Science online, don't drink the sapa edition

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

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

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.

Change happened

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 ...

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

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

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?

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

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

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

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

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

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.”

Self-deception

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

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

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

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.

Science online, top speed edition

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

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

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

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

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

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.