Textbook vs. Frontier

The Hwang Woo Suk stem cell research scandal has triggered quite a bit of concerned introspection in the scientific community. Orac has some useful comments on a good article in the NY Times that makes the distinction between “frontier science” and “textbook science”, where much of the current stem cell research is clearly on the frontier.

Much of science at the very frontiers turns out not to be correct. However, the way it is all too often reported in the press is that it is correct. We in science understand the difference between textbook science and the sort of frontier science that makes it into journals like Science. Indeed, we often lament that the very highest tier journals, such as Nature, Science, and Cell, tend to be too enamored of publishing what seems to be “sexy science,” exciting or counterintuitive results that really grab the attention of scientists–in other words “cutting edge” or frontier science. Such journals seem to pride themselves on publishing primarily such work, while more solid, less “sexy” results seem to end up in second-tier journals, which is why they are so widely read and cited.

I would add another factor, though: Hwang Woo Suk’s results were not at all unexpected, did not contradict any accepted scientific concepts, and were dramatic because they represented a methodological breakthrough. In a way, it was almost a “safe” category in which to cheat: lots of people are trying to transform adult cell nuclei into totipotent stem cells, it looks like a problem that’s just going to require a lot of trial-and-error hammering to resolve, and what Dr Hwang did was steal priority on a result he could anticipate would be “replicated” (or more accurately, done for the first time) in short order. This is one of the hardest categories of science to police, I would think. It’s frontier science all right, but it’s only one step beyond the textbook.

Orac’s comments about those sexy hot scientific results that get into the top-ranked journals also applies to weblogs. I’m guilty of the same thing: the articles I tend to summarize here are the ones that push at the edges of what we know, rather than the ones that consolidate what we already knew, which actually represent the majority of what I read. The solid stuff that is packed with gobs of detailed data on expression patterns of a single gene, for instance, is hard to make exciting to a general audience—when the conclusion of a long paper is that Hox1 represses transcription of Pax1/9 in the endoderm, it takes an awful lot of background exposition to try and make that interesting.

For the creationists out there, by the way, most of evolutionary biology is solidly in the “textbook science” category, which is one of the reasons biologists are so baffled about why the general public embraces criticisms of it.

Orsten fossils

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Bredocaris admirabilis

Ooooh, there’s a gorgeous gallery of Orsten fossils online. These are some very pretty SEMs of tiny Cambrian animals, preserved in a kind of rock called Orsten, or stinkstone (apparently, the high sulfur content of the rock makes it smell awful). What are Orsten fossils?

Orsten fossils in the strict sense are spectacular minute secondarily phosphatised (apatitic) fossils, among them many Crustacea of different evolutionary levels, but also other arthropods and nemathelminths. The largest fragments we have do not exceed two mm. Orsten-type fossils, on the other hand, have the great advantage in being three-dimensionally preserved with all surface structures in place and thus easier to interpret than any other fossil material. Orsten fossils are preserved virtually as if they were just critical-point dried extant organisms. Details observable range down to less than 1 µm, and include pores, sensilla and minute secondary bristles on filter setae and denticles. Orsten fossils also give an insight of meiofaunal benthic life at small scale, including preservation larval stages, and hence a life zone inhabited by the earliest metazoan elements of the food chain.

It’s a good browse over there. I think it’s useful to remember that the majority of the fauna of the world both extant and half a billion years ago is and was tiny and unfamiliar.

Department of Provocative Imagery

OK, that settles it. I’m in the wrong research field.

They found breasts moved in a 3D figure of eight and that uncontrolled movement strained fragile tissues and ligaments.

The study suggested as a woman runs a mile, her breasts bounced 135 meters.

The report found each breast moved independently of the body by an average of 9cm for every step taken on the treadmill.

With the average breast weighing between 200 and 300 grams, this movement puts great stress on the breast’s fragile support structure—the outer skin and connective tissues known as Cooper’s ligaments.

I suspect the analysis was…mesmerizing.

The wording was a little unfortunate—I pictured the subject dribbling a pair like basketballs as she runs.

(via Matt Dowling)

Hemichordate evo-devo

Every biology student gets introduced to the chordates with a list of their distinctive characteristics: they have a notochord, a dorsal hollow nerve cord, gill slits, and a post-anal tail. The embryonic stage in which we express all of these features is called the pharyngula stage—it’s often also the only stage at which we have them. We terrestrial vertebrates seal off those pharyngeal openings as we develop, while sea squirts throw away their brains as an adult.

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The chordate phylum has all four of those traits, but there is another extremely interesting phylum that has some of them, the hemichordates. The hemichordates are marine worms that have gill slits and a stub of a tail. They also have a bundle of nerves in the right place to be a dorsal nerve cord, but the latest analyses suggest that it’s not discrete enough to count—they have more of a diffuse nerve net than an actual central nervous system. They don’t really have a notochord, but they do have a stiff array of cells in their proboscis that vaguely resembles one. They really are “half a chordate” in that they only partially express characters that are defining elements of the chordate body plan. Of course, they also have a unique body plan of their own, and are quite lovely animals in their own right. They are a sister phylum to the chordates, and the similarities and differences between us tell us something about our last common ancestor, the ur-deuterostome.

Analyzing morphology is one approach, but this is the age of molecular biology, so digging deeper and comparing genes gives us a sharper picture of relationships. This is also the early days of evo-devo, and an even more revealing way to examine related phyla is to look at patterns of gene regulation—how those genes are turned on and off in space and time during the development of the organism—and see how those relate. Gerhart, Lowe, and Kirschner have done just that in hemichordates, and have results that strengthen the affinities between chordates and hemichordates. (By the way, Gerhart and Kirschner also have a new book out, The Plausibility of Life (amzn/b&n/abe/pwll), which I’ll review as soon as I get the time to finish it.)

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Firefly squid

This is a beautiful little animal with a brief and brilliant life.

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Watasenia scintillans is a small (mantle length,~6 cm; wet weight,~9 g), luminescent deep-sea squid, indigenous to northern Japan. Females carrying fertilized eggs come inshore each spring by the hundreds of millions, even a billion, to lay eggs in Toyama Bay (max. depth, 1200 m) and die, thereupon completing a 1-year life cycle.

Watasenia possesses numerous (~800), minute dermal light organs (photophores) on its ventral side. Other organs are scattered over the head, funnel, mantle, and arms, but none is found on its dorsal side. There are five prominent organs beneath the lower margin of each eye. They all emit a bluish light. A cluster of three tiny black-colored organs (<l mm diam) is located at the tip of each of the fourth pair of arms. They emit brilliant flashes of light which are clearly visible to the unaided eye even in a lighted room. Some of the flashes have a cadence resembling that of a terrestrial firefly flashing at night, and thus the squid is known in Japan as the “firefly squid” or “hotaru-ika.”

A billion die every year as a natural part of their lifecycle; all those glittering little creatures dying profligately—Nature is both exuberant and pitiless, it seems.

Tsuji FI (2005) Role of molecular oxygen in the bioluminescence of the firefly squid, Watasenia scintillans. Biochem Biophys Res Commun. 338(1):250-253.