March 3, 2007

Gutless Clams and One Researcher's Shame

There has been much talk about transparency and the distribution of literature in the scientific community and online, specifically when it comes to commercial publications versus open access journals like PLoS. With the recent move of more and more scientists to the blogosphere, we have the rare chance to see just such a discussion in real time, straight from the involved parties, as you will see below.

Jonathan Eisen and other researchers at UC Davis sequenced the genome of a giant deep sea clam (Calyptogena magnifica), which entirely relies on "gardens" of chemosynthesizing bacteria for its food (more here and here).

“The energy from hydrogen sulfide is used to drive carbon fixation in much the same way that chloroplasts carry out carbon fixation,” said Eisen. The symbiotic bacteria also fix nitrogen and produce amino acids, vitamins and other nutrients required by the clam.


Studies of the deep sea have implications for studying the origins of life, Eisen said. Life on Earth may have got its start with microbes living on such chemical reactions, before the evolution of photosynthesis.

“And they’re just plain interesting,” Eisen added.

It's not the only clam that plays host to food synthesizing symbionts, however. Tridacna clams (including the five foot, 500 pound T. gigas or giant clam) play host to symbiotic zooanthellae, colorful dinoflagellate algae, which photosynthesize food for the giant mollusk while it sun bathes in the shallow waters of South Pacific coral reefs. (Zooanthellae are a classical example of host-symbiont relations in sessile organisms.)

“The difference here is that while plants get their energy and carbon via photosynthesis by chloroplast symbionts, this clam gets its energy via chemosynthesis,” said... Eisen.

Eisen, it turns out, is a fairly active blogger. On his blog, The Tree of Life, Eisen laments his colleagues' decision to publish the article in Science:

[...] my collaborators failed to keep me in the loop that the paper was accepted in Science. Thus I did not find out about the paper until I did a google search for some other reason and noticed this Deep-Sea News Blog which had a story, well, about the paper in Science. It would of course have been nice to know the paper was accepted and coming out. It would have been even better to have seen the page proofs, which might have given me the chance to catch some little and not so little mistakes (e.g., the paper claims that this species has the largest genome of any intracellular symbiont sequenced to date - which is unfortunately not true).

Eisen would have rather been published in an Open Access journal:

I tried and tried to get Irene Newton the first author to submit this to another journal. But in the end, she did the brunt of the work, and thus she and her advisor, Colleen, got to pick the place.

[...] by choosing to publish the paper there [in Science] but not elsewhere, the field of deep sea symbionts may have been hurt rather than helped.

How could a Science paper hurt the field? Well, for one, Science with its page length obsession forced Irene to turn her enormous body of work on this genome into a single page paper with most of the detail cut out. I do not think a one page paper does justice to the interesting biology or to her work. A four page paper could have both educated people about the ecosystems in the deep sea, about intracellular symbionts in general, and about this symbiosis in particular. The deep sea is wildly interesting, and also at some risk from human activities. This paper could have been used to do more than just promote someone's resume (which really is the only reason to publish a one page page in Science).

You can read his entire post about the paper here (Eisen also has a nice embedded video of Calyptogena).

In the past, problems like these would be publicly addressed in letters to the editor, most likely published in scientific publications. This is a painfully slow process, relatively speaking. As soon as he heard about his paper being published under the wire, as it were, Eisen was able to respond publicly, sharing a perspective that was once confined to a lab or a community or a trade-specific publication.

Over the next decade (maybe less?), it will be interesting to watch how perspectives like Eisen's affect publication policy and the proliferation of info within the scientific community, and between scientists, writers and the public.


  1. Interesting. I sure hope open access becomes the norm. Since I'm not taking classes this semester, I can no longer access my university library's online journal database from home. I can drive 30 minutes to the school, search for papers, save them as PDFs, then mail them to myself, but that's just stupid. It seems like scientific journals would want to make information available to as many people as possible, especially with the debate about how scientifically illiterate most Americans are. And really, subscriptions to Science, Nature, and other good journals are just not affordable to many of us who are not working scientists (but still interested in reading journal articles).

  2. I agree Jen. I don't know how many times I "reach" for an article online to discover that I don't have access. It's truly irritating.