Denim and Tweed

Science online, don't drink the sapa edition

2012-01-27T08:05:00.000-06:00

Wood thrush, or mercury-poisoning canary? Photo by dermoidhome.

New at Nothing in Biology Makes Sense! Making sense of humans' role in the extinction of North America's big ice age mammals and the evolution of multicellularity.
Splenda suddenly doesn't seem so bad. The ancient Romans created the world's first artificial sweetener. It was a lead compound. And we can still see the resulting poisoning in Roman skeletal remains.
Not a feeding frenzy; more like a bridge club. Observational evidence suggests that sharks have social lives.
Silvery spring. Increasing—and worrying—levels of mercury have been detected in common songbirds in the northeastern U.S.
Sleep on it. Separating good ideas from bad ones requires taking time to not think about them.
Black, apparently. Reconstructing the color of Archaeopteryx feathers.
However, the Moon must still hit your eye like a big pizza pie for amore as we know it. Life as we know it probably doesn't require the Moon as we know it.
In your pants. Are modern grooming habits creating an extinction crisis?
Infant mortality, mental illness, and drug use. Just some of the bad things that increase along with greater income inequality.
Calibrated unfocusedness. Jumping spiders judge distances using blurry vision.

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Counterfactualizing for truth

2012-01-26T08:05:00.000-06:00

Something kind of incredible is going on over at Ta-Nehisi Coates's place: Bouncing off some typically reprehensible and ahistorical remarks by Ron Paul—who apparently thinks that (1) the U.S. Civil War was started by the North, (2) for the express purpose of ending slavery, even though (3) nonviolent means, such as "compensated emancipation," could have accomplished that end—Coates is not simply rounding up the contrary evidence, but actually trying to work out whether and how a nonviolent end to the "peculiar institution" could have worked. It's like a Harry Turtledove novel, except fascinating and good and informative.

Nevertheless, the saving of people is, indeed, a noble goal, and Paul is not without at least the rudiments of a case. Enslaved black people were constructed into an interest representing $3 billion. ($70-75 billion in 21st century money.) But including expenditures, loss of property, loss of life (human capital,) the war, according to Ransom, costs $6.6 billion.

The numbers are clear--the South's decision to raise an army, encourage sedition among its neighbors, and fire on federal property, was an economic disaster for white America. Moreover, the loss of 600,000 lives, in a war launched to erect an empire on the cornerstone of white supremacy and African slavery, was a great moral disaster for all corners of America.

In the most crude sense, it would have been much "cheaper" for the government to effect a mass purchase. But how?

Spoiler alert: compensated emancipation doesn't look very practical, especially considering that Southern slaveholders were pretty damned hostile to the idea. But getting to that conclusion is enlightening, and the discussion in Coates's famous comments section is as well worth your time as the posts. ◼

Baby steps versus long jumps: The "size" of evolutionary change, and why it matters

2012-01-25T08:05:00.000-06:00

Evolution can make leaps—but how frequently? Photo by Flavio Martins.

Does evolutionary change happen in big jumps, or a series of small steps? The question may seem a little esoteric to non-scientists—how many mutations can dance on the head of a pin?—but it has direct implications for how we identify the genetic basis of human diseases, or desirable traits in domestic plants and animals.

That's because the evolutionary path by which a particular phenotype, or visible trait, first evolved in a population is closely related to the genetics that underlie the trait in the present. Phenotypes that arose in a single mutational jump will probably remain connected to one or a few genes with large effects; phenotypes that evolved more gradually do so because they are created by the collective action of many genes. So what kind of evolutionary change is most common will determine which kind of gene-to-phenotype relationships we should expect to find.

In an excellent recent review article for the journal Evolution, Matthew Rockman, a biologist with the Department of Biology and Center for Genomics and Systems Biology at New York University, makes the case that the era of genomics has, so far, been much too focused on finding genes of large effect. Fortunately, Rockman also sees the beginnings of a new movement towards acknowledging the importance of small-effect genes—one which may ultimately make genomic association studies more useful.

Read more ...

Change happened

2012-01-24T21:41:00.001-06:00

Between this and a kick-ass State of the Union address, I'm feeling pretty damned optimistic, all of a sudden. It's a weird sensation. I think I may be a bit light-headed. ◼

I want to see mountains again ...

2012-01-24T12:39:00.002-06:00

Watch this on full screen mode, or don't watch it at all. All of a sudden, I need an excuse to go west.

Via Line Out. ◼

Nothing in Biology Makes Sense: Making sense of the origins of multicellularity

2012-01-24T11:06:00.000-06:00

Experimental evolution of multicellularity. Photo by Nothing in Biology Makes Sense!

In this week's new post at the group blog Nothing in Biology Makes Sense!, Sarah Hird discusses the recently published experimental evolution study that used laboratory yeast to tackle one of the biggest questions in reconstructing the history of life:

Some of the biggest questions in evolutionary biology deal with the origin of life. For example, if I go back one generation, I find my parents. Two generations, my grandparents. Ten generations are human beings who may or may not have looked like me. Five hundred thousand are, oh, I don’t know. Maybe a bipedal hominid? Anyway, if we continue going backward like this, we inevitably get to time zero and encounter some big-time questions that can really cause a brain to cramp up.

I promise you, if you read the whole thing, you will not experience brain cramps. Quite the opposite, in fact.

In other news, Nothing in Biology Makes Sense! has put out a call for guest contributors. If you work in biology—anything from medicine to plant breeding—and you've been thinking about giving this science blogging thing a try, send us an e-mail! ◼

Winter weather warning

2012-01-23T08:18:00.000-06:00

Between the fact that it's been a record-setting-ly mild winter, and the fact that I usually take the bus, I'd gone nearly seven months living in Minnesota without this happening.

Time to cross another item off the ol' bucket list. ◼

Nothing in Biology Makes Sense: Did humans send North America's large mammals to extinction?

2012-01-23T08:05:00.000-06:00

Are ancient humans to blame for mammoths' extinction in North America? Photo by W9NED.

After a beginning-of-semester scheduling hiccup, the group blog Nothing in Biology Makes Sense! is up and running for the spring, starting with a great post by contributor Noah Reid. Noah breaks down a big, complex study that applied species distribution modelling, paleontological data, and ancient DNA analysis to try and determine whether humans were responsible for the mass extinction of North America's ancient large mammals.

With the ending of the ice age, which began around 21,000 years ago, many of these species experienced dramatic declines or went extinct. Woolly Rhinos, Mammoths, Glyptodon, and Megatherium went completely extinct, while Bison, Reindeer, Musk Oxen and wild Horse went through serious declines and range contractions.

These population declines roughly coincided with another major event in earth’s history, the global expansion of modern humans. Because of this synchronicity, there has long been debate about whether either is the cause. Did humans fuel their global expansion by hunting these animals to extinction, were they victims of a changing climate, or was it some combination of the two?

To find out, go read the whole thing. ◼

Science online, missing #Scio12 edition

2012-01-20T08:05:00.000-06:00

How many eggs shall I lay? I'll ask the neighbors. Photo by yanajen.

Raise a glass (or two or three) for us absentees. I couldn't make it to Research Triangle Park this year, but the #Scio12 hashtag is nicely busy.
With, hopefully, lots of extra lives. Why classes should be a little more like video games.
Keeping up with the neighbors. Flycatchers decide how many eggs to lay in a given season by watching other birds.
Awkward! Yes, that ostrich is indeed flirting with you.
Sound advice. When choosing graduate advisers, prioritize personalities over projects.
I am become life ... One of the most enthusiastic funders of synthetic biology is the U.S. military. One goal: greener munitions.
The truth, putting its boots on. Assessing the fallout from The Atlantic's bunk report on miRNAs and GM food.
Eureka! Yeast that clumps! Multicellularity, evolved in a test tube.
Boom. With citations. In which Kate Clancy and Scicurious bury Jesse Bering's "deep-thinking hebephile" column under a great big pile of data.
For straight couples, that is. The per-coital act risk of HIV transmission, calculated.

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On strike against PIPA

2012-01-18T08:00:00.000-06:00

On strike! Photo by The Kheel Center at Cornell University.

If you like this whole Internet thing we've got going, let me suggest that you take the time while your favorite sites are on strike to call your Congresspersons, and tell them to vote against PIPA.

Legislation called the PROTECT-IP Act (PIPA) in the Senate and the Stop Online Piracy Act (SOPA) [Ed: the House version, SOPA, is no longer a going concern.] in the House are purported to be a way to crack down on online copyright infringement. In reality the bill is much broader. It would empower governments and corporations to take down virtually any website, create new liabilities and uncertainties for web innovators, and make the web less safe. According to the varied and multitudinous reasons large numbers of sites and individuals are opposed to the bill, it betrays basic American tenets, such as free speech, prosperity, and national security.

Thanks. ◼

Shit scientists say

2012-01-17T10:56:00.001-06:00

So this means the "shit X says" videos are pretty much done, right?

Also, for the record, it has been years since I've said or written the word "utilize" non-ironically. ◼

We still have a dream

2012-01-16T08:05:00.000-06:00

And when you're finished listening, check out On the Media's great description of how Dr. King went off script at the best possible moment—and what happened after. ◼

Excuses, excuses

2012-01-14T12:23:00.002-06:00

Separating the sheep from the goats. Original photo by Nick in exsilio.

I'm not a believer, but I reserve the right to appropriate the religious literature with which I was raised for my own ends. That's pretty much what Jesus and xkcd did, anyway. And once I thought of this one, I had to write it down.

When the Son of man shall come in his glory, with all his holy angels, then shall he sit upon the throne of his glory.

And before him shall be gathered all nations, and he shall separate them one from another, as a shepherd divides his sheep from the goats.

And he shall set the sheep on his right hand, but the goats on the left.

Then shall he say also unto them on the left hand, “Depart from me, you who are cursed, into everlasting fire, prepared for the devil and his angels.

For I was hungry, and you gave me no food; I was thirsty, and you gave me nothing to drink;

I was a stranger, and you did not invite me in; naked, and you did not clothe me; sick, and in prison, and you did not visit me.”

Then shall they answer unto him, “Lord, we did indeed see you hungry and thirsty, a stranger, naked, and sick and in prison. We’ll totally cop to that.”

And the Lord shall say, “Wait, that’s not in the script.”

Read more ...

Self-deception

2012-01-13T15:10:00.002-06:00

Over on the recently launched Queereka, an interesting discussion of cognitive biases in the context of life in the closet:

People who comment on how cute you look in that dress, for instance, would be confirming that you perform best as female. If, like me, you are convinced you should be and will be attracted to men, you will remember best the men you did like, ignoring the majority of men who were not sexually attractive to you. The important thing is that the people you try to like are in the arbitrary associative category, “men,” which overlaps somewhat with the category of “male.”

I also appreciate the comparison between the closet and the TARDIS. Both are bigger, and more impressive, on the inside. ◼

Science online, pseudonymous micro-RNAs edition

2012-01-13T08:05:00.000-06:00

Embrace the mask. Photo by Annamagal.

Welcome to postdoc-dom! DNLee takes a fresh Ph.D. to the Oklahoma State University.
Recognition by his colleagues, finally. The American Astronomical Society will honor gay rights pioneer Frank Kameny.
Suck it, George Lucas. This one's real. Astronomers have produced a data-based rendering of sunset on an extrasolar planet.
Oops. Lizards on closely-studied islands have become scared of scientists.
Ten-hut! Just like ants, at least one species of bees produces soldiers.
Time to get a pseudonym? A survey of online comments sections finds that pseudonymous commenters are better than those posting anonymously or under their real names.
Arming the locals. Infectious bacteria can pass on virulence genes to native gut bacteria.
But he still sounds like an asshole. Richard Owen was no creationist.
Quelle surprise. The genomes of two centenarians reveal no Medelian genes for long life.
An oldie but a goodie. What can we tell about ancestral human mating behaviors from population genetics?
Oy. An article in The Atlantic connects some dubious dots.
Moral of the story: put the good stuff in Figure 1. Why reading scientific papers doesn't mean what you might think—and shouldn't.

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Fixing evolutionary psychology

2012-01-11T08:05:00.000-06:00

Story time. Photo by McBeth.

Over at Neuroanthropology, Greg Downey's launching an ambitious project: making evolutionary psychology less ... shitty.

More specifically, and more politely, Downey thinks (as I do) that evolutionary biology can tell use some valuable things about human nature; but he's concerned (as I am) that the most visible representatives of an academic field which takes the evolution of human nature as its central question often apply an impoverished understanding of evolutionary biology to telling titillating (and usually unsubstantiated) adaptive fairy tales. Which fairy tales all seem to take place in a sort of dark Lake Wobegon, where all the women are weak and choosy, all the men are strong and horny, and children are barely more than notches on the bedpost of natural selection.

Against the strong man/choosy woman story, Downey proposes the "long, slow sexual revolution." The central idea is that, as our ancestors' intelligence increased toward modern humanity, their interest in, understanding of, and uses for sex and sexuality changed:

The idea of the ‘long, slow sexual revolution,’ I think, provides a simple and balanced umbrella for pulling together contradictory elements of our sexuality, gender relations, and reproductive strategies. Everyone knows that the more recent ‘Sexual Revolution’ didn’t erase pre-existing sexual mores and patterns, but rather mixed with them, producing a conflicted, sometimes-unpredictable pattern of sexual expression. Starting with a ‘sexual revolution’ rather than the Men-are-from-Mars-Women-are-from-Venus story means less erroneous leaping to stereotypes to undo when we teach or communicate about human evolution. [Emphasis sic.]

In one of many insightful points, Downey draws in Emily Willingham's recent post on family planning before the Pill—humans have had the intelligence, and the means, to use sex for more than making babies since (probably) before the dawn of recorded history.

That's really only the jumping-off point of a post that delves deep into the problems of evolutionary psychology and what might be done about them. And it's the first part in a promised series! So go read the whole thing, and keep an eye out for future installments. I'll certainly be watching with interest. ◼

You should read: Reamde

2012-01-09T09:39:00.000-06:00

Reamde. Photo by jby.

Neal Stephenson's latest novel, Reamde, opens in a self-consciously stereotypical image of rural America: three generations of the Forthrast family engaged in recreational firearms practice in the midst of an annual reunion on an Iowa farm. The next thousand pages follow two members of that family out of the Midwest and across the globe.

Reamde zips from Iowa to Seattle, the mountains of British Columbia, urban China, the Isle of Man, the Philippines, a trailer park in Missouri, and a survivalist compound in north Idaho. The engine driving this jet-setting plot is a computer virus, the eponymous Reamde, propagated through a fictional massively multiplayer online game. Reamde reaches out across the Internet to entangle the creator of that online game and his niece with Russian gangsters, a Hungarian hacker, Chinese professional gamers, a Wales-born Al Qaeda terrorist mastermind, British and American intelligence agents, rural U.S. militia members, and two fantasy authors—one outrageously highbrow, the other hilariously low.

Read more ...

Science online, top speed edition

2012-01-06T08:05:00.001-06:00

Running. Photo by Mark Sadowski.

Diff'rent strokes for diff'rent muscles. Most human leg muscles operate efficiently in walking and running, but different muscles are at peak efficiency at different speeds.
Harm reduction reduces harm. Aggressive and innovative public health measures in British Columbia has dramatically cut new HIV infections.
Getting to zero. What to do about false positive tests for HIV infection.
Not so vestigial after all? The function of the human appendix may be in recovery from gastrointestinal infections.
Someone's gotta provide those articles. A consideration of whether it's okay to write for Playboy.
Or, you know, there's more to "fitness" than sperm motility. In which being attracted to deep-voiced men may not make adaptive sense.
A depressing thought. Could failures of antidepressants in placebo-controlled tests be due to bad patient sampling?
That's one fast camera. New optical and computational tools can capture light waves in motion.
Convergence in the slow lane. Two-and three-toed sloths have apparently evolved their similar forms independently.
Requiescat. Pioneering geneticist James F. Crow.
The power of branding. An elaborately double-blind trial demonstrates that professional violinists can't tell a Stradivarius from a brand-new violin.

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Carnival of Evolution, January 2012

2012-01-05T08:05:00.000-06:00

Lignum vitae est. Photo by Niels Linneberg.

Whoops. I totally failed to point out that the latest Carnival of Evolution is up at The EEB & flow. With bonus historical perspective:

523 BCE
Anaximander: "Thales, my teacher, how is it that animals take their form?"
Thales: "Anaximander, all matter is an aggregation formed from a single substance, water, and qualities are obtained through need"
Anaximander: "Ah yes, water, I will now think about how air can be the primordial substance."

Fortunately, there's also lots of much more recent material, which is the whole point of a monthly compilation of all things online and evolution-related. Included are a couple of my latest posts, and Luke Swenson's great post (for Nothing in Biology Makes Sense!) explaining how biologists can trace the evolutionary past of an HIV infection to identify its source. Go take a look, if you haven't already. ◼

Iowa hangover

2012-01-04T10:42:00.001-06:00

So last night a tiny fraction of the population of a not-very-populous but otherwise unobjectionable Midwestern state demonstrated they've never Googled Rick Santorum. Or maybe that they'd rather vote for a hateful, race-baiting asshole than a Mormon. One state down, forty-nine to go.

So here's a nice animation of imagery from my favorite movie ever, to help take the edge off. In the grand scheme of cosmic history, the Iowa caucuses are much less stressful.

2001: A Space Odyssey from Joe Donaldson on Vimeo.

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Hello out there! The D&T 2011 reader survey

2012-01-03T08:05:00.000-06:00

Hmm. Out there looks ... familiar. Photo by tom jervis.

After crunching the traffic numbers yesterday, it's time to look at the results of my reader survey. With caveats for sample size, it appears my audience looks a lot like me: male, queer, young-ish, North American, English-speaking, and white. Here's the Google Documents graphical summary of the fifty-four responses. (Or you can inspect the spreadsheet with the raw responses here.) Let's start with the demographic bullet points I just mentioned:

Male. Of the 54 respondents, 20% (11) are female and 80% (43) male; no-one identified as transgendered. My readership is less gender-diverse than the current U.S. Supreme Court!
Queer. Twenty-eight respondents (52%) said they are attracted to the opposite sex, which is a majority—but much less so than in the general population. Nineteen (35%) said they are gay or lesbian; seven (13%) said they are bi.
Young-ish. A strong majority of respondents said they were either single (23; 43%) or married without children (19; 35%). That squares with the age distribution of respondents, for which the largest group are between 26-30 (16; 30%), and 65% (35) are under age 40. (There's an interesting bimodality to the age distribution though—there's a second, smaller peak in the 55-60-year-old bin.)
North American. Sixty-one percent of respondents (33) are living in the U.S; another 9% (5) are in Canada or Mexico. I'm going to bet most of those are in Canada, based on the next point.
English-speaking. Eighty-nine percent (48) grew up speaking English. Which makes sense, since that's the language I write in. This and the previous point also square with Google Analytics results, which find the overwhelming majority of site visitors are from the States, followed by England, Canada, and Australia.
White. Ninety percent of folks (47) identified as white/Caucasian. More people chose "other" (3) than any of the other racial/ethnic categories I provided.

I'm sure I'm not the first to point this out, but

2012-01-02T13:12:00.000-06:00

A surge by Santorum is a sign you're doing something wrong, regardless of whether we're talking about the voting booth or the bedroom. Please take note, Iowa Republican caucus-goers. ◼

State of the blog, 2011

2012-01-02T08:05:00.000-06:00

The quantified blog. Photo by hyperboreal.

Happy New Year! Time for some quantitative navel-gazing, which now counts as a Denim and Tweed New Year's tradition, since I've done it twice before. Tomorrow, I'll take a look at the responses to my first-ever reader survey, but right now, I'm just going to go through the metrics I've used before.

In 2011, I wrote 198 posts for this site. According to Google Analytics, these attracted 73,899 page-views by 24,025 unique visitors. That's an average of 373 page-views per post, and an increase in traffic of 161% over 2010, when I had 28,308 page-views. For some perspective, it's about two orders of magnitude less than John Scalzi's visitation rate. But not too bad, if I do say so myself.

More detail after the jump.

Read more ...

Best of lists, 2011

2011-12-31T08:05:00.000-06:00

Presented in no order of precedence, quality, or importance:

Kate Clancy rounds up online writing about ladybusiness anthropology—and I'm honored to have my own work listed alongside great pieces by folks including Emily Anthes, Jennifer Oulette, and Emily Willingham.
Southern Fried Scientist ranks the top science hashtags on Twitter this past year.
Ed Yong picks his favorite Not Exactly Rocket Science posts—there's everything from microscopic wasps to skull cups and out-of-body experiences.
Brian Switek digs up (sorry!) the top dinosaur news.
Alex Wild delivers a compilation of amazing insect photography. My favorite is the army ant soldier.

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Science online, auld lang syne edition

2011-12-30T08:05:00.000-06:00

I think it's safe to assume this quail is totally high right now. Photo by Hiyashi Haka.

Last call! If you haven't taken my reader survey yet, you have until the end of tomorrow! Thanks to everyone who's already answered!
Do this now, please. Pitch in to help Jacquelyn Gill fund her trip to Science Online 2012.
#UnBerable. More responses to Jesse Bering's latest embarrassment: Kate Clancy advises an anonymous Evidence-Free Science Provacateur and PalMD suggests Scientific American reconsider its relationship with Bering.
Guess tenure hadn't been invented yet. How Charles Babbage tried to remove Isaac Newton's calculus methods from Cambridge.
Video NSFW if you're a quail. What we can learn from studying the mating behavior of cocaine-addicted quail.
Ugh. Satellite images document the spread of operations at the Alberta tar sands.
Latina mortua est. Vivat lingua Latina! Botanists decide it's okay to name new species without describing them in Latin.
It should be the same kind as ecology ... What kind of science, if any, is economics?
A handy checklist. How to apply for a position as a grad student or postdoc.

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Stand up and be counted—take my reader survey!

2011-12-27T10:41:00.001-06:00

Just a brief reminder: my reader survey is still open for responses! I'm going to keep it open (and probably prod you for answers) through the 31st. So please follow that link and tell me about yourselves and what you think of Denim and Tweed. It's all quite anonymous, and you can skip any question you'd rather not answer. Thanks in advance! ◼

Has Jesse Bering jumped the shark yet?

2011-12-26T08:05:00.000-06:00

Photo via Octopus Overlords.

I have a history with Jesse Bering's evolutionary psychology writing, and I do, in fact, have better things to do over the holidays than deal extensively with his latest offense against evidence-based reasoning. But this one is pretty egregious: Bering pretends to be an advice columnist counseling a (hopefully imaginary) "hebephile" that there is a perfectly good adaptive explanation for lusting after "very young girls," even if our insufficiently evolution-conscious society frowns on it. Oy.

Bering cites a previous column arguing that attraction to young adolescents could be adaptive because youth correlates with fertility. Said column is conspicuously devoid of biological data. However, five minutes with Google found me an abstract that puts the age at which women's fertility is up to full adult capacity at about six years after their first periods. Given an average age of menarche at 12.5 years, that means it should be most adaptive to lust after, um, 18- to 19-year-olds.

Read more ...

A Calvin and Hobbes-ian season's greetings

2011-12-25T08:05:00.000-06:00

Via Lost in Transcription. Happy holidays! ◼

Science online, you'd better not pout edition

2011-12-23T08:05:00.000-06:00

How would you measure scientists' performance?. Photo by MarcelGermain.

Tell me who you are, and what you think! Have you taken the D&T reader survey yet? Please do!
Making sense of your holiday gift list. At Nothing in Biology Makes Sense!, Will Godsoe suggests some books for the biologist in your life.
Tinker, tailor, soldier ... Most people have difficulty remembering other folks' names, but much less remembering their jobs or hobbies.
Paging Marshall McLuhan. Kevin Zelnio's vision for online science outreach.
All that is advantageous does not fix. The evolutionary importance of drift, succinctly explained.
With video, this time. Scicurious takes on that study of fear and reproductive output in song sparrows.
To the victor ... Crickets that win fights with other crickets become more aggressive afterward.
What's in your metric? Counting journal articles as a metric of scientific achievement still makes sense.
Neat! Circuits made with gallium-indium alloy can heal their own cracked wires.
Looks like the TSA could use some peer review. Those body-scanning machines at airports are, in many cases, not as effective as a pat-down.

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Twelve months of Denim and Tweed, 2011

2011-12-22T08:05:00.000-06:00

Following DrugMonkey's lead, here's the first sentence posted to this site every month in 2011. (I've cheated a bit by skipping over boring introductory material in one or two cases.)

January: Happy New Year, everyone!
February: My dear Hooker, I was grateful for your very kind wishes; and for the book about the Anoles of the West Indes, which I expect I shall read with much enjoyment.
March: Plants' ancient relationship with animal pollinators is pretty crazy, when you think about it.
April: In which a new technology loses its shine.
May: What has two thumbs and forgot to submit to the Carnival of Evolution this month? This guy.
June: Greg Laden hosts this month's Carnival of Evolution, the monthly compendium of online writing about descent with modification and all its consequences, complications, and controversies.
July: So counterintuitive, it's counterfactual.
August: The latest edition of the Carnival of Evolution, a monthly collection of online writing about evolution and all its ramifications, is online at Sandwalk.
September: The September issue of the Carnival of Evolution is online now at The End of the Pier Show.
October: It's been ages since I posted a recipe, but I'm still doing lots of cooking.
November: This week at Nothing in Biology Makes Sense, the big science post comes from ... me.
December: Via Scott Chamberlain: A species of ants that lives in and around carnivorous pitcher plants isn't entirely freeloading.

Hey, I really kept on top of the Carnival of Evolution, eh? I did this last year, too. More quantitative navel-gazing coming in the new year. ◼

Take the D&T reader survey!

2011-12-21T08:05:00.000-06:00

Surveying. Photo by danakin.

Inspired by previous efforts at other blogs, and spurred by Kevin Zenio's recent post on the importance of reader feedback, I've decided it's well past time to find out more about who's reading Denim and Tweed. I get some sense of the size and diversity of my readership from Google Analytics, and from who decides comment on or tweet about or "like" individual posts. However, it's pretty clear that some number of you read without responding in any medium I can see, and those are the folks about whom I'm most curious.

So if you would please take a minute or two to fill in this handy online form, I would be exceedingly grateful. None of the questions are required, but answers to all of them would be informative. This is your chance to let me know who's out there, and what you think of what I'm doing here at D&T. ◼

Science online, the pain of defying gravity edition

2011-12-16T08:05:00.000-06:00

Hummingbird in flight. Photo by Jason Paluk.

Congratulations! The winners of this year's NESCent science blogging contest have been chosen.
We're really not that expensive. Want more scientific discoveries? Well, then maybe we should pay for more scientists.
Darwin wasn't a jerk. Nineteenth century shipping timetables confirm that Darwin didn't screw over Alfred Russell Wallace.
“The bird is so small and light that its bones are largely transparent to X-rays,” he said. X-ray video reveals the mechanics of hummingbird flight.
Say it ain't so, Marty Stauffer! Lots of wildlife photography is staged. But that's probably not a big deal.
Another reason to keep it natural. Most humans' body hair is lousy for insulation, but it does help deter parasites.
For example, the pain of lying on a slight incline for hours? Microgravity environments may interfere with how astronauts perceive pain.
One of these things is not like the other. A checklist for distinguishing real science from pseudoscience.
A useful skill, in a herbivore. Sheep can differentiate between different kinds of food plants.

Video this week: tool use by an orange-dotted tuskfish. Specifically, the fish breaks open a clam by hitting it against a rock. Who needs opposable thumbs?

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#OccupyAmazon round 2: Cheap books are great, but someone's paying the difference

2011-12-14T08:05:00.000-06:00

Brick-and-mortar. Photo by ImaginaryGirl.

Bouncing off the same NY Times op-ed that I did yesterday, Slate's Farhad Manjoo says, screw indy booksellers. They're not cheap or efficient enough. Here's the core of his price argument:

A few times a year, my wife—an unreformed local-bookstore cultist—drags me into one of our supposedly sacrosanct neighborhood booksellers, and I’m always astonished by how much they want me to pay for books. At many local stores, most titles—even new releases—usually go for list price, which means $35 for hardcovers and $9 to $15 for paperbacks. That’s not slightly more than Amazon charges—at Amazon, you can usually save a staggering 30 to 50 percent. In other words, for the price you’d pay for one book at your indie, you could buy two.

And here's efficiency:

Compared with online retailers, bookstores present a frustrating consumer experience. A physical store—whether it’s your favorite indie or the humongous Barnes & Noble at the mall—offers a relatively paltry selection, no customer reviews, no reliable way to find what you’re looking for, and a dubious recommendations engine. Amazon suggests books based on others you’ve read; your local store recommends what the employees like. If you don’t choose your movies based on what the guy at the box office recommends, why would you choose your books that way?

Manjoo also makes the point that indie bookstores aren't really selling local products—their bread and butter is sales of the same nationally distributed books that fill up Amazon's top sellers list. And since Amazon offers those books at a better price point, they're available to more people who want them, and that's all you need to sustain a literary culture, right?

Read more ...

#OccupyAmazon by occupying real bookstores

2011-12-13T13:10:00.000-06:00

Uncle Hugo's, where it is entirely possible to trip over a stack of Asimov novels and break a model of the ship from Lost in Space if you're not careful. Photo by Olivander.

You may have heard that Amazon.com took its competition with brick-and-mortar booksellers to a new level this holiday season, offering a discount to people who go into a store and scan a product with Amazon's smartphone app to find out what price Amazon was offering for the same wares (presumably cheaper, and free of local sales tax). If you're not sure why this is an asshole move on the part of the gargantuan online retailer, you've got a good one in this op-ed by Richard Russo, who talks to a number of other authors, all of whom have done pretty well thanks to sales via Amazon, about the whole business. Money quote from Ann Patchett:

"... If you like seeing the people in your community employed, if you think your city needs a tax base, if you want to buy books from a person who reads, don’t use Amazon.”

I bought a lot of books as gifts this holiday season, and I'm glad to say I bought none of them from Amazon. Instead, I went to the collegiate used bookstore the Book House, the "indie behemoth" Magers & Quinn, and the astounding nerdcave that is Uncle Hugo's. I probably paid a bit more, and I'll have to figure out how to fit all the books in my carry-on instead of shipping them ahead of me, but I had a lot more fun doing the shopping, too. ◼

Frightened birds make bad parents

2011-12-13T08:05:00.000-06:00

Song sparrow chicks. Photo by Tobyotter.

Predators have an obvious impact on their prey: eating them. But if the threat of predators prompts prey species to change their behavior, those behavioral changes can also affect prey population dynamics [$a]—and thereby, potentially, the prey's evolution—even if the predators never actually catch any prey.

This is the effect documented in a short, sharp study just published in Science, in which Liana Y. Zanette and her coauthors show that song sparrows raise fewer chicks if they simply think that there are predators nearby [$a].

The team's experimental design was simple but probably pretty work-intensive. Over the course of one summer on several small islands off the coast of British Columbia, they watched song sparrows choose mates and build nests. Once nests were established, the team surrounded them with anti-predator defenses: netting and electrified fences. They confirmed that these measures kept predators out with regular video surveillance. And then they turned on the loudspeakers.

Read more ...

Holiday baking

2011-12-12T08:00:00.000-06:00

Grandma's date pudding. Photo by jby.

I could frankly do without a lot of holiday-time rituals, but I'm perfectly happy to have the excuse for baking. This year I made cranberry orange bread for the folks in my lab, following a great recipe in Mark Bittman's magisterial How to Cook Everything. I've also taken a crack at Ma Savage's Christmas Snowballs for one party, and for the departmental party, I dug up a family tradition: Grandma Bender's date pudding.

My mom's mom has a pretty serious sweet tooth, and so I learned to love this recipe—cubes of rich, sweet, date cake layered in sweetened whipped cream—as part of the main course for Thanksgiving and Christmas dinners. Nowadays, I cut the sugar from the whipped cream, and it still goes over quite well as a dessert. It's also possible to substitute in whole wheat or spelt flour, which only makes the cake denser and richer. Recipe follows:

Read more ...

Science online, ancestral penis reconstruction edition

2011-12-09T08:05:00.000-06:00

You want to dissect my what?! Photo by GAC'63.

I made the cut. The finalists for this year's Open Lab compilation of online science writing have been announced, along with many deserving runners up.
This week, at Nothing in Biology Makes Sense! Luke Swenson described how understanding evolution lets scientists estimate the age of an HIV infection.
It flows! Well, flowed. The Mars rover Opportunity has found gypsum, a mineral that can only form in the presence of liquid water.
Meanwhile, even further out in space. The Kepler telescope identifies an Earth-sized planet at about the right distance from its sun for liquid water.
One nucleic acid is not like another. The nematode worm Caenorhabditis elegans can transmit traits to its offspring that aren't encoded in its DNA.
See also, graduate school. Medical school as a constellation of brief, intimate moments.
See what happens when you don't take source-sink dynamics seriously? Herbivorous insects are evolving resistance to genetically modified Bt corn in the U.S.
Collaborators! Invasive fire ants may be invasive because they work well with aphids.
Which pretty much explains HuffPo science writing. Some guy at the Huffington Post thinks science writing would be better if science writers stopped listening to scientists.
Hehe. Ostrich penises. A new detailed study of ostrich penises improves our understanding of bird evolution.
Getting warmer. Peak attendance dates at national parks have moved about four days earlier over the last 30 years.

Video of the week, via Open Culture: Robert Krulwich describes behavioral experiments that dissected how ants navigate. (You may remember this as the subject of one of Jason Goldman's earliest posts.)

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Can't keep us apart: Brood parasitic birds have specialized on the same hosts for millions of years

2011-12-07T08:05:00.000-06:00

A male greater honeyguide. Photo via Safari Ecology.

Brood parasitic birds lay their eggs in other birds' nests, a lazy approach to parenting that shapes the behavior and evolution of brood parasites in all sorts of interesting ways.

Brood parasite chicks often kill their adoptive nestmates, and can grow up confused about their species identity. To better trick their hosts into accepting "donated" eggs, many brood parasites have evolved eggs that mimic the hosts'—and some hosts have evolved contrasting eggs in response. A recent genetic study now shows an even subtler pattern arising from this host-parasite coevolutionary chase: lines of parasitic females that have specialized on the same host species for millions of years.

Read more ...

Open Lab 2011 finalists: I'm in a book (again)!

2011-12-06T19:02:00.001-06:00

I've already tweeted about this last night, as soon as I got the e-mail—but Jennifer Ouellette has just made it official with the complete list of science blog posts chosen for Open Lab 2011. And among them is my long discussion of natural selection and homosexuality. It'll be great to see that piece in actual dead-tree print. It'll be even better to see it alongside top-notch writing from such a long list of folks whose work I admire. ◼

Nothing in Biology Makes Sense: Tracing the evolutionary history of HIV infection

2011-12-06T09:24:00.001-06:00

The molecular structure of HIV. Photo by PHYLOMON!.

In the latest post at the group blog Nothing in Biology Makes Sense!, contributor Luke Swenson describes how biologists can reconstruct the evolutionary history of HIV to estimate when the virus make the jump from chimps to humans, or even when a single patient became infected.

Although HIV evolves rapidly, it does so at a fairly constant rate. In essense, you can use this constant rate to act like a clock to tell you roughly how many changes accumulate over a year. Then, by figuring out the number of changes it would take for both sequences to converge on a single identical sequence (their most recent common ancestor, “MRCA”), you can get an estimate of the date that the MRCA existed at.

This is one of the best cases I know about in which evolution directly informs medical practice and treatment, and it's well worth reading the whole thing. ◼

Diversity in Science Carnival No. 11: Native American Heritage Month edition

2011-12-05T12:07:00.001-06:00

There's a new edition of the Diversity in Science blog carnival out today, too: Urban Scientist DNLee rounds up stories of Native Americans in science, technology, engineering, and mathematics disciplines for Native American Heritage Month. It includes meditations on the value of cultural diversity in science, celebrations of individual scientists, and discussion of scientific insights from Native cultures that we're still just beginning to recognize. ◼

Carnival of Evolution, December 2011: A very special carnival of evolution

2011-12-05T10:55:00.001-06:00

Forty-two. Photo by Valerian Gaudeau.

The new Carnival of Evolution, freshly posted over at the Ocelloid, is the forty-second iteration of the monthly roundup of online writing about evolution, the universe, and everything. Well, maybe not everything.

Highlights include, but are not limited to, Larry Moran illustrating the difference between census population size and effective population size, Hannah Waters on the evolutionary context of grieving, and Jenna Gallie's description of her own research on rapid adaptive evolution by E. coli. There are also multiple contributions from Nothing in Biology Makes Sense!, in case you haven't already seen them. Go read the whole thing, and don't forget your towel. ◼

Science online, gesturing ravens edition

2011-12-02T08:05:00.000-06:00

Raven in flight. Photo by ingridtaylar.

In mice! Gene therapy has proven effective at preventing HIV infection.
Still no opposable thumbs, thank heavens. Ravens gesture to other ravens with their beaks.
Awww. The embryonic development of anoles, imaged.
Eight-month-old infants understand justifiable meanness.
A gene "for" many things, or nothing? Mutations to a single gene may cause many different malformations.
But only until the flavor runs out. Chewing gum helps you concentrate.
Romans weren't so careful about "leave no trace." European plant communities still show the effects of ancient Roman settlements.
I mean, seriously. Gender-specific science kits are not a good way to get girls into science, and not really helpful for boys, either.

And lastly, here's video of a starfish-inspired "boneless" robot in action. Good luck getting to sleep tonight!

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Pitcher plant ants keep their host clean

2011-12-01T09:09:00.001-06:00

Via Scott Chamberlain: A species of ants that lives in and around carnivorous pitcher plants isn't entirely freeloading. They also clean the walls of the plant's pitfall trap, keeping it nice and slippery for insect-trapping.

Of course, the ants have a vested interest in keeping the trap effective, since they eat some portion of the critters caught by their host. But it seems pretty straightforward to think that this helps the pitcher plant, too. A more definitive test would be to compare the survival and seed production of pitcher plants grown with and without a colony of ants to keep them clean. ◼

Nothing in Biology Makes Sense: Sexual selection and the lek paradox

2011-11-29T09:20:00.001-06:00

A peacock, which made Darwin "sick." Photo by aussiegal.

This week at the collaborative blog Nothing in Biology Makes Sense!, guest contributor Tom Houslay makes sense of costly mating displays:

Time and again in the animal kingdom, we see exaggerated ornaments, vibrant colours, and fantastic acoustic and visual displays. Frogs and crickets advertise their whereabouts with loud calls, fireflies flash patterns with bioluminescence; greater sage grouse strut brazenly in open pastures. While they undoubtedly brighten up the world around us, these behaviours and morphologies can seem not only unnecessary, but downright detrimental to the survival of an individual. How, then, can their existence be resolved with our knowledge of evolution?

To find out how a single showy trait can come to "capture" all the genetic variation in a population, read the whole thing. On an almost totally unrelated note: if I ever open a gay bar, it will definitely be called Lek. ◼

Advertising equality

2011-11-25T22:20:00.001-06:00

I'm with Queerty on this one: the Australians make a much better ad for marriage equality than us schlubs in the States.

Go ahead, take a moment to find a tissue.

If anyone asked my opinion, though—which they haven't—I'd say that there's an important point missing from this ad, and from most of the pro-equality campaigns I've seen. That point is that gays, lesbians, and transgendered folks are already living stories like the one so movingly depicted above, and making lifelong commitments to each other, without waiting for anyone's permission to do it.

My ideal advert for equality would simply be a series of short clips of committed queer couples—maybe just sitting there looking back at the camera, maybe recounting bits of the joys of life together. Each couple has accompanying subtitles: Alice and Rose, together 14 years, or Rob and Michael, together 5 years.

The point being, gay marriages already exist, and in many cases have been existing longer than a lot of the straight couples in the audience have been together. And it's long past time for the government to acknowledge them. ◼

Science online, pepper sprayed turkey edition

2011-11-25T08:05:00.000-06:00

Happy Thanksgiving, U.S. readers. Photo by Bemzilla.

This week at Nothing in Biology Makes Sense! Fruit flies prefer mates with the same gut bacteria.
Worst pets ever? An online ant supplier provides invasive pests.
Powers combined. The fungus killing frogs worldwide may have originated as a hybrid between non-lethal species.
The developmental regulatory systems that determine biological sex before birth don't stop after birth.
Planning ahead. The U.S. Defense Department's research arm is thinking about life after antibiotics.
Hell, yes. Should pepper spray be subjected to clinical trial?
Maybe. Can a genetic marker predict your impulsivity?

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How to interview for a faculty job

2011-11-23T08:56:00.001-06:00

This is billed as "how to get a faculty job in 20 not-so-easy steps," but it's actually all about what to do when you're invited out for an interview, which seems to me* to be eliding some even less easy steps, but whatever. It is, in fact, quite funny, and much of it is good advice for academic job interviewing at all levels, e.g.:

5. Wear a catheter. Your interview will consist of 1-2 days of 20-minute meetings scheduled back-to-back with absolutely anybody they could cram onto your schedule. There will be no bathroom breaks, no water breaks, and no insulin injections. This is exacerbated by the fact that every single one of the people you meet will want to take the 20-minutes as their coffee break. In the end, most of the interview will be a blur, except that you will be able to find the coffee cart from any point on campus blindfolded.

See also, the advice on the "interview dinner." ◼

----------------
* At this stage of the game, I would be so thrilled to be asked for a phone interview I might just ignore the call when it came, so as to preserve the blessed event as the current pinnacle of my job-hunting success.**

** No, of course I would not actually do this, because I would very much like a faculty job, thank you.

Nothing in biology makes sense: Gut microbes and mate preference

2011-11-22T11:20:00.001-06:00

Will this male fruit fly pick a mate based on what she ate? Photo by Max xx.

This week at Nothing in Biology Makes Sense!, Sarah Hird tackles a series of studies suggesting that fruit flies may pick mates reared on similar diets because their gut microbes make them do it.

In 1989, Diane Dodd reared fruit flies (Drosophila pseudoobscura) from a common stock on two different food sources: starch and maltose. She found that after multiple generations of isolation on their separate substrates, starch-flies preferred to mate with starch-flies and maltose-flies preferred to mate with maltose-flies. The result was robust and repeatable, but the reason why and its mechanism were unknown.

To find out how the mechanism was discovered, go read the whole thing. ◼

Science online, sexist mosquitoes edition

2011-11-18T08:05:00.000-06:00

Lab mouse. Photo by Rick Eh?.

What's next, a Nature centerfold? Janet Stemwedel, Anne Jefferson, Christie Wilcox, the Lab Lemming, and Paul Anderson, among others, respond to Jurassic-era "humorous" sexism in the pages of Nature. Kate Clancy proposes occupying the Nature Publishing Group.
This week at Nothing in Biology Makes Sense! Making sense of the latitudinal diversity gradient.
Some folks' bootstraps are shorter than others'. Academic life isn't so easy when you don't enter academia from the middle class.
Diversity matters. The heavy use of standardized lab mice in biomedical research may have some undesireable consequences.
And so ad infinitum. An amber-preserved spider has amber-preserved mites.
Not just in the usual way, either. Mosquitoes engineered to fight malaria may suck.
Power laws, and laws of power. What probability distributions can tell us about causes of income inequality.
Backyard science! A plan for behavioral observations of birds at your bird feeder.
Watch your glass, gals—and guys. "Date-rape" drugs may cause quite a lot of accidental deaths.
Annals of unsurprising results. Scientific evidence (such as it is) suggests that religion doesn't make you more moral.
Less than you might think. The evidence that women in close regular proximity synchronize their menstrual cycles.

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Hey, what happened to the header?

2011-11-17T23:32:00.001-06:00

In a word, this.

If that sounds like a bad idea to you, too, tell Congress. I have. ◼

Tell Congress to increase NIH funding

2011-11-16T10:04:00.000-06:00

Cross-posted from Nothing in Biology Makes Sense!.

For your consideration: a Change.org petition asking the U.S. Congress to increase funding to the National Institutes of Health by 3% in next year's Federal budget. NIH is one of the biggest sources of public research funds in the U.S., and its support goes well beyond things immediately connected to human health and medicine—I did many analyses for my dissertation research on Joshua trees and yucca moths on a supercomputing cluster supported, in large part, by NIH funds.

Some would argue that the private sector should take over some of the lost funding for academic, basic research. The sad fact is that the private sector does not support the type of basic research that the NIH does; they take the results NIH-funded research and apply it to drug development. In addition, many entities in the private sector are currently slashing their Research & Development (R&D) budgets! For example, Pfizer recently cut its R & D budget by 1.5 billion.

Consider the following numbers. For 2011 budget, U.S. spending on:
Social security was $2564 per citizen (20.8% of the budget)
Defense was $2203 per citizen (18% of the budget)
Medicare was $1569 per citizen (12.8% of the budget)
Medicaid was $1172 per citizen (7.8% of the budget)
NIH was $99 per citizen (0.8% of the budget)

The original idea, as I understand it, is for this to be an "open letter" to Congress from working scientists across the nation, but supportive non-scientists should definitely sign on, too. ◼

Nothing in Biology Makes Sense: Making sense of the latitudinal biodiversity gradient

2011-11-15T15:00:00.001-06:00

Tropical forest along the Inca Trail in Peru. Photo by TheFutureIsUnwritten.

This week at Nothing in Biology Makes Sense!, Noah Reid describes a new study that tries to explain the latitudinal biodiversity gradient—that is, the reason why a tropical rainforest has so many more species than, say, the mighty forests of British Columbia.

Almost invariably across taxonomic groups, hemispheres and continents, as one moves from polar regions towards the equator, species diversity increases (see the figure for a depiction of global bird diversity). The concept of diversity here can be broken down into three parts: “alpha diversity” or the diversity of species in a single location; “beta diversity”, or the turnover of species observed when moving among locations; and “gamma diversity” or the diversity of species found in an entire region. The latitudinal diversity gradient holds true for all three elements.

To find out what the new study reveals, go read the whole thing. ◼

Science online, rats and rice edition

2011-11-11T08:00:00.000-06:00

Rice. Photo by tamaki.

More on "pox parties." They're really a bad idea and almost certainly illegal.
Paging Dr. Roughgarden. Some male marsh harriers look like females—and coexist peacefully with "regular" males as a result.
We are what we eat, part 2,357. MicroRNAs from rice migrates into your tissue in the course of digestion, and may alter your own gene expression.
Giving that Thanksgiving "hand turkey" a new significance. The success of sumo wrestlers can be predicted from their handprints.
Rats on a rising tide. The expansion of humans across the globe is closely tracked by the expansion of rats.
In which Siri exorcises the ghost of HAL. The iPhone's new virtual assistant, considered anthropologically.
Another reason to buy organic. Up to three quarters of honey sold in the US doesn't contain any pollen—possibly to cover up illegal imports.

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Nothing in Biology Makes Sense: Treating depersonalization disorder

2011-11-08T09:01:00.000-06:00

Barnacles. Photo by JustCallMe_Bethy.

This week at Nothing in Biology Makes Sense!, my brother Jonathan Yoder—a third-year medical student—makes his science blogging debut with a post on the treatments available for depersonalization disorder, a condition in which patients feel disconnected from their own bodies.

There are currently no definitive treatments that have been developed regarding DPD. This is due largely to the fact that there is no well-defined pathology regarding its onset. Given its estimated prevalence of 0.8-2.0% in the general population, it is about as widespread as schizophrenia. Yet little research has been done to understand its root cause and treatment.

Jon's post is a view inside evidence-based medicine, in which a physician weighs peer-reviewed scientific results to decide on a treatment strategy. Go read the whole thing. ◼

Not that I watch Monday Night Football, either

2011-11-07T12:14:00.000-06:00

Slacktivist Fred Clark, as ever, draws an apt comparison:

This suggests that anyone who hopes to become an ethical person would be better off watching football on television every Monday night than attending worship at a Southern Baptist church every Sunday morning. Monday Night Football might not make you a better person, but the Southern Baptist Convention has long employed an “ethics” spokesman who seems determined to make you a worse one.

Actually, now that I think of it, much of what I like about the Slacktivist is his apparently limitless ability re-frame Christianist bigotry as a failure to behave by standards of basic human decency. Jesus said of simple courtesy, "even the pagans can do that." Fred Clark says, "Hey, folks? The pagans are doing it better." ◼

Science online, a pox upon your pox parties edition

2011-11-04T08:05:00.000-05:00

Halloween hangover, anyone? Photo by bunnygoth.

Spooky science. The Scientific American network goes all Halloweeny.
Dumb, dumber, downright dangerous. Parents who refuse to vaccinate their children try to immunize them by mailing around childhood viruses.
Carnival time! The November 2011 Carnival of Evolution is up at The Mermaid's Tale.
Last ditch effort. To save bats from white-nose syndrome, researchers propose building an artificial cave.
Helping science, helping himself. Participating in cognitive research helps a man with schizophrenia cope with his condition.
Alongside or, you know, underfoot. A newly discovered fossil was a ferret-like mammal that probably lived alongside dinosaurs.
Whale folksongs? Sperm whales' songs are probably culturally transmitted.

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Nothing in Biology Makes Sense: Timing is everything

2011-11-01T09:27:00.002-05:00

A euglossine bee gathers scent compounds inside an orchid. Photo by Alex Popovkin, Russian in Brazil.

This week at Nothing in Biology Makes Sense, the big science post comes from ... me. It's about a big new study of orchids and the perfume-collecting euglossine bees that pollinate them.

The study by a team out of Harvard—lead-authored by Santiago R. Ramírez—tests three predictions arising from the proposition that bees and orchids are equally dependent on the scent-collection mutualism. First, as I noted above, a mutually-dependent relationship should mean that bee and orchid species often form in tandem, and that the euglossine bees and the orchids have spent most of their histories together. Second, the euglossines should rely mainly on scents from orchids, not from other sources. Finally, euglossines and orchids should show similar degrees of dependency. An orchid that relies on only one bee species should use a bee species that only collects scent from that one orchid; bees that collect scent from multiple orchids should use orchids that are, themselves, involved with multiple bee species.

To find out whether or not these predictions are borne out, go read the whole post. ◼

I get e-mail

2011-10-31T10:04:00.001-05:00

Submitted without comment, except to note that I've been science-blogging for, like, three years now, and this is, to the best of my memory, the first time I've gotten this sort of e-mail. I'm not sure how that reflects on me, or on my readership.

hi i am a biology student doing an assignment on diversity and evolution

can you please tell me about the variation within weevils. how it came about and stuff like that

Thank you

--
Cheers
[Name redacted]

And my response, in its entirety:

Hi, [Name redacted],

Well, I'm not an expert on weevils, although I've written about some specific work other people have done on specific species of weevils ([long URL]) and about that group of beetles in general ([long URL]). But I'm sure you've already read those posts, since you e-mailed me using the blog's address. I would suggest that you start your research by following up on the papers I cite in those posts, however. (I'm attaching PDF copies of each.)

Also, "variation within weevils" is an extremely vague, and potentially very broad, topic. Weevils are, after all, one of the most diverse groups within the beetles, which are themselves the most diverse group of animals on the planet. So unless you want me to pick your topic, too, I think maybe you'd better do some additional reading and figure out exactly what it is you want to do your assignment on.

cheers,
Jeremy

Okay, fine, I will make one comment, in two parts: (1) [Name redacted]'s e-mail address is an academic one, and (2) the complete text of everything I've written on the subject of weevils is quite thoroughly indexed by Google, and therefore easily findable by both inquiring students, and suspicious professors. ◼

Good news, everyone!

2011-10-29T10:24:00.000-05:00

The academic-history-politics-awesomeness blog The Edge of the American West is back, baby. And they're turning the sacred words of Abraham Lincoln into Wordles.

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Science online, fish out of water edition

2011-10-28T08:05:00.000-05:00

Fish, out of water. Photo by las - initially.

Tradition! Cultural transmission means that different chimpanzee troupes use different food-gathering tools.
Reality's liberal bias persists. A formerly climate-skeptical physicist checks the data himself, and confirms that Earth is getting warmer.
Legless flopping is phylogenetically conserved. Mosquito fish, which routinely leave the water to evade predators, aren't much better at moving around on land than fish that don't jump onto shore.
Leave it to Nobel Prize winners. Two Nobel Prizes were hidden from the Nazis by dissolving them in acid—then later reconstituted and recast.
This is why I don't read HuffPo. On Huffington Post, a "holistic podiatrist" is qualified to tell you that vaccines and scientifically tested medicine don't work.
Do it for the fun, not the fame and fortune. A hard-nosed consideration of the costs and benefits of blogging, for a scientist.
Looks like a good read. A new book traces the origins of HIV in humans, back as far as 1921.

And now, video of one gecko saving another from an attacking snake.

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Nothing in Biology Makes Sense: Two parasites, one host

2011-10-25T12:25:00.000-05:00

Daphnia, a water flea. Photo via Nothing in Biology Makes Sense!.

This week at Nothing in Biology Makes Sense!, the still shiny new collaborative science blog, contributor Devin Drown describes what happens when two different parasite species infect the same water flea.

Octosporea bayeri needs the host to produce offspring for vertical transmission, that is the host and parasite have an aligned interest in producing offspring. On the other hand, Pasteuria ramosa is using host resources, including the reproductive tissues, to produce spores for infecting other hosts. Because of the alignment of interests between host and the vertically transmitting parasite, the question becomes: does infection by O. bayeri provide host protection from future infection by P. ramosa?

The answer, of course, is in the full post. ◼

The joy of sex (well, one, anyway): Fewer parasites

2011-10-25T08:05:00.000-05:00

Natural selection does not necessarily love sex. Photo by xcode.

Hey, don't knock [selfing]! It's sex with someone I love.
—Woody Allen, in Annie Hall

Sex is a puzzle to evolutionary biologists. I don't mean that we're socially awkward—I mean that sexual reproduction, which involves mixing your genes with someone else's to produce one or more children, seems to be at odds with natural selection. Every child produced by sexual reproduction carries only half the genetic material of each of her parents; but parents who can make children without sex pass on all their genes to every child.

Over time, individuals who can make babies without sex should become more common in the population than individuals who have to have sex to reproduce, simply because every baby produced without sex "counts" twice as much for its parent. We know of cases (for instance, stick insects) where asexual reproduction has apparently evolved and spread multiple times.

And yet, not only is sexual reproduction widespread in the natural world, there are many species of living things in which some individuals reproduce sexually and some reproduce without sex, and the two types coexist more-or-less stably. This is particularly common in plants, but it's also seen in lots of other taxa. That suggests there must be something useful about sexual reproduction that offsets the cost associated with making only half a copy of your genome for every child you have.

One popular hypothesis is that sexual reproduction helps generate new combinations of genes to fight parasites and diseases—this is called the Red Queen Hypothesis, after the character in Through the Looking-Glass who tells Alice that "... it takes all the running you can do, to keep in the same place." Sex, the thinking goes, means that your children are more likely to have new parasite-fighting gene combinations, and that populations can "run faster" in the coevolutionary race against parasites. And now, a new study in a population of peculiar little fish provides some reasonably direct evidence [$a] for that proposed benefit of sex.

Read more ...

CreatureCast: Strangler figs

2011-10-23T12:46:00.000-05:00

Kevin Zelnio's post about the need for evolutionary biologists to approach outreach like viral marketing reminded me about CreatureCast, a frickin' awesome project by the Dunn Lab at Brown University, which has scientists talking about their work in bite-sized videos illustrated with whimsical animation. Here's one on strangler figs:

If this isn't a good argument for adding a little money to your next grant to support an undergrad video production or communication major as a "broader impact," I don't know what is. ◼

Science online, vitamin vacuity edition

2011-10-21T08:05:00.000-05:00

Pills. Photo by aSIMULAtor.

Nothing in Biology Makes Sense! I launched a shiny new group blog this week. Is it in your RSS feed yet?
Rant(s) of the week. Scicurious shreds a truly awful discussion of birth control methods; Kate Clancy piles on, and Michelle Clement explains why girlybits aren't scary.
See also, connected to natural selection, however tenuously. A not-all-that-recent study shows that people are more likely to believe claims about human psychology if they're connected to neuroscience, however tenuously.
Wait. There are also vitamins in food? Vitamin pills are probably not as magical as vitamin pill manufacturers would like you to think.
Like sex, and death. Some of the more puzzling features of complex life may be explained by the interaction of the nuclear and mitochondrial genomes. (In part.)
More bloodflow = ?? The colorful blobs on functional MRI brain scans, explained.
With videos and LOLsagegrouse. Why doesn't sexual selection eliminate heritable variation in sexual traits?
First step to smallpox-ville? An experimental malaria vaccine is proving effective in trials.

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Big news, everyone!

2011-10-18T08:05:00.000-05:00

There's a new science blog in town. Er. Online. Nothing in Biology Makes Sense! is what happened when I asked a bunch of my friends—collaborators, "sibling" grad students, and, yes, my brother the medical student—to pitch in their time and expertise in a collaborative science blog. Some of us have a lot of experience writing about science online, and some of us are trying it out for the first time.

The site's name, of course, is a tongue-in-cheek reference to Theodosius Dobzhansky's famous statement that "Nothing in biology makes sense except in the light of evolution." In that spirit, I'm hoping the diverse expertise of contributors to Nothing in Biology means that we'll help each other make sense of the living world, together.

(I'll continue posting here at D&T, too, though probably at the same reduced frequency I've managed lately. Nothing in Biology is a group blog; D&T is still my personal home on the web.)

We launch today with a post on the importance of evolution in human medicine—have a read, make a comment, and, if you like what you read, like us on Facebook and share the link! ◼

"Losing Control"

2011-10-17T21:01:00.001-05:00

Via Leonid Kruglyak: Hey, a romantic comedy about a Ph.D. student (in, from the trailer, some flavor of biochemistry) considering an unexpected marriage proposal. I am constitutionally suspicious of the genre, but it is long past time a movie tapped the comedic potential of emergency showers. ◼

Science online, unhelpful anthropomorphism edition

2011-10-14T08:05:00.000-05:00

Young chimpanzees at play. Photo by Tambako the Jaguar.

The correlations are suggestive, except when they're not. Thoughts on a study that connects "maternal" feelings to hormone levels and "feminine" facial features, by Kate Clancy and Scicrious.
Shiny! Paleontologists reconstruct the colors of a fossilized moth.
You have to admit, it'd be pretty cool. Other paleontologists basically invent a giant superintelligent prehistoric squid out of thin air.
Raising the wrong kind of awareness. Seeing chimpanzees in entertainment programming may be setting back efforts to save wild chimps.
Welcome to the future, if your insurance covers it. Genetically-engineered adult stem cells cure a genetic liver disease.
Not so much a needle as the whole haystack. Sequencing the genome of the bacterium responsible for bubonic plague suggests that there isn't just a single gene that made it so deadly.

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Coming out day: A few more things

2011-10-12T09:03:00.000-05:00

Yes, National Coming Out Day was "officially" yesterday, but these are worth following up with:

It's the little things. Great new posts by Gerty-Z on how helpful straight allies can be, and Zwitteronique on the everyday bother of being out.
Rest in peace. Queer rights pioneer (and astronomer) Frank Kameny died yesterday, at age 86.
The truth shall make you free. John Smid, the former executive director of one of the oldest "ex-gay" quackery outfits in the US, admits that sexual orientation—including his own—isn't changed by therapy.
And ANOTHER thing. (Added 0935h.) A matter-of-fact listing of some ways in which gays, lesbians, bisexuals, and transgendered folks aren't full and equal citizens.

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Happy National Coming Out Day

2011-10-11T10:17:00.000-05:00

Photo by massdistraction.

October 11 is National Coming Out Day, a day for gay, lesbian, bisexual, and transgendered folks to come out, and to recognize the importance that coming out and being out has had in the our progress towards full civil equality.

Being open about our lives and loves is an everyday task, but it has real political implications—straight people who know they have a queer friend or family member are much more likely to support treating us like full and equal citizens, and queer kids growing up in a far from queer-friendly world need all the positive examples and encouragement they can get. For more in the way of the latter, there's It Gets Better, and the Pride Month Diversity in Science Carnival, hosted right here at Denim and Tweed. For more on the political side, let me suggest the national campaign Freedom to Marry, the kick-ass folks at the ACLU; or Minnesotans United for All Families, the campaign to stop an anti-marriage amendment to the state constitution.

Oh, and if you happen to have just come out today—congratulations! ◼

Science online, whales' teeth and hand driers edition

2011-10-07T08:05:00.000-05:00

"... all they’re doing is shooting a blast of hot bacteria full force onto your hands." Photo by eatmorechips.

Much like my transition to regular coffee drinking. Ancient proto-whales' transition from terrestrial to aquatic life is recorded in their teeth.
Non-anthropologists should also take note. Anthropology gets a dressing down, from an anthropologist.
So is it possible to get high on fake weed? The placebo effect may work through the same biochemistry as a marijuana high.
Pretty fast, all things considered. The path of a publication, traced from initial observation to acceptance, over a mere three years.
Hot-air driers: gross as well as ineffective. The disease-fighting possibilities, and failures, of public restroom design.
Science writers commemorate teachers who got them started.
I, for one, etc. A new brain-machine-brain interface gives monkeys prosthetic limbs with a sense of touch. (See also.)
Eventually. Tortoises are not social animals, but they can learn by watching other tortoises.
With nuance. Charles Darwin, animal rights advocate.

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Carnival of Evolution, October 2011

2011-10-06T09:14:00.001-05:00

Photo by Dave77459.

The Carnival of Evolution, a monthly roundup of online writing about the science and politics of evolutionary biology, is now up at EvoEcoLab—apparently this one is the 40th edition! Check it out for posts by Jerry Coyne, Ed Yong, Greg Laden, and yours truly. ◼

It's that time of year again!

2011-10-04T08:05:00.000-05:00

The Portland Marathon two years ago. Looks fun, right?.

This weekend I'm flying out to Portland for the 2011 Portland Marathon, my third. It's been a bit tricky keeping up with my training on top of moving to a new town and starting up a postdoc with a whole new study system, but I think I'll be ready. While I pack, why not check out my post on the occasion of last year's Seattle Marathon, in which I discuss what I've learned over a couple years of long runs and leg cramps. It all still applies.

I can make it through even a half-marathon on a good breakfast and carefully-judged pre-race hydration, but to go much longer I need more food (and water) mid-run. The long-term exercise involved in a long race is fueled by a combination of fat reserves and glycogen stored in the liver and muscle tissue. Glycogen is the more efficient fuel, so as exercise intensity increases, muscles draw on it more heavily.

For far more detail on evidence-based endurance training approaches, I suggest Dave Munger's great science-based running. See you in 26.2 miles! ◼

The best chocolate chip cookies I know how to make

2011-10-03T08:05:00.000-05:00

Cookies! Photo by jby.

It's been ages since I posted a recipe, but I'm still doing lots of cooking. So, here's another staple in my personal recipe book: chocolate chip cookies. I found the recipe on AllRecipes.com, but I've incorporated a couple of stylistic quirks from the New York Times food section.

First, I refrigerate the dough at least overnight, or up to 48 hours, before baking. This lets the liquid (mainly eggs) integrate with the flour, for better texture. It also breaks up the work so it doesn't take a whole afternoon at once.

Second, I make them big. I form balls of dough a little less than the size of a golf ball, so the entire recipe makes exactly 24 cookies, at a rate of six to a cookie sheet-ful. Big cookies end up with a range of texture from a crisper edge to a chewy center, which you can't get if you make them too small. And I can tell you from personal experience that big cookies make a serious impression when you bring them to a lab meeting, or (as I did with these) your dissertation defense.

Follow the jump for the recipe!

Read more ...

Science online, miraculous maps edition

2011-09-30T08:05:00.000-05:00

Nothing like the real thing. Photo by Jamie Anderson.

It's a magical-seeming discovery! The molecular biology of miracle fruit, which makes sour taste sweet.
For one thing, you can't get lost in a map. Seeing a place is not the same as physically moving around within it—on a neurological level.
I'm just catching up on these, I know. Sarcozona interviews Jeremy Fox, Zen Faulkes, and Jean Burns.
When you've got eight to start with ... Spiders deal with missing legs pretty quickly.
Shiny! Fossilized in the right conditions, beetles keep their colors for millions of years.
Sample size matters. A Bayesian perspective on understanding Amazon seller ratings.
Top-notch long form. The biologist behind "arsenic life," profiled.
Jurassic cluck. A paleontologist wants to recreate dinosaurs from chickens.
Knowing the limits. Defining expertise in terms of what you don't know.
More than a pinch. The salinity of the world's oceans, measured from orbit.
No fruit salad is safe. The latest food-bourne illness outbreak is from contaminated cantaloupe.

And now video, via Kevin Zelnio, of the sand tiger shark's embryonic, siblicidal cannibalism. Ew?

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What does evolution have to do with the cost of police in Switzerland? Probably not much.

2011-09-27T08:05:00.001-05:00

Lucerne, Switzerland. Photo by Jamie McHale.

So a little while ago, I was perusing the latest from PLoS ONE while doing some low-attention-requiring lab work Monday afternoon, and a title caught my eye: "A test of evolutionary policing theory with data from human societies." Oh, hey. That looked interesting.

The paper's author, Rolf Kümmerli, claims to have found evidence for a particular kind of evolutionary model of cooperation in recent economic data from Switzerland. The problem Kümmerli addresses is a classic one: from the perspective of natural selection, individuals (apparently) have little evolutionary incentive to cooperate, unless they're relatives. And yet, we see cooperation in human societies.

One solution to this quandary has been group-level selection, which is a whole 'nother kettle of worms . Another is that policing behavior could evolve to help keep groups of less-closely-related people cooperative. Of course, modern human societies are a long way past the days when most of us lived in villages that were also basically big extended families. Kümmerli proposes that we might use some sort of rule of behavioral thumb to (unconsciously) assess how likely it is we're interacting with close relatives—which is less likely in bigger communities, and communities with larger immigrant populations.

Er, what?

Read more ...

Science online, Easter Island sustainability edition

2011-09-23T08:05:00.000-05:00

Easter Island. Photo by vtveen.

Easter Island is no Greenland. The collapse of Polynesian society on Easter Island may not have been due to ecological damage, but a terminal case of Europeans.
Angry Birds can't do that. Players of an online game have resolved the structure of a key HIV protein.
The kids are all right. David Dobbs draws together emerging research on the brains of teenagers.
You're running late. But so is everyone else. Our perception of the present is really a remembrance of the immediate past.
Fortunately, I hear that the honey badger doesn't care. The popular idea that honey guide birds lead honey badgers to beehives is probably a myth.
Hold your horses, Jean-Baptiste. Heritable epigenetic changes to gene expression may not have much impact over evolutionary time.
Predator becomes prey. Ground beetle larvae prey on much larger frogs and toads by luring them in for an attack.

And finally, via SciAm, the peacock spider. Check out that thorax!

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Reasons to download the entirety of the "Savage Lovecast" archives, in order

2011-09-19T08:05:00.000-05:00

Dan Savage. Photo by soundfromwayout.

8. Because you're training for a marathon/ putting in a lab-work marathon/ cleaning house/ doing anything that's better with someone talking in your earphones, and you're just not getting enough with NPR, Slate, and that one about the things from the British Museum—and you've already used up all the Audible.com freebies offered via those podcasts

7. To hear Dan take a victory lap after Rick Santorum lost his Senate seat (while trying not to dwell on how U.S. politics have changed/not changed/gotten ten times worse since then)

6. As part of creating a drinking game for a sex-ed themed cocktail party (maybe you're hosting a fundraiser for Planned Parenthood?)

5. For the episode recorded immediately after Thanksgiving dinner

4. To pin down the exact moment of origin of the phrase "tech-savvy at-risk youth"

3. For every time Dan has a special guest/ co-host/ foil

2. Because back in the day Dan and/or the TSARY weren't so selective about which calls deserved an answer

1. For the old, Monty Pythonesque brass band intro music

It's all available via www.thestranger.com!

Edit, 2011.09.29: Corrected link to the Savage Love archives. Oops! ◼

At long last, an answer!

2011-09-16T12:11:00.000-05:00

To my exasperated question:

Comic from Darwin Eats Cake.

It's ... actually kinda plausible. But I think that, if Guillaume manages to overcome his vexation, he might also note that there's probably some sort of marginal fitness benefit associated with landing a regular gig at Slate. ◼

Science online, tastefully uphostered placeboes edition

2011-09-16T08:05:00.000-05:00

No in-flight drinks on this trip. Photo by pheanix.

Take note, Book of Leviticus. Menstruating women are not poisonous.
Oops? As many as half of all neuroscience papers may make a basic statistical error.
Talk about commitment. Migrating birds supply themselves with water by breaking down their own muscles.
Well, why not? The placebo effect may be as much about waiting room décor as it is about a well-designed sugar pill.
First, remove the stack of unread manuscripts from thine own inbox. Is peer review broken, or are we all just lousy peers?
Billions. The costs of introduced insects, estimated.
Not a monster-themed alternative history, either. Abraham Lincoln, forensic meteorologist.
Hundreds of billions. The economic return on investment of ones of billions in NIH research funding, estimated.
Wait. Rats' ears can ring? A possible cure for ringing ears, demonstrated in rats.
Prince, biologist, geologist, anarchist, fan of Adam Smith and Jean-Baptiste Lamarck. Eric Michael Johnson interviews the author of a new biography of Peter Kropotkin.
Might be pretty humid, though. Astronomers identify an exoplanet about the right distance from its primary to support life as we know it.
Brains aren't as hard to come by as we thought. A new phylogeny of the molluscs supports four independent origins of complex brains.

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Passwords and eviction notices: How do plants keep their bacterial partners honest?

2011-09-13T08:05:00.000-05:00

The nodule-y roots of a soybean plant. Original photo by Pro-Soil AG Solutions.

Nitrogen is one of the elemental building blocks of life as we know it—it's a basic component of amino acids, which are in turn the building blocks of proteins, which form the building blocks and moving parts of every living cell. The nitrogen interwoven in our tissues originated as part of the atmosphere we breathe, but the path from atmosphere to living flesh is far less direct than drawing a breath. Atmospheric nitrogen becomes useful to us animals only via an intimate relationship between a plant and bacterial growing in its roots.

The bacteria, called rhizobia, have the rare ability to "fix" free-floating nitrogen into biologically useable form. In return for this nitrogen source, the host plant allows the rhizobia to infect a specialized knob of root tissue, a root nodule, which it supplies with sugar for the benefit of its nitrogen-fixing guests. The plant uses the fixed nitrogen to make proteins for its own use, and anything that eats the plant afterwards benefits.

If all this sounds familiar, it's because the interaction between plants and rhizobia is the focus of my developing postdoctoral research, and I've been writing about it as I've done more reading about it. Specifically, I've been interested in how plants might be able to make sure their root nodules house helpful bacteria rather than freeloaders, who enjoy the sugar supply inside the nodule without fixing nitrogen in return.

I've discussed a couple of different mathematical models that suggest some options. However, models are really just formal ways to follow through the implications of a particular idea, not necessarily descriptions of what actually transpires between a plant and the rhizobia inside its roots. So I thought it might make sense to step back and survey what we presently know about what goes on inside those root nodules.

Read more ...

Ten years

2011-09-11T08:05:00.000-05:00

Ten years ago today, I was in organic chemistry lab when the prof walked in and mentioned, somewhat casually, that an airplane had apparently hit one of the World Trade Center towers in New York. We all assumed it was some accident, and I distinctly remember picturing a small private plane of some sort.

By the time I was done synthesizing and purifying and precipitating, I returned to the dorm to find everyone gathered around CNN, watching looped footage of not one but two full-sized commercial airliners striking the towers.

Ten years later, it seems the entire United States is still gathered around 24-hour cable news, still watching the planes strike the towers. If, like me, you find it easiest to contemplate those ten years in numbers, Wired's Danger Room has compiled an elegant series of infographics illustrating the costs and consequences of the last decade.

Graphic by Danger Room.

It's only data. It cannot, of itself, tell us whether the last ten years were well spent. ◼

Science online, hyphenated surnames edition

2011-09-09T08:05:00.000-05:00

A caribou in Denali National Park, Alaska. Photo by blmiers2.

Biodiversity riches needn't beggar their neighbors. Longstanding conventional wisdom that protected wild areas depress the economies of nearby communities turns out to be untrue.
You say you want a revolution? Humans may riot not because we're evolved to riot; but because we're not evolved to deal with stressful times.
Not unlike wearing a wedding band. The decision to take your spouse's last name when you marry may say a lot about you, except when it doesn't.
And, yes, like humans. Even though it sounds like whistling, dolphins form sound by vibration, just like other mammals.
Interesting yes, but not quite enlightening. It's no surprise that conservatives and liberals think differently, so it's probably not surprising that their brains look different.
To panic, or not to panic? A conversation about the upcoming, highly-researched pandemic film Contagion.
Simultaneously awesome and disgusting. A virus prompts caterpillars to climb to the top of a tree, then melts their flesh.

Science online, hungover ticks edition

2011-09-02T06:05:00.000-05:00

Nasty stuff, regardless of where you drink it. Photo by Darby Rose.

Which is why I stick with gin and tonic. "Four Loko" might not be extra-intoxicating because it combines caffeine and alcohol, but because it doesn't taste alcoholic.
Go easy on the pawpaw, too. Too many carrots can, in fact, turn you orange.
When he helps with the cover-up, I think probably yes. When a graduate student falsifies results, is his or her advisor responsible?
Forty. Percent. Profits. The case against for-profit academic publishing. (But see also.)
Good digestion goes a long way. Mice fed "probiotic" bacteria seem to be less stressed out.
I'm sure we're all glad to know that the tick phylogeny is now much clearer. A rare and unique species of tick has been rediscovered in South Africa almost thirty years after it was last seen.
"We had Kate Winslet learning how to pipet." The new film Contagion aims to accurately portray an emerging epidemic.
Especially great if you're shopping for a graduate advisor. If you haven't already, go check out Sarcozona's ongoing series of interviews from the ESA meetings.
Yes, it's a link to another linkfest. Ed Yong picks his favorite online science writing of August 2011.

Carnival of Evolution, September 2011

2011-09-01T08:05:00.000-05:00

Photo by joiseyshowaa.

The September issue of the Carnival of Evolution is online now at The End of the Pier Show. Okay, it's not as glamorous as the better known September issue, but it's still the number one spot for a month's worth of online writing about descent with modification and all its scientific, cultural, and political ramifications. A few highlights:

ItTakes30 on the cool new study of cooperation in biofilm-forming bacteria.
Zen Faulkes on how tiny worms evade an ensnaring fungus.
Jerry Coyne points out a probable case of sympatric speciation in palms.

Cheese curds and pigeons and butter sculptures

2011-08-31T08:05:00.000-05:00

Oh, my. I spent Saturday—yes, pretty much all of it—at the Minnesota State Fair with friends. I have to admit, it was impressive. The livestock barns were bio-geeky fun, and the food (sampled strategically, in moderation) was uniformly good, especially the milkshakes at the dairy barn. Deep-fried cheese curds are amazing, and I do not want any more until next year.

Anyway, I've finally gotten around to weeding through the photos I took, so here you go. Check out the QR code made out of seeds from the "seed art" competition (which is far from the most peculiar and specific competitive category we encountered) and the sheep in vaguely sinister protective coveralls.

Making themselves at home: Spider mites disable plant defenses, then spin their own

2011-08-30T06:05:00.000-05:00

Tomatoes, one of many plants that play unwilling host to red spider mites. Photo by sylvar.

Plant-eating insects must overcome some of the cleverest weaponry in the living world—from poisonous latex to sticky hairs—just to find a meal or a place to lay eggs. Many deal with their host plants' toxic defenses by digesting them or sequestering them safely for personal use, but the red spider mite Tetranychus evansi simply turns them off.

Tetranychus evansi eats a wide range of plants, from tomatoes to potatoes. One female mite can eat enough to lay 50%-70% of her weight in eggs every day, and while that isn't much on the scale of a single, miniscule red mite, it adds up quickly when colonies build into dense clusters on host plants, sucking them dry and covering them in webs of spun silk.

Most host plants respond to such an onslaught by ramping up production of chemicals that make them unpalatable to herbivores, or that interfere with the mites' ability to digest plant tissue. However, a team of Dutch and Brazilian biologists recently found that T. evansi somehow short-circuits this response [$a].

Read more ...

Science online, did the earth move for you? edition

2011-08-26T05:05:00.000-05:00

Beerquake. Photo by dongga BS.

Boy, did I ever pick the right time to visit North Carolina. If only there were some sort of widely-available medium through which working geologists could explain what shook up the East Coast on Wednesday ...

Darwin and Boyle were way into dice-playing. Biology and chemistry are more than just extra-complicated physics, because they deal in randomness.
Introducing Ms. Homunculus. Scicurious discusses a new map of brain regions activated by stimulation of the vagina.
Mad science in a good cause. A proposed new treatment for malaria would work by microwaving the patient.
Maybe what they need is a well-written Wikipedia page? People who grew up with Internet search engines don't know how to use them effectively. (See also.)
One thing's for certain: there's more taxonomizing to be done. A new study suggests that taxonomy isn't endangered after all; but see also.
The "underwater view" will haunt my dreams. Lampreys really, really hate the smell of rotting flesh.
It comes in pints! The new Sam Adams Boston Lager Glass (TM) may not be the paragon of beer-containment that it claims, but it is the latest in a long history of cups, beakers, and tankards.
Defining a new adaptive zone for evolutionary ecology. The observation that anoles living in different micro-habitats had different body types, and that those body types might be related to life in the micro-habitats, was first published fifty years ago.
That burbling sound is "Thus Spake Zarathustra" playing underwater. Now dolphins are using conch shells as tools.

Finally, from a compilation of timelapse videos of plants, here's climbing morning glory. Tropisms in action!

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Science online, hard at work edition

2011-08-19T07:05:00.003-05:00

Yes, I've actually kept busy enough this week to make it all the way to Friday without compiling the weekly linkfest. So, er, here's the best thing not related to next-generation sequencing I did manage to see all week: Julia Child explaining the Miller-Urey experiment, then making her own "primordial soup."

Video via Ferris Jabr. That original experiment turned out to be more successful than originally known. ◼

#NGS11 day one: The wrath of Moore and Kryder

2011-08-15T18:44:00.000-05:00

The future is in the cloud? Photo by Extra Medium.

Biologists are about to have access to all the genetic data we could ever want. Unfortunately, once we have that data, we have to figure out where to put it—and some way to sift out the bits that answer the questions we want to answer.

That's the first day of the NESCent workshop in next-generation sequencing methods in a nutshell.

Brian O'Connor, who gave the morning lectures, framed the immediate future of biology as a race between technologies for collecting genetic sequence data and technologies for storing and analyzing that data. Moore's Law is that computer processor speed (really, the number of transistors packed into a single processor chip) doubles about every two years; Kryder's Law is that computer storage capacity roughly quadruples in the same amount of time. But in the last few years, and for the foreseeable future, DNA sequence collection capacities are growing on the order of ten times every couple years.

In other words, there may very well come a day when the cost of storing and using a genome (or genomes!) belonging your favorite study organism will exceed the cost of obtaining those data.

Read more ...

Sequencing: The Next Generation

2011-08-14T20:51:00.001-05:00

Sighted in the woods near Northgate Park, Durham. For real. Photo by jby.

I'm spending the next two weeks in Durham, North Carolina, for the NESCent workshop on next-generation sequencing. Which is to say, a workshop about collecting great big genetic datasets, and what you can do with them once you have them. I'll be stretching my programming skills to the maximum, and hopefully getting a head start on some ideas I've had for good old Medicago truncatula.

If time permits, I may take a page from Carl Boettinger's literally open lab notebook and post some notes and thoughts here as the workshop progresses, but it's looking likely to be a full two weeks, and time may very well not permit. ◼

Science online, gluteal symmetry edition

2011-08-12T08:05:00.004-05:00

Is that a tennis ball in your pocket, or asymmetric hypertrophy of your iliopsoas? Oh. It's a tennis ball. Photo by Steve9091.

Quick, tell Coach Schtitt to change up the drills. Something about the athletic demands of tennis leads high-level players to develop asymmetric bums.
Nothing revolutionary comes easy. Engineering grain plants that can host nitrogen-fixing bacteria would be an historic breakthrough for agriculture, but it won't be simple.
Try not to forget. Memory really doesn't work the way most people think it does, in a lot of important ways.
Like my relationship status with "food miles." Even when you do the math, figuring out what lifestyle choices are most sustainable is complicated.
But even so ... It's pretty clear that biking to work is the greenest choice available.
Fitness measures are harder to get than you'd think. A large-scale experiment in Nebraska will finally directly test the hypothesis that light-colored mice are better camouflaged on light sand dunes.
Oops. Pheromone-based traps for Japanese beetles not only don't work, they attract more beetles.
Question left begging: which is scarier, a brown recluse, or MRSA? Lots of reported spider bites might actually be soft-tissue bacterial infection.

Another one for the reading list

2011-08-10T08:05:00.000-05:00

So, I've known for some time that On the Media co-host Brooke Gladstone has a new book out, and that it's a meditation on media in quirky graphic-novel form, but I didn't really know I needed to read it until I saw this trailer. ◼

Flowers stay open for pollinators, not daylight

2011-08-09T08:06:00.003-05:00

A honeybee explores the depths of a dandelion, one of the species used in Fründ et al.'s experiments. Photo by je-sa.

If you've ever stopped to admire morning glory flowers opening first thing in the morning, then noticed they've closed by evening, you're at least dimly aware of one of the longest-established ideas in plant biology: that flowers open and close on a reliable daily schedule. Different species are open at different times of day, of course, but each flowering plant has its preferred open period, and it sticks to that schedule during its flowering season.

This idea led Carolus Linneaus, the father of modern biological taxonomy, to propose an Horologium florae, or "floral clock" using plantings of species with known flowering times to mark the hours. You can find his table of proposed species in the online version of Linneaus' 1783 treatise Philosophia Botanica, if you're not averse to Latin. Studies of flowers' daily schedules go back to well before English was the language of international science, and continue to the present day [$a].

Yet no one seems to have spent much time considering how flowers' schedules might respond to the activity of their very reason for being: pollinators. Flowers don't open just to be open in a particular kind of sunlight—they're open to attract animals that can carry pollen to another plant, and maybe leave some, too. If a flower receives enough pollen to make seeds by noon, why would it stay open until two o'clock?

According to some new experimental results, the answer to that question is that they don't [$a].

Read more ...

#ESA2011 #ESA11: Who to follow

2011-08-08T09:26:00.001-05:00

Update, 9 August 2011: I seem to have picked the wrong hashtag--there's more activity at #ESA11.

Western scrub jay. Photo by Minette Layne.

The annual meeting of the Ecological Society of America is underway in Austin, Texas, this week. If, like me, you're not anywhere near Austin, do not despair. There are people who will use the Internet to tell you what is going on at the meetings anyway, out of sheer enthusiasm for ecology! Here are the ones I'm following:

Thanks in part to readers like you, Sarcozona will be covering the meeting at Gravity's Rainbow. Zen Faulkes of NeuroDojo has apparently been there since Day 0. And Jeremy Fox has been anticipating the meeting for the last week over at the OIKOS blog. Finally, you can follow the official ESA twitter feed and the hashtag ~~#ESA2011~~ #ESA11 for continuous updates. ◼

Paying up

2011-08-06T14:53:00.000-05:00

So one major credit rating agency has announced it has a bad feeling about the long-term value of U.S. government debt. Whatever could our government—which is to say, we, the U.S. public—have done to warrant that? How about refusing to collect revenue that could pay down existing debt:

(Via.)

Sure, government spending increases debt, and the U.S. government spends money to do lots of things I'd be happy to stop doing. But government does lots of things that any sane person agrees are necessary—paying for police and firefighters, building roads, preventing people from pissing in my drinking water—and even if we cut all those basic services to zero, we still wouldn't have a balanced budget. (Non-defense discretionary spending for 2010 ≈ $530 billion; 2010 federal budget deficit ≈ $1,294 billion. Everyone can agree that 530 is not larger than 1,294 ... right?)

When the government borrows, it borrows against tax revenue that it could, theoretically, collect to pay off the debt. Our collective decisions as U.S. citizens, expressed via elections—with admittedly varying degrees of accuracy and wisdom—have run up historically high national debt while driving the proportion of national income collected as taxes to a historical low. If you were loaning more and more money to a friend who kept working fewer and fewer hours a week, wouldn't you start to get a bit edgy?

And if all this sounds a bit abstract, here's a nice concrete number: the increased cost of U.S. debt associated with that credit rating agency's bad feeling comes to about $322 per U.S. citizen. If I'm not mistaken, that's a pretty big chunk of the refund I got back when the last round of big tax cuts took effect, ten years ago—and it's just the start. ◼

Science online, migrating sushi edition

2011-08-05T08:05:00.038-05:00

You must admit, it doesn't look comfortable. Photo by Soller Photo.

A movable feast. The neurochemical explanation for those viral videos of dancing squid sushi.
Or, you know, don't fragment the habitats. To offset the effects of habitat fragmentation and help natural populations adapt to changing climate, just add gene flow.
The knight's burden is a heavy one, literally. Was medieval chivalry undone by the sheer weight of knights' armor?
Coming soon: age-defying low-iodine diets. Axolotls are neotenic salamanders, meaning they become sexually mature without developing the "adult" characteristics other salamander species typically have—unless you dose them with iodine.
Reviving, not revived. After being fished nearly to extinction, the Atlantic cod population—and rockfish, and haddock—may finally be reviving.
We traded guts for brains. Compared to other mammals, humans have unusually big brains for our body size, which means that we also have rather odd bodies.
And we're not talking about "Tag" body spray. The African crested rat deters predators by slathering itself in poison.
These congratulations will not be withdrawn later. Retraction Watch completed its first year of following up on post-publication reviews and refutations this week—well done!

Carnival of Evolution, August 2011

2011-08-01T12:56:00.000-05:00

Grizzly bear. Photo by Alaska Dude.

The latest edition of the Carnival of Evolution, a monthly collection of online writing about evolution and all its ramifications, is online at Sandwalk. Check it out to learn why genetic testing for grizzly bears is important, what new fossil may have taken the place of Archeopteryx in the evolutionary history of birds, and what pioneer of evolutionary biology will soon be on a U.S. postage stamp.

Science online, urban evolution edition

2011-07-29T08:05:00.025-05:00

Freddie Fungus and Alice Algae have no likin' for prions. Photo by 0olong.

Genetically determined, except when it isn't. The evolutionary context of misogyny.
Queering evolution? The new frontier for evolutionary biology may be tracking adaptation to human-built environments.
Mad lichen disease? Some lichens can apparently break down prions.
Really, where would it have gone? That big underwater plume of oil spilled into the Gulf of Mexico is still there.
No surprise to field scientists, I suspect. Commercial GPS systems have some downright dangerous issues with their databases for rural and wilderness areas.
"This was the original peer review: immediate and open" The increasing use of online platforms for post-publication peer review may be taking scientific discourse back to its Enlightenment-era roots.
Guess I'd better get some more gel packs. Carbohydrate supplements during exercise do, in fact, help you work longer.
I'm sure that if/ I took even one sniff/ It would bore me terrifically, too ... Pair-bonding with a mate seems to make voles less prone to amphetamine addiction.
Time to revise the bat "pollination syndrome." A bat-pollinated tropical vine has leaves that collect and reflect its pollinators' echolocation signals.

Of mice and men, making a living in rarefied air

2011-07-26T08:53:00.000-05:00

High-elevation populations of deer mice have evolved "stickier" hemoglobin to cope with the thin atmosphere. Photo via Animal Diversity Web.

It's easy to walk through the woods and fields of North America and never spot Peromyscus maniculatus, the deer mouse, but you've probably heard them scampering off through the leaf litter or under cover of tall grass. They're exceptionally widespread little rodents, found in forest undergrowth and fields from central Mexico all the way north to the Arctic treeline. In all this range, they look about the same: small and brown, with white underparts and big, sensitive ears.

That apparent sameness is deceptive, however.

A big, varied range presents lots of different environmental conditions to which a widespread species must adapt. And when that big, varied range includes the Rocky Mountains, one of those environmental conditions is as basic as the air itself. At high altitudes, atmospheric pressure is lower, which means lower partial pressure of oxygen, the gas that makes life as we know it work.

The fundamental problem at high altitude is to pull more oxygen from thinner air. Natural selection is good at solving problems, and it has multiple options for adapting a mammal to thinner air at high altitudes, to the extent that these traits are heritable. Selection could favor individuals who more readily respond to thin air by breathing faster and deeper, pulling in more air to make up for its lower oxygen content. Or selection could favor individuals who produce more red blood cells, so that a given volume of blood pumped through their lungs picks up more oxygen. Or, at the most basic level, selection could favor individuals whose individual red blood cells are better at picking up oxygen, via a new form of hemoglobin, the oxygen-binding molecule that packs every red blood cell.

Read more ...