Tuesday, May 29, 2012

Garfunkel and Oates on 29 versus 31

So, what's the difference between being 29 and 31? Two years, you say? Well, that sounds just like you, you idiot.  Here's the right answer:

Friday, May 18, 2012

FBI Profiles Scooby Doo Terrorist as "All Ron Paul Supporters"

So, the FBI is offering a reward of $150,000 in their search for the person responsible for mailing 380 letters over the past four years. Each letter contained a white powdered substance that was not anthrax, but resembled anthrax in that it was white and powdery.

According to the FBI website:
During the week of May 7, 2012, over 20 letters containing white powder were received by early childhood development centers, elementary schools, and an aerospace-related business. 
The most recent batch of letters contained this Scooby-Doo-rich gem:
Try singing this to the tune of the Scooby Doo song. It works better than you might think.
The FBI has also helpfully published a profile of the suspect, just like on Criminal Minds. The profile lists seven characteristics, which could have been presented much more succinctly by simply stating that the mailer was a Ron Paul supporter:

The difference with this guy is that he is doing IRL what most Ron Paul supporters only do in internet comment threads.

via Boing Boing.

Wednesday, May 16, 2012

FDA Recommends more Judicious use of Antibiotics in Agriculture

So, the FDA recently put out its report recommending that the agriculture industry reduce its use of antibiotics. Specifically, they urge that the use of antibiotics that are also used to treat humans be used more "judiciously."

There are two specific widespread practices that the FDA aims to discourage: 1) the use of antibiotics to make animals gain weight faster, and 2) prophylactic use of antibiotics to prevent the outbreak of a disease, even in the absence of any indication that such an outbreak is likely. Both of these are commonly achieved by feeding animals a constant, low dose of antibiotics in their feed or water. This constant-low-dose scheme is, of course, optimal, assuming that your goal is to maximize the rate at which bacteria acquire antibiotic resistance.

As per the FDA's website, the plan is this: "implementing a voluntary strategy to promote the judicious use in food-producing animals of antibiotics that are important in treating humans," which basically means leaving it up to the food producers themselves. So, you can fully expect that absolutely nothing will happen, and that you will still die a very slow, painful death from a virulent antibiotic-resistant bacterial infection.

Nature Reviews Microbiology has just published an editorial on the topic in which they point out that these steps by the FDA are not nearly enough, and they provide this depressing tidbit:
In 1977 the FDA began a process which could have resulted in a similar ban to that seen in the EU, by issuing notice of their intention to hold hearings into the withdrawal of approval for the use of penicillin and tetracycline in animals. However, these hearings never took place, and in December 2011 the agency announced that these notices had been formally withdrawn. 
Really, FDA? Are you really that incompetent and corrupt? Don't answer that, it was a rhetorical question.

Anyway, here's a strip that appeared last year at Darwin Eats Cake, where Andy and Eleonora debate the use of antibiotics in agriculture. It's from back before I increased the font size, so it is easier to read on the original site.

Best URL for sharing (or reading, really): http://www.darwineatscake.com/?id=34
Permanent image URL for hotlinking or embedding: http://www.darwineatscake.com/img/comic/34.png

Tuesday, May 15, 2012

Time-lapse map of Europe, 1000-2005

So, this is a pretty cool thing. In three and a half minutes you can watch a thousand years of European history unfold before your eyes. The one downside is that there is no timeline with a little running dude, or date-o-meter, or something to let you know where you are (when you are, said Inspector Spacetime). If you know a smattering of history here and there, you can pin it down though.

It looks like the progression of time is not completely uniform, though. If you're interested, here's a little guide for you

1066 = 0.05 (Norman conquest of England)
1204 = 0:18 (Fourth crusade sacks Constantinople)
1478 = 1:11 (Conquest of the Novgorod Republic by Ivan III)
1580 = 1:32 (Union of Spain and Portugal)
1603 = 1:37 (Unification of England and Scotland under James I)
1795 = 2:24 (Third Partition of Poland)
1812 = 2:33 (French Invasion of Russia)
1914 = 2:53 (Start of World War I)
1942 = 3:06 (Farthest German advance in WWII)
1990 = 3:15 (Reunification of Germany)

Ooh, and, as I was writing this, the creator posted another version, which is much slower, running for 11 minutes, and more zoomed in.

Sunday, May 13, 2012

Happy Mother's Day -- Biology Style

So, happy Mother's Day to all the moms out there, but especially to my mom, and to my kid's mom, who are both awesome, even in the pantheon of moms.

How better to celebrate than with a nerdy biology song? No better, that's how.


via Joanne McMaster.

Friday, May 11, 2012

Why Romney's bullying is a big deal

So, for the past couple of days I've been trying to figure out whether or not the latest Romney scandal is a big deal. On the surface, the answer may seem obvious. I mean, the story of the time when a young Mitt Romney had a gang of his friends hold down a boy while he forcibly cut his hair has dominated the news cycle for a couple of days, competing successfully with Barack Obama's declaration of his personal belief that same-sex marriage should be allowed.

What I am wondering is whether or not the story is going to remain in the public consciousness for more than a few days, and whether it will actually substantially alter the public perception of Romney and influence the outcome of the election in the fall. The fact is that every day there is some scandal or crisis that dominates the news cycle, sending pundits scurrying to their typewriters (metaphorically) to write about how the the news of the day is a game changer, and how the outcome of the campaign hinges on how they respond over the next few hours. Most of these crises fade away to be replaced by the next crisis, and don't seem to have any lasting impact on the election dynamics.

There is a part of my that thinks that the haircut scandal may be different.

The difference, I think, is the tangibility and violence of the act.

Most of the short-lived crises that crop up in election cycles do not really have gut-level impact. Maybe one candidate served on a corporate board with someone who was accused of insider trading. That is a situation that is so disconnected from the lives of most people that, while they might understand it intellectually, it is unlikely to resonate emotionally. Or maybe another candidate had an affair in the past. Affairs are much more universal, but that universality also mitigates our outrage. Everyone has friends who have, or have had, marital difficulties, and most of us understand that relationships are difficult and complicated, and that those situation are rarely simple.

Perhaps more important is the fact that we have have a very strong cultural narrative of infidelity followed by redemption. It is not hard to come up with examples of movies, television shows, and novels where there is infidelity in a marriage, but the cheater learns the error of their ways, makes amends, and winds up with a stronger marriage as a result.

Contrast these two situations with the Romney haircut scandal. It seems to be a clear case where Romney was a bully. Bullying is a cultural universal. It is something that everyone can picture from their own personal experience. Furthermore, pretty much everyone thinks of themselves as having been on the receiving end of bullying (even many of the people who were also the bullies at some point). So, while there may be a few people who identify and sympathize with Romney, everyone can identify and sympathize with John Lauber, the boy whose hair was forcibly cut by Romney.

Adding to the emotional resonance is the extreme violence of the incident. I actually have a bit of a hard time picturing the scene. Not because it is so very foreign, but because it makes me queasy to think about it. Here's the description from the Washington Post:
“He can’t look like that. That’s wrong. Just look at him!” an incensed Romney told Matthew Friedemann, his close friend in the Stevens Hall dorm, according to Friedemann’s recollection. Mitt, the teenage son of Michigan Gov. George Romney, kept complaining about Lauber’s look, Friedemann recalled.
A few days later, Friedemann entered Stevens Hall off the school’s collegiate quad to find Romney marching out of his own room ahead of a prep school posse shouting about their plan to cut Lauber’s hair. Friedemann followed them to a nearby room where they came upon Lauber, tackled him and pinned him to the ground. As Lauber, his eyes filling with tears, screamed for help, Romney repeatedly clipped his hair with a pair of scissors. 
It's a scene of extreme violence. A group of boys tackling another boy and pinning him to the ground. The pinned boy screaming for help and starting to cry while his hair is forcibly cut with a pair of scissors. I'll posit that if picturing the scene doesn't make you feel sick, either you're a psychopath, or you're not really picturing it.

The other thing about this that spell trouble for Romney is the cultural resonance of the scene. In contrast with the infidelity-and-redemption trope, try to picture the haircutting scene in a movie. This is exactly the sort of scene you can imagine being used as short-hand near the beginning of a movie to quickly establish characters. Now, think about what the scene would actually be telling us about those characters.

It is not hard to imagine one of the cronies, one of the gang of kids holding John Lauber down, being sympathetic. He might be a character who is not really bad, but was weak, and got caught up in the moment. Maybe by the end of the film this character redeems himself by standing up to the group of bullies who were his former friends.

But what about the kid who was holding the scissors? I have a hard time picturing that kid as a redeemable character. He's the kid who is rotten to the core, the one against whom other characters' redemptions are measured. That is the image of Mitt Romney that has just been presented to us.

That's not to say that, in real life, a kid who callously engages in acts of cruelty can't learn empathy and set his bullying days behind him. But I don't think that's the narrative of least resistance. That means, I think, that it is incumbent on Romney to demonstrate that he has totally changed between then and now.

The problem is that Romney has done absolutely nothing to suggest that he did learn anything from the experience, or that he has acquired more empathy than he seems to have had as a teenager. So far, his responses have been the usual political denial-of-recollection and non-apology:
I don’t recall the incident myself, but I’ve seen the reports and I’m not going to argue with that. There’s no question but that I did some stupid things when I was in high school and obviously if I hurt anyone by virtue of that, I would be very sorry for it and apologize for it.
Contrast this with the people who were interviewed for the original Washington Post piece, who are still haunted by the cruelty that they witnessed and facilitated. So far, they seem to fit pretty well into the narrative of the henchman-bullies who did some cruel and callous things, but who learned from the experience became better people as a result. One of them went so far as to seek out John Lauber and apologize to him (years later, but presumably prior to Lauber's death in 2004).

There seem to be three possible interpretations of Romney's response, none of which paint a flattering picture of the presumptive Republican nominee:

One possibility is that Romney is being honest, that he doesn't remember the incident. That he, in fact, probably never gave it is second thought, and doesn't really fully understand, even now, why people think it is such a big deal. This would speak to a troubling, pathological lack of empathy on Romney's part. Unfortunately for Romney, this picture resonates with his image as a child of privilege who feels no moral obligation to other people.

A second possibility is that Romney recalls the incident, and maybe even feels bad about it, but that he is trying to manage the political impact of the story by minimizing it. That would speak a little better to Romney's capacity for empathy (and long-term memory), but still paints a picture of someone whose sense of entitlement (and political ambition) far outweighs any sense of morality.

A third possibility is that Romney genuinely feels bad, but is unwilling to say so because he feels that he need to pander to the anti-homosexual contingent in his base. That would make Romney a bit less of a monster personally, but fits neatly with his image as a candidate who has no core values, and who is willing to say or do anything in the name of getting elected.

Maybe I'm wrong, and next week this will be forgotten as we're all talking about the lost thirteenth tribe of Kardashians. But to me, this story is so visceral, and so resonant with everything else we know about Mitt Romney, that it just might stick around.

Update: The original title of this post was "Why is Romney's bullying is a big deal?" Which is, um, derp, is not very grammaticish.

Thursday, May 10, 2012

Best headline of year changed by Seattle Times

So, there is an article up at the Seattle Times with the following title: "All 6 Wash. congressional Dems favor repeal of gay-marriage ban."  The article was written after Norm Dicks, a democrat representing Washington's sixth congressional district, joined other Washington Democrats in saying that he would support the repeal of DOMA.

This is great news, and just the most recent in a long list of Democrats who have come out in support of marriage equality in the wake of Obama's announcement yesterday declaring his personal support.

The only sad part of the story is that the seems to have abandoned their original headline, which was "With Dicks in, all 6 WA congressional Democrats favor repeal of gay-marriage ban."

via +K. O. Myers.

Sunday, May 6, 2012

500-mile limit on e-mail

So, this is old news. Actually, it's ancient in internet terms, as it happened sometime in the mid 1990s. But, it's new to me, so maybe it's new to some of you, too.

This is a story from Trey Harris, who was in charge of the e-mail system at the University of North Carolina. He was contacted by a department chair who claimed that no one in his department could send e-mails more than 500 miles.

Before you object that, you know, that's not how e-mail works, let me assure you that not only was it true, but Harris managed to figure out what was happening. Here's an excerpt:
"What makes you think you can't send mail more than 500 miles?"
"It's not what I *think*," the chairman replied testily.  "You see, when we first noticed this happening, a few days ago--"
"You waited a few DAYS?" I interrupted, a tremor tinging my voice.  "And you couldn't send email this whole time?"
"We could send email.  Just not more than--"
"--500 miles, yes," I finished for him, "I got that.  But why didn't you call earlier?"
"Well, we hadn't collected enough data to be sure of what was going on
until just now."  Right.  This is the chairman of *statistics*. "Anyway, I asked one of the geostatisticians to look into it--"
"--yes, and she's produced a map showing the radius within which we can send email to be slightly more than 500 miles.  There are a number of destinations within that radius that we can't reach, either, or reach sporadically, but we can never email farther than this radius."
Read the whole thing here. There's also a FAQ if you want more technical details.

via Kottke.

Thursday, May 3, 2012

Blue-eyed-people-are-all-related zombie news

So, you know how sometimes at night you're lying in bed when you burp, but then the burp turns out to actually be you throwing up into your mouth just a little bit, and it tastes like a combination of whatever you ate for dinner and evil? Well, this is sort of like that.

Four years ago, a group of researchers from the University of Copenhagen published a nice paper on the genetics of blue eye color. In that paper they look at a bunch of Danish families in which some people have blue eyes and some have brown eyes (or, combination blue-brown eyes, which, for purposes of this study, are treated as non-blue). They also look at a small sample of non-Danish blue-eyed folks: five from Turkey and two from Jordan.

The paper makes a compelling case that the pure blue eyes phenotype depends on a particular nucleotide substitution that alters regulation of the gene OCA2. Furthermore, there is an extended haplotype around the key mutation that is shared by everyone in their sample (a few people have additional nucleotide substitutions that most likely post-date the key functional mutation). This suggests that, while there are many genes that contribute to eye color variation and to pigmentation in general, there may be a single critical mutation responsible for all of the blue eyes out there. Which is pretty cool.

For reasons that I still don't understand, this study has popped back into the news recently. In particular, an article that looks to have been written back in 2008 in USA Today was "updated" in February, and has resurfaced on AOL, which describes it as a "study from USA Today," and warns people with blue eyes about the dangers of falling in love with another blue-eyed beauty. Presumably because of incest (also shown is a clip from HLN -- the artist formerly known as CNN Headline News -- featuring the anchor doing a whole "ick" thing).

In worst-of-media-coverage-of-science fashion the reports that I have found (both from 2008 and from 2012), coverage focuses on stuff from the paper that is tangential, irrelevant, or wrong.

First, "all blue-eyed people are related." Where to start. The researchers suggest that the mutation might have arisen 6000-10000 years ago in the Black Sea region, prior to the Neolithic agricultural expansion into Europe. If we assume a generation time of, say, 25 years, that is 240-400 generations. If we look back that far in the past, even just to the 6000 year mark, each of us has 2^240 ancestors. That's 1.7 x 10^72, which, you will notice, is not just much larger than 7 x 10^9 (the current population of the whole world), but is close to the ballpark of the total number of atoms in the universe.

The fact is, once you go back more than a few hundred years, each of us has a list of ancestors that features the same people over and over again. Not only are we all related, we are all related over and over and over again. While your brother may not be your cousin, your tenth cousin is quite likely to be your seventh cousin as well.

So, yes, all blue-eyed people are related, but there is not really anything here to suggest that they are significantly more closely related than any two people.

Second, both the 6000-10000 year timeframe and the Black Sea origin of the mutation -- both of which featured heavily in press coverage of the paper -- are completely unsupported by anything in the data. What the authors actually say is this:
The mutations responsible for the blue eye color most likely originate from the neareast area or northwest part of the Black Sea region, where the great agriculture migration to the northern part of Europe took place in the Neolithic periods about 6–10,000 years ago (Cavalli-Sforza et al.1994).
The high frequency of blue-eyed individuals in the Scandinavia and Baltic areas indicates a positive selection for this phenotype (Cavalli-Sforza et al. 1994; Myant et al. 1997). Several theories has been suggested to explain the evolutionary selection for pigmentation traits which include UV expositor causing skin cancer, vitamin D deficiency, and also sexual selection has been mentioned. Natural selection as suggested here makes it difficult to calculate the age of the mutation.
That is, we don't know how old the mutation is, and have not tried to perform any sort of analysis to ask the question. That's fine, because what the paper actually does is provide us with a basis for asking these sorts of questions, although that will require more extensive sampling.

The supposition here is based solely on the fact that there was this expansion of agriculture (along with, to a not-fully-characterized extent, an expansion of the genes of the people who developed that early agricultural technology), and that stuff in Europe probably came with that.

The actual way to ask the question would be to go and sequence the DNA of a bunch of folks from all across Europe. To first approximation, we might assume that the mutation first arose in the region where the blue-eyes haplotype shows the greatest within-haplotype genetic diversity. For example, if the mutation first arose near the Black Sea, we should see more genetic variation right around the key mutation among blue-eyed people near the Black Sea. If the allele arrived more recently in Sweden, blue-eyed Swedes would be more genetically similar to each other in the same genomic region, simply because there would have been less time for differences to accumulate.

All else being equal, we might expect the geographical origin of a particular mutation to be at the central point of its range, or near the place where the mutation has reached its highest frequency. That supposition would place the origin somewhere near the Baltic (rather than the Black) Sea. But, there is good reason to believe that this mutation may have been subject to selection. The blue-eyes allele also affects other aspects of pigmentation, and lighter coloring is thought to have been favored at higher latitudes due to the reduced incidence of sunlight.

The fact that we think that natural selection would have pushed the mutation northward means that that its origin was probably somewhere to the South of its current center. Exactly how far depends on a bunch of details, like the strength of selection, and how that strength of selection changes as you move from South to North.

The problem is that, to do it right, you would have to build a model that explicitly incorporates the agricultural expansion and natural selection acting on OCA2, with the strength of selection favoring lighter pigmentation depending on latitude. Maybe also the fact that there are other genes affecting pigmentation. It is something that is doable, especially now that we have a specific gene to focus on, but at this point what we have is a bunch of speculation.

So, to recap, 1) Cool paper. 2) Sex between blue-eyed people is not incest. 3) We have no idea when or where this mutation came from, but it is now conceivable that we could ask the question. 4) Embarrassingly bad science reporting spontaneously rises from the grave four years later and tries to eat your brain.

Eiberg, H., Troelsen, J., Nielsen, M., Mikkelsen, A., Mengel-From, J., Kjaer, K., & Hansen, L. (2008). Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression Human Genetics, 123 (2), 177-187 DOI: 10.1007/s00439-007-0460-x

Wednesday, May 2, 2012

Ronin Institute post at Wired

So, yesterday I posted about the white paper that Sam Arbesman and I wrote about fractional scholarship for the Kauffman Foundation. Well, we also wrote a piece for Wired, which Sam has posted there now.

The best part is that it features a picture of a statue of Ben Franklin, and right under the picture it notes that the article was co-authored with Jon Wilkins (me). Go read it. Go!

Tuesday, May 1, 2012

Happy May Day from Occupy Darwin Eats Cake!!

So, today is May Day!! Hopefully, you are out General Striking right now, or will be later today. If you're stuck inside, are far away from one of the occupied cities, or just want to feel like you're saving civilization in a way that doesn't involve getting wet, I have assembled here a retrospective of Occupy comics from Darwin Eats Cake. Links to individual comics will open in a new window

Here are all of the "Occupy Darwin Eats Cake" strips, where the cast abandoned me last fall to join in the protests at Zuccotti Park, along with the Occupy-related strips that have come up along the way:

The Economic Brain
Episode 1
Episode 2

And remember, sharing is caring!

White Paper on Fractional Scholarship

So, I've been working with the incomparable Sam Arbesman to write up some thoughts on the concept of "fractional scholarship." Basically, the idea is that there are a lot of people out there who have the expertise and the interest to contribute to scholarly research, but for whom, for whatever reason, the seventy-hour-a-week academic lifestyle just doesn't work. We need to develop mechanisms that will allow people to participate in research at ten, twenty, or thirty hours a week, and to get paid for doing it.

Obviously, someone working only ten hours a week would get paid a lot less than a university professor, which is part of what makes this such a powerful model. Keep in mind that a typical university professor probably does not spend much more that ten hours a week actually doing research anyway, what with all the personnel-management and bureaucratic tasks that take up so much of their time.

Basically, all the people out there (and there are tens of thousands of them) who got a PhD, but then dropped out of academia (e.g., to have kids) represent a vast underutilized intellectual resource that is trading well below its actual value. Tapping in to that resource is one of the things that we hope to do with the Ronin Institute.

Check out the full white paper at the Kauffman Foundation website, here.