john hawks weblog

paleoanthropology, genetics and evolution

open access

  • Sit down and shut up

    Tue, 2012-05-08 23:22 -- John Hawks

    Carole McGranahan describes a memorable case where academics shut down public discussion of their work: "Dialogue with the Public: Adam Yauch and Academic Snobbery". The subject of the story is the recently deceased Beastie Boys member Adam Yauch.

    Before anyone on the panel could reply, one of the conference organizers—a Harvard professor—stood up and said forcefully that this was an “academic conference” and that “emotional” questions would not be entertained. He made it clear we were here to discuss real politics in an academic, dispassionate manner. That is: in discussing politics we were to be apolitical.

    A celebrity unrecognized by the academics, asking a simple question.

  • Turning around the profits

    Sun, 2012-04-22 14:55 -- John Hawks

    The absurdity of academic publishing is starting to get attention from the mainstream press. From The Economist: "Open sesame".

    PUBLISHING obscure academic journals is that rare thing in the media industry: a licence to print money. An annual subscription to Tetrahedron, a chemistry journal, will cost your university library $20,269; a year of the Journal of Mathematical Sciences will set you back $20,100. In 2011 Elsevier, the biggest academic-journal publisher, made a profit of £768m ($1.2 billion) on revenues of £2.1 billion. Such margins (37%, up from 36% in 2010) are possible because the journals’ content is largely provided free by researchers, and the academics who peer-review their papers are usually unpaid volunteers. The journals are then sold to the very universities that provide the free content and labour. For publicly funded research, the result is that the academics and taxpayers who were responsible for its creation have to pay to read it. This is not merely absurd and unjust; it also hampers education and research.

    I expect that universities will begin to compete for prestige as the publishers of top open access journals, instead of as subscribers to expensive pay-for-access journals.

  • Our plenary session gets coverage

    Fri, 2012-04-13 15:22 -- John Hawks

    I don't have much time to come up for air this week, it's been an incredibly busy and exciting meeting so far. But I wanted to take a moment to pass along this link, in which Ann Gibbons describes last night's plenary session for Science: "Anthropological Casting Call".

    Paleoanthropologist John Hawks of the University of Wisconsin, Madison, explained that he organized the 12 April share-and-tell session of published fossils at the annual meeting of the American Association of Physical Anthropologists because many members have never even seen casts of important fossils, including Lucy, the 3.1-million-year-old member of Au. afarensis. As he lined up three skulls that showed changes in the evolution of the members of the human family from 1.8 million to 1.6 million years ago, Hawks said that seeing the fossils is the best way to learn about human evolution. "There are people in this association who are responsible for teaching evolution in the U.S. who have not even seen a cast of Lucy," he said.

    What an incredible crowd we had -- at one point around 200 people, crowding around the biggest collection of fossil casts that has ever been assembled at the meetings. Here's a photo from my phone; I wish I had a wide-angle lens to get the entire crowd, as this is less than half of the room!

    Plenary cast session
  • A plenary of plenty

    Wed, 2012-04-11 00:41 -- John Hawks

    I've arrived in Portland, Oregon today for the annual meeting of the American Association of Physical Anthropologists. This is really a central highlight of the professional year for biological anthropologists like me, and it's always great to see old friends, to meet new ones, and to see the exciting work that many people are doing.

    It has been great for me today because almost everybody I've run into in the hallways has told me how interested and excited they are to see the AAPA Plenary Session this Thursday evening. "Plenary" means that nothing else is formally going on at the same time, so everyone at the conference can in principle attend. At many meetings, plenary sessions are stodgy affairs in which the hoopdedoos of the field stand up to pronounce their latest opinions in front of a captive audience. The AAPA has always done something different with the plenary session, giving an opportunity for the lighter side of science, sometimes entertainment, sometimes issues.

    This year, Karen Rosenberg approached me with an idea that is really different from anything the association has done before. Last year, the Institute of Human Evolution at the University of the Witswatersrand donated a set of casts of the Malapa hominin skeletons to the Association. It was a great act of generosity, but also a message about the importance of disseminating these materials to professional anthropologists. Over the past twenty years, we have been incredibly fortunate to recover a vast and growing hominin fossil record. Our traditional way of educating ourselves about these materials is to distribute casts, as pictures cannot really substitute for examining the physical form. But our distribution system has not kept up with the pace of discovery. Too many professional anthropologists today are teaching human evolution without ever having the chance to examine even casts of the materials. Karen asked, why couldn't we invite other people to bring casts of fossil specimens and have an open lab night for the association?

    I thought this was a really inspired idea, and I set at the project with all my Andy Hardy "Let's put on a show!" enthusiasm. It has been a lot of behind the scenes work, with the generous help of some people who have really gone beyond all expectations. As I gathered more participants, I really saw a spirit of openness that has emerged in institutions across the U.S. and on many continents. Some casts are being brought by meeting participants on behalf of international institutions, others are sending their own to the meetings specially for the session.

    The list of participants has become very impressive, including:

    • Kenya National Museums
    • National Museum of Georgia
    • Croatian National History Museum, and the Museum of the Krapina Neandertals
    • National History Museum, London
    • Turkana Basin Institute and Stony Brook University
    • Institute of Human Evolution and University of the Witswatersrand
    • Luigi Pigorini National Museum of Prehistory and Ethnography
    • Max Planck Institute for Evolutionary Anthropology
    • Boston University
    • University of Delaware
    • University of Kansas
    • University of Michigan
    • University of Oregon
    • University of Pennsylvania
    • University of Texas, Austin
    • University of Wisconsin-Madison

    I'm sure that I have forgotten some as I've been tabulating them, and I will continue to update as I add institutions for the online component of the session. As you can see, it's a great list, and right now I only wish I had time to have gotten materials from even more. If the session is a success, maybe the AAPA will make it a regular event, and we can bring even more materials. It really wasn't all that hard, once we got started.

    I really wanted to add to the session one other thing -- a way to connect the session to people who cannot attend the meeting. We can't bring casts everywhere, but I can highlight some of the public resources that exist online for sharing anthropological materials with other professionals and the public. I'll be highlighting a series of those resources here over the upcoming weeks, forming a continuing online exhibition to coordinate with the physical plenary session at the meetings.

    As you have probably noticed from the blog, I've been doing a lot of thinking lately about how to maximize the scientific value of conferences. How can we take a traditional conference and make it more useful for the participants, while broadening it to people who cannot attend? It's clear that our association has a professional need to make sure that human evolution and human biology are being communicated at institutions by experts who have seen the evidence. We can make the opportunities for this exchange of information. As an association we can do something to serve those institutions who cannot afford the newest and largest collections of materials themselves. And as I'll be featuring online resources, many of our institutions are already doing great work bringing photos and models of materials to students and the public.

    I hope that I can spread some of the excitement about what's going on now in human evolution. I don't know what to expect for a crowd in the room on Thursday evening, but if you're at the meetings, unless you're at one of the best-stocked cast laboratories in the country (and maybe even then) I can guarantee we've got some casts you haven't seen. I have some graduate students who are itching to help people learn about things, and hoping we can bring a real spirit of openness and learning to the session.

    Synopsis: 
    How we put together an open cast lab for the AAPA meetings in Portland
  • Wiki into journal

    Thu, 2012-04-05 20:22 -- John Hawks

    PLoS Computational Biology has started a new collaboration with Wikipedia, in which short review articles called "topic pages" will be peer-reviewed, given journal references, and simultaneously put on Wikipedia to further its content in computational biology. From the journal editorial by editor Shoshana Wodak and colleagues [1]:

    Topic Pages are the version of record of a page to be posted to (the English version of) Wikipedia. In other words, PLoS Computational Biology publishes a version that is static, includes author attributions, and is indexed in PubMed. In addition, we intend to make the reviews and reviewer identities of Topic Pages available to our readership. Our hope is that the Wikipedia pages subsequently become living documents that will be updated and enhanced by the Wikipedia community, assuming they are in keeping with Wikipedia's guidelines and policies, either by individuals, or, perhaps as is already happening in medicine and molecular and cell biology, by something more organized, or with a more formal review structure. We also hope this will lead to improved scholarship in a changing medium of learning, in this case made possible by the Creative Commons Attribution License that we use.

    The first of these topic pages appears in the current iteration of the journal, by Spencer Bliven and Andreas Prlić [2]. It is interesting to see a journal article following the basic outline of a Wikipedia entry, but also refreshing because it gets to the point. I would seriously consider writing this kind of publication, which would have much greater impact than the typical review article.


    References

    1. Wodak SJ, Mietchen D, Collings AM, Russell RB, Bourne PE. Topic Pages: PLoS Computational Biology Meets Wikipedia. PLoS Computational Biology. 2012;8(3):e1002446.
    2. Bliven S, Prlić A. Circular Permutation in Proteins Wodak S. PLoS Computational Biology. 2012;8(3):e1002445.
  • Floating to the top of the data

    Sun, 2012-02-12 20:10 -- John Hawks

    The New York Times writes today about "Big Data" and its effects on disparate fields of science and public policy: "The Age of Big Data".

    For my money, this quote should be at the beginning of the article instead of embedded near the end:

    Big Data has its perils, to be sure. With huge data sets and fine-grained measurement, statisticians and computer scientists note, there is increased risk of “false discoveries.” The trouble with seeking a meaningful needle in massive haystacks of data, says Trevor Hastie, a statistics professor at Stanford, is that “many bits of straw look like needles.”

    Big Data also supplies more raw material for statistical shenanigans and biased fact-finding excursions. It offers a high-tech twist on an old trick: I know the facts, now let’s find ’em. That is, says Rebecca Goldin, a mathematician at George Mason University, “one of the most pernicious uses of data.”

    The article begins by hyping the career prospects for graduates who can analyze large datasets. I would emphasize that good analytical skills don't emerge naturally from working with data, they must be learned as part of one's scientific training. The top hazard working with large datasets is that they can temporarily knock out your BS meter.

    We are obviously in the realm of big data now in paleoanthropology, as we grapple here to compare genomes that sum into the terabytes. I periodically link to stories about open access in astronomy precisely for this reason: those instruments generate terabytes of data and more every night.

  • American Anthropological Association keeps it from the people

    Thu, 2012-02-02 16:34 -- John Hawks

    Last month, the White House Office of Science and Technology Policy solicited comments concerning open access publication policies for federally funded research. I submitted a comment to a related solicitation, concerning open access to data from federally funded research ("Public interests in data from federally funded research"). But the open access publication comments are also interesting to me, and the OSTP has just released the full list of comments to the public ("Public Access to Scholarly Publications: Public Comment").

    Included in the list is a comment written on behalf of the American Anthropological Association by its executive director, William E. Davis, III (PDF of comment). The letter is a defense of closed-access journal policies, and includes many statements that I view as disputable.

    For example, Davis addressed the embargo period for open access to journal articles. The NIH access policy allows this embargo period for journals to restrict exclusive access to subscribers for 12 months after publication.

    First, after twelve months much of the content in many STM fields is old news. An embargo period of 12 months often has little effect on the financial models upon which publishing in STM fields is based. In anthropology, however, where over 90 percent of downloads occur after 12 months from the date of publication and the cited half-life of our quarterly journals is over 10 years, a 12 month embargo period does nothing to hep protect our subscriptions.

    May I offer an alternative view of this problem? I suggest that the closed access policy has contributed to the irrelevance of AAA journals. Nobody outside the AAA membership notices when papers of note are published there. The AAA journals, including American Anthropologist have effectively cut themselves off from the rest of the academic world. The "half-life" is high not because new papers are steadily building more citations, but instead because their impact is anommalously slight compared to papers from 50 years ago.

    Instead of making its journals more rich and relevant, the AAA leaches vampire-like its past icons. Instead of giving libraries reasons to support its efforts, the Association depends on its university-based members to argue with their libraries' acquisitions staff to keep the journals despite their poor impact.

    Others have focused on this passage in the letter, which is particularly grating:

    We know of no research that demonstrates a problem with the existing system for making the content of scholarly journals available to those who might benefit from it. In a recent article published in the Journal of the Medical Library Association, authors Philip Davis and William Walters conducted a literature review and concluded that "...recent studies provide little evidence to support the idea that there is a crisis in access to the scholarly literature." A separate earlier study found that 93% of the researchers surveyed reported easy access to original research articles in journals. This study surveyed 3,800 researchers and evaluated their access to 18,000 journals. It is worth keeping mind [sic] that this same study found that 62% of these scholars enjoyed easy access to data sets, data models, and the research compendium of other scholars. AAA independently corroborated these results in a survey about anthropological information with its members, who reported in February 2009 very high levels of access to peer-reviewed journals and scholarly monographs.

    I think the most appropriate response to this passage is parody. Consider: "We know of no research that demonstrates a problem with the existing system of providing health care information to indigenous peoples.... A study of indigenous people covered by health plans found that 93% of them enjoy easy access to such information."

    The American Anthropological Association over the past several years has shaped policies that keep peer-reviewed AAA publications accessible only by members and large institutional subscribers. Past and ongoing journal issues are walled within the Association's "AnthroSource" archive, available with association membership or to institutional subscribers for a hefty fee.

    In 2007, when the AAA more than doubled the institutional subscription prices for its flagship journals, I ran some numbers on open access publication. Even using high-end price schemes, it was clear that open access electronic journals could be provided free worldwide for an annual cost of $10 per AAA member. That would represent a substantial cut in the cost of society membership, considering the current membership dues include a hefty subscription subsidy. Instead of moving toward an open access model of publication, the Association chose to provide its publisher partner (Wiley) with the opportunity to market AnthroSource and association-sponsored journals to libraries. For this, the Association receives some income, printing, and bit-moving services. Not too impressive, considering the low actual bit-moving requirements for these journals.

    Overall, the AAA statement is a defense of their current policies and an argument against being required by federal policies to release any content to the public. I believe it does matter. Anthropologists have increasingly been courted by NIH funding programs directed toward "ethical and social impacts" of biomedical research. Skimming the acknowledgements section of the American Anthropologist today will not find many references to NIH, but other federal funding programs are prominently represented. Anthropological research has always been supported by the public, both as funders and participants. The AAA has kept its head low until now, but if federal policies shift any further, they will find themselves subject to the embargo or other open access requirements.

    I am disappointed that AAA does not step forward into the lead on this issue. Public access to research results is the right direction for anthropological research. Davis is obviously wrong to write that "easy access to original research articles in journals" is available to the communities affected by anthropological research. Surely the legacy of distrust left by past elitism by anthropologists are evident to everyone?

    It is inevitable that we will move in the direction of greater and more open access to our research. The only question is whether today's institutions will be the ones to make the transition possible, or whether we will replace them with new ones. New journals and organizations springing up to support effective online communication and collaboration are very compelling for young academics looking for a more vibrant research community. Maybe the AAA's final transmogrification will be to Archie Bunkerhood.

    UPDATE (2012-02-04): The American Anthropological Association Executive Board has issued an attempt to clarify the organization's position: "American Anthropological Association Position on Dissemination of Research".

    Acknowledging the Association's commitment to "a publications program that disseminates the most current anthropological research, expertise, and interpretation to its members, the discipline, and the broader society," but also the need for a sustainable publication strategy, and building on the Association's support for a variety of publishing models, the AAA opposes any Congressional legislation which, if it were enacted, imposes a blanket prohibition against open access publishing policies by all federal agencies.

    This obviously raises the question of what they thought they were doing before, in their statement to the White House. In my view, the current position is weak beyond reason, but it does stop short of actual malevolence.

    More voices on this issue:

    Daniel Lende: "American Anthropological Association Takes Public Stand against Open Access"

    Doug's Archaeology: "American Anthropology Association FAIL!!!! This Time on an Epic Scale"

    Dienekes Pontikos: "The American Anthropological Association opposes open science"

    Savage Minds: "News: AAA Response about Public Access to Scholarly Publications", and "How do we mobilize anthropologists to support open access?"

    Synopsis: 
    A White House request for comment on access to journal articles brings an unexpected comment.
  • Open science interview

    Mon, 2012-01-30 10:46 -- John Hawks

    NPR's Science Friday interviewed open science advocate Michael Nielsen last week: "Can science be done without secrecy?" I like the headline.

    FLATOW: Why are scientists the last ones to get in on this?

    NIELSEN: Well, it's kind of funny. I mean, they certainly helped bring us the Web back in the early '90s. Unfortunately, they're pretty bought into doing things in the standard way, the way they've done them for centuries, which is you do your work in the lab, you get all your results, you write them up in a paper and possibly several years later, it all appears for your colleagues to digest at that point.

    And, you know, that's a great system if you're back in the 1600 or 1700s, but today we've got better tools, but people still haven't adopted them.

    It's a long, thoughtful interview. I want to point to a later part also:

    FLATOW: Mm-hmm. Is it - do you find that there is resistance to the way - to changing the way, the old way, of things being done? Are older scientists resistant to change and becoming part of this process?

    NIELSEN: I'm not so sure I'd say resistance so much as it's just difficult to see how to cause a large-scale change. How do you get everybody simultaneously to adopt the new way of doing things? And so some people will kind of throw up their hands and say, well, it just can't be done. Probably the people actually get that the most from, scientists who are sort of in their mid-career. They're doing post docs or they're at the end of their graduate studies. And while they're subject to the system, they don't really feel like there's very much they can do to change it. When I talk to younger scientists, they're often very enthusiastic. And sometimes, when I talk to much more senior scientists, because they feel like they have some power to actually change the system, they can actually be quite enthusiastic.

    Some thoughts on this later. For now, let me point again to my "Public interests in data from federally funded research."

  • "Journals seem noticeably less important than 10 years ago."

    Mon, 2012-01-16 16:56 -- John Hawks

    As ScienceOnline2012 gets underway later this week, the New York Times is running an article about open science: "Cracking open the scientific process". The article spends many paragraphs promoting a social networking startup for scientists called ResearchGate, which honestly strikes me as having a not-very-useful approach to openness. For example:

    Dr. Rajiv Gupta, a radiology instructor who supervised Dr. Madisch at Harvard and was one of ResearchGate’s first investors, called it “a great site for serious research and research collaboration,” adding that he hoped it would never be contaminated “with pop culture and chit-chat.”

    I doubt that a walled garden where scientists share their reprints is the wave of the future. The "answering questions" aspect of the site seems similar to the Faculty of 1000 and similar concepts. Such sites aim to make social sharing into a virtue for scientists by credentialing them. On the other hand, if a social network for science can succeed in filtering out politics, that might be worth paying for.

    There are many other things in the article. One thing that shocked me: The open access fee for Nature Communications is really $5000. Holy cow. For $5000 I could pay someone to sit in a coffee shop all day and hand-type the contents of my article into personalized e-mails to everyone who reads it. What the heck is that about?

Pages

Subscribe to open access

Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.