In defense of Matt Kaplan

Recently I responded negatively to an article in the Economist about research in my former lab. My complaints were, 1. sensationalistic title, 2. oversimplification, 3. sexing up the subject matter, and 4. failure to credit first author. Several respondents convinced me I was being too harsh, so I've retracted the post and apologized to Matt. The problem is that the Economist's Editors, not authors, choose titles, and Editors also have a significant influence on the tone and content of the article. The issues are not really Matt's fault.

The issues I raise are actually part of a dilemma for many science writers: what is an acceptable level of detail in an article? Naturally not all readers can be expected to understand science writing at the level of Science and Nature, but does science writing in the Economist need to be dumbed-down? The editors apparently think so. The sad thing is that they are probably right. Many people have a difficult time understanding even rudimentary science. Take for example the recent experience of the British National Lottery. In their game, Cool Cash, players scratch away a window to reveal a temperature. If that temperature is lower than temperature on the card, the player wins. The problem is that many players could not determine which number was smaller: -7 or -8.

Matt wonders, "if sacrificing some detail [is] acceptable to reach a wider audience? Is it right that editors have total control of titles to popularise complex science? Do they really know better than the journalist?"

My opinion is that there is that, beyond a certain level, sacrificing detail is counter-productive because the science itself is mis-represented, giving the reader a false understanding of science and the state of scientific knowledge. Easy to say, of course, but what is that level. I don't think there are any easy answers. Publishers know that if their readers cannot understand the material, they probably won't buy the work. Ultimately the consumer is responsible for the content because they exercise choice in the marketplace.

I, and Matt, would be very interested in what others have to say.

Photo from the Onion.

What would you improve?

Mark Hoofnagle at Denialism has a neat article on what would you improve if you could redesign the human body. I'm fine with an appendix, I'm not female so I don't really care about childbirth, and I'm still fairly young so I am not really concerned with my prostate. However, I would like to upgrade my senses. I'd like eyes like a hawk, ears like an owl, touch like a star-nosed mole, and a nose like bloodhound.

Birds have acute vision, but also can see ultraviolet light. Their world must be especially colorful. How cool is that?

Besides having rather keen hearing, Owls have asymmetrical ear openings permitting it to precisely locate things even in the absence of visual cues. My hearing isn't so great so this would be nice for me.

Star-nosed moles have rather exquisite senses of touch since they are functionally blind.

Bloodhounds have exceptionally sensitive noses. Imagine being able to figure out where your partner is in the grocery store by following their scent? I guess the drawback is that garbage will smell pretty bad...

Presumably it is possible for humans to evolve all these traits given enough time and the proper selective forces. In fact, it is likely that many of our senses have degenerated via relaxed selection over the millennia.

I'd also like to be able to jump higher than four inches, but let's leave that for another time...

Drawing from WikiCommons.

Author Order

EMBO Reports Science and Society section has an interesting note about author position in publications. Wren et al. 2007 note that a prominent publication trend is "author inflation", where the number of authors per paper is growing. This is probably linked to the increase in complexity of biological research and the trend towards greater collaboration across disciplinary boundaries. Naturally everyone wants the coveted first or last author spots, but those are in short supply, so more researchers are listed in the middle author spots. Given that there are, on average, more authors, what happens to those in the middle? Wren et al. report that the perception is that the more authors there are, the less each middle author contributed.

Wren et al. provide some valuable advice for untenured faculty and grad students: if possible, become corresponding author.

"Respondents reduced last-author credit when the corresponding author was the middle author. This suggests that candidates for promotion or tenure would be well advised to highlight publications on which they acted as corresponding author, especially if they were not the last author."

I found this surprising since I thought that nobody paid attention to who was corresponding author. At any rate, I am in favor of clearly delineating contributions in the paper itself, preferably on the first page, but not many journals require this.

Night on the Town

Friday night a couple of friends and I received an after-hours tour of one of my favorite places in the world, the American Museum of Natural History. It's really nice to tour the museum when there are no screaming kids running around. One of the highlights was a trip to the roof where we had a view much like the one above (I was kicking myself for not bringing my camera). The other highlight was viewing the hominan phylogeny now including the purported newest member, Homo floresiensis in the Hall of Human Origins. Since the first reports of the little man; some have suggested that it is a clear cut case of microcephaly and over-eager anthropologists. There has been a lot of back and forth on this hypothesis, but if in fact the skull is that of a new human species, it doesn't look anything like that of the more recent hominids. Actually you have to go back to Australopithecus before you really see something that looks similar to H. floresiensis. Now wouldn't that be stunning; a new genus of hominids contemporaneous with Homo ~20k years ago!

John Hawks has a superb series of posts on H. floresiensis.

Top photo by ezola.

This Week's Citation Classic

Readers of this blog may notice that my choices for classic papers come mainly from the evolution, ecology and molecular biology literature. This is not to imply that findings in other fields are less important, but rather that my command of the literature in other fields such as phylogenetics, developmental biology and cellular biology is less apt. However, even a caveman such as myself is familiar with the Homeobox discovery.

McGinnis W, Levine MS, Hafen E, Kuroiwa A, Gehring WJ. 1984. A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes. Nature 308: 428-33.

Homeotic genes determine when, where and how animal body segments develop. In other words, they tell cells in the developing embryo what kind of structures to make, i.e. legs, head, arms etc. Mutations in homeotic genes can result in dramatic changes in animal body plans, such as the antennapedia in the fruit fly that causes legs to develop instead of antennae (see photo). These genes, as the Nobelist Edward B. Lewis discovered, usually are co-linear in space and time with their segments of activity.
Many homeotic genes contain a common motif, a region termed the homeobox. This 180bp sequence encodes a 60 amino acid transcription factor, a protein that switches on and off other genes by binding to the relevant regions of DNA. The awesome thing about the Homeobox is that they are evolutionarily highly conserved, as McGinnis et al. discovered. The homeobox of the fruit fly is nearly identical to that of a wide variety of animals including the mouse and even humans! This is extraordinarily strong proof of common descent. Next time you see a fly, think about how you and she share a very similar stretch of DNA, the Rosetta Stone of life.

The master himself, PZ Meyers, covers Homeobox here.

Top photo from NIH. Fruit fly head showing the effects of the Antennapedia gene. This fly has legs where its antennae should be. Embryo cartoon from NobelPrize.org.

Biology and Art

I love reading bioephemera; Jessica always has interesting things to say about biology and art (and her artwork is amazing). I was impressed at the insight in her latest post. It taught me a thing or two about detachment and human nature. Don't take my word for it, get over there and read it.

Jessica Palmer
Bee and Echinacea
watercolor on Strathmore paper
2007

This Week's Citation Classic

Fraenkel-Conrat H. and Williams R.C. (1955). Reconstitution of active tobacco mosaic virus from its inactive protein and nucleic acid components. PNAS USA 41: 690-698.

This week's citation classic is probably the coolest experiment you've never heard of. Fraenkel-Conrat and Williams literally took a virus apart, separated its components, then put it back together again. Granted TMV is a relatively simple virus, consisting of 2130 molecules of coat protein and one molecule of genomic RNA 6390 bases long. Nonetheless, this experiment caused quite a buzz in the scientific world.

Gunther Stent wrote to Sidney Brenner, "Frankel-Conrat seems to have done the biggest thing with TMV since Stanley crystalized it. He can add soluble TMV protein to soluble TMV RNA, aggregate the whole mess into rods of which 0.1% are infective!!! Naturally, you don't believe it--nor did I or anyone else, but unless he has made up the whole thing it seems that it must be true. You can't beat that for laughs, can you buddy?"

It was true.

First Fraenkel-Conrat and Williams treated TMV with a mild acid. This treatment eliminated the charges that held the virus together. Then they separated and purified the protein. In parallel, they treated TMV with a detergent to strip away the protein, and recovered the RNA. After these steps, the viruses were no longer infective. Then they mixed the whole mess together again, and lo and behold! Reconstituted viruses!

The following year, Fraenkel-Conrat hybridized the viruses by mixing protein from one strain with RNA from another. Not only did he get viable viruses, he also was able to show that progeny viruses always had the same type of protein coats as the parent strain that donated the RNA. Thus proof that RNA was the genetic material for these viruses.

Photo of Tobacco Mosaic Virus from NIH.