metascience

Alan Boyle covers a talk by Donald Kennedy, editor-in-chief of Science that augurs changes to come in the publication of pop science:

However, during a Q&A session, Kennedy suggested that the print version of a Science paper might be written in a shorter, "more user-friendly" style - with the full blow-by-blow account appearing in the online version. The online archive would also provide video, complex graphics and other supplemental materials that just can't be put into the on-paper publication, he said.

Kennedy's main theme was that with the rise of online research distribution and 24/7 news distribution, scientific discoveries aren't likely to fit into an "only-on-Thursdays" package.

"It's going to create a problem for the people who try to manage science news," Kennedy said. "My guess is that the embargo system will either be abandoned, in which case it'll be a free-for-all ... [or] it's certainly likely that embargoes will be shortened, and the distribution of news to mainstream news media - which used to happen in clumps so that embargoes for an entire clump could be organized - is going to happen in driblets. So there will have to be a more confusing embargo environment."

The talk was for an audience of people interested in science reporting, and Boyle discusses the issues well from that perspective.

I have to say that as a scientist I am really divided. Papers in anthropology in Science and Nature in particular have a poor track record over the past several years. A very high proportion of the papers I am prepared to evaluate have big (and often glaringly obvious) flaws. In many instances, I've pointed those out on the weblog, so it's no surprise.

But it is compounded by one of the trends that I really hate is the trend toward hiding details of the paper in online supplements of one kind or another. Papers with hidden details are impossible to evaluate quickly, and the more difficult they are to judge, the fewer independent people will try to evaluate them. Fewer eyes means a smaller chance of catching errors. That may be good for some authors, and good for the journal, but it's bad for science.

On the other hand, if the paper version of Science had breezier articles that were more accessible to nonspecialists, I would be much more likely to subscribe. Presently, I only read the journal online through my university subscription. Although I am interested in solid state physics breakthroughs, I'm not equipped to follow a research paper in that field or in many others. The occasional news article or "perspective" by some other scientist is just not enough value added.

I've always loved Scientific American because it specializes in articles written by professionals for a more general audience. But I certainly can't see the percentage for Science or Nature to follow that model -- I can only imagine trying to find enough new research from good writers to fill a weekly magazine.

The model that Kennedy talks about, with the online version of a paper as the "archival" version does have the merit of possibly eliminating the "supplementary information" problem. Just have the online paper be longer. Maybe a system where papers accepted in Science are understood to be two parallel developments -- a "real" research paper and a "lite" version -- would work. But I'd bet they'd have to assign "real" writers to many of the papers to get them up to readability!

I think the biggest difference they could make would be to open up the review process. The linked article does talk about this concept some. As an associate editor of PLoS One, I have some experience with the more open discussion system, and I think it's vastly preferable. With something as high-profile as Science, you would probably want a moderator for continued online discussions of the new research, but it creates the opportunity for a real marketplace of ideas. I like the open marketplace model; it lets the good ideas come to the surface.

The article expresses some worries that people won't be able to deal with the "messy process" of science. Personally, I think it's dishonest to pretend science is anything else. And it's not like closing the reviews and hiding information makes things look neater. Frequently, the product is a flawed research article that is exposed on somebody's blog within a day of publication. That doesn't make anybody look good.

Except, maybe, the blogger!

I think it's a good idea to set out with a purpose for the new year. If there is one thing that describes the important work underway, it is bridging the gap between the natural history of humans and our molecular makeup.

Except, well, "bridging the gap" is way too overused. It's like "building bridges to the 21st century" and the like. Plus, it has this huge structural connotation. It takes a lot of people working together to build a bridge. Everybody knows that.

That's why it's such a good metaphor: plausible deniability. "Hey, the bridge didn't get built? What are you looking at me for? I'm supposed to build a bridge all by myself? Get outta here!"

So I'm picking "be a gap junction". Let's look at what they are:

A gap junction is a junction between certain animal cell-types that allows different molecules and ions to pass freely between cells. The junction connects the cytoplasm of cells.

It makes a certain kind of connection between two things, allowing things to flow between them -- like a bridge. But it's tiny and operates rapidly, on a molecular scale. It's an individual, although it may work collectively with others.

For me, the gap junction is a perfect embodiment of this year's theme -- making connections between human molecular evolution and human natural history.

The evolution of our molecules has been coming rapidly into focus. Much more information about the broad scale of human molecular evolution will be coming online this year. There aren't so many people who can take this information and find the aspects of human natural history that it can address. The important changes in human evolution -- beyond the brain to other aspects of our biology, such as life history, diet, and social strategies -- are just as much a black box to many molecular biologists as genomics has become to many traditional anthropologists. There is something interesting there, no doubt, but what is it?

That's my field. That's what I'm working on. It's really exciting.

I bring this up not only because of the New Year, but also because of this article by Carl Zimmer in the current PLoS Computational Biology. It may not be a journal you typically read, but it's open access and worth a look.

Zimmer sets out to describe the dichotomy between natural historians -- paleontologists, field biologists, ecologists, and the like -- and molecular biologists. He gives a quick account of the hippo-whale problem, but it is in no sense exceptional -- anthropology has it's own examples of phylogenetic discord between molecular and paleontological specialists, such as Ramapithecus. The point is that there are increasingly two kinds of data -- molecular and natural historical -- and nobody is a specialist in both:

This experience made a strong impression on me. I was struck by the divide between these two kinds of biologists. Each group had a profound confidence in their own sources of information, and an abiding skepticism about the other's. As I learned more about the history of modern biology, I realized that this rift did not begin in the 1990s. It was already present in the 1950s, as molecular biologists began championing their new science over more traditional ways of understanding life.

Harvard University's biology department was a microcosm of this conflict. James Watson, fresh from discovering the structure of DNA, breezed into the department in 1956 with revolution on his mind. “It was time to sweep beyond mere description of animals and plants and move into a new biology based on chemistry and physics,” as Watson's biographer, Victor McElheny, writes [4].

Needless to say, the Harvard naturalists were not happy. Edward O. Wilson, entomologist, ecologist, and sociobiologist, pushed back hard. “Watson, having risen to historic fame at an early age, became the Caligula of biology,” he writes in his autobiography, Naturalist. “It was foolish, we argued, to ignore principles and methodologies distinctive to the organism, population, and ecosystem, while waiting for a still formless and unproved molecular future” [5]. The struggle only ended when Harvard's biologists agreed to split their department in two.

The Watson-Wilson dichotomy is an emblematic example, in that the real problem is as more due to personality and temperament than to the inherent difficulty of the subject. How many molecular biologists are requiring their students to learn about the fossil record? How many natural historians have been requiring molecular biology and genetics of their students? The answer is not zero -- indeed, far from it. But one or two courses in genetics generally give a good grounding in the molecular biology of ten years prior. The fossil record doesn't change so quickly, but a full theoretical grounding in the means of analyzing fossil samples takes a long time. It is very easy to pick and choose hypotheses and worry about the niggling doubts later.

As Zimmer points out, this problem of training leads to absurd extremes. Imagine a paper summarizing the evolution of a mammalian family -- one richly represented in the fossil record -- that doesn't include a single fossil.

One example of this new ambition was a paper published earlier this year on the evolution of cats [6]. The scientists offered a sweeping scenario for cat evolution, complete with migrations of cats out of Asia into the New World and back, along with the emergence of the major groups of felids, ranging from ocelots to bobcats to lions. The scientists based their scenario entirely on an analysis of cat DNA. They did not consider a single fossil of a cat, nor did they have a paleontologist expert on cats as a coauthor. Cat fossil experts inform me that fossils of true cats as old as 17 million years have been discovered in North America. The geneticists put the arrival of cats in North America at only 8 million years ago. Whether or not the DNA results are correct, it is striking that the report does not even mention the existence of fossils that do not fit the pattern.

Zimmer has written much about natural history, and has great sympathy for the paleontologists he has worked with. So the article's theme is the value of natural history knowledge as applied to molecular information (he refers to this as "computational biology", but that gives the lab guys short shrift). As an example, he describes the evolution of early vertebrates: Molecular information shows evidence for genome duplication between present-day jawed vertebrates and the agnathans. As Zimmer points out, this led the hypothesis of a sudden burst of evolution leading to the features of jawed vertebrates, but paleontology shows that the jawed vertebrates emerged gradually in the fossil record over a long time, with different features emerging at different times. In this instance, a "striking" hypothesis from considering molecular features in isolation is easily disproved by looking that the fossil record.

This is the frontier of human evolution: integrating the data from human genomics with our knowledge of human prehistory. The days when we had to argue about the phylogeny of a single gene are long behind us. Anthropological genomics is about being a "gap junction" -- taking specialist knowledge of human prehistory and applying molecular information to test evolutionary hypotheses.

And if single genes are behind us, so are single events. "Out of Africa" doesn't explain everything, nor does the origin of Homo, the origin of the hominids, or any other single event. When we were limited to one gene, we were limited to one event, more or less. More than likely, that one event really was about natural selection and the phenotypic expression (or linkage) of the gene. Genomics has opened new doors that let us examine the evolution of phenotypes over hundreds of thousands of years. We can examine the differences between loci in their genealogical patterns, and in some cases we can link those differences to demographic events.

It's about finding diversity among the evolutionary histories of different genes, and linking that diversity to the diverse causes of our own evolution. This will be the year that a true anthropological genomics begins to emerge.

References:

Zimmer C (2006) The Genome: An Outsider's View. PLoS Comput Biol 2(12): e156 DOI: 10.1371/journal.pcbi.0020156

I've had a few queries this week asking why I write "Neandertal" instead of "Neanderthal."

Probably most readers are familiar with the issue. For the background on the problem, I recommend the FAQ at TalkOrigins:

The first such fossil was discovered in 1856 in the Neander Thal, or "Neander Valley" in German, and became known as "Neanderthal Man". In 1904, German spelling was regularized to be more consistent with pronunciation, and "thal" became "tal". In 1952 Henri Vallois proposed that it should be spelt as the Germans spell it, and the "-tal" spelling has become widely used since then. The "-thal" spelling persists most strongly in England.

Anybody who writes much about Neander-types has to confront this issue. Science fiction writer Robert J. Sawyer has a thoughtful discussion where he concludes that "Neanderthal" with a "TH" is the most popular and least likely to confuse.

There is surely truth to that -- after all, I'm sure I wouldn't have readers writing in asking why I wrote "Neanderthal" with a "TH."

But I have a couple of reasons why I prefer my "Neandertal" with a "T":

1. William King was the first to make a taxonomic name for the group we call Neandertals. He named it Homo neanderthalensis -- that's "neanderthalensis" with a "TH". By the almighty rules of taxonomic nomenclature, that's the name our poor heroes are stuck with (instead of Schwalbe's vastly better, but slightly later, Homo primigenius, for instance). So using "Neandertal" with a "T" is an act of taxonomic subversion. Let's call it a pique.
2. "Neanderthal" with a "TH" has an ordinary English meaning that is well understood by everybody -- it means "stupid," "clumsy" and "brutish" all in one! Since that's not ordinarily what I mean when I'm describing Neandertals, I take advantage of the unfamiliarity of the alternate spelling to get people to think about them in a different way.

Now, I know that some folks like their hominids Hobbesian, and the "TH" surely fits that bill. Personally, I would say that the "T" works when it startles, but fails when it confuses. I like the aesthetic, but I myself may have to change it for a trade book. I'll be happy when we can stop talking about them as misunderstood and start talking about how we understand them.

But never forget: all the cool kids write it with a "T".

The Times Online has a short profile of Chris Stringer, with relation to the ancient Britain project. I just love the way it starts:

Shortly after marrying an archaeologist, Agatha Christie remarked: "An archaeologist is the best husband any woman can have. The older she gets, the more interested he is in her."

Professor Chris Stringer considers this as he makes his way through a maze of steel cupboards at the back of the Natural History Museum. His partner, Angela, is approaching her fiftieth birthday, but to interest him professionally she would need to be a good deal older: "Any younger than 10,000 years and I lose interest."

That is soooo cute!

(via Palanthsci)