Wednesday, February 21, 2007

Why I am ashamed to have a paper in Science

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:

Below I have embedded a video of a dissection of what I think was a deep sea Calyptogena, just for the fun of it.

This was taken during a deep sea cruise I managed to get on. For mroe detail on this cruise, see the NOAA Ocean Explorers site here.


  1. Do you have a suitable 'Author's own version of accepted paper'?

    According to RoMEO ( you could at least stick that up on here...perhaps?

  2. Yes, well, since I was not included when the paper was resubmitted or edited, I do not have that but can try and get it

  3. I like the idea -- just like movies have director's cuts, we should have author's cuts of papers.

    Maybe we could even record commentary tracks: "When I was writing that paragraph my daughter was crying and that's why it isn't as clear as it could have been. Now this paragraph over here is clearly an homage to Woese & Fox, 1977, and I'd imagine most of you at home got the joke. You probably didn't see the secondary reference to Crick, 1958, though"

  4. This cuold definitely one up PLoS One ...

  5. Well, the papers can be extended with blog posts, just like the one you just posted. For my last paper I tried to explain a little bit where the ideas for the work came from in blog.Something like a "making of". Right now the only problem is that it is not easy to get all these blog extensions visible near the papers. I have several greasemonkey scripts to overlay postgenomic blog comments into the publisher's websites but it should be the other way around. It should be up to the publishers to offer to the readers aggregated blog comments.

  6. Jonathan, why didn't you simply remove your name from the paper in protest, so as not to continue your association with such a non-open journal?

  7. You know, I have done that in the past, but never had the chance to do this here since it was resubmitted without my knowledge. I really figured it would not get accepted and they said the next choice could have been be an Open Access journal. I guess I have not yet become as radical as I would like to be. However, I am not sure removing my name does anything useful in this case --- but it would probably have been the right thing to do.

  8. I did a tally for citations for JA Eisen since 2000 (when open access actually started becoming a choice). Note how few open source papers there are in this tally. Ashamed of being in Science - really? What specific feelings changed between the eighth publication (supposedly guilt free) and the ninth guilt ridden entry?

    The stats are below...the numbers do all the talking!

    citations in peer reviewed journal publications:
    PLoS Biology : 5
    Science: 9
    PNAS: 7
    Genomics: 2
    App Environ Microb: 1
    PLoS Genet: 1
    Photosyn Res: 1
    Int J Syst Evol Mic: 1
    Nature: 5
    Genetics: 1
    Nature Biotech: 2
    J Bact: 3
    PMB: 1
    Environ Micro: 1
    Methods Enzym: 1

    PLoS Biology 2
    OMICs: 1
    Genome Biology: 1
    Science: 2
    J Bact: 1
    Theo Pop Bio: 1
    PNAS: 1
    Nature: 3
    COPB: 1
    COGD: 1
    COM: 1
    Res Mic: 1
    COSB: 1

  9. What an absolutely absurd and misleading comment. Sure it is true that I have published many papers in Science and Nature and other non Open Access journals. But look at the dates. How misleading can you try to be? Yes, I did not convert to Open Access immediately upon it being an option. But I did convert in ~ 2004 and now only publish in OA journals when I have control. For example of my last 10 papers (see below), 5 are in PLoS Biology, one is in PLoS Genetics and one is in PNAS (these are all OA). One is in AEM, which some would count as OA. The three non OAs are the Science paper you refer to, an OMICS commentary that I tried to get the authors to submit elsewhere but failed and a Genomics paper that I also failed to get the authors to submit elsewhere. Admittedly I could have removed my names form those papers, which in fact I regret not doing, but ALL papers I have major influence on go to OA journals.

    Here are my last 10 papers:
    1. Eisen JA.

    Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes.
    PLoS Biol. 2007 Mar 13;5(3):e82

    Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC.
    Abstract The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific.
    PLoS Biol. 2007 Mar 13;5(3):e77

    Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC.
    Abstract The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families.
    PLoS Biol. 2007 Mar 13;5(3):e16

    Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM.
    Abstract The Calyptogena magnifica chemoautotrophic symbiont genome.
    Science. 2007 Feb 16;315(5814):998-1000.

    Goldman BS, Nierman WC, Kaiser D, Slater SC, Durkin AS, Eisen JA, Ronning CM, Barbazuk WB, Blanchard M, Field C, Halling C, Hinkle G, Iartchuk O, Kim HS, Mackenzie C, Madupu R, Miller N, Shvartsbeyn A, Sullivan SA, Vaudin M, Wiegand R, Kaplan HB.
    Abstract Evolution of sensory complexity recorded in a myxobacterial genome.
    Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15200-5. Epub 2006 Oct 2

    Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E.
    Free Full Text Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.
    PLoS Biol. 2006 Sep;4(9):e286.

    Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjolander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C.
    Abstract Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).
    OMICS. 2006 Summer;10(2):231-7. Review.

    Hamilton EP, Dear PH, Rowland T, Saks K, Eisen JA, Orias E.
    Free Full Text Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome.
    Genomics. 2006 Oct;88(4):443-51. Epub 2006 Jun 19.
    PMID: 16782302

    Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, Eisen JA.
    Abstract Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters.
    PLoS Biol. 2006 Jun;4(6):e188.
    PMID: 16729848

    Penn K, Wu D, Eisen JA, Ward N.
    Abstract Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts.
    Appl Environ Microbiol. 2006 Feb;72(2):1680-3.
    PMID: 16461727

  10. Hi Jonathan.. I'm very pleased with your point of view, wich, by the way, lead to profound questions about science (the millenary practice). I'm a graduating student from Brazil, and we know, most than everyone, that free information is crucial to development of science and humanity itself. A humanity worried not just with profits and good looking careers, but essentially with ethics and a global purpose.

    ps: Sorry about my poor english. Good luck.

  11. thanks for the support ... it seems to me that many many many people in the rich countries take a very self centered view of science ... there are many phenomenal scientists in places that cannot afford subscriptions to all the latest journals ... the world would benefit greatly by allowing ALL people better access to scientific discoveries

  12. Dear Jonathan,

    Almost four years have passed since your post was published about your article published in Science (mentioned in - but we at InTech Open Access publishers were so amused and impressed that we just had to write and give you a big shout out!

    We send you our warm regards from Croatia and wish you all the best your scientific and publishing endeavours.

    Nataly Anderson


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