Sunday, December 30, 2012

Scocca on Toy Gender Apartheid

So, here's an awesome piece to make you feel shitty about whatever you bought your kids for Christmas. Tom Scocca has written an excellent screed about "Toy Apartheid" and the cultural enforcement of gender norms on young children. Here are a couple of highlights:
Christina Hoff Sommers—who has made a nice career in the Boys' Toys section of the opinion-having business by arguing over and over that men have been victimized by feminism—explained to the readers of The Atlantic's website how dangerous this intervention in the toy-marketing business really is. "[N]othing short of radical and sustained behavior modification" can change children's "elemental play preferences," she wrote. And:
The Swedes are treating gender-conforming children the way we once treated gender-variant children.
They are calling them special epithets and beating them up and sometimes killing them? (Also: "Once"? Do tell.) But no, sorry, what she means is that these scheming Nordic elites are trying to modify the poor children's natural behavior. Only they aren't even doing that, really. They're just putting some different photos in the toy ads.
Here, he responds to an anecdote Sommers tells about the time that her granddaughter, when given a toy train, placed it in a baby carriage and covered it with a blanket:
But as the sociologists say: so fucking what? What's the damage if little Eliza wants to rock Baby Train to sleep? Baby Train is snug and warm, and is also an inanimate object. Little Eliza is enjoying herself. Why does her grandmother have to be an asshole about it?
And here is, I think the correct response to anyone who uses anecdotes about children to justify gender conformity as "natural":
Children are stupid and rotten and conformist, and elevating their weakness to a point of pride is insane. Trying to make them to stop being that way isn't confusing or cruel; it's one of the basic duties of being a parent and adult. Any pundit who starts holding forth on the superior behavioral wisdom of small children deserves to be bitten by one.
I miss when he had a regular blog at Slate sooo much.

Wednesday, December 19, 2012

Epigenetics and Homosexuality

So, last week featured a lot of news about a paper that came out in the Quarterly Review of Biology titled "Homsexuality as a Consequence of Epigenetically Canalized Sexual Development." The authors were Bill Rice (UCSB), Urban Friberg (Uppsala U), and Sergey Gavrilets (U Tennessee). The paper got quite a bit of press. Unfortunately, most of that press was of pretty poor quality, badly misrepresenting the actual contents of the paper. (PDF available here.)

I'm going to walk through the paper's argument, but if you don't want to read the whole thing, here's the tl;dr:

This paper presents a model. It is a theory paper. Any journalist who writes that the paper "shows" that homosexuality is caused by epigenetic inheritance from the opposite sex parent either 1) is invoking a very non-standard usage of the word "shows," or 2) was too lazy to read the actual paper, and based their report on the press release put out by the National Institute for Mathematical and Biological Synthesis.

That's not to say that this is a bad paper. In fact, it's a very good paper. The authors integrate a lot of different information to come up with a plausible biological mechanism for epigenetic modifications to exert influence on sexual preference. They demonstrate that such a mechanism could be favored by natural selection under what seem to be biologically realistic conditions. Most importantly, they formulate their model into with clear predictions that can be empirically tested.

But those empirical tests have not been carried out yet. And, in biology, when we say that a paper shows that X causes Y, we generally mean that we have found an empirical correlation between X and Y, and that we have a mechanistic model that is well enough supported that we can infer causation from that correlation. This paper does not even show a correlation. It shows that it would probably be worth someone's time to look for a particular correlation.

As a friend wrote to me in an e-mail,
I found it a much more interesting read than I thought I would from the press it's getting, which now rivals the bullshit surrounding the ENCODE project for the most bullshitty bullshit spin of biology for the popular press. A long-winded-but-moderately-well-grounded-in-real-biology mathematical model does not proof make.

Okay, now the long version.

The Problem of Homosexuality

The first thing to remember is that when an evolutionary biologist talks about the "problem of homosexuality," this does not imply that homosexuality is problematic. All it is saying is that a straightforward, naive application of evolutionary thinking would lead one to predict that homosexuality would not exist, or would be vanishingly rare. The fact that it does exist, and at appreciable frequency, poses a problem for the theory.

In fact, this is a good thing to keep in mind in general. The primary goal of evolutionary biology is to understand how things in the world came to be the way they are. If there is a disconnect between theory and the world, it is ALWAYS the theory that is wrong. (Actually, this is equally true for any science / social science.)

Simply put, heterosexual sex leads to children in a way that homosexual sex does not. So, all else being equal, people who are more attracted to the opposite sex will have more offspring than will people who are less attracted to the opposite sex.

[For rhetorical simplicity, I will refer specifically to "homosexuality" here, although the arguments described in the paper and in this post are intended to apply to the full spectrum of sexual orientation, and assume more of a Kinsey-scale type of continuum.]

The fact that a substantial fraction of people seem not at all to be attracted to the opposite sex suggests that all else is not equal.

Evolutionary explanations for homosexuality are basically efforts to discover what that "all else" is, and why it is not equal.

There are two broad classes of possible explanation.

One possibility is that there is no biological variation in the population for a predisposition towards homosexuality. Then, there would be nothing for selection to act on. Maybe the potential for sexual human brain simply has an inherent and uniform disposition. Variation in sexual preference would then be the result of environmental (including cultural) factors and/or random developmental variation.

This first class of explanation seems unlikely because there is, in fact, a substantial heritability to sexual orientation. For example, considering identical twins who were raised separately, if one twin is gay, there is a 20% chance that the other will be as well.
Evidence suggests that sexual orientation has a substantial heritable component. Image: Comic Blasphemy.

This points us towards the second class of explanation, which assumes that there is some sort of heritable genetic variation that influences sexual orientation. Given the presumably substantial reduction in reproductive output associated with a same-sex preference, these explanations typically aim to identify some direct or indirect benefit somehow associated with homosexuality that compensates for the reduced reproductive output.

One popular variant is the idea that homosexuals somehow increase the reproductive output of their siblings (e.g., by helping to raise their children). Or that homosexuality represents a deleterious side effect of selection for something else that is beneficial, like how getting one copy of the sickle-cell hemoglobin allele protects you from malaria, but getting two copies gives you sickle cell anemia.

It was some variant of this sort of idea that drove much of the research searching for "the gay gene" over the past couple of decades.  The things is, though, those searches have failed to come up with any reproducible candidate genes. This suggests that there must be something more complicated going on.

The Testosterone Epigenetic Canalization Theory

Sex-specific development depends on fetal exposure to androgens, like Testosterone and related compounds. This is simply illustrated by Figure 1A of the paper:
Figure 1A from the paper: a simplified picture of the "classical" view of sex differentiation. T represents testosterone, and E represent Estrogen.

SRY is the critical genetic element on the Y chromosome that triggers the fetus to go down the male developmental pathway, rather than the default female developmental pathway. They note that in the classical model of sex differentiation, androgen levels differ substantially between male and female fetuses.

The problem with the classical view, they rightly argue, is that androgen levels are not sufficient in and of themselves to account for sex differentiation. In fact, there is some overlap between the androgen levels between XX and XY fetuses. Yet, in the vast majority of cases, the XX fetuses with the highest androgen levels develop normal female genitalia, while the XY fetuses with the lowest androgen levels develop normal male genitalia. Thus, there must be at least one more part of the puzzle.

The key, they argue, is that tissues in XX and XY fetuses also show differential response to androgens. So, XX fetuses become female because they have lower androgen levels and they respond only weakly to those androgens. XY fetuses become male because they have higher androgen levels and they respond more strongly to those androgens.

This is illustrated in their Figure 1B:
Sex-specific development is thus canalized by some sort of mechanism that they refer to generically as "epi-marks." That is, they imagine that there must be some epigenetic differences between XX and XY fetuses that encode differential sensitivity to Testosterone.

All of this seems well reasoned, and is supported by the review of a number of studies. It is worth noting, however, that we don't, at the moment, know exactly which sex-specific epigenetic modifications these would be. One could come up with a reasonable list of candidate genes, and look for differential marks (such as DNA methylation or various histone modifications) in the vicinity of those genes. However, this forms part of the not-yet-done empirical work required to test this hypothesis, or, in the journalistic vernacular, "show" that this happens.

Leaky Epigenetics and Sex-Discordant Traits

Assuming for the moment that there exist various epigenetic marks that 1) differ between and XX and XY fetuses and 2) modulate androgen sensitivity. These marks would need to be established at some point early on in development, perhaps concurrent with the massive, genome-wide epigenetic reprogramming that occurs shortly after fertilization.

The theory formulated in the paper relies on two additional suppositions, both of which can be tested empirically (but, to reiterate, have not yet been).

The first supposition is that there are many of these canalizing epigenetic marks, and that they vary with respect to which sex-typical traits they canalize. So, some epigenetic marks would canalize gonad development. Other marks would canalize sexual orientation. (Others, they note, might canalize other traits, like gender identity, but this is not a critical part of the argument.)

The model presented in this paper suggests that various traits that are associated with sex differences may be controlled by distinct genetic elements, and that sex-typical expression of those traits may rely on epigenetic modifications of those genes. Image:
The second supposition is that the epigenetic reprogramming of these marks that normally happens every generation is somewhat leaky.

There are two large-scale rounds of epigenetic reprogramming that happen every generation. One occurs during gametogenesis (the production of eggs or sperm). The second happens shortly after fertilization. What we would expect is that any sex-specifc epigenetic marks would be removed during one of these phases (although it could happen at other times).

For example, a gene in a male might have male-typical epigenetic marks. But what happens if that male has a daughter? Well, normally, those marks would be removed during one of the reprogramming phases, and then female-typical epigenetic marks would be established at the site early in his daughter's development.

The idea here is that sometimes this reprogramming does not happen. So, maybe the daughter inherits an allele with male-typical epigenetic marks. If the gene influences sexual orientation by modulating androgen sensitivity, then maybe the daughter develops the (male-typical) sexual preference for females. Similarly, a mother might pass on female-typical epigenetic marks to her son, and these might lead to his developing a (female-typical) sexual preference for males.

So, basically, in this model, homosexuality is a side effect of the epigenetic canalization of sex differences. Homosexuality itself is assumed to impose a fitness cost, but this cost is outweighed by the benefit of locking in sexual preference in those cases where reprogramming is successful (or unnecessary).

Sociological Concerns

Okay, if you ever took a gender-studies class, or anything like that, this study may be raising a red flag for you. After all, the model here is basically that some men are super manly, and sometimes their manliness leaks over into their daughters. This masculinizes them, which makes them lesbians. Likewise, gay men are gay because they were feminized by their mothers.

That might sound a bit fishy, like it is invoking stereotype-based reasoning, but I don't think that would be a fair criticism. Nor do I think it raises any substantial concerns about the paper in terms of its methodology or its interpretation. (Of course, I could be wrong. If you have specific concerns, I would love to hear about them in the comments.) The whole idea behind the paper is to treat chromosomal sex, gonadal sex, and sexual orientation as separate traits that are empirically highly (but not perfectly) correlated. The aim is to understand the magnitude and nature of that empirical correlation.

The other issue that this raises is the possibility of determining the sexual orientation of your children, either by selecting gametes based on their epigenetics, or by reprogramming the epigenetic state of gametes or early embryos. This technology does not exist at the moment, but it is not unreasonable to imagine that it might exist within a generation. If this model is correct in its strongest form (in that the proposed mechanism fully accounts for variation in sexual preference), you could effectively choose the sexual orientation of each of your children.

Image: Brainless Tales.
This, of course, is not a criticism of the paper. The biology is what it is. It does raise certain ethical questions that we will have to grapple with at some point. (Programming of sexual orientation will be the subject of the next installment of the Genetical Book Review.)

Plausibility/Testability Check

The question one wants to ask of a paper like this is whether it is 1) biologically plausible, and 2) empirically testable. Basically, my read is yes and yes. The case for the existence of mechanisms of epigenetic canalization of sex differentiation seems quite strong. We know that some epigenetic marks seem to propagate across generations, evading the broad epigenetic reprogramming. We don't understand this escape very well at the moment, but the assumptions here are certainly consistent with the current state of our knowledge. And, assuming some rate of escape, the model seems to work for plausible-sounding parameter values.

Testing is actually pretty straightforward (conceptually, if not technically). Ideally, empirical studies would look for sex-specific epigenetic modifications, and for variation in these modifications that correlate with variation in sexual preference. The authors note that one test that could be done in the short term would be to do comparative epigenetic profiling of the sperm of men with and without homosexual daughters.

As Opposed to What?

The conclusions reached by models in evolution are most strongly shaped by the set of alternatives that are considered in the model. That is, a model might find that a particular trait will be selectively favored, but this always needs to be interpreted in the context of that set of alternatives. Most importantly, one needs to ask if there are likely to be other evolutionarily accessible traits that have been excluded from the model, but would have changed the conclusions of the model if they had been included.

The big question here is the inherent leakiness of epigenetic reprogramming. A back-of-the-envelope calculation in the paper suggests that for this model to fully explain the occurrence of homosexuality (with a single gene controlling sexual preference), the rate of leakage would have to be quite high.

An apparent implication of the model is that there would then be strong selection to reduce the rate at which these epigenetic marks are passed from one generation to the next. In order for the model to work in its present form, there would need to be something preventing natural selection from finding this solution.

Possibilities for this something include some sort of mechanistic constraint (it's just hard to build something that reprograms more efficiently than what we have) or some sort of time constraint (evolution has not had enough time to fix this). The authors seem to favor this second possibility, as they argue that the basis of sexual orientation in humans may be quite different from that in our closest relatives.

On the other hand this explanation could form a part of the explanation for homosexuality with much lower leakage rates.

What Happened with the Press?

So, how do we go from what was a really good paper to a slew of really bad articles? Well, I suspect that the culprit was this paragraph from the press release from NIMBios:
The study solves the evolutionary riddle of homosexuality, finding that "sexually antagonistic" epi-marks, which normally protect parents from natural variation in sex hormone levels during fetal development, sometimes carryover across generations and cause homosexuality in opposite-sex offspring. The mathematical modeling demonstrates that genes coding for these epi-marks can easily spread in the population because they always increase the fitness of the parent but only rarely escape erasure and reduce fitness in offspring.
If you know that this is a pure theory paper, this is maybe not misleading. Maybe. But phrases like "solves the evolutionary riddle of homosexuality" and "finding that . . . epi-marks . . . cause homosexuality in opposite-sex offspring," when interpreted in the standard way that I think an English speaker would interpret them, pretty strongly imply things about the paper that are just not true.

Rice, W., Friberg, U., & Gavrilets, S. (2012). Homosexuality as a Consequence of Epigenetically Canalized Sexual Development The Quarterly Review of Biology, 87 (4), 343-368 DOI: 10.1086/668167

Update: Also see this excellent post on the subject by Jeremy Yoder over at Nothing in Biology Makes Sense.

Tuesday, December 11, 2012

Having your awesomest grad school experience

So, welcome back for the third installment of me dispensing advice that no one asked for. Previous advice included two guides, the first to help you decide whether or not you should go to graduate school, and the second to help you to pick a program (and advisor).

Now, let's fast forward to the point where you're in grad school, and you're thinking to yourself, "I wonder what advice that nice young Jon Wilkins would have to help me get the most out of grad school, now that I'm here and all."

Well, you're in luck, because here it is:

The Lost in Transcription Guide to Having Your Awesomest Grad School Experience Ever: A Guide

I'm going to assume that you're already familiar with the basics here. You already know that grad school is hard work, that it requires dedication and creativity and the ability to maintain the veneer of work-life balance. In fact, I'll assume that you have already mastered the seven habits of highly effective people (list-making, delegation, pretending to pay attention during meetings, not hitting Reply All, fiber, shaking the toner cartridge, and Adderall). Rather, I'm going to let you in on the stuff that I was told, or figured out, that applies specifically to grad school and might not be obvious.

1. Attend Talks, but not too many

If you're at a large university, you'll find that there are a crap ton of talks. There are departmental seminar series, topical seminar series, special colloquia, journal clubs, lab meetings and on and on. You could easily spend all of your time going from talk to talk.

The more likely outcome is that you will be so overwhelmed that you will avoid going to talks altogether.

This is a mistake. When you're deep in your research, it will always seem like whatever you're working on is more valuable than some talk. In the short term, that's probably right. Attending talks is part of the long-term game. You go to talks with the hope that they will plant a seed in the back of your mind. That seed might not grow into anything for years. But eventually, when the time is right, it will blossom into a beautiful, original idea.

You will then harvest that beautiful idea and drain all the beauty out of it as you grind it up to fit it into a grant proposal.

One great piece of advice I received was to pick one seminar series (maybe a different one each semester) and go to every talk in the series. This forces you to stretch a little bit, attending some talks you might otherwise skip, while keeping a lid on the total number of talks.

Critically, don't pick more than one series. You'll still probably find another talk or two each week that you go to for various reasons. Maybe someone famous is speaking, or maybe the talk is closely related to your work, or maybe your advisor is worried that there won't be enough people in the audience, or maybe that cute boy from your stats class is going to be there. Ha ha, I'm kidding, of course. There are no cute boys in your stats class.

If you find yourself going to more than three talks a week, you should either raise your standards or paint eyeballs on your eyelids, because there is no way you're staying awake through all that.

2. Ask Questions

When you're going to the too many talks that you go to, because you are ignoring my earlier advice, try to make yourself ask a question. You don't need to ask a question every time. I mean, you don't want to be that guy. But set hard goals for yourself, like, if you didn't ask a question at the last talk, you have to ask something at this one.

The point here is not to draw attention to yourself, or to make sure that your advisor knows you are at the talk. (If this is important, you've chosen the wrong advisor.)

One very tangible benefit of asking questions in talks is that it keeps you awake. Even if you are in a field where people hold all of their questions till the end, pressing yourself to come up with a good question is a great way to keep yourself engaged.

The other thing asking questions does is help you to start thinking of yourself as a peer in your field. This is maybe the most important transformation you will undergo as a graduate student. As an undergraduate, you probably functioned mostly as a receptacle (for knowledge and/or beer). By the time you receive your PhD, you should be comfortable functioning as a real member of the scholarly community. When you start grad school, you probably view your advisor, and all professors, as some other species. By the time you finish, you should view them as an older, more experienced (and, in my case, better looking) version of yourself.

A lot of grad students feel like they should not ask questions during talks because they should leave that to the people who know more. That's not peer thinking.

Also, like Big Bird says, asking questions is a good way to find things out!

If you're having trouble coming up with questions, consider developing some questions that work in any talk. For example, if you work in Theoretical Ecology, try "What happens if you put that on a lattice?" If you're in Statistical Physics, try "What happens if you substitute one of the generalized forms of entropy?" If you're in Evolutionary Psychology, try "How does that correlate with the 2D:4D digit length ratio?" I'm certain that you can come up with the analogous question for your own field.

3. Decide when to Graduate

In some systems, like in the UK, there is a standard PhD length. In the US, however, the PhD tends to be more of an open-ended affair. It might take three years, or it might take ten. If you ask how long your PhD should take, the answer will probably be some variant of "as long as it takes to complete your dissertation."

The secret is that there is no rule about what constitutes enough work to qualify as a dissertation.

There might be standards and norms. For instance, in my field, the rule of thumb is that you write three papers. Then, you write and introduction and a conclusion, staple them all together, and you're done. But I have known people who have graduated with as many as ten papers, and as few as zero. Some advisors or departments might have stricter guidelines, but even in those situations, you probably have some say in when you graduate.

The advice I was given was this: Decide when you want to finish. Then, a couple of years before that, start talking about this as your graduation date. Soon, everyone will be convinced that you should actually finish then, including your advisor, and, more importantly, yourself. Next thing you know, you're staying up all night to meet this totally artificial deadline. Moreover, however much work you have accomplished by that point (within limits), your committee is going to look at it and say, "Um, I guess that looks like a dissertation."

So, how do you decide when to graduate? Well, it depends in part on what you want to do next. If you want to go on in academia (or an analogous, high-end research career), you want your CV to kick ass. You want to have good publications and something that looks like momentum moving forward.

That means you should not graduate too soon. There's a weird thing. People tend to judge your CV by your rate of productivity: papers per year, or years per book, or something like that. But this rate-based evaluation does not kick in until after you get your PhD. In my experience, the person who published four papers during a three-year PhD comes off as only marginally more impressive than the person who published four papers during a seven-year PhD. Similarly, the seven-year, five-paper candidate often outshines the four-year, four-paper candidate.

On the other hand, grad school might convince you that you want to do something different. Maybe you'll want to switch fields, or go into industry, or leave research altogether. Maybe you're going to go into science writing, or go back to Law School and work in patent law. If you're following one of these paths, the most important thing is going to be the fact of your PhD. If you graduate without publishing, it might make your ascent up the academic career ladder more difficult, but it won't prevent you from forcing people to call you "Doctor" at parties.

Only good taste can do that.

4. Avoid the Lobster Pot Mentality

Academia is competitive. I mean, it would be really cool if we all got sinecures that let us work on whatever we wanted, and if we all wanted to work on things that were different enough that no one ever got scooped, but related enough that we could all collaborate in some sort of glorious transdisciplinary daisy chain.

Sadly, the reality is that there are limits to all of the resources most coveted by academics: jobs, grants, awards, prestige. If you continue on in academia, you're going to spend the rest of your career competing with your peers for money, space, and recognition.

Here's the thing, though. You don't need to start stabbing people in the back yet.

It is easy in graduate school to let your horizon shrink. Sometimes it will feel like you need to be competing with the other grad students in your program for everything: grades, attention, approval.

Avoid this impulse as much as you can. Your peers from grad school are going to be some of your best friends in your life, and they are going to be your closest allies in your career. Years from now, they're the ones who are going to suggest your name when someone in their department is assembling a list of speakers for a symposium. They're going to tend to give you the benefit of the doubt when they're reviewing your papers or grant proposals.

Sure, maybe it sucks to feel like your advisor's second best student. Just remind yourself of the long-term benefits. Someday, that best student is going to be your best opportunity for name dropping. "Oh, yeah, I went to grad school with her. Why yes, I am pretty cool. Thank you for noticing."

5. Don't Learn a Skill

You might think that learning a skill is the whole point of grad school. You would be wrong. The point of grad school is to learn to be a scholar. A danger, especially in the experimental sciences, is in focusing on developing a set of technical skills at the expense of the conceptual skills that lie at the core of what you need to be learning.

I mean, sure, it's really cool that you've mastered using this multi-million dollar piece of equipment, and maybe you've even gotten some cool results out of it. But there are two specific dangers here.

First, technology changes. No matter how cool that machine is, a few years from now it is going to be obsolete. If your expertise is really wedded to the machine, you become obsolete as well. However, if you can keep your eyes on the forest, you will have learned a much more valuable set of skills about how to pose and answer interesting questions. Those skills will transfer over to the next generation of technology just fine.

Second, if you have an unscrupulous advisor, you can find yourself painted into a corner, spending your grad school years effectively as an underpaid laboratory technician. In fact, I have seen cases where a grad student will master a particularly fickle piece of equipment. That grad student then becomes a critical resource for the lab, and their advisor will delay their graduation, so that they can keep milking that piece of equipment for data. Worse yet, you can get stuck being a sort of data mule, playing second fiddle on projects for other students and postdocs, at the expense of developing your own research program.

6. Don't Be a Helper

Look, if you've gone to grad school, you probably have certain personality traits. You've probably got an impulse to respect authority, and you've always liked to please your teachers. This is part of how you got those good grades.

Some grad students tend to take this to extremes, and fall into a "helper" role. This could mean taking on part of your advisor's teaching load. It could mean acting as a sort of lab mom/dad. No doubt, your advisor feels overworked and stressed out. If you take some of their stuff off of their plate, they will probably be grateful, and will praise the crap out of you. In general, though, this is not healthy for your own career.

This depends, of course. For example, if your long-term goal is to work at a small college where you mostly teach, taking on additional teaching in grad school might be a good thing. However, you need to make sure that you are getting the credit for it.

7. Be the Youiest You You can Be

Yes, really.

Grad school tends to have a homogenizing effect. Sometimes this is okay. Some things really need to be homogenized, like how we format our bibliographies, or we calculate our p values. However, there are also a lot of things that get homogenized that really don't need to be.

More specifically, don't get caught up in other people's definitions of success. Just because everyone else in your lab wants to get that prestigious postdoc at Johns Hopkins does not necessarily mean that this is what you want.

Also, develop your own interests. People tend to converge on a narrow definition of what constitutes an "interesting" question in their field. This leads to situations where everyone is racing to answer the same question. If you have a different perspective, embrace it. You're much more likely to do something truly original that way.

Even if you're wrong, and the question that everyone else is asking really is more important, you should still follow your own interests. The fact is, you are going to do more good for the world working on something that you're passionate about, even if that something is objectively dumb. So go for it.

Yes, go ahead and get that pierced.

No, I'm not going with you.

Friday, December 7, 2012

Scholarship quotation

So, I've started reading Mr. Timothy by Louis Bayard. No spoiler alert necessary, since I'm only on page 36, but I did want to share this:
This, I believe, is the mark of a true scholar: to be unfazed by the world's skepticism.

Saturday, December 1, 2012

2012 Gift Guide for Population Geneticists

So, it's that time of year again, when you have to come up with gift ideas for the population geneticist in your life. Personally, I like cash, but if you insist on coming up with personalized gifts, here are some ideas for you:

1. Mathematical Population Genetics, by Warren Ewens

This book was originally published in 1979. When I was in grad school, it had been out of print for years. People would pass around xeroxed copies that had been made from other xeroxed copies.

Finally, a couple of years ago, the second edition came out. So now the population geneticist in your life can own their very own book-shaped copy.

Of course, it's a little bit pricey. Fortunately, there are plenty of other gifts on this list for the folks about whom you don't care enough to buy this book. :(

2. The Gospel of the Flying Spaghetti Monster, by Bobby Henderson

Okay, cheapskate, maybe this is a little bit more your speed. This is the perfect gift for the pastafarian population geneticist.

Or it could be a good evangelical gift for those who have not yet been touched by his noodly appendage.

And look, it comes with one of those little ribbon things that means you don't have to use your wadded up Starbucks receipt as a bookmark!

3. Gene Pool Shirt

Get it?

It's a jean shirt!

With a pool ball on it!

Great conversation starter!

Also comes in Flaming 8-Ball!

4. Obnoxious Car Decals

There are a number of different aggressively obnoxious things that you can get for your car, like a T-Rex eating a Jesus fish. But if your goal in life is to get your headlights smashed by some nice religious folk, nothing will beat this "Procreation Car Emblem."

If you're in the mood for something a little more subtle, there are some good options in the "Customers who bought this item also bought" section.

5. Remarkable, by Lizzie Foley

Okay, okay, I know what you're thinking. That this is shameless promotion of my wife's book, and has nothing to do with population genetics.

Yes, fine, it's shameless, but it's a great book, perfect for the population geneticist with one or more F1s a home (ages 8 and up!). And it does feature a cameo appearance by population geneticist and UCLA Professor John Novembre. For reals!

Also, the story features boy and girl identical twins. So, analyze that.

6. DNA Earrings

What's that?

I can't hear you.

I've got DNA in my ear.

7. DNA Portraits

Okay, check this out. You send in a swab of DNA, and $199, and they'll send you a giant picture of a gel, which is I guess is supposed to be some fraction of your genome? Maybe? It looks like there are supposed to be eight sample lanes, and it's that old-school sequencing analysis where each dideoxynucleotide terminator gets its own lane. So this might be about forty bases of sequence. Maybe?

To be honest, though, this looks a lot more like a protein gel to me. Maybe they use your DNA, clone a little tiny homunculus of you, grind it up, trypsin digest it, and this is that gel.

If that wasn't bad enough, you also have the option of getting your DNA made into a giant QR code poster (that no one will ever scan).

For the money, I'd go with two copies of the Ewens book.

8. Personalized Genetic Analysis

The classic here is 23 and Me.

Okay, maybe you're thinking, no, a real population geneticist would not want one of these goofy personalized genetic analysis things. Those are for amateurs, mere heredity enthusiasts. Will my population geneticist friend be offended by the ridiculous pinpointing of their Y-chromosome and mitochondrial ancestry, or the ridiculous breakdown of racial composition, or the ridiculous risk-factor analysis?

Well, that's the beauty of this gift. If they are the wild-eyed, naive sort of population geneticist, they're just going to be so gosh-darned excited to get all that cool information. If they're the bitter, cynical sort of population geneticist (most of them, in my experience), you'll be giving them the gift of feeling knowledgable and superior!

If you want to surprise them, order the kit and swab their cheek while they're sleeping.

If you really want to surprise them, order a second kit, swab a random guy, get the results, and claim that the results are from their father.

9. Darwin Eats Cake Stuff

Yeah, you thought plugging my wife's book was shameless? I'll show you shameless! Check out these new items from the official Darwin Eats Cake store:

Look! It's a mug illustrating the academic funding cycle: papers->money->caffeine->papers.
Also works for non-population-geneticist academic types.

Look! It's a trucker hat featuring Guillaume the Adaptationist Goat's credo!

Look! It's a t-shirt featuring J B S Haldane's moustache in a jar!

Don't see anything you like? You can check out the comics and contact the "artist" here to submit special requests.

10. Ronald Reagan Riding a Velociraptor with a Machine Gun

Okay, so this one really has nothing to do with population genetics, but it is 100% pure awesome.

Prints available in 11x17 or 24x36 from SharpWriter at deviantART.

Other ideas? Leave them in the comments.

Bad Kid Jokes

So, here's a Tumblr that will entertain you for a while. According to its creator
I moderate jokes on a Kids Jokes website. A lot of joke submissions can't be published because they're offensive (to kids, or to parents who would hear them repeated at home), or they don't make sense... so I publish them here instead. I have not edited or made up any of these jokes.
Some of them are genuinely offensive in a way that seems to dovetail nicely with the spelling. Many, however, are pure joy. Here are a few samples
What does your mum need to make her fase very dirtey
SHE needs to go in the bin 474844747474747474474747474 times
knock knock
my penas and butt
what happens when you eat 100 tacos and 500 foooodz?
mum; we can eat camels you know honey
When I was young I used to pray for a bike, then I realized that God doesn’t work that way, so I stole a bike and prayed for forgiveness.
why did mr potateo run from the cops? because he killed mrs carrot face and robbed mrr broccili pants.
Enjoy (via Boing Boing)

Wednesday, November 28, 2012

Where Should YOU go to Grad School? A Guide

So, you've come here because you read the Lost in Transcription Guide to Whether or Not YOU Should go to Graduate School, and, at the end of having read said guide, you (YOU) concluded that yes, you (YOU) would give grad school a whirl.

Now you're looking down the barrel of grad school applications and trying to decide where to apply.

Or maybe you're looking down the much happier barrel of multiple grad school acceptances and trying to decide where to go.

[Already decided? Jump to this guide on how to do grad school like a boss!]

Well, luckily for you, Lost in Transcription is here for you with

The Lost in Transcription Guide to Where YOU Should go to Graduate School

Okay, let's start with the disclaimer. This guide will be most directly relevant to people looking at grad schools in the US and in the sciences. However, many of the considerations will be at least partly applicable more broadly.

Consideration 1: Reputation

In academia, just as in a pre-Joan-Jett Main-Street America, reputation matters. But what reputation, exactly? Is it your university, your department, or your advisor? And how much does it matter?

Look, in an ideal world, your prospects after grad school would be determined by the quality of your work. And yes, that is the most important thing. But the fact is, when you apply for a postdoc or a job, the people who are going to be reading your CV and your lovingly crafted research description are mind-bogglingly busy. They are also all flagrant (if sometimes closeted) Bayesians. They are going to look at where you went to school and who your advisor was, and they are going to construct a mental picture of you.

Yes, it sucks. And it is a bunch of crap. But the reality is that most academics, in addition to being overly busy, are ridiculously status conscious. So, while this shouldn't be your primary consideration, it should probably factor in. As unfair as people's biases and preconceptions (sometimes) are, you want to do what you can to be on the right side of them.

Of course, what I am calling "reputation" here is going to be at least reasonably well correlated with "quality," which is a perfectly legitimate consideration. If you go to a higher quality program, you will tend to have smarter colleagues, better classes, and a broader and more interesting set of advisors and projects to chose among. Unless you have a seriously unhealthy big-fish-in-small-pond fetish, you're going to want to be surrounded by the highest-quality people and resources you can find. You'll be more challenged to push yourself, and you'll learn more.

But let's get back to the question of which aspect of quality/reputation you should focus on. For undergraduates, the most important consideration is the reputation of the school as a whole. For postdocs, it is probably the reputation of the individual advisor. As a graduate student, both of those matter, but the most important reputation by far is that of the department.

If you go to a top-notch department at a university that is otherwise known primarily for its binge drinking, you're golden. We have a collective societal ranking of the prestige of various universities that is fairly well reflected in things like the US News and World Reports rankings. Most people have a sense (rightly or wrongly) that Stanford outranks Lehigh, and that Michigan outranks UNLV when it comes to academics. But in the world of grad school and beyond, those rankings, the ones we all know, really don't matter that much.

Every field will have its own ranking of schools and departments, and it is this ranking that will shape your experience and job prospects. For example, it is fairly common for large state universities to have a few "flagship" departments where they focus a lot of resources. These departments are every bit as good as the best departments at the most prestigious universities.

That is, don't go to Harvard just because it's Harvard. (And don't go to Yale just because you didn't get into Harvard -- Snap!) The prestigious universities are prestigious not because their good departments are better than the good departments elsewhere. They are prestigious because they have a larger number of good departments. But in grad school, you're really going to be in one department. If you're a molecular biologist, the presence of Nobel Memorial Prize winning economists on campus is not going to impact you much.

The only place where having gone to a prestigious school (as opposed to a quality department) is going to help you is in name dropping at cocktail parties. However, there is a much easier way to impress people at cocktail parties: don't be the jackass who is always telling everyone where they went to school.

You can easily find rankings of various departments online, and this is worth doing, just to get a sense of the lay of the land. You can also look up the faculty in the corresponding department at a few different colleges and universities. See where they went to grad school. If you have a strong sense of where you want to wind up, focus on that sort of place. For example, if you think that you would really like to teach at a small liberal-arts college, look up faculty at small liberal-arts colleges.

Most importantly, ask around. Make appointments with professors and ask them for a list of good departments. Ask your TAs. If you know someone who knows someone, ask them to put you in touch. I know it might feel like you are imposing on their time, but you're really not. Academics love ranking things, and they love love love passing judgement. Asking an academic to rank the departments in their field is like asking a normal person to judge a wet t-shirt contest. So don't be shy.

The final thing, though, is to make sure you don't take the details of those rankings too seriously. At the end of your research, you want to have a sense of what schools have quality departments, but there will be no legitimate sense in which the number three department on your list is objectively and quantifiably better than the number six department. Your goal should be to assemble an unordered list of "good" places. Then, if you are accepted into more than one of them, let these other considerations guide you.

Consideration 2: Your Advisor

This is important. Graduate school, and academia more generally, is built on this weird feudal system that more closely resembles the medieval system of guilds than anything else. Your advisor will hold tremendous sway over your life during graduate school, and over your career trajectory when you finish.

Why are we covering this here, though? We're supposed to be picking a school not an advisor.

Well, depending on your field, as well as on the school you wind up at, the two choices might go together. At some places, you may be accepted by the department, and then have the opportunity to get to know various faculty members before committing to one. In some cases, though, you will be accepted directly to work with a specific advisor, or at least provisionally, so that it would require a bit of effort to change.

Either way, it's an important part of the decision process.

The game here is not to find the best possible advisor. The game here is primarily one of "Do No Harm." There are a lot of advisors who are going to be good enough. And the fact is, you are not going to spend nearly as much time with your advisor as you probably think you are.

There are a few advisorial archetypes that you particularly want to avoid. Note that these are not mutually exclusive.

1. The Narcissist
This is a remarkably common personality type among academics. In many fields, particularly in the sciences, the "productivity" of senior researchers is actually measured by the productivity of the people who are working under them. In a lot of experimental sciences, in particular, faculty members write papers and grants and manage lab personnel, but may not have been engaged in hands-on research themselves for years.

That means that your advisor's success is tied up with your success. Fundamentally, this is a good thing, as you are both pulling in the same direction. At some point, though, your interests and your advisor's interests will begin to diverge. It is at this point that, if your advisor is a narcissist, you are totally screwed.

If your career is not prestigious enough, the narcissistic advisor will be pissed off because you have embarrassed them. If you are successful, well, at some point, you are going to become one of your advisor's competitors. Either way, they are going to turn on you.

The key to rooting these people out is to ask them about their former students. Ideally, you want the advisor who comes off like the proud grandma or grandpa when they're talking about their fledged advisees. Do they seem to talk about them as if they were people? Or do they seem more like statistics and trophies?

2. The Best Friend
Now, on its surface, this seems like someone you should want as an advisor, right? It is also the sort of advisor that everyone thinks they want to be. The problem is, the vast majority of us need an advisor who is willing to hold our feet to the fire a little bit. Grad school will probably be the most unstructured thing you have done in your life. Most people struggle a bit with learning the tricks of motivation, focus, and self control that are required to make good academic progress. While you're trying to learn these things, you don't want an advisor who is all, "What? You're spending this week at home in your pajamas watching TV? Just like last week? That's cool. See you whenever."

You need an advisor who has enough authority and emotional distance from their students that they can say, "You know what, you need to do this over. At this point, it's just not good enough." Yes, it totally sucks to have someone tell you that, especially when that person is your boss. But the thing that sucks even more is when no one ever tells you that, and you wind up being completely unemployable because you never learned how to do rigorous, high-quality work.

3. The Slave Driver
This is the flip side of the best friend, of course. You really do want an advisor who will push you, but not one who will be controlling and abusive. One thing to look for is a distinction between quality and quantity.

Some groups have a culture where students and postdocs feel they need to be seen in the lab. They will work in the lab on Saturday in the hopes that their advisor comes in and sees how industrious they are being. You hear some professors talking about wanting to be able to look at their lab at 10 pm on a Friday and see all the lights on. If students are trying to hide their hobbies from their advisor, out of a fear that having other interests will make them look lazy, this is a bad advisor.

4. The Pre-Retiree
Some time in their careers, most academics reach a point where they're just, like, "Fuck it." For some people this happens the day after they get tenure. (NB: These people are in the minority, but are well on their way to ruining tenure for everyone else.) For most people, it happens much later though, and within a few years they go emeritus. The trick is not going to work with someone who is still in that window between intellectual retirement and actual retirement.

This is especially dangerous in the case of famous, well respected senior researchers. The idea of working with a living legend can be incredibly attractive. But if they have lost interest in their research, then they are going to be shutting down their group, if they have not already begun to do so. They won't be taking more students, so your life will get lonelier and lonelier. Also, there's this dangerous path where you wind up abandoning your own research and editing their memoirs.

5. The Letch
This, I think, is much less of a problem than it used to be, but it is certainly still there. Most universities now have sufficient protections in place that if you have trouble with sexual harassment, you can probably find a fair amount of support. Also, I think that our culture has evolved enough that most of your fellow students will also tend to be supportive. But none of that is going to make a harassment situation not horrible. And if the harassment is from your advisor? Well, best case scenario, you probably wind up switching advisors, and maybe losing a year or two. Basically, avoid at all costs.

How to avoid this, though. Basically, you want to rely on the rumor mill. That doesn't mean that you have to take every rumor about every professor at face value. But you should absolutely not fall for the old, "You shouldn't spread rumors. Nothing was ever proven. It's so unfair to sully his name." bullshit.

Talk to grad students who have been around the department for a few years. Talk especially to students in other groups. Ideally, talk to them at some sort of social event where there is alcohol involved. Grad students actually love to gossip.

Of course, it is possible that there will be a story out there, and that a particular faculty member will have been accused of something, but will, in fact, be blameless. If you hear a specific story, ask around some more. If there's another side, someone will probably give it to you. If no one in the department offers any sort of defense of the professor, that does not necessarily mean they're guilty. But it does mean that no one likes them enough to defend them, which is a data point in its own right.

If there is more than one story, run.

And before you start quoting some "innocent until proven guilty" nonsense, recall that choosing to work with a different PhD advisor is not the same thing as putting someone in prison. You have every right to err on the side of caution.

So those are a few of the advisors you don't want to work with, but what are the positive traits that you can look for in an advisor?

1. Are their students happy?
And by this, I don't mean rolling-into-the-lab-at-noon-still-drunk happy. I mean, are they optimistic and enthusiastic about their projects? The ideal lab will have people who are eagerly working long hours, not because they are scared of their advisor, but because they can't wait to get the results of their experiments. Part of this is going to be driven by the mix of students and postdocs who happen to be there, but part of it will be a reflection of the advisor's managerial style. If you can find a lab like this, jump at the chance to join it.

2. Do you connect?
It is not as simple as there being good advisors and bad advisors. A lot of it is about a match between you and them. Are you snarky and sarcastic? Don't go with a super-earnest advisor, no matter how much everyone talks about how nice they are. Are you thin-skinned? Don't go with the gruff professor, even if they do have a heart of gold.

3. Do they have a plan?
A good thing to ask a potential advisor is how they imagine your grad career being structured. The details of their answer are not necessarily that important. There are many paths to a successful PhD. However, if they don't have any ideas, that should raise a red flag.

4. Where do their students go?
With the exception of very new faculty, you can look at a potential advisor's track record. What have their students gone on to do? Remember, there is no one right answer here. If all of their students go on to be professors at major research universities, that's great -- so long as you are sure that you want to go on to be a professor at a major research university. It might also mean that if you decide you want to go into science writing, you're going to catch hell.

In my view, the ideal track record would have a majority of people who have gone on to successful, traditional academic careers, but also people who have gone on to do other things. Perhaps most important, though, is how the advisor talks about their non-traditional students. Do they seem ashamed and embarrassed? If so, that's maybe a problem. Even if you think you want a traditional career right now, who knows what you'll think in five years. Make sure you find an advisor who will support whatever path you choose to follow.

Consideration 3: Your Project

This seems really important, right? I mean, what you actually work on for your PhD has got to be one of the most critical considerations, right?


Wrong wrong wrong wrong wrong.

This might actually be the least important consideration. Sure, you can factor it in if you want, but you should rank it somewhere below the quality of the linoleum in the hallways.

Remember that thing that people say about undergraduate education, that what you're really doing is "learning how to learn"? Well, grad school is sort of like that. The most important thing you do in grad school is learn how to be a researcher.

When you break it down, doing independent research actually takes a lot of different skills. You learn how to read up on a topic, teaching yourself what the state of the art is. You learn how to identify an interesting open question. You learn how to pose that question (or some aspect of that question) in a way that you can answer it in a reasonable amount of time. You learn to actually do the research. You learn how to write about your research clearly. You learn how to speak about it clearly. You learn how to respond to challenges and criticisms, both in person and in writing. You learn how to identify when a project is a dead end. You learn how to salvage what you can and apply it to the next question.

The thing is, of all of those skills, "doing the research" is the only one that is specific to your particular project. Everything else in the list will transfer over, even if you completely change fields.

Let's say grad school takes an average of about six years. It is typically the case that 90% of the stuff that goes into your thesis will be things you do in the last year and a half. That's because most of what you're learning is how to be a researcher. Once you get that down, you do a little research, write it up, and graduate.

So what happens if you finish your PhD and decide that you want to work on something different? Well, you change. In fact, lots and lots of people make big shifts in what they work on when they do a postdoc. Obviously, if you switch fields, you're going to have to spend some time learning the new one. The thing is, while it took you four years to learn what you did about your field in grad school, once you've finished, you'll be able to accomplish the same thing in a new field in like six months. In part, you will have developed an intuition for how to zero in on the relevant information in the literature. In part, you will have learned how to stop yourself from playing Halo when you're supposed to be reading papers.

The point is this: Maybe you have strong opinions about what you want to research. That's cool. But the fact is, you know almost nothing. Most likely, this thing you want to research is one of a very small number of things you've been exposed to.

Maybe you had a positive experience working in a insect biomechanics lab for a semester. Or maybe you had a really hot TA in a your evolution class, and he/she works on insect biomechanics. And now you think that insect biomechanics is the most important topic in biology, and that working on it is your life's calling.

I want to offer you an alternative explanation. What you have actually learned about yourself is that you can get excited about academic research. In all likelihood, you would have had a similar response to any number of topics. So keep your mind open. Find a program that makes you happy, and one day you will be the hot TA.

If, after finishing your PhD in yeast senescence, you still think that insect biomechanics is the bees' knees (see what I did there?), go do a postdoc in it. You might even find that some of the things you learned about yeast give you an interesting new perspective on the insect biomechanics problem.

Consideration 4: Location

Unless you completely ignore consideration number 2, you are not going to spend all of your time working in your advisor's salt mines. Don't get me wrong. Graduate school tends to be pretty all-consuming. And there are some people who seem perfectly happy with spending basically all of their time at the lab (or the library, or the steam room, or whatever).

Personally, though, I'm a fan of a more process-based perspective. Remember, grad school is not just five (or seven, or nine) years on your way to a stressful career, it is five years of your life. If you have outside interests that you love, I think it would be a mistake not to take those into consideration.

If you love skiing, and there is a good program in your field in Colorado or Utah, that is a perfectly legitimate consideration. If you can be happy on the weekends, it will help to carry you though the dark time in your fourth year when you realize that your entire thesis has been built on a faulty assumption. (Yes, this will happen. Just think of it as the Kobayashi Maru part of your PhD training.)

The thing that I would discourage you from, though, is a vague sense of regional loyalty. You know, like where you've always lived on the West Coast, so you're only going to apply to West Coast schools.

All you're really doing here is limiting your own experience. Also, if you are aiming towards an academic career, you're probably going to have to learn to be flexible in where you're willing to live (unless you wind up going Ronin). The academic job market is a national one. In fact, it is increasingly becoming an international one. For many people, the possibility of traveling to and living in a variety of places is one of the appeals of the academic lifestyle. If that is really not attractive to you, think carefully before you commit to this path.

Of course, maybe you have other constraints and considerations that have you anchored to a particular location (like maybe an ailing parent). Obviously, in this case, you should go wherever works, and put all your effort into choosing a good advisor.

Consideration 5: Your Peers

This is easily, in my opinion, the most important factor to consider. Yes, you're going to be doing your own independent research. Yes, you're going to be taking classes from the faculty. Yes, you're going to receive at least some mentorship from your advisor. But whatever you learn in those contexts is going to pale in comparison to what you learn from other graduate students and postdocs.

There are the more senior members of your group, who are actually going to teach you things. If they are nice, and smart, and engaged, you are going to learn a lot more.

There are the other students who come in with your cohort. You are going to spend hundreds and hundreds of hours with these people. You are going to take exams with them. You are going to practice giving talks in front of each other. You are going to drink beer with them (wine if you're in the humanities). You're going to play poker with them. It's reasonably likely that you're going to wind up getting married to one of them. It's even more likely that some of them are going to get embarrassingly drunk at your wedding.

Thirty years from now, these are the people you're going to be connected to via whatever replaces the thing that replaces Facebook.

Of course, you won't be able to pick exactly who your peers are. But a lot of programs have some sort of interview visits or recruiting visits. If you have this sort of opportunity, take it. And don't just look at the program and the faculty. Also look at the other interviewees/recruits. Are there people here with whom you could imagine forging lifelong friendships? If you can't imagine it, maybe this won't be the place for you.


So, young Gradawan, imbued you now have been with all the wisdom required to choose the right graduate program for YOU! Be sure to write in to let me know how it works out!

Tuesday, November 27, 2012

The NY Jets Almost Make Me Want to Watch Football

So, I've never really been a big Football fan ("American Football" for our international readers). But, as a lifelong Chicago Cubs fan, if I were to start following Football, I've found my team in the New York Jets.

Check out this awesome play from this week's Jets game. Jets QB Mark Sanchez tries to carry the ball up the middle, but runs smack into the rear end of one of his offensive linemen, who then falls over backwards and winds up sitting on him. During the collision, Sanchez fumbles the ball, which is returned for a Patriots touchdown.

The official story seems to be that Sanchez was sliding. I've watched this several times, and it really looks more like he was just not paying attention to where he was going. It's like watching pee-wee league, but with 250-pound toddlers (i.e., awesome).

Here's the GIF version of the money shot from Deadspin. I could watch this all day long.

All. Day. Long.

Monday, November 26, 2012

Two new characters at Darwin Eats Cake

So, if you're a regular reader of Darwin Eats Cake, you'll already know that two new characters have been introduced to the strip: R A Fisher's Pipe and J B S Haldane's Moustache.

If you're not a regular reader, you should be, because it will make me happy (and it is, after all, the holiday season), and also because Robert Gonzales once called it "my [meaning Robert's] new favorite webcomic" over at io9.

For those of you who are not population geneticists, or at least evolutionary biologists, Fisher and Haldane are two of the major figures of the "modern synthesis" in evolution in the first part of the twentieth century. This was basically the integration of the Mendelian idea of the gene with the Darwinian idea of gradual change via natural selection. Fisher, in addition, created a whole lot of modern statistics, which have found applications far outside of evolutionary biology.

R. A. Fisher smoking his pipe. Not a euphemism.
J. B. S. Haldane, um, I guess, having his mustache. Note the lack of "o" in the American spelling of mustache.
Fisher loved himself a good smoke. In fact, late in his life, he publicly challenged research purporting to show a causal link between smoking and lung cancer. Oops.

Haldane once chased my former officemate and his mother down the street in a rainstorm in Calcutta to offer them an umbrella.

These two anecdotes provide all the information you need to accurately reconstruct the political views of each.

Fisher passed away in 1962, and Haldane in 1964. Fortunately, one of the most salient features of each was preserved in a jar for posterity. And now, half a century later, the two have reunited to bring you their genetically inspired comedy stylings.

Here's what you've missed so far:

Best URL for sharing:
Permanent image URL for hotlinking or embedding:
Best URL for sharing:
Permanent image URL for hotlinking or embedding:
Best URL for sharing:
Permanent image URL for hotlinking or embedding:

Monday, November 19, 2012

Do Heart Transplants Cause Lesbian Bestiality? We Investigate!

So, this video is straight-up awesome, as is the song, which was the inspiration for the video. Over at Boing Boing, they have an interview with songstress Kim Boekbinder, artist Molly Crabapple, and animator Jim Batt, who collaborated to put this thing together. The interview also features behind-the-scenes photos, which give a sense of the scale of the project. The figures look to be maybe six inches tall, while the paper-craft buildings are maybe three-feet tall.

If they're smart, they'll auction off the set, for which someone would certainly pay 10 kajillion dollars.

Speaking as a biologist, I should note for the record that I am unaware of any replicated, double-blind studies showing a statistically significant association between organ transplants and having steamy lesbian pirate sex with cats.

Update: I just went and checked out the dedicated website (, which has a series of blog entries following the project from its beginnings in May 2010 to July 2012. Awesome.

Sunday, November 18, 2012

Should YOU Go to Grad School? A Guide

So, it's that time of year again, when thousands of college seniors emerge briefly from their beer-bong haze long enough to ask themselves, "What the hell am I going to do next year?" At times like this, for many of you, your thoughts may turn to graduate school, and to the question of whether or not you should go there. Some of you are imagining grad school as an opportunity to continue doing whatever you've been doing for the past four years. Some of you are imagining a path to riches paved with scholarly articles on the mating habits of the Brazilian Wandering Spider. Some of you are all, "I don't know, I guess it's a thing to do."

If you clicked on this post, then you're probably feeling torn about whether or not grad school is right for you. I'm going to say that the answer is probably yes. But that's because I loved grad school. Also, according to my wife, I have poor Theory-of-Mind skills, so I have a hard time picturing that you would not, also, love grad school. But it is just possible that you might not.

So perhaps a more detailed analysis is in order.

Well, here is a comprehensive guide to whether or not YOU should go to graduate school:

[Note: if you're already in grad school, check out this guide to making grad school AWESOME]

The Lost In Transcription Guide to Whether or Not YOU Should Go to Graduate School

Consideration 1: Lifetime Earnings

Okay, the first thing you might want to consider is your lifetime earnings potential. On the one hand, earning an advanced degree is correlated with higher salaries. On the other hand, you'll spend the next several years earning only a small salary, or even going into debt, depending on your field (and lifestyle). Furthermore, if you get started on a money-earning career now, you'll have that many more years of seniority. How do these things balance out?

Well, if you're eagerly looking to this paragraph for detailed economic analysis of the effect of having a PhD on your lifetime earnings, then the answer to whether or not you should go to grad school is an easy one: You should not go to grad school.

If your primary consideration looking forward is monetary, this is not the right path for you. Yes, most PhDs are able to earn a very comfortable living, certainly substantially higher than most jobs. However, most of these PhD careers require long hours and a willingness to move thousands of miles for a job. If you have the intelligence and work ethic and commitment to make a go of a PhD-type career, but your primary consideration is monetary, then there are other, better paths for you. Go work for a consulting firm, or start working your way up the financial analyst ladder. If you want more school, go to a professional school (e.g., Business, Law, or Medical). These will also lead to careers with long hours, but your earnings upside is much greater, as is the degree to which you will be able to tailor your career to other considerations, like living close to / far from your in-laws. Or, if you're really set on grad school, at least consider engineering, where you can go off and make a bundle of money working for a defense contractor.

If lifetime earnings potential is at the top of your list of considerations, do not, under any circumstances, enter a graduate program where the best-case-scenario outcome has you teaching Medieval German History to a bunch of bored premeds fulfilling a distribution requirement.

Consideration 2: Your Deathbed

Previously, writing about work-life balance, I quoted someone (whose name I could not remember) who said something like this:
You know, I don't think anyone has ever been lying on their deathbed and said, 'Boy, I wish I had published just one more paper.'
While I think that this statement is a reasonable prediction for most people on their deathbeds, it is not entirely universal. I remember one time at a dinner I was seated next to Daniel Aaron (an Emeritus Professor of English at Harvard). At one point he said that he was beginning to reread Proust's Remembrance of Things Past (a.k.a., In Search of Lost Time) in the original French, because he wanted to make sure that he read the whole thing one more time before he died. (He would have been about 92 at the time. He is still alive, at 100, so I assume he accomplished it. He probably also got to rewatch all twenty seasons of Law & Order on DVD.)

Does this story resonate with you? Imagine that you have just learned there is an asteroid heading towards earth, and you have thirty-six hours to live. Would you rush to grab your Greek edition of The Republic? Would you see if you could crack that one really hard problem from this week's problem set?

If you answered yes to the you-appropriate analog of these questions, then you have your answer: You should go to grad school.

Take out loans if you have to. Sell plasma. Live the life of the mind. Die a happy pauper. Stop reading this. Go.

But what about the rest of us?

Okay, most people won't fit into either of the two easy cases above. For the remainder here, I'm going to assume that you're smart and a little bit dorky, or, you know, "academically oriented." You can picture becoming a professor, or working at a national laboratory, but you can also picture not becoming either of these things. I'm going to assume that you enjoy classes and reading and research projects and such. If these assumptions are wrong, well then no, you should not go to grad school. But you're probably not even reading this.

Okay, moving on.

Basically, my short answer is sure, why not. Particularly if you can go to grad school for free, with some sort of stipend, then yes, give grad school a shot, but keep your options open. Be ready to bail, and remember that you don't have to go right away.

Let's unpack this.

Consideration 3: Can You Go for Free?

I know we already said that you should not go to grad school if money was your primary consideration. But even if it is not primary, for most people it is at least a consideration. This is a place where there is huge variation among fields and among universities. If you're in the sciences, there tend to be a lot of opportunities to go to grad school in such a way that your tuition is paid for, and you will, in fact, receive some sort of a stipend. If you get a fellowship from the NSF or NIH, this might be on the order of $30,000 a year. If not, you might be looking at more like $15,000 a year.

Now, that's not a ton of money, but $15,000 is about what you would be making if were working a full-time job at minimum wage. And, with a little ingenuity, you can stretch those dollars pretty far. At many universities, there will be opportunities for subsidized on-campus housing if you're willing to hold undergrads' hair while they vomit. If not, you can probably find some other grad students to share housing with. Also, you will quickly learn which seminar series provide free food.

Depending on where you are, you may have to do some teaching, grading, etc. as part of your stipend package. If you're in the social sciences or humanities, this is more likely, and the teaching load might be heavy.

Here's the thing, though. Taking classes, teaching undergrads, and grading papers is going to be a more varied and interesting job than most things you could be doing for minimum wage. Let's say that you wind up teaching (or grading for) a couple of classes each semester, all while taking classes of your own and trying to do your own research. Does working at Starbucks sound better or worse than that to you? This will give you your answer as to whether or not to go to grad school. The fact is, the job you're facing down as a grad student is a lot like the job you're looking at having for the next forty years. If that's not appealing, get out now.

But what about something where you have to pay out of pocket. Honestly, I would be skeptical. I mean, if you come from money, fine. Otherwise, the only way this makes sense is if you already learned that you should attend grad school after reading consideration 2, above. In which case, I already told you to quit reading. Get out of here!

Consideration 4: Take a Process-Oriented View

A lot of people, when they think about grad school, focus on the long-term goal: the faculty job, or the pharmaceutical-company job, or the government-agency job, or whatever. In general, goal-oriented behavior is a good thing, and your capacity to pursue long-term goals is probably one of the reasons why you're in a position to consider grad school in the first place.

But remember what Aerosmith said: "Life's a journey, not a destination." Someone else probably said that, too, but whatever.

Let's say you're in your early twenties. Using ballpark numbers, you might spend the next five years in grad school, and maybe another three, or five, or eight as a postdoc, depending on your field. Let's say you retire between sixty-five and seventy.

That's forty-five years of working, ten of which will be training for your career. That's not the majority, but it's a huge fraction, and you should make an effort to be happy, not just working towards something that you think will make you happy.

Here's the good news. Grad school can actually be a lot of fun. You're surrounded by smart people. It's like college, but without the jocks and the frat boys and all the other assholes who used to call you Poindexter. You'll make lifelong friends among your grad school cohort. You'll hang out together and watch reality television and play poker and volleyball and drink beer.

This, of course, depends in part on your choice of field, school, and advisor. That's a topic for a different post, however. The point is that grad school, when well chosen, can be a great time. Even if you wind up with a shitty advisor, the students will often bond together over the shared trauma. But what if grad school sounds appealing, except that you hate having a great time? Well, if you're not confident in your ability to choose an advisor who will make you completely miserable, consider Chemistry.

Consideration 5: You Don't Have to Stay

You're reading this because you're not sure if you would like grad school. Here's the thing. Going to grad school is a good way to find out if you'll like grad school. Grad school is quite a bit different from undergrad, but it is, in some ways, not that different from what you would be doing after finishing grad school. It also gives you opportunities to see close up what postdocs and professors do (or close-ish, anyway).

So, one thing you can do is start grad school. If it's not working out for you, leave. Many PhD programs have some sort of a terminal masters degree. In some cases, you actually earn the masters in the normal course of pursuing the PhD. In others, the masters is awarded if you pass your exams, but drop out before doing your dissertation. Either way, that means that after a couple of years, if you decide this isn't for you, you won't leave empty handed. The people in your field and in your lab will tell you that the masters degree is a sign of failure, and within the academic community of that field, it is. But here's the thing, if you're leaving that academic field, who cares! People outside in the rest of the world will recognize your masters degree for what it is, an indication that you went out and gained a whole lot of knowledge about something.

Alternatively, you can leave your grad program and join another one. I started off in a PhD program in Biochemistry. After two years, I changed fields, schools, and cities, because after that time I had a much better sense of what I wanted to get out of school.

So if you think you might like grad school, give it a go, but keep the escape hatch in mind. This sounds easy now, but may not seem so easy later. There is a lot of myopia in grad-school culture, and a lot of echo-chamber nonsense. People tend to get tunnel vision, and buy into the idea that there is one true, golden path for success. If you start to stray off of that path (like by thinking about leaving with a masters), everyone will try to discourage you: your advisor, senior grad students and postdocs. They might even stage an intervention.

Just remind yourself that Stockholm is not only the place where they give out the Nobel prizes, it is also the name of a syndrome.

Consideration 6: You Don't Have to Go Right Now

Consideration 5 was really sort of an argument for jumping into grad school if you are leaning that way. But what about if you're leaning the other way? Here's the other thing to keep in mind: grad school will still be there next year. Probably even the year after that. Have you always wanted to spend a summer working on a fishing boat? Go for it. Did you want to backpack across Asia? That sounds exhausting to me, but, hey, why not!

You meet a remarkable number of twenty-two year olds who feel an enormous pressure to get their careers started. I just want to shake them and say, "What the hell? You're twenty two!" Let's say you take five years off before starting grad school, and then follow the standard career path. Most of it will be exactly the same, except that, instead of being a Full Professor somewhere for twenty years before retiring, you'll be a Full Professor there for fifteen years before retiring. No one cares, even you.

Recall again, that if you really are that desperate to publish five more papers in your life, you should already have stopped reading and started applying.

There are also ways to sort of hedge your bets. Like, apply to work as a lab technician in a lab in some country you've always wanted to visit. I did this before grad school. The country was the United States, which is sort of lame, but I'm sure you could do better. If you're in the humanities, apply to be whatever the equivalent of a lab technician is in your particular field. Unless the equivalent is "prostitute." Don't do that.


So, now that you've read through the entire Lost In Transcription Guide to Whether or Not YOU Should Go to Graduate School, you know whether or not to go. Still not sure? Perhaps you didn't read carefully enough. If you've read this guide three times, and are still not sure, send fifty dollars, and I will refund half your money.

For those of you who have decided on grad school, check back here for the Lost In Transcription guide to choosing a graduate school program and advisor. (UPDATE: It's HERE!)

For those of you who have decided against it, check back here for instructions on how I like my coffee.