Denim and Tweed

Science online, through a panopticon darkly edition

noreply@blogger.com (Jeremy Yoder) — Fri, 14 Jun 2013 13:00:00 +0000

About that study of queer-identified folks in STEM: It's off to a great start.
No prior (heh) experience needed. A nice introduction to Bayesian statistics.
But it's maybe okay if you don't mind being arrested by mistake. Why ubiquitous survelliance is a problem even if you don't mind being watched—and that's before we account for the how hard it is to prove innocence once suspicion is sparked.
In mice. Gene knockouts that cause obesity and obssessive-compulsive behavior cancel each other out.
At a zoo, even! Advice on finding a post-PhD career outside academia.
Bout damn' time. How television weather-people are coming around on global warming.
What one thing should change in undergrad classes? Maybe you'd remove all the desks.
You're out of luck if you work with plants. When scientists take the Up-Goer Five challenge
SCOTUS tries to rule on the Central Dogma. The U.S. Supreme Court rules that naturally occurring DNA sequences may not be patented. But the text of the decision [PDF] is drawing complaints from people who know actual biology, and one justice admitted in his concurrence that he doesn't understand the science.

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Queer in STEM, one month in

noreply@blogger.com (Jeremy Yoder) — Wed, 12 Jun 2013 14:37:00 +0000

Over at the blog for the Queer in STEM study, I've just posted an update on the project's progress about a month after we first launched it. In short: it's going really amazingly well.

Back on May 7, we opened an online survey of folks working in science, technology, engineering, and mathematics who identify as lesbian, gay, bisexual, trans*, and queer. As of today, 1,523 people have answered the call—out of which, 1,180 participants have completed the key survey questions on their identity and experience.

Our "snowball sampling" method of asking participants to pass along links to the study has been extremely successful: we know that the survey has been mentioned in at least 185 tweets, recommended 467 times on Facebook, and shared 20 times on Google+. We've been linked from websites we know well—like It's Okay to Be Smart and Minority Postdoc—and also from new friends like Geek Feminism, The Asexual Agenda, the University of North Carolina at Charlotte, Lab and Field, and many, many folks on Tumblr.

To find out what's next for the project, and to help spread the word (or even answer the questionnaire, if by some tiny chance you haven't yet), go read the whole thing.◼

Science online, the wrong kind of fan mail edition

noreply@blogger.com (Jeremy Yoder) — Fri, 07 Jun 2013 13:00:00 +0000

Not at all the way it works in science. A brief guide to the way evolution works in science fiction.
Woah. A project in nanotech fabrication captures images of the breakup and formation of carbon-carbon bonds.
Yeah, don't do this. Where "this" is e-mailing perfectly nice scientists and science writers and asking them to do your homework for you.
Sweet. Candy company Mars launches a project to sequence the genomes of crops that are staples in the developing world.
"... except perhaps, for Google+ posts." Social media postings correlate with formal citations of scientific papers.
Star Trek is for nerds; Star Wars is for geeks. The difference between nerds and geeks, quantified.
Want to eat like a hunter-gatherer? First you've got to decide which kind of hunter-gatherer you are.
"Evolutionary traps" When human-created environmental change turns adaptations into maladaptations.
Color, insulation, even defense. What use were feathers before dinosaurs evolved flight?

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New, rigorous study looks for genes associated with education—but doesn't find much

noreply@blogger.com (Jeremy Yoder) — Sat, 01 Jun 2013 18:25:00 +0000

Late update: Michelle Meyer, who sits on the advisory board of the consortium responsible for the study discussed below, briefly discusses the results on her blog, and links to a Frequently Asked Questions document [PDF] meant to accompany the study, which makes some reasonable and sensible points about how best to understand the findings. A point I didn't emphasize originally is that the small effect size of the sites identified suggests that a lot of previous "sociological genetics" studies are now called into question—because their sample sizes were far too small to detect such subtle effects.

A few months ago, I roundly thrashed a study that attempted to identify genes associated with educational achievement. It was, to put it mildly, shooting fish in a barrel: that paper was published in a journal that doesn't handle much (if any) genetics research, the sample size was small, the genetic data was sparse, the analysis applied to the genetic data didn't test for what the authors wanted to test for, and the authors ignored basic statistical practice when they interpreted the results.

This week, though, there's a new study of the genetic basis for educational achievement that is the mirror-image opposite of the one I beat up: it's online ahead of print in Science, it has a great big sample size of 101,069 participants and a built-in "replication" sample of 25,490 more, it works with good genome-wide genetic data, and it looks to be both admirably careful in its statistical work and cautious in its conclusions—which is consistent with the inclusion, in the paper's lengthy author list, of some folks who know what they're talking about when it comes to association genetics.

So, naturally, I wanted to write something about this study as a nice example of what's possible when genetic analysis is done right. Unfortunately, the actual results of the study don't give me much to discuss—because, for all its rigor and caution, it doesn't find much in the way of genetic explanation for educational achievement.

Read more ...

Science online, visibly relevant edition

noreply@blogger.com (Jeremy Yoder) — Fri, 31 May 2013 13:00:00 +0000

This week, at The Molecular Ecologist: I review a book that rebuts Stephen Jay Gould's paleontological perspective.
Or ringworlds. The search for alien civilizations may be simpler if we look for Dyson spheres.
"They told me I made a bomb on school property ..." Kiera Wilmot speaks out.
Depends what you mean by "phytonutrients." Are the wild ancestors of dometic crops more nutritious?
Oops. Guy calling for more scientific outreach seems not to know much about scientific outreach.
Of course I was going to link to this. Failed experiments are the Kobayashi Maru test of science.
Score (yet another) one for Charles Darwin. Phylogenetic diversity predicts primary productivity.
Dolphins are assholes. Which is why you'd have to be nuts to invite some to your childbirthing.

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The Molecular Ecologist: Relentless Evolution

noreply@blogger.com (Jeremy Yoder) — Tue, 28 May 2013 13:36:00 +0000

When I was just starting graduate school, one of the first things I wanted was readings to get me up to speed on the current state of research on the evolution of interactions between species. My dissertation advisor handed me The Geographic Mosaic of Coevolution, by John Thompson (who, it should be said, had been my advisor's postdoctoral mentor). Thompson turned out to be just the author for the job, wrangling a huge body of research into a clear, straightforward text, and all in support of his argument that metapopulation dynamics—populations linked by migration across a landscape of varied environments—are the engine driving much of evolution.

Now, Thompson's published a new book, titled Relentless Evolution, which pretty much picks up where The Geographic Mosaic left off. And I've reviewed it for The Molecular Ecologist.

Gould’s “paradox of the visibly irrelevent” holds that, if we are to understand the river of evolutionary history, we must look below the spume and spray of year-to-year adaptative change to find the deeper currents that can, over time, carve canyons. In his new book Relentless Evolution (University of Chicago Press, $35.00 in paperback), John N. Thompson makes the opposing argument with gusto: To Thompson, studying the roiling eddies that Gould dimissed as transient and superficial is the only way to understand the deeper currents, and the river’s course ahead of us.

Should you run out and buy a copy? If you're even slightly on the fence, I suggest you go read my whole review.◼

Science online, on the road edition

noreply@blogger.com (Jeremy Yoder) — Fri, 24 May 2013 13:00:00 +0000

This week, at Nothing in Biology Makes Sense! Tracing the origins of the fungus among us.
Yay! Charges against DIY chemist Kiera Wilmot have been dropped, and she's going to space camp.
Wow: "75 percent of all tornadoes on Earth occur in North America." For the devastating tornadoes that hit Oklahoma this week, some meteorlogical context.
Yum! Acacias ensure that no one steals the food rewards provided for mutualistic ants by making poisonous food rewards.
Good enough is good enough. The magic of evolution revealed in the inefficiency of an adaptation to poisonous environments.
It would make sense. Could immune response influence human reproductive function?
Whoops. Sweetened poisons have selected for cockroaches that can't stand glucose.

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Science online, where no one has gone before edition

noreply@blogger.com (Jeremy Yoder) — Fri, 17 May 2013 13:00:00 +0000

Congratulations! To the winners of the first ScienceSeeker Awards.
It was only logical. How DNA barcoding may be making (one of) the capabilities of Mr. Spock's tricorder a reality.
I'm shocked. Shocked! Pest control company distributes guide to "USA spiders" including species not found in the U.S., misinformation about toxicity.
For a given value of "fame." Towards a mechanistic theory of fame in science.
Perspective. Why barns are traditionally painted red, in the most ultimate sense.
Cool. Land plants detect attacking aphids on other plants via mycorrhizal fungi.
Good luck? On the widely-reported Chinese study of genetic variation underlying intelligence.
Haven't we already decided that's bad? How discussion around that widely-reported Chinese study of genetic variation underlying intelligence is getting worryingly eugenical.
Skeptically. How to write about science—as well as how to read about it.
Oy. How really not to write about science—by taking scientists' words completely out of context.

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Equality

noreply@blogger.com (Jeremy Yoder) — Mon, 13 May 2013 23:47:00 +0000

Almost exactly six months after the election in which Minnesotans decided they didn't want their state constitution to ban the legal recognition of same-sex relationships, their elected representatives provided that very recognition.

Last Thursday the state House passed a bill allowing the state to recognize same-sex couples in all the same ways it recognizes straight couples; today the Senate passed it, too; and tomorrow Governor Dayton will sign it into law. It's almost exactly two years since another bunch of state legislators passed bills to amend the state constitution with a ban on same-sex marriage—which makes this some kind of record turn-around.

Read more ...

Science online: Opening lab closets everywhere edition

noreply@blogger.com (Jeremy Yoder) — Fri, 10 May 2013 13:00:00 +0000

In which I take a crack at social science. I'm collaborating on a survey of queer folks working in STEM fields! Have you taken it yet?
Which history goes back farther than you knew. A historical perspective on colony collapse disorder in bees.
Chicken, egg? When Republican voters understand climate science, they want someone to do something about climate change.
Not even the real-world-possible version from 2001. Why the International Space Station doesn't have artificial gravity.
Holy poop! Scicurious reveals her "real" name.
It's not going away any time soon. More on political interference with peer review.
But still not the original human language! Linguists identify 23 words in European, Asian, and Inuit languages that have shared roots in a common ice-age-era language.
The better to evade bats with, my dear. Drab little moth sets record for sensitive hearing.
See also Ecclisiastes. Scientific fraud: all of this has happened before.
It's the little things. On making a lab a nice place to work.
More sampling = better, as usual. Ground-truthing the data in public databases of plant traits.
An object lesson in coalescent processes. Why it's not all that impressive to discover you're descended from Charlemagne.

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"This is water," now in convenient filmic format

noreply@blogger.com (Jeremy Yoder) — Wed, 08 May 2013 18:18:00 +0000

Via Slate's Brow Beat blog, and just in time for graduation season, David Foster Wallace's perennially apt commencement address has been adapted into a video.¹

And, lest you think that this only applies to all those bright-eyed twenty-year-olds in the silly hats, see also.◼

¹ There are actual, onscreen footnotes, even though I'm pretty sure the original didn't have any, but I guess they're there because, DFW.

Holy poop! Scicurious is pseudonymous no more

noreply@blogger.com (Jeremy Yoder) — Wed, 08 May 2013 14:57:00 +0000

Super-blogger Scicurious is taking off the mask. Metaphorically speaking.

Her full statement is over at her Scientific American blog.

I've known Scicurious as an Internet friend for years now, even met her at ScienceOnline, and gone running with her, and I never knew "real" name. She was totally cool about the use of the pseudonym, politely but firmly protective of her other identity. But it's still very nice to meet Bethany Brookshire. It feels, just a little bit, like she's come out of ... well, maybe not the closet. Some sort of smaller-than-necessary, confining space with opaque walls. Er.

Anyway: Congratulations, Bethany! It turns out that I love your work.◼

New project: Surveying LGBTQ folks working in science

noreply@blogger.com (Jeremy Yoder) — Tue, 07 May 2013 15:05:00 +0000

I'm pleased and excited to announce that a project I've been working on for the last few months is finally ready to launch: A new, nationwide survey of queer folks working in science, technology, engineering, and mathematics.

Read more ...

Carl Zimmer on the evolution of feathers, animated

noreply@blogger.com (Jeremy Yoder) — Sat, 04 May 2013 15:30:00 +0000

Clever, informative, beautiful.

Via CZ, and many of the more discerning parts of the Internet.◼

Carnival of Evolution, May 2013

noreply@blogger.com (Jeremy Yoder) — Fri, 03 May 2013 19:22:00 +0000

I am reliably informed that the monthly round-up of online writing about evolution is available now at DNA Barcoding. Reserve a nice long block of time to peruse the links—this month's carnival is bigger on the inside.◼

Science online, meddling Congresspeople and deceptive orchids edition

noreply@blogger.com (Jeremy Yoder) — Fri, 03 May 2013 13:00:00 +0000

This week, at Nothing in Biology Makes Sense! I explain why I think we should study the evolution of human sexuality.
And, at the Molecular Ecologist: I fret about Congressional interference in NSF's grant review process.
With an apperance by some guy with a really weird middle name. A nice extended meditation on the biological basis of sexual orientation.
Something to keep in mind while teaching: It hurts to feel stupid.
The solution for bad science: more science. How the emergence of evolutionary biology overturned a major "scientific" justification for slavery.
Mr. President, we must not allow an implementation gap! Is there a gap between ecological theory and conservation practice?
NSFW if you're an orchid; just embarrassing if you're a bee. How orchids trick bees into mating with them. With video!
And it has ~~nothing~~ everything to do with the fact that she's black. Sixteen-year-old girl faces felony charges for DIY chemistry experiment. See also, also, and also. If that sounds crazy to you, there is a petition you should sign.
Because, fitness. A nexus of recent human evolution might just be pregnancy.

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Felony experimentation

noreply@blogger.com (Jeremy Yoder) — Thu, 02 May 2013 16:02:00 +0000

This story is, rightly, blowing up the science-y internet:

Kiera Wilmot got good grades and had a perfect behavior record. She wasn't the kind of kid you'd expect to find hauled away in handcuffs and expelled from school, but that's exactly what happened after an attempt at a science project went horribly wrong.

Wilmot apparently mixed some "household chemicals" together inside a small plastic bottle, producing a reaction that caused the bottle to explode. She told police that she meant it as a scientific experiment—clearly she was curious to see what would happen, which makes it an experiment in spirit, even if it didn't take place in a lab. The chemicals involved aren't specified, but anyone who grew up among nerdy teenagers probably remembers doing exactly this, and probably can recall the recipe. Trouble is, Wilmot did it on school grounds, outside of a supervised science class. And the response of the folks who run her school was totally fucking disproportionate:

After the explosion Wilmot was taken into custody by a school resources officer and charged with possession/discharge of a weapon on school grounds and discharging a destructive device. She will be tried as an adult.

One of the people who might have something to say about this said this:

"She made a bad choice. Honestly, I don't think she meant to ever hurt anyone," principal Ron Pritchard told the station. "She wanted to see what would happen [when the chemicals mixed] and was shocked by what it did. Her mother is shocked, too."

And now a sixteen-year-old girl with no prior behavioral problems and good grades is at risk of acquiring the kind of criminal record that screws up job interviews, credit checks, and applications to college. All for setting up an experiment you can see performed in any number of YouTube videos.

And, oh yeah, Kiera Wilmot is African American. DNLee digs into the sad, infuriating racial component of this whole sad, infuriating mess over at Scientific American, and this is really her wheelhouse. My only contribution to that part of the conversation is: I grew up in a rural, predominantly white, predominantly middle-class school district. Among my friends, when I was sixteen, were any number of white, male, middle-class kids who set up "experiments" far more dangerous than what we're told Kiera Wilmot did. They set off explosions with household chemicals, firecrackers, model rocket engines—and none of them were charged with felonies.

I'm pretty sure none of them would've been charged with felonies even if they'd set off one of these experiments on or near school grounds. Yes, they might've been suspended a day or two, or made to attend a safety lecture, but no one dismissed the destruction of their future with the blandly hateful accusation that they "made a bad choice."

Because they were white, teenaged, middle-class boys in a rural school district, and blowing things up was just what white, teenaged, middle-class boys did. Everyone knew that.

There is, at least, a Change.org petition. I'd suggest that you sign it.◼

Science online, green-blooded rat ticklers edition

noreply@blogger.com (Jeremy Yoder) — Fri, 26 Apr 2013 13:00:00 +0000

This week, at Nothing in Biology Makes Sense! Does science promote morality?
And at The Molecular Ecologist: I demonstrate how to make species distribution models in R.
Good luck! Physicians at the University of Minnesota are going to try to cure another patient of HIV infection using a bone marrow transplant.
Best experimental treatment ever? Need to de-stress your rat? Try a daily tickle party.
For a general audience—but most of this also applies for scientific ones. David Dobbs on how to write about science.
"So, we have red blood because Nature started making O₂ with chlorophyll." The biochemistry of blood in science fiction movies.
Definitely significant. Or trending that way, at least. A list of statistical weasel-words.
"That was the only way we could get them to pay attention." How a groundbreaking book about the AIDS crisis spread a lie about the diseases' origins.
Seriously, this is asinine. How not to treat your graduate students, episode 2,573.
And they don't look that much nifty-er. "Forests" planted on the terraced sides of skyscrapers cost a lot more than actual on-the-ground forests.
Clever girls! Groupers use gestures to coordinate their collaborative hunts with moray eels.
Or, Jeremy Fox aims for the head. A couple of new papers help to slay the zombie of the local-regional richness relationship.

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Zombie skunk cabbage!

noreply@blogger.com (Jeremy Yoder) — Wed, 24 Apr 2013 14:38:00 +0000

In a new episode of the botanical web-video series "Plants Are Cool, Too!" Chris Martine points out that skunk cabbage was a zombie long before zombies were cool.

Representative quote: "Smell that—smells just like skunk!" "Suurrre does!"◼

Nothing in Biology Makes Sense: Science and morality

noreply@blogger.com (Jeremy Yoder) — Tue, 23 Apr 2013 17:34:00 +0000

Over at Nothing in Biology Makes Sense, Amy Dapper takes a look at a new study suggesting that thinking about science might promote moral behavior.

In all four experiments, the authors found exposure to scientific thinking led to more moral behaviors. Study participants that were exposed to the scientific priming (or in the first experiment, that had greater previous exposure to science) reported date rape as being more wrong, were more likely to report that they would participate in prosocial behaviors and divided the $5 more evenly between themselves and the anonymous participant.

Of course, I'm flabbergasted by these results, because all of the scientists I know are selfish, amoral hedonists—that's why we're all clamoring for cushy, overpaid jobs on the tenure track. But maybe you should go read the whole thing and see what you think.◼

The Molecular Ecologist: Using R to model the spatial distributions of species

noreply@blogger.com (Jeremy Yoder) — Tue, 23 Apr 2013 15:06:00 +0000

This week at The Molecular Ecologist, I'm showing how to use the popular open-source statistical programming language R to estimate species distribution models.

Species distribution models (SDMs) are handy any time you want to extrapolate where a species might be based on where you know it actually is. Maybe you’re trying to figure out where would be fruitful to do more sampling; maybe you want to know where your favorite critters probably lived back during the last ice age; maybe you want to know what regions will be suitable for your favorite critters after another century of global climate change.

Given how widely useful SDMs are, it's very nice to be able to estimate them using multiple methods implemented within a single open-source framework. To get a taste of the capabilities provided by R and a select set of add-on packages, go read the whole thing.◼

Some not entirely unsolicited advice for science blogging success (for a given value of "success")

noreply@blogger.com (Jeremy Yoder) — Mon, 22 Apr 2013 13:00:00 +0000

Recently I recieved a very nice e-mail asking for advice about blogging, and after I'd written up a response I realized I was most of the way to a blog post. So, waste not, want not. First, the original question, then my response, which I've edited to protect the innocent (i.e., not me), and also to turn up the snark a bit more than I care to in an actual personal interaction:

... as a highly successful blogger maintaining and contributing to multiple well-followed blogs, we were wondering if you had any tips for us on a. how to better promote our blog and b. get more people commenting?

First, let me take a moment to bask in the phrase "highly successful blogger," which: hahahahaHaHA. John Scalzi is a highly successful blogger. When I can pull down pageviews within an order of magnitude of his, we'll talk about "highly successful." (I'm not bitter—John Scalzi is, objectively, at least that much more awesome than me. Seriously, did you read this short story he wrote on Twitter over the course of a flight last week?)

But more seriously: now that I've been writing online since midway through grad school (since, eek, 2006), there are some people who care what I have to say, and come by to read it; I've had some writers who I deeply, deeply respect say some nice things about some of my work; and I've even been asked to go to other online places to do the kinds of things I used to do entirely on my own site. And that does make me happy, and I consider it's a pretty great outcome from just writing about whatever I wanted to here in my own little corner of the Internet.

But yeah, I do more than just the writing.

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The third week of April in Minneapolis

noreply@blogger.com (Jeremy Yoder) — Fri, 19 Apr 2013 13:42:00 +0000

Apparently we've officially gotten 10 inches of snow. Further north, it's up to 22. I'm ready for this to be done. I was about a month ago.

More photos at my Flickr stream, because what else can I do?◼

Science online, two months to Snowbird edition

noreply@blogger.com (Jeremy Yoder) — Fri, 19 Apr 2013 13:00:00 +0000

This week at Nothing in Biology Makes Sense! We're looking ahead to the Evolution meetings.
And, at ProfHacker: I review a book about teaching science.
Maybe! Does your brain know whether you're reading a piece of paper or a screen?
Not that we couldn't do a lot better. U.S. policies for reducing carbon pollution are a scattershot mess, but they seem to be working.
No, really. Why we should treat science and math literatcy more like basketball.
With a lot of money on the line. The U.S. Supreme Court heard oral arguments this week in a case that could decide whether it's legal to patent a human gene.
So to speak. Even when you have all your publication-ducks in a row, how do you decide which ducks go first?
Yum! Scicurious review's Mary Roach's new book Gulp.
In a lineage this young, are we surprised? Human origins are turning out to be more of a mosaic than a clean-cut family tree.
No kidding. For more students to go into science careers, maybe there need to be more science careers?
Well, Earth-scale-ish. Kepler space telescope finds evidence of not one but two Earth-scale planets orbiting in another star's "habitable zone."
More on E.O. Wilson vs. math. Maybe what he really doesn't understand is how collaboration works.
Aww. Zoobooks! The journey to field studies of lions in Kenya starts with a subscription to Zoobooks.

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I read a book!

noreply@blogger.com (Jeremy Yoder) — Thu, 18 Apr 2013 14:30:00 +0000

It's called Making Scientists: Six Principles for Effective College Teaching (buy it over on Indiebound). It's about teaching science to undergraduates, which is a thing I've been trying to do, lately. And I wrote a review for ProfHacker.

In their new book Making Scientists: Six Principles for Effective College Teaching, (Harvard University Press, $24.95) Light and Micari argue that undergraduate education in the sciences should go beyond imparting a basic set of knowledge, and make learning science more like the experience of doing scientific research.

If teaching science to undergraduates is also a thing you do, may I suggest you go read the whole thing?◼