Nothing in Biology Makes Sense: Circumcision and microbial ecology

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Banana Peel What? Photo by photograφ.

Over at Nothing in Biology Makes Sense!, Sarah Hird describes a new study of what happens to the microbial community of the human penis when you make a … let’s say a certain change to its environment?

They begin by sampling the penile microbiota of 156 uncircumcised men. Approximately half of the men are then circumcised and all subjects are resampled after one year (presumably enough time that behavior is unaffected by the procedure).

Yeah, it’s maybe not surprising that circumcision would change what kinds of bacteria hang out in the region formerly covered by the foreskin. But apparently that change may contribute to the reduced rate of HIV transmission associated with circumcision. To find out how, go read the whole thing.◼

Science online, anthropocentrism and budgetary doomsday edition

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Lab Mouse checkin out the camera Another victim of the shutdown. Photo by Minette Layne.
  • This week at The Molecular Ecologist Is the ultimate model organism for molecular genetics Homo sapiens?
  • This week in shutdown science: The CDC sits out an outbreak of drug-resistant salmonella, experiments on hold, lab mice euthanized and an entire season of Antarctic research cancelled.
  • Not like they have much state funding to lose, these days. Public universities are looking for ways to be less, um, public.
  • Of course, it can be both! Is behavioral genetics “taboo,” or just bad science?
  • From the personal to the general. The New York Times Magazine goes in-depth on underrepresentation of women in science.
  • Because bunnies! The Central Limit Theorem turns out to be adorable.
  • This sounds … familiar. The Great Library of Alexandria wasn’t destroyed by a fire, but by budget cuts.
  • Literally, because he says he can’t. Why Malcolm Gladwell can’t be trusted.
  • About 35 years. A new study estimates how long global warming can continue before average temperatures exceed historical highs.
  • It’s more likely to be MRSA. No, that’s almost certainly not a brown recluse bite.

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The Molecular Ecologist: Is Homo sapiens a model organism?

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New York City Photo by Bikoy.

Over at The Molecular Ecologist, guest contributor Jacob Tennessan suggests that for those of us who study the genetics of natural populations, the ultimate “model organism” may be … us.

Thus, the field of human population genetics has always been a step or two ahead of the molecular ecology of wildlife. Common techniques like mitochondrial- or microsatellite-based phylogeography analyses were pioneered with data from humans. Research into human molecular ecology has yielded countless fascinating stories that provide a baseline for what to expect when examining other taxa. Some are well-known textbook examples, like the sickle-cell hemoglobin balanced polymorphism that conveys resistance to malaria, or the human global diaspora reflected in sequence diversity that traces back to “mitochondrial Eve” and “Y-chromosome Adam.”

Does that make Homo sapiens a “model organism” in the same sense as fruitflies and Caenorhabditis elegans, or more of a proving ground for new molecular methods? Go read the whole thing, and tell us what you think in the comments.◼

2013 Twin Cities Marathon, in photos

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2013.10.06 - Balloon Arch Photo by jby.

So, that marathon I ran this morning? Went pretty damn well. My official time is 3 hours 19 minutes 55 seconds, which is a personal record marathon time—by about ten minutes! I attribute this to (1) spectacular autumnal weather—clear, cool, and perfect for running; (2) some half-arsed attempts at speed training I did over the winter; and (3) actually paying attention to my pacing, instead of my usual marathon strategy of just running as fast as I can until I end up barely able to walk the last mile.

I didn’t do much tweeting from the course, but I did take a bunch of photos—the camera on my new iPhone is a lot better than my old one. So here they are, with a reconstructed transcript of my internal dialogue:

“The best thing about a marathon in my hometown is, I can walk to the starting line. It was near the Metrodome. And the weather’s nice and clear! But, eek, I only have about 25 minutes to stand in the porta-potty line …”

2013.10.06 - Metrodome Photo by jby.

“Whew. All set. Time to head to the start line.”

2013.10.06 - Headed to the starting line Photo by jby.

“And we’re off! Next stop, Saint Paul.”

2013.10.06 - And we're off! Photo by jby.

“Yay, marathons! Here’s Hennepin Avenue. I’m going to see Wicked in a couple weeks!”

2013.10.06 - South on Hennepin Photo by jby.

“And here’s the Basilica.”

2013.10.06 - Basilica I Photo by jby.

“I’m a sucker for Baroque architecture.”

2013.10.06 - Basilica II Photo by jby.

“Ooh, the Walker Art Museum.”

2013.10.06 - Walker Art Museum Photo by jby.

“And now we’re at the lakes! This is just like my usual Sunday runs.”

2013.10.06 - Lakeside I Photo by jby.

“There’s the skyline across Lake Calhoun.”

2013.10.06 - Lake Calhoun Photo by jby.

“And now the trails around Lake Harriet.”

2013.10.06 - Lake Harriet Photo by jby.

“Is this Minnehaha Parkway? I’ve never run here before.”

2013.10.06 - Parkway Photo by jby.

“Balloon arch!”

2013.10.06 - Balloon Arch Photo by jby.

“Almost to the halfway mark. Whew.”

2013.10.06 - Almost halfway! Photo by jby.

“Oof. Sixteen miles in two hours. I’m right on pace.”

2013.10.06 - Mile 16 Photo by jby.

“Crossing the Franklin Avenue Bridge. I’ve done this hundreds of times before … but it hurts a lot more this time.”

2013.10.06 - Franklin Avenue Bridge Photo by jby.

“Gee, thanks for the reminder, sponsor I’ve never heard of. Six miles to go, mostly uphill.”

2013.10.06 - Gee, thanks. Photo by jby.

[Five and a half miles of incoherence and pain. Otherwise known as Summit Avenue.]

“Finally, the cathedral. All downhill from here. Ow.”

2013.10.06 - Cathedral Photo by jby.

“I can see the State Capitol!”

2013.10.06 - Final stretch Photo by jby.

“Getting closer …”

2013.10.06 - Finish line in sight Photo by jby.

“The finish line! Does that clock really say 3:20?”

2013.10.06 - Crossing the finish Photo by jby.

“Ow. Owowowowow. Now where’s the chicken broth table?”

2013.10.06 - State Capitol Photo by jby.

“Of course they make me climb a staircase to get to the bus back to Minneapolis. Ow.”

2013.10.06 - Finish line festival I Photo by jby.

And that’s the lot. Next year, I’m going to have to do a marathon out of state for a change. Maybe Chicago?◼

Marathoning, yet again

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Tomorrow morning I’m running the Twin Cities Marathon—a mere two and a half years, and three other marathons, after I moved to the Twin Cities. What can I say? Scheduling is tricky.

I’ll be bringing my phone, so there may be live-tweeted photos if I’m feeling comfortable enough for that. Certainly the forecast—cool and cloudy but not actually raining—is perfect weather for both a very long run and for nice photos of the prettiest parts [PDF] of Minneapolis and Saint Paul. But I’m really hoping to crack my current time record of about 3 hours 30 minutes, so the only mid-race updates may be the ones available via the marathon website.

In the meantime, I have one last very short run to go do, to keep the ol’ joints loose.◼

Science online, shutdown edition

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Aedes aegypti mosquito A safer DEET successor can’t arrive soon enough. Photo by Sanofi Pasteur.

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Nothing in Biology Makes Sense: On the origins of bacon

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Pig Photo by mgabelmann.

Over at Nothing in Biology Makes Sense! Noah Reid takes a look at a new study of the recent evolutionary history of pigs:

Domestic pigs are in the family Suidae, which includes the babirusas, warthogs, the endangered pygmy hog (whose generic name is, Porcula, seems a likely candidate for America’s next tragic children’s cereal) and the domestic pig’s close relatives in the genus Sus. Depending on where you draw the lines, there are around 7 species in Sus. With the exception of the wild boar (Sus scrofa) their natural ranges are restricted to Southeast Asia west of Wallace’s Line.

Because domestic pigs are prone to going feral and getting, um, re-familiarized with their wild relatives, unravelling their history using genetic data is tricky business. To see what the new study found, go read the whole thing.◼

The Molecular Ecologist: Interview with Loren Rieseberg

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Sunflower (closely) Photo by ToOb.

This week at The Molecular Ecologist, we’re kicking off a new interview series, “People Behind the Science,” by John Stanton-Geddes. The inaugural interview is with Loren Rieseberg, the Chief Editor of Molecular Ecology and an expert in the evolutionary consequences of hybridization between species.

When I arrived at Washington State University (WSU) in the fall of 1984 to begin my PhD, my advisor, Doug Soltis, handed me a copy of Verne Grant’s Plant Speciation and told me to find a problem. I was especially intrigued by Grant’s discussion of the potential role of hybridization in adaptation and speciation.

The interview ranges from Rieseberg’s philosophy for Molecular Ecology to which one paper (out of over 300 he’s authored!) that he wishes more people would read. So go read the whole thing.◼

Science online, black hole at the (other) end of the universe edition

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Beer Trio Horizontal Dude, if you don’t brew it in your gut, you can’t really appreciate the bouquet. Photo by Lindsey Gira.
  • This week at The Molecular Ecologist: Take your coding to the next level with Software Carpentry.
  • And, at Nothing in Biology Makes Sense! Taking a big-data approach to understand the role of reproductive isolation in species formation?
  • New update from Queer in STEM: Examining the outness of queer folks at STEM workplaces.
  • “This collection is among the first to reveal all major evolutionary stages of feather development in non-avian dinosaurs …” Dinosaur feathers found preserved in amber.
  • Best or worst infection ever? A brewer’s yeast infection of the gut can make the ultimate micro-brew.
  • Gee whiz. An editor at Nature goes right off the rails.
  • One jab to rule them all? The basis for a “universal” flu vaccine may finally have been found.
  • Optical illusion of the week. Here is a moth that looks like a leaf with curling edges.
  • With charts! Why infographics are bad for conveying, you know, info.
  • Sure, why the hell not? Did the universe begin in a five-dimensional black hole?
  • Whew. Turns out that distance running doesn’t increase your risk of arthritis.

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Nothing in Biology Makes Sense: Can we separate reproductive isolation and species formation?

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fork in the road Photo by dkwonsh.

This week at Nothing in Biology Makes Sense! Noah Reid takes a look at a study that attempts to disentangle the effects of reproductive isolation between species and the rate at which new species are formed. Why would you want to do that? So you can tell whether the former causes the latter!

RI [reproductive isolation] is often thought to be important in diversification because some theory predicts that even low levels of intermating between populations can prevent divergence from occurring and because hybridization between divergent populations can cause them to homogenize, or cause one population to become extinct. If these factors commonly prevent speciation or cause incipient species to go extinct, one might expect a positive correlation between the rate of evolution of RI and DR [species diversification]. This paper is the first test of this prediction.

But, of course, a lot of biologists would say that the evolution of reproductive isolation is the evolution of a new species … so things get a bit complicated. Go read the whole thing, and see what you think.◼