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23. The Microbial Commons: Journals and Professional Societies – Samuel Kaplan50 University of Texas at Houston Medical School I was chair of the Publications Board of the American Society for Microbiology (ASM) for nine years, so I am very familiar with ASM journals. The nine peer-review journals and two review journals were publishing annually approximately 55,000 pages as of several years ago. This is a lot of information. Digitally, the materials are posted on HighWire Press and in PubMed Central, as well as through Google, so this content is very well available. It is also available through PubMed International, which makes literature in PubMed available in other countries. Last year on HighWire Press alone, there were 18.6 million PDFs downloaded. To me, that spells access. About 40 percent of the manuscripts submitted to our peer-review journals are accepted. We could make our journals more “boutique” by lowering the acceptance rate, but we feel that a scientific society should encompass the broadness of the field, i.e., covering the field of microbiology. For us, this is a very important reason for our being. More than 50 percent of our publications now have foreign authors, a figure that has increased steadily over the past decade and a half. Fifteen years ago, approximately 30 percent of accepted publications were from foreign authors. The journals are important to scientists in various ways. In order to get grants, for instance, you need publications in good, peer-review journals. The quality of manuscripts and where they have been published also affects career advancement. This is not free, of course. Those 55,000 pages—print, as well as digital—cost about $20 million yearly. It is a big operation, and it costs a lot of money to get this kind of quality. It is impossible to imagine such an operation without the effort and structure that is put into it. If we were to stop printing paper copies, the cost would drop to about $13 million yearly. I tried very hard to get rid of print journals for the ASM before I stepped down as chair of the Publications Board. However, it was felt we could not drop print even though getting rid of that format would have allowed us to perform a variety of other activities. I should note, however, that the digital form of the journal, not the print journal, is now the official copy of record. How do the ASM journals fit into the microbial commons? We have 144 editors and a stable of 28,000 reviewers, of which 13,000 were actually used in the past year. So if you are thinking about supplanting the established journal process, you should think carefully about the magnitude of that undertaking and how this could be accomplished. Thanks to the National Library of Medicine, all of our journals are digitally archived and available, beginning with the first publication of the Journal of Bacteriology in 1916. We have standardized the literature across the field. Researchers, who communicate, need to have a sense of how to talk to one another in a field, so all of our journals try to standardize that process. This is not always successful, but there is a reason for having print journals or, if not print, at least a recognized subscription and editorial process. 50 Presentation slides available at isionSelectionMethod=Latest. 165

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The journals also provide quality control and readability. We have over 60 people on staff, a large number of whom are involved in copyediting. Although it costs a lot of money to copyedit journals, it is important. Moreover, the fact that more than half of our articles are now authored by foreign nationals makes the issue of copyediting and readability in English much more important across the field. Furthermore, the journals provide control over the format and presentation of figures and tables. Despite the many pages of information we provide concerning how to submit a paper and what format the figures and tables should take, they come in as a hodgepodge. So unless somebody does the work to put them all into a consistent format, readability would be impossible. Journals also digitize content for broad distribution. Soon, perhaps, the print version will be dropped altogether in favor of the digital format because this would make it possible to be involved in more areas, such as the gray literature, data mining, and other functions that can only be done online and that are not available through the print journal. Journals also help with nomenclature in microbiology. This is vital in dealing with the coming avalanche of digital information. There are 40 terabytes of genes coming down the road, and you have to call them something. It is no good simply to have a million genes and wish to communicate about them. They have to have names. There has to be some way of recognizing these genes, which means that nomenclature is a critical issue, but it does not arise de novo, nor is it maintained within a vacuum. The ASM journals try very hard to standardize nomenclature according to the old Demerec’s rules, but it is simply impossible. Last year there were 540 manuscripts published where nomenclature was a serious issue in terms of trying to standardize what people call genes. In establishing a microbial commons, this is something that should be addressed up front. What do you call genes? You can have digital identifiers which are a best effort to identify a gene, but within such a context there are some genes that are known with 100 percent certainty, there are many genes where the probability of their function is less than 60 percent, and there are many, many genes whose functions are unknown at any level of probability. This is a real problem and only getting worse. Without rigid structural context, we only will exacerbate this problem. Finally, as has been mentioned several times in this meeting, journals play a major role in making sure that biological materials are shared. We have a strict rule in all of our ASM journals: If you do not provide the materials to the community that you published about, you are not going to publish in an ASM journal again. Indeed, we very often get complaints from researchers who tell us that they have had difficulty getting the biological material from a cited author. If the report was published in an ASM journal, we will write to the author and remind the author of our rule. We cannot take the author to court, but we try to use whatever powers we have (denial of future publication in an ASM journal) to ensure the sharing of biological materials. We also try to use the power that we have to make sure that the materials and methods are completely described. We have refused to publish papers—even otherwise scientifically acceptable papers—where authors have not provided enough detail concerning the materials and methods. What should journals do to further the advance of science? Here is my personal wish list assuming that all were digital and we did not have the constraints of print copy. I would start with free and immediate availability. If you are a member of the ASM, you can get immediate digital access to all 55,000 pages for $235 a year. That may seem like a lot of money, but an iPod costs $200, and everyone seems to have one. 166

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In addition, everything we publish is put on PubMed Central. When I took over as chair of the ASM Publications Board, all our journal content was made freely available after one year through PubMed Central. We reduced that period to six months, and then to four months free, during my tenure. When I left the Publications Board, they increased it back up to six months. I also would like to remove all copyright restrictions. The only time that I know of that the ASM journals enforced any copyright restriction has been when a commercial publisher has used some of our material without the appropriate attribution. We did not seek to charge a fee, but only to require the appropriate attribution. I would like to be able to crosslink our content with that of all the other microbiology journals. I would like to be able to link references and tables of contents. I would like to incorporate unsolicited peer review and the gray literature. You can only do this, however, if everything is digital. I would certainly like to encourage data mining, and I would like to arrange for the development of “critical tables”. This is my pet peeve. Physicists and chemists have critical tables: You can find the boiling point of anything; you can find the molecular weight of anything or the refractive index. For the genome projects, I would like to see a series of “genomic critical tables”. It is already possible for me to click on E. coli and see what pathways it has and so on, but I would like to be able to do more. I would like, for example, to start with something like the enzyme lysine decarboxylase, then click on that and find all the organisms that have lysine decarboxylase in order to find out the map position of its cognate gene. I would like to be able to find out many things about that enzyme and to find out its nomenclature as well as its molecular size, pH and temperature optima, as well as regulatory elements and so much more. Returning from this ideal world to the real world, I am going to touch on several issues facing scientific publishing, and I will begin with the cost of content. When print was the only option, the cost of content or of getting access to content was based upon the “three-legged stool” model. The three legs were subscriptions to libraries or institutions, subscriptions to members, and page charges to authors. Now, institutions are rebelling, and everyone is saying the literature should be free. Even members of the ASM find it pricey to pay $235 to get all this content. So, with the advent of open access, the question has been raised, Why not have the author pay the full cost? Here is the problem. Recently Nature announced that it will cost $3,000 to have an article published under open access conditions and, in general, the going price seems to be somewhere between $2,800 and $3,500 to have an open access article published. If you as a researcher publish 10 articles a year, that is $28,000 to $35,000, but even three per year would be costly. No study section at the NIH that I know of is going to give you $35,000 in your grant for publication costs. The NSF is even worse. When we raised the page charges of certain high-impact ASM journals from $55 to $75 we got a flood of complaints from prospective authors saying it was outrageous and they would never publish in those journals again. Given that the total price might have been around $800, imagine what they would have said if it was $3,000? So, we are going to have to address this issue. One way or the other, it costs money to publish. So who is going to pay if the authors cannot or will not do it? Protection against misuse is going to be another major issue. This is something that the organized journals do very well. If, for example, an author ever came to us and said, “I just saw my figure published in another paper,” we would approach the editor or the publishers of that paper and investigate the situation. 167

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The detection of falsification and plagiarism is another job of the scientific journals. This is a real problem. Believe it or not, it happens a lot. It takes a concerted effort, costing time and money, to perform the necessary sorts of policing activity, and it cannot be done in a lackadaisical fashion. Dual use refers to situations where a given scientific finding can be used for good—the purpose of its publication—or it can be used for evil, say, to make some bioweapon. No one has mentioned such dual use regarding the microbial commons and open access, mainly because it has not been on people’s radar screens recently, but if there is another anthrax incident or something similar, it will quickly get attention. As soon as you were to start releasing all of this information free without any oversight— which, by the way, is what I believe should be done—then the issue of the “bad guys”, whoever they are, using that information for evil purposes becomes a concern. Thus dual use poses a real threat to open access. From my perspective, one of the most important issues is journals’ income and the role of professional societies in promoting science. Professional societies do many things beyond publishing journals and holding meetings. There is a collective membership, for example. The ASM has about 40,000 members, but in a sense that membership extends out to all the people who publish in ASM journals or attend ASM meetings, which by the way, are both populated by a minor fraction of members of the ASM. The ASM has educational programs that range from kindergarten to high school, and we spend a lot of money on those programs. We serve on government panels, for example. When the government asks someone from the ASM or its leadership to serve on a panel or committee, or to represent the government overseas on some issue, the government does not pay for it. The travel expenses come out of ASM money. This is part of what we do to promote the field of microbiology. We interact and cooperate with other societies, as well. We hold joint meetings and have joint publications with other professional societies. We develop standards for quality control. We lobby the government on behalf of microbiology and of biology in general. We spend considerable sums to enhance the profession in terms of CMEs (educational credits required to enhance the professionalism of scientists and technicians) and other things. We provide scientific information to the public in many forms, such as the Microbe Minute on National Public Radio. The Wash Your Hands Program, which began 8 or 10 years ago, was an ASM-sponsored program. The journal of tomorrow, as I see it, will be one that is fully digital and that is interactive at all levels with the community at large. When considering the establishment of a microbial commons, there are a number of questions we should be asking: Who contributes to this commons, and how do they contribute? What will the content be? Will recognition be attributed, and by whom, from whom, and to whom? Who will pay for the cost of the commons? Who will provide the upkeep? Who will validate, vet, verify, and provide access to the commons? Who will maintain the commons over time and so much more, as described above? 168