Oh, hey. This sounds familiar.

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Minnesota’s not the only state putting people’s civil rights up for a majority vote this election. Over on the Slog, Eli Sanders reports on working the phones with the campaign in support of Washington’s initiative R-74, which would make civil marriage available for same-sex couples in that state. (Contrast with Minnesota: here, we’re fighting against a ballot initiative that would put a ban on same-sex marriage in the state constitution.)

Sanders goes into rather more detail about specific calls than I did, probably because he’s a real journalist. I like this one:

Then, Ronald in Suquamish. I apologized for calling him during the dinner hour.

“Go ahead,” he replied. “I’m old, I like to talk.”

Ronald is 80. He told me that if I promised not to vote for Republicans “who are going to cut my Social Security,” he’d promise to vote to approve R-74.

But this wasn’t really a “persuasion” type of situation. Ronald had already come around to supporting marriage equality on his own. He’d met his first gay people while serving in the Navy, where he worked on submarines. “In fact, I got knocked on my butt by a lesbian in a bar in New York, in my uniform,” he told me. “I asked her girlfriend to dance. She let me have it. Knocked me right on my can.”

This is probably as good a time as any to note that my little fundraising project, in which I’m running the Mankato Marathon (in less than two weeks!) in support of the marriage-equality campaign here in Minnesota, Minnesotans United for All Families, is over halfway to my goal of $500! Thanks yet again to everyone who chipped in — and the rest of you, what’re you waiting for?◼

Science online, Friday coffee break edition

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Scream Someone just saw his report from “23andMe,” I guess. Photo by CHRISTOPHER MACSURAK.
  • At Nothing in Biology Makes Sense! God fails a standard information-theoretic test.
  • At the Molecular Ecologist: Reduce sequencing error with a new “duplex tag” method.
  • The only thing we have to fear is variation at adrenaline receptor loci. Against fearmongering over personal genomics.
  • Encouraging words for job application season. You don’t know how your story ends.
  • We’re number one? Study by Dunkin’ Donuts concludes that scientists drink more coffee than members of any other profession.
  • So say we all. Space operas, graded by accuracy of physics portrayed.
  • Three out of four cases. A large majority of scientific paper retractions are due to fraud.
  • Jumping gigawatt! Experiments that are so crazy, they just might work.
  • Proposed, then scuttled in Congressional absurdity. A multi-location National Park to commemorate the Manhattan Project.
  • Or, you know, human. Ayn Rand’s individualism doesn’t work so well if you’re a hunter-gatherer.
  • The early bug gets the bite. The use of insecticide-infused bed nets at night prompts mosquitoes to bite during the morning.
  • Historical contingency. What killed the electric car, the first time around.

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Notes on a model species

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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.”

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Nothing in Biology Makes Sense: God’s AIC score

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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

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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

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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

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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

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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.


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

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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!

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(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.◼