All posts by jonfwilkins

academia, Ronin Institute

The case for independent scholarship, #1: Everything

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So, as regular readers already know, I have recently founded a nonprofit institute that is dedicated to supporting and promoting independent scholarship — that is, scholarly research outside of the standard system of research universities and government laboratories.

(Sounds cool, right? Want to know more? Drop by the webpage of the Ronin Institute.)

Why do we need to promote independent scholarship? Well, there are a lot of great reasons, and they’re the topic of my new series: The case for independent scholarship, where I’m going to break those reasons down for you. But, for those of you who can’t wait to read about all of those compelling reasons in detail, here’s a précis of the coming argument. Whether you are a scholar yourself, a financial supporter of scholarship, or just someone who believes that things should be done better in the future than in the past, here is why you should be looking beyond the standard academic model.

  • Independent scholarship is cheaper and more efficient. Research universities and government laboratories support huge, bureaucratic infrastructures that must be fed by siphoning funding away from research.
  • Independent scholarship is more democratic. Along with the bureaucracy of large research institutions comes hierarchical structures that can limit academic freedom.
  • Independent scholarship is more humane. The independent-scholarship model avoids many of the problems of the traditional academic lifestyle, which is often at odds with other goals, such as being an involved parent. Independent scholars can set their own hours to accommodate other priorities, and are not as geographically restricted as traditional academics — thus avoiding the academic “two-body problem.”
  • Independent scholarship is more transdisciplinary. The departmental structure in universities — or whatever bureaucratic structure exists in a particular institution — tends to create artificial barriers to exploration and collaboration. Some institutions have taken steps to encourage interdisciplinary research, but the independent scholar is naturally situated to pursue the most interesting questions without any artificial constraints.
  • Independent scholarship can exploit untapped intellectual resources. In the United States alone, there are tens of thousands of people with PhDs who are not making use of their PhD training. The independent-scholarship model allows people with training in and passion for a subject to contribute to their field, even if only in a part-time capacity.
  • Independent scholarship does not need to be profit driven. Increasingly, hiring and tenure decisions at universities are driven by funding considerations. Independent scholarship can be driven by important questions, rather than by the need to develop and justify large research budgets. 
  • Independent scholarship honors donor intent. For philanthropists who support research, donations to universities are always problematic, since the fungibility of funds means that donations rarely go 100% to support the program(s) that the donor cares about. Independent scholarship can be structure in a scalable way, so that donations translate directly to increased support for those research projects that are most important to the donor.
  • Independent scholarship is more open. The independent-scholarship model aims to break down the distinctions between the ivory tower of academia and the broader population of intelligent, educated individuals who are eager and able to contribute to scholarly discourse.
In upcoming installations of this series, I will devote one or more posts to each of these bullet points and more, bringing in some detail and statistics to illustrate each. 
biology, evolution, Politics, sex

Post-copulatory female choice in crickets and Missouri

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So, maybe you’ve seen the news today about Representative Todd Akin. He’s the republican nominee for Senate in Missouri, running this year against Claire McCaskill. In an interview he said that he opposed abortion in all circumstances, with no exception for rape, because rape does not lead to pregnancy, see, because, “If it’s a legitimate rape, the female body has ways to try to shut that whole thing down.” (Quotes on Jezebel, video here.)

After realizing that he sounded like a complete shithead, even for a contemporary Republican (and probably after receiving a scolding from national Republicans), he issued a statement in which he claims that he “misspoke,” which is politician speak for, “I accidentally said what I actually thought, and then discovered that it will negatively impact my election chances, so I’m going to lie now. No backsies!”

Although, to be fair to Akin, nowhere in his statement did he back down from the position that abortion should be outlawed without exception, merely that he would advocate for “justice.” Also, jobs!

Setting aside for the moment the woeful state of politics, is it true, or even possible, that the female body could have “ways to try to shut that whole thing down”?

Actually, in a lot of non-human animals, something sort of like that does exist.

In species where polyandry (where females mate with multiple males) is common, there is often competition for reproductive access both before and after copulation, where one male may participate in a larger share of a female’s reproduction. In many cases, this is going to be something like sperm competition, where differential reproductive success depends on traits associated with the sperm, and by extension, with the competing males. This is not really what we’re talking about, though.

In a few cases, you can actually get “post-copulatory female choice,” where it is clearly the female deciding whether or not to allow fertilization. One such set of cases occurs in some spiders and crickets, where the male transfers a spermatophore to the female. This is basically a bag full of sperm that is attached to the female during copulation. She may then modulate the success of the sperm through the amount of time she permits it to remain attached to her.

For example, here‘s a paper on field crickets that shows not only that females modulate spermatophore retention time in response to male song quality, but that this modulation is contingent on the female’s prior experience. This is important because it emphasizes the aspect of female choice.

But what about humans? Well, actually, yes. Human females have the capacity to engage in post-copulatory female choice, such that they do not necessarily have to give birth to their rapist’s child. It’s called safe, legal abortion. It still exists in this country, but if too many more Todd Akins get elected, the American female body will no longer have “ways to try to shut that whole thing down.”

Rebar, D., Zuk, M., & Bailey, N. W. (2011). Mating experience in field crickets modifies pre- and postcopulatory female choice in parallel Behavioral Ecology, 22, 303-309

Behavior, biology, comic, Darwin Eats Cake, evolution, science

The selfish herd

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So, one of the most interesting questions in evolutionary biology is the origin of collective behaviors. This can be the complex division of labor that we see in social insects and human societies, flocking behavior in migratory birds, or microbial formation of biofilms. It can be predators engaging in collective hunting, or prey engaging in collective being hunted. It’s this last one that we’re going to be talking about today.

As with many questions in evolutionary biology, there are a couple of dimensions that people are interested in untangling: proximal and ultimate causation. Proximal explanations focus on the “how” part of the solution, as in, “what are the molecular, genetic, etc. mechanisms and environmental cues that result in this behavior?” Ultimate explanations focus on “why,” in the evolutionary sense of “what were the selective pressures that led to the evolution of this behavior?”

Herding or flocking behavior is a classic case. For example, why do sheep hang out in a big group, in contrast to say, leopards, which tend to be pretty solitary? There are a number of possible (and not mutually exclusive) ultimate explanations, but the most talked about one is probably defense against predators.

Best URL for sharing: http://www.darwineatscake.com/?id=135
Permanent image URL for hotlinking or embedding: http://www.darwineatscake.com/img/comic/135.png

Back in the mid-twentieth century, it was common for biologists to talk in fairly loose terms about collective behaviors having evolved as a result of their benefits to the group. Then, in 1966, G. C. Williams published Adaptation and Natural Selection, which dropped a lot of truth into the community. In particular, it emphasized the gene-centered view of natural selection that hit the public consciousness with Richard Dawkins’s 1976 book, The Selfish Gene, and which has remained the dominant paradigm in evolutionary biology ever since.

Williams demonstrated that group selection, while possible, will generally be a much weaker force than selection acting on the individual. Therefore, it is good practice to look for evolutionary explanations at this lower level. Given plausible adaptive stories at the individual and group levels, one should favor the individual-level story. While the two stories might not be mutually exclusive, individual-level selective pressures are more likely to have played an important role in  the evolution of any particular trait than group-level selective pressures (all else being equal, of course).

In 1971, W. D. Hamilton published a theoretical analysis that brought this individual-level perspective to herding behavior. Hamilton argued that all you need is for animals to be trying to evade predators as individuals. If there are other individuals of their type around, they just need to try to position themselves between other individuals. Here’s how Hamilton draws it:

This frog wants to position itself between the two frogs on the right. That way, when the sea snake comes up, it will eat one of the frogs at the edge, and the one in the middle will be safe.

All you need is for everyone to follow one simple rule: when a predator comes, position yourself between two other individuals. What you get then is a tight cluster of individuals.

You can actually try this at home. You probably need about eight or ten people. So, most of you might not be able to try this at home, but you could maybe try it at school or work. Have each person pick two other people in the group (but don’t tell who your picks are). Then, everyone tries to get between the two people they picked. What you’ll get is something a lot like a cluster of frogs climbing all over each other to get away from a sea snake.

Frogs maneuvering to get between other frogs results in the formation of a clusterf**k of frogs. I know, right? I was surprised, too, but my herpetologist friends assure me that “clusterf**k” is the official collective noun for a group of frogs. Don’t even ask about sea snakes. You don’t want to know.

Bonus activity: after you’ve disentangled yourselves from the frogpile, try this one. Each person picks two people again, labeling them “A” and “B” (in your head). Again, no one needs to say whom they picked. Now, each person should position themselves so that their “A” person is between them and their “B” person. If it helps, imagine that “A” is Mitt Romney, that “B” is the American People, and you are Mitt’s tax returns. Your job is to position yourself so that Mitt keeps the American People from seeing you. I won’t spoil how it comes out.

So, Hamilton’s model provides a nice, simple model that can produce the observed behavior. The model is attractive because (1) it requires selection only at the level of the individual, and (2) it requires each individual only to follow a very simple behavioral rule. The collective behavior is an emergent property requiring no coordination at the group level.

Now, there’s a new paper out that is attempting to look at this empirically, in sheep. The study involves strapping adorable GPS backpacks on a bunch of sheep (Figure 1c, below) and then letting a sheepdog chase them around.

You can look at the movies here. It’s only a brief communication, and does not really nail anything down, but the authors interpret their results as broadly consistent with the selfish herd model. In particular, they are able to see that individual sheep seem to be trying to get to the center of the flock.

The cool thing is more the potential for this type of experiment. Yes, Hamilton’s model is attractive and parsimonious, but if we want to understand the rules that actually govern the behavior of sheep when they are faced with a predator (or, in this case, an annoyator), we will need to get good quantitative data on individual behaviors in a variety of contexts.

Plus, look at that little GPS backpack!

I’ll leave you with this.

Best URL for sharing: http://www.darwineatscake.com/?id=136
Permanent image URL for hotlinking or embedding: http://www.darwineatscake.com/img/comic/136.jpg

King AJ, Wilson AM, Wilshin SD, Lowe J, Haddadi H, Hailes S, & Morton AJ (2012). Selfish-herd behaviour of sheep under threat. Current biology : CB, 22 (14) PMID: 22835787

Hamilton, W. D. (1971). Geometry for the Selfish Herd Journal of Theoretical Biology, 31, 295-311 DOI: 10.1016/0022-5193(71)90189-5

Sports

The two-athlete rule is the way sports work

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So, if you’ve been following the olympics at all, you’ve no doubt been exposed to the outrage at the fact that Jordyn Wieber won’t be competing for the United States in the all-around gymnastics final. If you haven’t been following that closely, here’s the recap.

Yesterday featured the qualification round in women’s gymnastics. One point of this round is to determine which 24 athletes will compete in the all-around final. Basically, it is the 24 with the highest scores, but there is a cap of two athletes per country. The US gymnasts Gabrielle Douglas, Alexandra Raisman, and Jordyn Wieber finished second, third, and fourth. Because of the two-person cap, only Douglas and Raisman will be competing in the final. Obviously, given the rules, it was clear in advance that only two of the three could make it to the finals. What was surprising was the fact that the one left out wound up being Wieber, who was the 2011 world champion.

The (American) announcers at the venue started voicing their outrage at the two-gymnast rule, saying how ridiculous it was for the fourth-place finisher not to place in the top twenty-four, etc., etc.  This was followed by Bob Costas sitting down with Béla Károlyi to voice their outrage, with Costas scoffing at the ridiculousness of having a sport where you let anyone besides the best compete in the finals. Slate calls the rule “indefensible.”

Maybe I’m in the minority here, but it seems to me that this is pretty much how the olympics works. It also happens to be the way that most American sports work. The fact that we have divisions in baseball, basketball, football, etc. leads to exactly this sort of situation. In fact, prior to the introduction of the wildcard, this sort of thing happened all the time, where the two best baseball teams in the league would happen to be in the same division, so only one got to go to the playoffs. In fact, the outrage over this type of situation is exactly what prompted the creation of the wildcard in baseball (well, that and the desire for more playoff revenues). Now, I don’t know whether Bob Costas would be just as outraged as when, say, the best team in the NL Central is worse than the third-place team in the NL East, but I can’t say that I’ve ever heard him calling for the elimination of the division structure.

I think there are a couple of things going on here. First, the olympics represents two different, but related, competitions. Obviously, it is a competition among the best athletes in the world. At the same time, it is a competition among nations. If you want to have the best athletes in the world duke it out quotas or limits based on nationality, fine. What you have then, I believe, is something more like the world championships, which happen every year (I think), and are cared about by precisely no one outside of the gymnastics community. People care about the olympics in no small part because you have various nations sending their best, and pitting them against each other. Yes, the two-athlete cap in the gymnastics all-around final seems harsh, but I think it is inextricably tied up with the whole idea of what the olympics is.

The other thing is the tension between the desire to see the “best” athletes rewarded, and the sense that, in order to make a competition special, you require athletes to perform on a certain day. Clearly, much of the handwringing here is about the fact that Jordyn Wieber was supposed to be the best American. Presumably you can argue that, in a time-averaged sense, she is. But what are we supposed to do? We could say that Wieber is clearly really good, and deserves to be in the final. But, then, there’s really no point in having the competition. Why not just rank the athletes based on their track record and hand out the medals?

Basically, what fans (and TV executives) want is a nail-biting competition with huge stakes. Well, the way you do that is you collect some of the best competitors together, and then make them perform under pressure. You set up some rules to determine who is in and who is out, then you reset everything to zero and make the best prove it. If there is no chance for the favorite to fail, you really don’t have a sport.

The privileging of geographic diversity might be particularly salient in the olympics, but it is a critical feature of most professional sports, the world cup, and pretty much all of the sporting events that anyone cares about. You could argue that the World Series in baseball would be a more honest championship if it were simply a competition between the two teams with the best regular-season records. Maybe it would, but it would lose much of the charm and appeal of being the showdown between the American League and National League champions. Also, a huge number of games in the regular season would no longer matter.

There’s a sort of zero-sum game whenever you set up any sort of championship. The only way to increase the number of meaningful competitions is to increase the stochasticity in the system. If you’re going to have the qualification round at all in olympic gymnastics, you’ve got to have the two-person-per-country cap in place, or something like it. Yes, there are people arguing it should be three, as it was prior to 2004, but this actually more exciting and dramatic.

So, yes, this situation sucks for Jordyn Wieber, and for the fans who care a lot about the American medal count. But the bigger picture is this: the fact that it is possible for the reigning world champion to come in fourth and not make the 24-person finals is exactly what makes the olympics worth watching.

biology, evolution

How to pronounce "Muller’s Ratchet"

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So, how would you pronounce the name “Muller”? According to the standard pronunciation rules of American English, it should sound like a word that means “one who mulls,” with the “u” pronounced like the “u” in mullet. Curiously, however, when evolutionary biologists talk about “Muller’s ratchet,” more often than not they will pronounce the name so that it rhymes with “Bueller,” as in “Hermann Mueller’s Day Off.”

[Aside: Muller’s ratchet refers to a model in which deleterious mutations arise in a population, but there are no beneficial mutations. An individual’s fitness is a decreasing function of the number of deleterious mutations they possess. These deleterious mutations are held in check by purifying selection, such that there is a steady-state distribution of the population into fitness classes. The “ratchet” part refers to the fact that, in a finite population, stochastic fluctuations will eventually lead to the loss of the highest fitness class. The whole distribution then shifts down. This progresses in a ratchet-like fashion, and the fitness of the whole population declines over time. The take-home point is that purifying selection alone is not sufficient to preserve adaptation indefinitely. You also need some number of beneficial mutations to maintain fitness in the long run. Recombination can reconstitute higher fitness classes, reversing the ratchet in the short term, but still leaves the system susceptible to the stochastic fixation of deleterious mutations.]

If you ask one of these evolutionary biologists why they pronounce “Muller” like “Mueller,” they will often point you towards the umlaut on the u (or, somewhat equivalently, the e following the u). The thing is, there is no umalut, nor is there an e. Sometimes they will point to the fact that Muller was German, and that therefore, you know, it should sound more German. Except for the fact that Muller was not German. He was born in New York City. His parents were also born in the United States.

Now, according to Wikipedia:

H. J. Muller and science fiction writer Ursula Le Guin were second cousins; his father (Hermann J. Muller Sr.) and her father’s mother (Johanna Muller Kroeber) were siblings, the children of Nicholas Müller who immigrated to the United States in 1848.

That’s sort of cool about Ursula Le Guin. It also suggests that Muller’s grandfather was, in fact, named “Müller,” which would not really be pronounced the way that people say “Mewler,” but that would at least be the more standard Americanization of the name. What it looks like is that Muller’s grandfather changed his name (either by choice, or by orthographical fiat, as was often the case at Ellis Island). It would not surprise me if he pronounced it in the German fashion, but that the name became fully Anglicized over the course of the next couple of generations.

Of course, with names, I figure the rule is that the correct pronunciation is always how the person themselves pronounces (or, in this case, pronounced) it. On that point, all I can do is point to a seminar by Matt Meselson that I once attended. At the end of his talk, someone from the audience asked a question about “mewler’s ratchet.” Before answering, Meselson made the point that he had known Muller, and the Muller had pronounced it “Muller.” I have attempted to contact Muller’s surviving daughter for more direct confirmation, but have not heard anything back yet. If and when I do, I’ll post an update.

In the meantime, here’s a little mnemonic I’ve whipped up for you

There was once a professor named Muller
whose breakfast could not have been duller.
As his fitness crept down
with a ratcheting sound,
he said, “Man, I could go for a cruller!”

NB: I have also found no evidence that Muller ever lived in Nantucket.

culture, miscellaneous

Google Mall Reviews

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So, this will not come as a shock to those of you who know me, or who have seen me dressed, but I only go shopping for clothes about once a year. This weekend was one of those rare occasions, which meant that I had to look up our local mall on Google (Willowbrook, as featured on How I Met Your Mother).


What I did not expect was to come across a little treasure trove of user reviews. I can’t say why, exactly, but I find the idea of user reviews of a mall charming.

Sic, throughout:

This is like the best mall in the whole state of new jersey,i realy go up there for the ride is like an ahour and fourty something min. But i enjoy the view & i only shop or visit the apple store, like for instence i been waiting for a friend of mine’s to make up his freaking mind to go i been waiting for a weak or more on him, i can’t wait no longer i have to go up there so they can update my ipad2 . But yes sir! The best mall is willow brook mall!!!

I feel suffocated by the largescale consumerism and the mind boggling highway structure that surround this mall. 

Willowbrook Mall is suppose to be ghetto. LOL Also, this mall back in the day used to be good now it pretty much died out. The new hottest (GHETTO)mall in jersey LOL is Garden State Mall.

For comparison, here are a couple of reviews of Garden State Plaza (aka Garden State Mall), which, you may have heard, is the new hottest (GHETTO)mall in jersey LOL.

It’s the best mall in New jersey it has the biggest Johnny Rocket’s and the best Quiksilver and also Timberland is the best store to get your work boots

I rather be at the westchester mall y go to another state shop go truth bullshit of traffic and give them my money when I could spend’it in my owne state ny f.u

 and, for the final word on this most hottest (GHETTO) LOL of malls:

Liked: Hot chicks
Disliked: Service 
science

Copper nanotubes and acronym hilarity

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So, I just learned about this paper via the Twitter. It’s a short piece in the journal Chemical Communications entitled “Electrochemical synthesis of metal and semimetal nanotube–nanowire
heterojunctions and their electronic transport properties.” Nothing to see here, right? Well, the repeated references to copper nanotubes lead to fifty uses of the acronym “CuNT” in the three-page paper.

The paper is by a group of researchers in China, and I can’t quite decide if the lesson here is to run your acronyms past colleagues who are native speakers of various other languages, or if the lesson is to absolutely never do that, lest you should deprive the world of gems like this.

If you’re sufficiently juvenile that you’re still laughing about the copper nanotubes, the School of Chemistry at the University of Bristol has multiple web pages dedicated to molecules with names like “arsole,” “cummingtonite,” and “moronic acid.” Check it out.

via Colin Stewart via Ed Yong.

miscellaneous

They don’t make aristocrats like they used to

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So, today’s Telegraph includes the obituary of Count Robert de la Rochefoucauld, who died at the age of 88. The whole thing is worth reading, and I look forward to the movie version where he is played by Jason Bourne.

After France was invaded by Germany during World War II, Rochefoucauld joined the British Special Operations Executive (SOE), which engaged in various acts of espionage and sabotage during the war. Here are a few highlights from the obituary.

On joining the SOE:

After meeting de Gaulle to ask his permission to join British forces (“Do it,” came the reply. “Even allied to the Devil, it’s for La France.”) La Rochefoucauld began his training early in 1943 at RAF Ringway, near Manchester, where he learned to parachute and use small arms and explosives, as well as how to kill a man with the flat of his hand. 

On one of the two times he escaped execution:

En route to his execution in Auxerre, La Rochefoucauld made a break, leaping from the back of the truck carrying him to his doom, and dodging the bullets fired by his two guards. Sprinting through the empty streets, he found himself in front of the Gestapo’s headquarters, where a chauffeur was pacing near a limousine bearing the swastika flag. Spotting the key in the ignition, La Rochefoucauld jumped in and roared off, following the Route Nationale past the prison he had left an hour earlier.

He smashed through a roadblock before dumping the car and circling back towards Auxerre on foot under cover of night. He sheltered with an epicier. From Auxerre, friends in the Resistance helped him on to a train for Paris, where he evaded German soldiers hunting him by curling up underneath the sink in the lavatory. 

On the other time:

Cycling to Bordeaux to meet a contact who was to arrange his return to England, however, he ran into a roadblock, taken prisoner, and imprisoned at the 16th-century Fort du Hâ. His explanations that he had been out after dark on a romantic assignation were not believed and, in his cell, La Rochefoucauld considered swallowing the cyanide pill concealed in the heel of his shoe.

Instead he faked an epileptic fit and, when the guard opened the door to his cell, hit him over the head with a table leg before breaking his neck. (“Thank Goodness for that pitilessly efficient training,” he noted). After putting on the German’s uniform, La Rochefoucauld walked into the guardroom and shot the two other German jailers. He then simply walked out of the fort, through the deserted town, and to the address of an underground contact.

And loads and loads more. Read it.

via Kottke.

 

 

academia, Ronin Institute

Ronin on the Radio

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So, this is reposted from the Ronin Blog, presented here for you to enjoy in the default Blogger font, rather than the default WordPress font:

Buongiorno Ronineschi!

I had two opportunities to speak on the radio about the motivation and goals of the Ronin Institute this week.

Yesterday, I was on WBUR’s Radio Boston, along with Victoria Blodgett, Associate Dean and Director of Career Services for the Graduate School of Arts and Sciences at Yale. If you’re interested in listening, you can find the segment here.

On Monday, I was interviewed on New Hampshire Public Radio’s Word of Mouth (listen here). The WBUR segment is about 25 minutes, while the Word of Mouth segment is something like 10-12. 

The WBUR segment was called “nice and didactic” on twitter, which I choose to interpret as a compliment.