison of Ss derived from simulated scenarios and calculation of those same summaries on an observed, empirical dataset. In theory, simulation summaries are selected to provide maximal distinction amongst competing models. In practice, identifying these summaries isn’t always easy, and is the object of continued research3

For an introduction to ABC, and a description of the new approach, go read the whole thing.◼

Science online, organic marmots edition

Posted on by
Fresh Organic Strawberries Organic strawberries. Photo by VancityAllie.

◼

Carnival of Evolution, September 2012

Posted on by
Dinner! Photo by basykes.

The monthly roundup of online writing about descent with modification is online at the Stochastic Scientist. Dig in!◼

The Molecular Ecologist: Isolating isolation by distance

Posted on by
Linanthus parryae population Linanthus parryae. Photo by naomi_bot.

And now I present my first “real” post as a contributor at the Molecular Ecologist, a discussion of a new review article pointing out that population geneticists aren’t doing a great job dealing with one of the best-known patterns in population genetics, isolation by distance, or IBD. You may recall that I discussed IBD in a more historical context way back in the day on this very website. It’s simply a pattern in which populations located close to each other are more genetically similar than populations farther away from each other, which arises because most critters (or their seeds, or larvae, or pollen) are less likely to move longer distances. But IBD can be conflated with a number of other patterns population geneticists often try to detect:

So let’s say you’ve collected genetic data from sites on either side of a line you think might be biologically significant—a pretty standard-issue population genetics study. You run your data through Structure, and find two clusters of collection sites that line up pretty well with that Line of Hypothesized Biological Significance. As a followup, you conduct an AMOVA with the collection sites grouped according to their placement by Structure, and you find that the clusters explain a significant fraction of the total genetic variation in your data set. Therefore, you conclude that the LHBS is, in fact, a significant barrier to dispersal.

Except that as we’ve just discussed, everything you’ve just found could be a consequence of simple IBD plus the fact that you’ve structured your sampling so that your LHBS happens to bisect the landscape you’re studying. And just to add to the frustration, even if you’d started out by testing for IBD before you started with all of the tests for population structure, a significant result in a Mantel test for IBD wouldn’t necessarily mean that population structure wasn’t there.

To find out how the author of the new review article suggests we deal with the complications outlined above, go read the whole thing.◼

Big, bloggy news

Posted on by

Starting today, I’m officially part of the crew at the Molecular Ecologist, the group blog associated with the journal Molecular Ecology, as both a contributor and a sort of coordinator/administrator.

Molecular Ecology‘s managing editor Tim Vines first approached me about joining the site back at Evolution 2012, and I’m excited to start talking about the many wonderful uses of molecular genetic data with Holly Bik, Mark Christie, Nick Crawford, and Peter Fields. We’re hoping to bring in lots of guest posters as well. (And if you’re interested, send me an e-mail.) Although the Molecular Ecologist is affiliated with Molecular Ecology, the vision of the site is not to promote the journal itself, but to build a space for the community of scientists interested in the journal’s subject matter. As part of that effort, we’ve launched a Molecular Ecologist page on Facebook, and I’m taking over @molecologist on Twitter.

This doesn’t mean I’ll stop posting at Nothing in Biology Makes Sense!, much less here at D&T; the Molecular Ecologist is aimed at a somewhat different audience than either of my other online locales, and while this may spread me a little thinner, I expect I’ll be covering different topics at each site.◼

Science online, giant leap for mankind edition

Posted on by
Neil Armstrong on the Moon. Original image from NASA Goddard Photo and Video.
  • Requiescat. Neil Armstrong, the first human being to walk on the Moon.
  • This week at Nothing in Biology Makes Sense! The evolutionary history of lizards on Indian Ocean islands and the problems with the Paleo Diet.
  • Bees need somewhere to buzz. Cultivating hedges between fields to save pollinators.
  • Maybe not as complex as we think. How complex does a brain need to be to become self-aware?
  • We’re working for the weekend. Also over the weekend. Download statistics from Springer’s journal archives provide real-time evidence of workaholic scientists.
  • Sure, why the hell not? Do people become vegetarians because they’re more prone to disgust reactions?
  • This seems like a bad idea. A kennel club is attempting to breed dogs into a recreation of prehistoric dire wolves.
  • This seems like a worse one. Engineering a strain of bacteria that will eat plastic.
  • This increasing energetic investment will not stand, man. A long-standing hypothesis about human gestation comes into question.
  • I’ll have seconds now, please. Although abstemious diets can lengthen lifespan in other animals, they don’t work for primates.

◼

Nothing in Biology Makes Sense: Why the “paleo diet” doesn’t make sense

Posted on by
Nuts! Gathering hazelnuts is a nice way to spend an afternoon, but a lousy diet plan. Photo by ParaScubaSailor.

Just up at the collaborative science blog Nothing in Biology Makes Sense!: Sarah Hird takes down the “paleo diet” trend, which is based on eating what we think our ancestors ate before the invention of agriculture. Readers of D&T will recognize some of the points Sarah makes:

… this assumes that no evolution has occurred since the advent of agriculture. This is demonstrably false. One example of post-agricultural evolution is the human lactase gene, which breaks down lactose, the dominant sugar in milk. In ancestral humans this gene was turned off after infancy; those humans would have been “lactose-intolerant”. Most humans of European descent now have a mutation that keeps that gene turned on their entire lives. Not surprisingly, this gene spread throughout Europe at approximately the same time cattle were domesticated. There are other known examples of agricultural dietary adaptation, and doubtless more to be discovered. If we are going to use evolution to justify our dietary choices, why throw out the last 10,000 years of it?

That’s just a taste (heh) of Sarah’s objections; for the full case against trying to eat like a hunter-gatherer, you’ll need to go read the whole thing.◼