The Futile Cycle

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

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.

In the first major casualty of the etBLAST algorithm and Deja Vu database has been found at Harvard Medical School, where Prof. Lee Simon’s review paper has been found to have large sections copied from another professor’s paper.

I had hoped that Deja Vu would consist of articles from random foreign countries and small, obscure universities, but alas, I was perhaps a little naïve. Perhaps the good part about this will be that it encourages authors to be much more reluctant to plagiarize.

On the other hand, it depends on whether the journals care. Elsevier, in this case, did the right thing and acted upon the evidence to retract the paper, but other journals don’t have such “enlightened” policies. I heard once about a professor that was reviewing a manuscript for a journal when he found that the other author had plagiarized sections from one of the professor’s own papers! When the professor notified the journal editor, they informed him that this was commonplace, and that he should just review the article anyway.

What floats to the top in science is often beautiful, but there’s a lot of crap that sinks to the bottom.

Alas, I (as a poor, time-crunched graduate student) will not be able to make it to the North Carolina Science Blogging Conference, but they have a nice website that’s going to be aggregating a lot of the content surrounding the conference.

(Beware of that aggregating website; it seems to break on Safari, so use Firefox. Alas, Mac users do not seem to command respect and deference quite yet.)

The crystal structure of a human GPCR (beta 2 adrenergic receptor)

Crystal structures of membrane proteins are really hard to obtain, because they tend to slide and be too “slippery” to get them to pack into an ordered, structured crystal. GPCRs are even harder, because they’ve got so many moving parts that it’s much harder to prevent them from sliding against each other. This is an amazing achievement, but even now you can see that they weren’t able to get everything they wanted; the resolution of the structure is low (over 3 angstroms) and a lot of their protein still didn’t crystalize very well. Still, very impressive.

Not to generalize from one anecdote, but Doris Lessig, the 2007 Nobel Laureate in Literature, is a rather testy author. Is it just me, or are a lot of famous, “literary” authors annoyed by publicity? Maybe they’re shy? Consider the excerpt:

I asked [Doris Lessig] if she had heard the news and when she said no, I shared it with her.”Oh Christ!” she said in an exasperated tone that I certainly was not expecting. “[Speculation that I might win the prize] has been going on now for 30 years, one can’t get more excited than one gets.”….”Isn’t this a recognition of your life’s work?” I persisted.”Yes, it is. See, you’ve said it all for me,” the feisty and prolific author responded, turning to head indoors….Clearly, she was not going to make it easy. I managed to get her to turn around when she was half-way up the garden path by asking her if prizes meant anything to her, as obviously they were not the reason she wrote books.”Look, I have won all the prizes in Europe, every bloody one. I’m delighted to win them all, okay?”

As everyone probably already knows, the 2007 Nobel Prize in Medicine or Physiology went to Mario Capecchi, Martin J. Evans, and Oliver Smithies for developing a way to create transgenic mice by targeting genes. Smithies and Capecchi developed the methodology for creating cells which had specific genes knocked out, while Evans developed a lot of the methodology for using these techniques in stem cells to create live mice that would carry these induced mutations. The knock-out mouse is now one of the most versatile models we have for testing questions about genes and diseases. A good explanation of the process that they developed is explained here.

I know a lot of people just skim the press release, but there are some really interesting nuggets in the “Advanced Information” section of the announcement. For example, Evans first tried to use cancer cells to make mice, but (as you would expect), the cells were just too sick to actually make a good organism. So he actually went through and found the cells the we now use as “Embryonic Stem Cells,” which he used to create mice that were a mosaic of cells of two different mice.

Another thing was that Capecchi and Evans both wrote grants proposing this research (on gene targeting) to the NIH and the UK Medical Research Council (respectively), but both were rejected, because the reviewers thought it would be too hard and unlikely to succeed!

Finally, though this isn’t mentioned on the Nobel website, Capecchi had a really hard life as a child. His mother was arrested and put away in a concentration camp during World War II (for being an anti-Fascist bohemian), and he was left alone for four years as a street urchin. Fortunately, he was later found (very sick and malnutritioned) by his mother (who survived). He moved to the US, went to school, then college, worked under Jim Watson at Harvard, and then went on to have a massively successful career (though, as I mentioned above, not without a few hiccups along that path as well). It’s an amazing life story, and the Nobel Prize surely can’t go to a better person.

This year’s “Genius Grants” (MacArthur Foundation Fellowships) have been awarded, and one of the fellows is Michael Elowitz, a biologist at Caltech. He’s done some really amazing work on a subject near and dear to my own heart, which is on how genes interact, one branch of the so-called “Systems Biology.”

Some of his most famous works include the “repressilator”, work on competence in bacteria (PDF), and the theory (PDF) and measurement (PDF) of intrinsic vs. extrinsic noise in gene expression. All these major contributions, and he’s only 37!

Although systems biology is “hot”, not that many “systems biologists” work at the level of really fundamental, mechanistic biological questions (more common is a branch-off of bioinformatics and microarray analysis), so it’s great to see this kind of wonderful recognition for a really prominent figure in that arena.

Via Terra Sigilata, the amount of diacetyl artificial butter flavoring in microwave popcorn is apparently high enough to destroy your lungs, in a syndrome called bronchiolitis obliterans. It’s been well known that the compound will destroy the lungs of workers in factories, but this is the first reported case of a consumer being affected. Now, this is one reported case in the past umpteen-year history of microwave popcorn, so the risks are probably very low, but still, beware savoring the smell of microwave popcorn.

For some reason, many people who’ve bought iPhones early on are complaining now that Apple issued a $200 price cut. These people may sound like whiners, but really, it’s because what they’re buying is not just a phone they really like, but the prestige of being able to shell out $600 for a phone. It’s the brand, the exclusivity, the signaling, that they’re buying. Sure, the iPhone is more functional and much better made than most other phones, but several hundred dollars worth? It’s hard to say; individual preferences and weights strongly come into play there. For most people, I’d say it isn’t worth it, in the same way that the “hand-made quality” and “attention to detail” in an Aston Martin just isn’t worth the cost to most people.

So, that’s why consumers are complaining. The theory doesn’t make them any less whiney and pathetic, but it does explain why there’s so much backlash, and Apple does need to realize that it’s not just competing as a technology company, but as a fashion company, one in which price plays a large role in social prestige and branding.