It discusses the story of the discovery of the first hydrothermal vent oases back in 1977. I note this is near and dear to my heart. I worked as an undergraduate and then after graduating in Colleen Cavanaugh's lab at Harvard on chemosynthetic symbioses. And then amazingly I got to go on the 2002 deep sea cruise celebrating the 25th anniversary of the discovery of the vents. On that cruise Rosebud (mentioned in this article) was discovered.
I have always been fascinated by life in extreme places on the planet. And somehow I have managed to do projects on microbes from places like Antarctica, boiling hotsprings in Yellowstone and Kamchatka, acid pools, and more. The extremes are fascinating to me because they tell us a lot about the limits of life as well as indirectly about life in "normal" places.
And of course, I am not alone. Many many scientists are fascinated by life's extremes. But not everyone ends up studying life in extreme environments of course. One reason for this is that many extreme environments that might be of interest are kind of hard to study. Consider the deep sea. Not so easy to do work there and just getting samples can be a massive undertaking.
Just imagine though. What if there were a way to "tag along" on an existing project studying life's extremes at no cost to you or your grants? Even better what if there were a way to get extra funds to not just tag along on a project but to carry out detailed research at the same time?
As many of you know, I generally avoid writing about non open access publications here. But occasionally I make exceptions. And I am making one today. There is a wicked cool paper out in Nature today. Entitled "Hydrogen is an energy source for hydrothermal vent symbioses" comes from Nicole Dubilier, Jillian Petersen and others. It is about my favorite ecosystem(s) on the planet - hydrothermal vents. I became interested in these vents in 1989 when I met Colleen Cavanaugh who at the time was a Junior Fellow at Harvard. She told me about her work on bacteria that live inside tubeworms, clams and other creatures in the deep sea that are key to the lives of these animals. The bacteria are chemosynthetic (i.e., they use the energy of chemicals to drive carbon fixation). The animals have either no digestive systems or very degenerate ones and the bacteria function much like chloroplasts do for plants. The bacteria basically make everything for their hosts while the hosts collect energy (chemicals in this case) and oxygen and CO2 for the microbes.
After hearing Colleen tell me about her work on these symbioses and how at the time nobody knew much about the symbionts, I joined her new lab at Harvard (she was just appointed as a junior professor) and worked in her lab in my Senior year and after graduating (and ended up publishing my first paper on symbionts of a clam Solemya velum). I have been captivated by symbioses ever since. So much so that many years later I worked with Colleen, Irene Netwon, Tanya Woyke, Dongying Wu and others to sequence and analyze the first genome of any of the chemosynthetic symbiotic bacteria.
So I just had a paper published in Science last week. In many ways, it has all the makings of one of those papers I should be really proud of. First, it represents a collaboration with my undergraduate advisor, Colleen Cavanaugh, the person who inspired me to go to graduate school and who got me interested in microorganisms, which I have worked on ever since (I published my first scientific paper on work I did in her lab). The paper is on one of the coolest biological systems on the planet - bacterial symbionts of deep sea animals that allow these animals to function much like plants (they use chemosynthesis in much the same way plants use photosynthesis). Studies of the deep sea and of chemosynthesis are important for understanding the origin and evolution of life, for understanding global carbon cycles, for understanding the rules by which symbioses evolve and much more. And on top of all of this, the paper reports the sequencing and analysis of the complete genome of one of these symbionts (that from the clam Calyptogena magnifica) - and one of my main areas of research is on the evolution of the genomes of symbionts. And, the genome was sequenced at the Joint Genome Institute, where I now have an Adjunct Position and am working with extensively. All sounds good right? And, I should be happy to get a paper in Science too, right?
Actually, in reality, I am not pleased with how this paper has turned out. This is really due to two things. First, 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). Now, admittedly I was out sick for a while and maybe my collaborators just did not want to bother me with this information. More likely- people were just very busy - and this just slipped through the cracks.
But you know - it is a Science paper. I should be happy however it came into being right? Well, no. Completely and thoroughly wrong. You see, I do not support publishing things in Science. I object because Science is not 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. And in the time since Irene submitted the paper, I have become even more miltant against publishing in such non Open Access journals. Publishing in a non Open Access journal like Science make me feel icky in every way. In addition, by choosing to publish the paper there 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).
But of course, even more importantly, anyone without a subscription to Science, well, they can't even read the paper. And AAAS gets to decide what happens to the text and figures in the future. So - count this as one of my papers I am not really proud of. I love that I helped my Undergrad. advisor and one of my favorite people in the world do this work. But by it not being in an Open Access journal, I have unfortunately contributed to a system that I think is bad for the world. And I just fell icky.
Some news stories and blogs are coming out on the paper:
