The Futile Cycle

In the mix of the whole “Scienceblogs is white!!” non-event, Razib at Gene Expression had some questions to ask about the underrepresentation of Asians in blogging, even though Asians tend to be over-represented in science research. He speculates that maybe Asian American cultures tend not to cultivate literary talents as much.

I’m going to go out on a limb and speculate some more. I think Asian Americans tend to emphasize mathematical and technical fields because of social and migratory selection.

Namely, the over-representation of Asians in certain fields has to do with the immigrant language barrier. It’s hard to get a job if you don’t speak English well; part of being successful in the humanities is being able to communicate, as that’s largely what one does in those fields: communicate and analyze other people’s communications. On the other hand, technical fields, especially highly mathematical fields, tend to translate better across language barriers because mathematics is universal these days. Those immigrants who are able to obtain green cards or visas are those who have valuable skills that can translate immediately to results, and those skills tend to be technical.

You’d think that it would still be hard to survive any academic job without a good command of English, but immigrants can be amazingly resourceful, and academia can be surprisingly forgiving of bad speaking ability (let’s face it, professors are often not model speakers, even the native English speakers). I know that my dad had an insane amount of trouble learning english, but his mathematical ability was top-notch. He survived his thesis defense by writing down his entire presentation beforehand and memorizing it, word-for-word.

So what I’m saying is that the American barriers and limitations to immigration create an artificial, societal selection such that only those immigrants with technical abilities are able to pass through the immigration filter with any amount of ease.

This model, of course, makes some predictions. As English language teaching abroad increases, more immigrants and more minorities with backgrounds from those countries should start to appear in the humanities. In addition, this kind of filter effect should happen even with non-Asian ethnic groups, as long as there is some sort of language barrier. I’m curious as to how many British scholars, for example, populate the humanities compared to, say, German speakers (I’m trying to pick countries that have roughly the same overall economic status, and similar “white”-ness and cultural backgrounds). More Africans and Hispanics should populate the sciences compared to other disciplines, too.

The main problem with generalizing this model to other immigrant and minority groups is that there are fewer scholars that are, say, black, or Hispanic in academia, compared to Asians. There might be too much noise to definitively affirm or rule out this “filter effect” in such groups. There might be enough immigration, however, from Britain and Europe to do some sort of preliminary analysis.

A lot of news stories are once again talking about breakfast and its connections to weight and obesity. Consider this BBC article as one example. This Reuters article hypes breakfast as magically keeping teens skinny. The original Pediatrics journal article is here.

What’s wrong with all of this? The research doesn’t say whether eating breakfast makes someone lose weight. All it says is that skinnier teens eat breakfast more often than more obese teens, on average. That doesn’t mean that suddenly eating breakfast more will make you lose weight.

Consider, these details in the paper. People who eat breakfast more also: “more likely to be white, to come from a higher [socio-economic status], and to engage in higher levels of physical activity.” Hmmm, breakfast-eaters do more exercise, huh? I wonder if that has anything to do with the difference in weight…hey, will eating breakfast also make me white and wealthy? Awesome!

Sure, the authors try to correct for the physical activity differences in their regression, but no regression is perfect, and since all of the data is essentially self-reported, it’s hard to tell whether hours spent per week in “strenuous, moderate, and mild exercise” is really a good reflection of lifestyle choices. Maybe they take the stairs more often, or bike and walk more than those who don’t eat breakfast. Is running a mile moderate, strenuous, or mild exercise?

In addition, there are the classic correlation-versus-causation arguments: perhaps people who eat breakfast are just those who tend to have a higher metabolism naturally, and so they have the energy in the morning to get up early enough to eat breakfast. Or perhaps breakfast eaters are just more conscientious of their life choices, including sleeping, planning ahead, being less stressed, and so on, which might contribute to their lower BMI. Their eating breakfast in the morning could then be just one more symptom of their conscientiousness.

Though this article was published in the journal called Pediatrics, really this is just a sociological or economic study, not a medical study. Researchers and the news should stop hyping it as some sort of recommendation for preventing obesity. Breakfast isn’t a therapy just yet.

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Timlin, M.T., Pereira, M.A., Story, M., Neumark-Sztainer, D. (2008). Breakfast Eating and Weight Change in a 5-Year Prospective Analysis of Adolescents: Project EAT (Eating Among Teens). PEDIATRICS, 121(3), e638-e645. DOI: 10.1542/peds.2007-1035

All right, time to settle a vitally important issue in lab science.

I’ve heard people pronounce “autophagy” as both AW-tuh-fey-jee and uh-TAW-fuh-jee. Clearly, it should be pronounced as the former, like any normal person. The latter pronunciation makes the speaker sound pretentious and silly, whereas the former makes him or her sound practical and to the point, like a serious scientist.

Don’t come quoting to me from the dictionary, either. Do you say “HA-rass” for “harASS”, though that’s the way it is in the dictionary? No, of course not. Because you’d sound like a silly fop otherwise.

Besides, everyone pronounces “autophagosome” as AW-tuh-FA-go-some, and not uh-TAW-fuh-go-some. And no one says uh-TAW-mow-beel for “automobile.”

So there. Those who say “uh-TAW-fuh-jee” will be teased mercilessly.

In between running around to experiments, attending classes and seminars, reading the literature, eating, and sleeping, I’ve manage to catch chapters of Intuition, by Allegra Goodman. I started the book because of a glowing review from Dr. Free-Ride. I finished it last week, and I’ve been mulling it over in my head.

This book is quite possibly one of the best novels I’ve read in the past year (though, it’s looking like it might be the only novel I’ll read this year…).

It is set in Cambridge, Massachusetts, at a biomedical research institute that’s right next to Harvard’s campus. If this sounds familiar, that’s because the author did some research for the book at the Whitehead Institute, a huge biomedical research institute geographically in between MIT and Harvard. Allegra Goodman did some wonderfully thorough research for the book, because it abounds in the small details of a real lab. Old machines, nude mice, foil-capped bottles of reagents and media.

And the people, the characters, the scientists: how wonderful! They are the classical archetypes that anyone who’s worked for a while in academia would recognize instantly: the hard-working, technically brilliant East Asian immigrant, the powerful lab techs, the rising star who suffers from “imposter syndrome”, the senior post-doc who resents the rising star for all the breaks he’s had going to prestigious schools, the lab head who’s too scientifically cautious to promote her lab well, the star oncologist with a flair for selling the research (”a poet of the NIH form”) but with less-than-stringent scientific skepticism.

Yet, none of the characters are stereotypes. None of them fit their archetypes. All of the characters are quite real, with real motivations, dreams, emotions, and agendas. That, in the end, is probably what ignites the central conflict of the entire book. I will not divulge much about the book’s plot, as I suggest to all of you that you go out and read it if you haven’t yet.

Still, a little thought as to what I see from the book, without spoiling the book (I hope). It seems like the book makes plain that truth — even in science — is hard to know, as it is always seen through the eyes of a person, through a glass darkly. Even the events of the story, told from so many points of view, are not clear. Agendas are confused. All because of people.

The conflict between the exacting requirements of science and the people who actually synthesize and propagate the knowledge seems to be almost the central conflict in the book. Science — true science — happens on the scale of years and decades: ideas are proposed, experiments are done, hypotheses are rejected or accepted, experiments are replicated. Science takes time, and truth only emerges with a grain of certainty years after the fact.

But for many of us in science, especially in the present day, we are forced to live on a faster time scale. Grants are due, demanding results. Jobs demand papers. Papers, of course, require experiments. One can get scooped, if one doesn’t move fast enough. Scientists don’t have the luxury to wait for science proper to catch up, and so sometimes, in the milieu of researchers running back and forth in their frantic-paced lives, some can trip and get crushed under the slow-moving glacier that is real, absolute truth, not for evil or malicious intents in their souls, but for the fact that they, too, have dreams.

But the book does hold out hope. Although science is harsh, people are resilient, and that is why science is able to happen at all. The book is almost a tribute to scientists, and an acknowledgment of the many sacrifices that people make to pursue a career that they love.

Go read it. It is delightful!

This is really quite odd. In today’s Science
bacteria have been found to nucleate many ice particles in the atmosphere, including snowflakes. In other words, bacteria are raining and snowing from the sky!

There are two interesting new papers out in the newest issue of Molecular Cell, and one from Science a week back that’s online early:
An Important Role for the Multienzyme aminoacyl-tRNA Synthetase Complex in Mammalian Translation and Cell Growth: Seems that the two different forms of Arginine tRNA synthetase have different roles in the cell, one to make tRNAs for synthesizing proteins, and to make tRNAs for degrading them via the ubiquitin pathway!

Human Alu RNA is a Modular Transacting Repressor of mRNA Transcription During Heat Shock:
Non-coding RNAs have been shown to have transcriptional regulatory properties, but this particular paper discusses one that looks a lot like a protein, in the sense that it seems to have modular “domains.” Pretty neat work!

Selective Blockade of MicroRNA Processing by Lin-28: The main discovery of the paper is, of course, nicely summarized in the title. The idea is that Lin-28 prevents the biogenesis of let-7, one very well-studied (though not well-understood) family of microRNAs, by binding to the RNA and preventing Drosha and Dicer from gaining access to it.

Day to day, I work a lot with clear, colorless drops of liquid, shuttling them back and forth between small plastic vials. I also work with cells, but they just look like cloudy suspensions in strange-smelling liquids.

But every time I look at cells under a microscope, I can’t help but gaze in wonderment. Cells! Under a microscope!

Even better are images and videos online from the American Society for Cell Biology, which I found via Bitesize Bio. Make sure to check out the videos, some of which are absolutely spectacular and inspiring. Some of my favorites include watching rat heart cells beating in a Petri dish, seeing fish cells zooming across slides (especially check out how fragments of cells without a nucleus can still move around! Movement is thus, at least in the short term, independent of transcription), the movement of mitochondria within a cell, seeing chromosomes divide in real time using just light microscopy, and watching Drosophila embryo syncytial division (where all of the nuclei divide simultaneously, without cytokinesis).

Biology is an absolute wonder, and I hope you find these videos as inspiring as I do.

I’ve found a bunch of tools recently that have made organizing my life a lot easier, especially with integrating labwork into the rest of my life.

First up is Remember the Milk, which is a free, online to-do list manager. It’s simple, but very useful. I can create multiple lists, tag each list item, and create smart lists based on searches. It’s all done very well, including lots of AJAX-y goodness and keyboard shortcuts to boot. For FireFox users, it has nice integration with Google Gears for offline access. It also integrates into Gmail and Google Calendar, though I’ve used those features less. The only caveat I have with RTM is that I wish its keyboard shortcuts mimicked those in Gmail. Gmail’s shortcuts seem much more intuitive than RTM’s, such as using “x” instead of “i” to select or deselect items.

Having an online tool is really handy, as sometimes I don’t have my computer with me, especially in lab. My To-Do list, however, is only an internet connection’s away.

Next is Gmail. Yes, many people use Gmail, but I especially like to use Gmail to shuttle little bits of data back and forth as attachments on drafts of letters to myself. Very handy! And Gmail’s recent introduction of IMAP has made it a lot easier to keep track of my email from both my home computer as well as a lab computer.

Another amazingly useful tool is Google Calendar. It’s very handy to be able to check my schedule from any computer, but the main problem is that I like the way iCal is integrated into the rest of my system! It picks up dates and times from email read in Apple Mail, it integrates with the Address Book, and alerts are simple to create, making it so much easier to manage my time at my home computer.

So I use BusySync. The 2.0 beta (as I write this) includes Google Calendar synchronization, which is an absolute godsend. The synchronization is seamless!

RTM combined with Google Calendar + BusySync + iCal is a killer combination for me; I can keep track of experiments, time points, appointments, meetings, seminars, classes, and even the rest of my life regardless of what computer I’m on! And now that I use an electronic lab notebook published online (though under a password), I can access data and procedures from home, too, so that I can plan out experiments or process data and record it wherever I am. It’s glorious!

Alas, the only thing I can’t do is pipette my reactions or maintain cell culture from home…Hey Honda, any chance you might come out with an ASIMO Laboratory Rat model?

Since when do universities write press releases for review articles? Is it really necessary?

Via Pharmalot, apparently Pfizer is going to court to try to force the NEJM to release its confidential reviews of articles on Celebrex and Bextra, two of Pfizer’s products that have been targeted for lawsuits on their side effects.

Now, I’m not saying either way whether Pfizer is guilty of misinformation and such on Celebrex and Bextra, but this subpoena is just wrong. The scientific peer-review process has traditionally depended on confidentially to ensure candid and honest statements about the quality of research without fear of repercussions or retribution. It’s not perfect, but it’s sure a hell of a lot better than going without a peer-review system, and trying to break the confidential review system is like trying to force journalists to open up their sources. It stops the flow of good journalism, and it stops the flow of proper science.

Pfizer isn’t doing itself or the rest of the drug industry any favors, either. For whatever reason, people hate drug companies even more than they hate other companies (except maybe Big Tobacco), perhaps because they think that drug companies are evil machines sucking money out of sick and desperate people. That’s not true, and there are many noble people, including doctors and scientists, working hard out there in the drug industry to find the latest drugs to help people, but these kinds of antics from the top are just awful. I don’t envy the researchers at Pfizer, as they don’t deserve society’s scorn for all of this.