Notes on a model species

2012.09.20 - Seeds

Seeds. (Flickr: jby)

There are a couple of neat racks on my desk containing rows of plastic tubes, each tube with a drift of tiny, kidney-bean-shaped seeds at the bottom. These are seeds of Medicago truncatula, barrel medick. When I tell people about this plant I’m currently studying, I usually describe it as an unremarkable wildflower native to the Mediterranean. Or I note that it’s a close-ish relative of alfalfa (Medicago sativa).

Medicago truncatula does not have an especially grand heritage. It grows in dry, sunny places throughout the dry, sunny Mediterranean region, forming low tangles of trifoliate leaves and small yellow flowers that eventually ripen into tough, spiky, vaguely barrel-shaped fruits full of those tiny seeds. Some of the seeds on my desk are descended from plants that grew in places like the Temple of Apollo at Curium, Cyprus; but most are from less distinguished locales. In his 2011 monograph on the genus Medicago, Ernest Small quotes a description of M. truncatula‘s habitat as “sandy fields, wet grasslands, wet meadows, strongly overgrazed and degraded garrique, coniferous forests, grasslands, fallow fields, olive groves, and as a weed in cereal and crops and waste places.”

Continue reading

Nothing in Biology Makes Sense: God’s AIC score

The creation of Adam. Image via Web Gallery of Art.

This week at Nothing in Biology Makes Sense! Noah Reid takes a cue from Bill Nye the Science Guy and applies information theory to test whether a model of divine intervention fits a simple phylogenetic dataset.

Without getting into the details, we can think of information theoretic criteria for model selection as formally implementing Occam’s Razor: the simplest model with the most explanatory power is to be preferred. By preferring simple models, you guard against overinterpreting data, a pitfall that can make models poor predictors of new observations.

So, I realized as long as we can formulate any mathematical model of “The Hand of God”, rejectable or not, we can compare it to an evolutionary model in this framework. If, as Nye suggests, evolutionary theory is simple and powerful, and creationism is a model of fantastical complexity that doesn’t much improve our understanding of the data, information theory would help us sort that out.

If you want to settle the whole evolution-versus-creationism thing once and for all (okay, not really), or just learn how biologists use information theory to select models (really!), go read the whole thing.◼

5k down, 42 to go

2012.09.29 - Big Gay Racers Big Gay Racers. Photo by jby.

Saturday morning, I ran Big Gay Race with a whole bunch of friends and thousands of other Minnesotans. In spite of an early-season cold, I did the 5k run in 20:08, nine tantalizing seconds from a personal record. (Is Pseudophed a performance-enhancing drug? If so, it’s not performance-enhancing enough.)

The BGR was the first of two events I’m running in support of Minnesotans United for All Families and the fight against the proposed anti-gay-marriage amendment to the state constitution. With a bit more than a month to go before the vote, polling on the amendment is also tantalizingly close, a statistical dead heat at 49% for, 47% against, and 4% undecided.

Meanwhile, I’m just about ready to take something a little bit longer—the Mankato Marathon. I did what will probably be my longest pre-marathon training run—19 miles un-enhanced by cold medicine in beautiful autumn weather—on Sunday, and I do believe I’m ready to survive 26.2 miles (or about 42k) less than three weeks from now.

Denim and Tweed readers have already given $205 to MNUnited, for which I’m mighty grateful. But if you haven’t given yet, please help us make it to $500 with a donation of $5, or $10, or $25—we’re on the home stretch, and every little bit will make a difference.

Donate here.◼

Leaf-peeping on the run

2012.09.30 - Mississippi shores Autumn on the Mississippi. Photo by jby.

The camera on my iPhone (4, not even S) is really pretty lousy. But when I’m on the last long run before a marathon, it’s the camera I have with me. And it does give you some sense of how colorful things have become in the parklands that line the Mississippi River from Minneapolis to Saint Paul, my regular running route. More photos after the jump!

I like these cities.◼

New words

Climate hawk. Noun. A person who judges that the risks associated with climate change necessitate immediate, vigorous preventative action and investment. Analogous to “deficit hawk.” Climate hawks in the Senate have opposed the bill, saying it provides insufficient funding for wind farm development. [Source: Grist]

Malinformed. Adjective. Ignorant or misinformed on a topic, not through lack of access to knowledge, but as the result of active deception perpetrated by a newsmedia organization, a governmental institution, or oneself. I can’t have a civil conversation with someone so malinformed that he thinks that President Obama is a Muslim. [Source: Slog]◼

Science online, seeds of subversion edition

Sweet & Spicy Toasted Pumpkin Seeds Don’t roast all those pumpkin seeds—save some to plant. Photo by satakieli.
  • This week, at Nothing in Biology Makes Sense! The evolutionary origins (or lack thereof) of type II diabetes.
  • Caveat: adaptive evolution requires (1) heritable variation and (2) time. Make your home garden more self sustaining, and maybe better adapted to a changing climate by saving seeds.
  • In which “functional” means about 80% of what you thought it means. Further complaints about the spinning of ENCODE.
  • Wait, what? Yes, colonoscopies can (rarely!) cause patients to explode.
  • Yeah, you’re probably going to need to declare that in your conflict-of-interest statement. When your new study linking cancer and GMO corn is also central to your new book and documentary film.
  • Size labeling matters. People eat more cookies when they’re labeled “medium”.
  • But probably not, you know, a causative one. An association between type II diabetes and gut bacterial profile.
  • Paging Dr. Jones … Paging Dr. Indiana Jones. A Tibetan statue brought to Germany by the Nazis was made from a meteorite.
  • Wallace’s online. A new online archive of the work of Alfred Russell Wallace.

Video for the week: “Plants are cool, too!” is a botannical YouTube series. And yes, it’s cool. Here’s an episode featuring University of Idaho (go Vandals!) biologist Dave Tank, who acts as a tour guide through a famous fossil site not far from the UI campus.


Nothing in Biology Makes Sense: An evolutionary origin for diabetes?

550d - Bubblegum Bowl Photo by @Doug88888.

This week at the collaborative blog Nothing in Biology Makes Sense!, Jon Yoder (my brother) takes a look at the possible evolutionary origins of type II diabetes from his perspective as a medical student:

Currently, around 285 million people worldwide are affected and that number could potentially climb to 430 million by the year 2030. Diabetes also accounts for 12% of all health care expenditure. It is also a highly genetically associated disease, at least Type 2 Diabetes. Now, in type 2 diabetes the individual will have high levels of circulating insulin. Insulin is a key regulator of fat storage. It is released following meals in response to glucose from the meal and stimulates the uptake of that glucose into liver, muscle and fat. It also acts to antagonize other hormones that would breakdown and use the stored glucose as energy. So, this is where I got to thinking, if there is a gene that is linked evolutionarily to helping survive famine, is there a potential link between such genes and diabetes.

To find out more, go read the whole thing.◼

The Molecular Ecologist: Genes … in … space!

(A) Geography, and (B) genetics. Figure 2 from Wang et al. (2012).

I’ve got a new post up over at The Molecular Ecologist, discussing a new paper that tries to take a quantitative approach to a phenomenon that keeps turning up in human population genomic datasets, in which genetic data mirrors the geography of the places it was collected.

It’s something of a classic result in human population genomics: Go out and genotype thousands of people at thousands of genetic markers. (This is getting easier to do every day.) Then summarize the genetic variation at your thousands of markers using Principal Components Analysis, which is a method for transforming that genetic data set into values on several statistically dependent “PC axes.” Plot the transformed summary values for each of your hundreds of samples on the first two such PC axes, and you’ll probably see that the scatterplot looks strikingly like the map of the places where you collected the samples.

Of course “looks strikingly like” is not a very quantitative statement. To see how the new study deals with that problem, go read the whole thing. And yes, I manage to shoehorn in a reference to the Muppets.◼

Science online, roller derby to tenure edition

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.

Still running …

Me, running the Portland Marathon three years ago. Looks fun, right?.

Hey, remember that thing where I’m running a 5k, then a marathon, to raise money for the campaign against an amendment to the Minnesota Constitution that would ban same-sex marriage?

Well, so far readers have made some very nice contributions—$110, to be exact. Which is great! But I have reason to suspect that a lot of folks still haven’t chipped in. I know, I know. You, my readers, are about evenly divided between impoverished, ramen-subsisting graduate students and the kind of young, hip professionals who just blew their discretionary budget on a new iPhone—but you have five bucks, right? Minnesotans United for All Families, the campaign against the amendment, would be happy to have five bucks. It’s not a lot, but it would add up. The average post at D&T scores a couple hundred pageviews; if every page-viewing person kicked in a fiver, we’re talking folding money.

And what will your five bucks will go toward? More phone banks to make our case to each and every Minnesotan we can reach, more canvassing for support, and, as we get closer to the election, TV ads like this brand new one:

Seriously: go chip in five bucks?◼