john hawks weblog

paleoanthropology, genetics and evolution

metascience

  • What should be the shape of the science journal landscape?

    Tue, 2013-04-02 23:12 -- John Hawks

    Michael Eisen, one of the founders of the Public Library of Science, has thought a lot about how to make the system of scientific publishing better. He has posted the text of a presentation he recently gave, which explains many of the current problems with access and curation: "The Past, Present and Future of Scholarly Publishing". In this passage, he suggests a different system that would obviate the problems finding appropriate research among the 10,000 different journals of the current publishing environment:

    So what would be better? The outlines of an ideal system are simple to spell out. There should be no journal hierarchy, only broad journals like PLOS ONE. When papers are submitted to these journals, they should be immediately made available for free online – clearly marked to indicate that they have not yet been reviewed, but there to be used by people in the field capable of deciding on their own if the work is sound and important.

    The journal would then organize a different type of peer review, in which experts in the field were asked if the paper is technically sound – as we currently do at PLOS ONE – but also what kinds of scientists would find this paper interesting, and how important should it be to them. This assessment would then be attached to the paper – there for everyone to see and use as they saw fit, whether it be to find papers, assess the contributions of the authors, or whatever.

    This simple process would capture all of the value in the current peer review system while shedding most of its flaws. It would get papers out fast to people most able to build on them, but would provide everyone else with a way to know which papers are relevant to them and a guide to their quality and import.

    So far, this kind of value-added curation is not happening very much with PLoS ONE. I'm an associate editor and I still can't keep track of all the research in the journal relevant to me. But even though I have access to many paywall journals through my university library, I still love the ease of just clicking on a link to a PLoS article. It just works, no library proxy, no password, just text. Creative Commons text and graphics, that I can freely comment and reuse. The way science should be.

  • Centuries of grant writing

    Tue, 2013-04-02 15:40 -- John Hawks

    Jenny Rohn has an article on the wasted effort into failed grant writing, which is so full of good paragraphs it's hard to figure out which one to snip: "Show me the money: Grantwriting is taking over science". Here's one:

    There is some evidence that having the vast majority of scientists spend the vast majority of their time writing grants instead of doing and thinking science might be a tad inefficient, and not, perhaps, the best way to get science done. A recent correspondence in Nature about the Australian system, for example, reported that collectively, in 2012, researchers spent "more than five centuries' worth of time" writing or revising grants for the major funding scheme; as only 20.5% were successful, this account for a staggering four centuries' worth of wasted time.

    I suppose if we looked at the U.S. we'd be talking about the geological timescale.

  • The problem of Lance retraction

    Mon, 2013-03-18 14:46 -- John Hawks

    Retraction Watch comments on a provocative case: Should a scientific paper that measured Lance Armstrong's exercise physiology during his Tour de France days now be retracted in light of revelations about his use of performance-enhancing substances? "Lance Armstrong in the scientific literature: A 'reconsideration'". The comment is prompted by an editorial in the Journal of Applied Physiology, which published the initial research [1].

    Should Coyle’s paper therefore be retracted? We do not think so; the data are the data, free of author-related ethical concerns. His editorial seems to be the best solution, especially because there can be no definitive answer. How much of the subject’s performance was attributable to his genetics and training, compared to how much was contributed by possible doping, may never be known, but that does not constitute grounds for retraction.

    Interesting just how often the paper has been cited in the years since its 2005 publication, although I'm not familiar enough with the physiology literature to judge.


    References

  • The cost of plagiarism at NSF

    Fri, 2013-03-08 20:04 -- John Hawks

    I pass this along from ScienceInsider, really too irritated for clever comment: "NSF Audit of Successful Proposals Finds Numerous Cases of Alleged Plagiarism".

    The National Science Foundation (NSF) is investigating nearly 100 cases of suspected plagiarism drawn from a single year's worth of proposals funded by the agency.

    The cases grow out of an internal examination by NSF's Office of Inspector General (IG) of every proposal that NSF funded in fiscal year 2011. James Kroll, head of administrative investigations within the IG's office, tells ScienceInsider that applying plagiarism software to NSF's entire portfolio of some 8000 awards made that year resulted in a "hit rate" of 1% to 1.5%. "My group is now swamped," he says about his staff of six investigators.

    So...

    Between 1 and 1.5% of the NSF budget is going to fund obvious plagiarists. Obvious because they can be caught with standard plagiarism filters, which are not richly seeded with scientific papers.

    Because closed access stands in the way of incorporating much of the scientific literature into such databases.

    And this doesn't count the incidence of grants that are given to applications proposing work that is already done.

    The NSF budget is not evenly distributed among grants, and I suppose that many small grants probably contain more plagiarism than the few really big ones. Still, we're talking about $50 million or so.

    UPDATE (2013-03-09): A reader writes:

    I was just reading your post on plagiarism, and it made me recall something that happened to me years ago when I was a practicing biochemist. My boss received a grant to review on some work proposed by one of our competitors. He passed off a copy to me to look at (I was a postdoc at the time.) On reading the background section, there was a paragraph that sounded familiar. I did a little looking around on my computer and it turned out the reason the paragraph sounded familiar was that I had written it. But not in a paper - it was in one of our grant proposals. The material didn't concern any proposed experiments - it was just part of a short review of the state of the field, so we never did anything about it. I knew the guy who did this and he was quite capable of writing a decent paragraph himself, so I never could figure out why he borrowed my material. Anyway, it may not be enough to get all the literature in the database - they should have all the other grant proposals in there too.

    This is another essential area. Probably the most common outcome is people stealing ideas from other proposals. The texts of unfunded proposals are not available to the public, which may cut down on stealing but also impedes comparing funded proposals. I tend to think that the lower the success rate, the more likely we'll see substantial cheating of one kind or another.

  • If we can describe a poster as beautiful, it is because it communicates effectively

    Fri, 2013-03-08 08:06 -- John Hawks

    Zen Faulkes, on why beautiful, well-made scientific poster presentations are not just an exercise in catching attention for oneself: "More than marketing".

    I also had a little l’esprit de l’escalier on what a well-designed poster says about its creator. It shows that you understand what is important. A poster almost always demands you leave stuff out, which means you have to make decisions about what to include, exclude, and emphasize. Thus, you can only arrive at a beautiful, well-made poster if you have a deep understanding of the research you are presenting on it.

    A well-made poster shows mastery of the material, not just tricks to grab attention.

    It's that time of year again, when people are designing poster presentations for the AAPA meetings. If you haven't before, check out Zen's "Better Posters" site.

  • IRB review

    Tue, 2013-03-05 23:27 -- John Hawks

    Zachary Schrag points to a report by the American Association of University Professors , and gives a quoted excerpt that deserves to be forwarded on: "AAUP Publishes Final Report, Regulation of Research on Human Subjects: Academic Freedom and the Institutional Review Board".

    As things now stand, the IRB system assembles local committees whose members have no special competence in assessing research projects in the wide range of disciplines they are called on to assess, whose approval is required for an only minimally restricted range of research projects and who are invited to bring to bear in assessing them an only minimally restricted body of what they take to be information, who are only minimally restricted in the demands they may make on the researchers, and whose judgments about whether to permit the research to be carried out at all are, in most institutions, final. When one steps back from it, one can find oneself amazed that such an institution has developed on university campuses across the country.

    Different kinds of human research raise different kinds of ethical concerns. A good aspect of the IRB process is that the board members themselves often learn a lot about the ethical issues in other fields. But the composition of particular boards can make the process of review troublingly arbitrary.

  • Fieldwork survey for current and former student anthropologists

    Sat, 2013-03-02 14:26 -- John Hawks

    Kate Clancy directs readers' attention to a new research project examining the conditions under which students have field experiences in biological anthropology: "The Biological Anthropology Field Experiences Web Survey: Now Live".

    We (Kate Clancy, Katie Hinde, Robin Nelson and Julienne Rutherford) invite you to participate in our Biological Anthropology Field Experiences Web Survey. The Biological Anthropology Field Experiences Web Survey is designed to solicit input on the ways in which fieldwork does or does not provide a safe scholarly and research environment for all. Rather than determining the total number of instances, or percentage risk of a negative experience, our interest is in gathering stories to inform Field Directors, faculty mentors, and other researchers and students on the scope of the problem, and identify some of the main contributory factors to a negative environment, both to encourage improvement and to identify future areas for research.

    If you’re over 18 and have ever done research or been a student at a bio anthro field site, please take 20 minutes to fill out our survey.You can indicate interest at the end in participating in a follow-up phone interview. You can also enter the lottery at the end for a 1 in 10 chance of winning a $25 Amazon gift card.

    It's an important project that is attempting to extend an understanding of field mentoring experiences beyond anecdotes. We all know of really good and really bad field experiences of our colleagues (or ourselves). If you have fieldwork experience as a student -- whether or not you continued on toward more anthropology training -- I encourage you to fill out the survey. Obviously, more people who have stuck around for training in anthropology are likely to hear about this survey, so please try to spread the word as much as possible to those who may have gone on to different careers.

  • Anthropology's Spinal Tap problem

    Tue, 2013-02-26 16:25 -- John Hawks

    The Thesis Whisperer brings up the topic of prolonged rudeness in academic culture: "Academic assholes and the circle of niceness". When I write that it's time to "reclaim the name 'anthropology' from this earlier generation", I mean that the elite discourse within the field has become toxic. Rude behavior often yields short-term gains, but has obvious long-term costs for the discipline as a whole:

    How does it happen? The budding asshole has learned, perhaps subconsciously, that other people interrupt them less if they use stronger language. They get attention: more air time in panel discussions and at conferences. Other budding assholes will watch strong language being used and then imitate the behaviour. No one publicly objects to the language being used, even if the student is clearly upset, and nasty behaviour gets reinforced. As time goes on the culture progressively becomes more poisonous and gets transmitted to the students. Students who are upset by the behaviour of academic assholes are often counselled, often by their peers, that “this is how things are done around here” . Those who refuse to accept the culture are made to feel abnormal because, in a literal sense, they are – if being normal is to be an asshole.

    Not all academic cultures are badly afflicted by assholery, but many are. I don’t know about you, but seen this way, some of the sicker academic cultures suddenly make much more sense.

    Yes, anthropology has been affected. Picking academic vendettas used to be a great way to get famous. The students -- at least the normal students -- suffered. The field has selected for bad behavior.

    Many elite anthropologists still consider the New York Times to be an arbiter of quality work. That is, if you are featured in the Times, you are visible to the elite. Yet the Times itself has become actively hostile to cultural anthropology as a field, selecting the worst instances of bad behavior for promotion and coverage. Some of my friends have been agitated for the last week waiting breathlessly for the Times to publish letters decrying the recent coverage.

    Seriously.

    You know that scene in This Is Spinal Tap?

    David St. Hubbins: I do not, for one, think that the problem was that the band was down. I think that the problem *may* have been, that there was a Stonehenge monument on the stage that was in danger of being *crushed* by a *dwarf*. Alright? That tended to understate the hugeness of the object.

    Ian Faith: I really think you're just making much too big a thing out of it.

    Derek Smalls: Making a big thing out of it would have been a good idea.

    Yeah. That one. The curtain has risen on the old band, and they're playing behind a Stonehenge monument that can be crushed by a dwarf. Please, somebody, lower the curtain.

  • Sahlins and Chagnon

    Mon, 2013-02-25 10:10 -- John Hawks

    Essential reading today for anthropologists: Serena Golden's account of how Marshall Sahlins resigned from the National Academy of Sciences: "A Protest Resignation".

    Sahlins' resignation highlights two serious and ongoing debates within anthropology: one, the appropriate relationship -- if any -- between anthropologists and the military (Sahlins has previously expressed his opposition to any such involvement); two, the role of hard science within the discipline.

    ...

    Asked to offer his opinion on Sahlins' move, [Napoleon] Chagnon wrote in an e-mail, "I am surprised that Sahlins resigned from the NAS to protest my election last year to the NAS. One possible interpretation is that he is displeased with the gradual swing back to to the academic principle that scientists should tell the truth in their publications...."

    I think it's time to reclaim the name "anthropology" from this earlier generation.

  • White House policy on data access

    Sun, 2013-02-24 23:29 -- John Hawks

    The White House this week announced a new policy on public access to results from federally funded research. The announcement has gotten

    Michael Eisen comments: "No celebrations here: why the White House public access policy sucks".

    The administration fell hook line and sinker for the ridiculous argument put forth by publishers that the only way for researchers and the public to get the servies they provide is to give them monopoly control over the articles for a year – the year when they are of greatest potential use.

    Think about how absurd this is. Publishers, whose role should be to disseminate information as widely as possible, are now the only reason why the public will continue to not have access to research results their tax dollars paid for.

    Why is Eisen so exercised? Here's an excerpt from the White House policy memo describing the policy on publication access:

    In developing their public access plans, agencies shall seek to put in place policies that enhance innovation and competitiveness by maximizing the potential to create new business opportunities and are otherwise consistent with the principles articulated in section 1.

    Agency plans must also describe, to the extent feasible, procedures the agency will take to help prevent the unauthorized mass redistribution of scholarly publications.

    In other words, it's no longer just a matter of copyright agreements with publishers; now the federal agencies themselves must help police PDF sharing among researchers. I wonder where "mass redistribution" will kick in.

    Further, the memo does not set a 12-month access embargo as a maximum, it directs agencies to adopt the 12-month embargo as a guideline. There is a lot not to like in the memo.

    Most of the public attention to the decision has been directed at the effects on scientific publications. I have long been interested in a second area: the public access to data generated by federally funded research.

    The White House Office of Science and Technology Policy last year requested public comment on two questions: open dissemination of federally-funded research and open access to data resulting from federally-funded research. I commented last year in response to the OSTP request ("Public interests in data from federally funded research") about the value of data to scientists and others who are not members of federally funded labs. The present announcement from the White House did not indicate how these comments from last year may have contributed to the decision, but it includes general recommendations on both publication and data access.

    As it stands, the text of the memo essentially keeps in place the data access requirements established under the Bush administration. That is not a bad thing, and indeed the recommendations listed in the memo seem very reasonable. I quote them here at length:

    Each agency’s public access plan shall:

    a) Maximize access, by the general public and without charge, to digitally formatted scientific data created with Federal funds, while:

    i) protecting confidentiality and personal privacy,

    ii) recognizing proprietary interests, business confidential information,and intellectual property rights and avoiding significant negative impact on intellectual property rights, innovation, and U.S. competitiveness, and

    iii) preserving the balance between the relative value of long-term preservation and access and the associated cost and administrative burden;

    b) Ensure that all extramural researchers receiving Federal grants and contracts for scientific research and intramural researchers develop data management plans, as appropriate, describing how they will provide for long-term preservation of, and access to, scientific data in digital formats resulting from federally funded research, or explaining why long-term preservation and access cannot be justified;

    c) Allow the inclusion of appropriate costs for data management and access in proposals for Federal funding for scientific research;

    d) Ensure appropriate evaluation of the merits of submitted data management plans;

    e) Include mechanisms to ensure that intramural and extramural researchers comply with data management plans and policies;

    f) Promote the deposit of data in publicly accessible databases, where appropriate and available;

    g) Encourage cooperation with the private sector to improve data access and compatibility, including through the formation of public-private partnerships with foundations and other research funding organizations;

    h) Develop approaches for identifying and providing appropriate attribution to scientific data sets that are made available under the plan;

    i) In coordination with other agencies and the private sector, support training, education, and workforce development related to scientific data management, analysis, storage, preservation, and stewardship; and

    j) Provide for the assessment of long-term needs for the preservation of scientific data in fields that the agency supports and outline options for developing and sustaining repositories for scientific data in digital formats, taking into account the efforts of public and private sector entities.

    These recommendations are all basically already in the NSF data access policies, meaning that the new White House memo will maintain the status quo at that level.

    The problem is that the current policy is toothless. Continued data access is a very serious problem threatening the integrity of science. Self-archiving and institutional archiving have been sufficient to pass data management portions of grant applications, but have proven to be woefully insufficient to enable access to data. Meanwhile, some fields have intensive data collection but very little or no data entering the public domain as part of digital repositories. The recommendations listed above do nothing to change the current situation.

    Nevertheless there is some room within the recommendations for agency directors to take bolder action on data access. Section (j) perhaps provides the best hope. If federal funding agencies actually assess the long-term needs of each field supported by funding, many (including anthropology) will clearly benefit from the establishment of standard digital repositories.

    I hope that NSF will not sit on its current policy but will instead work to extend access more broadly. At the same time, I wish the White House had given clearer guidance to enable the creation of digital repositories and to require their standard use as a condition of continued funding of research projects.

    Synopsis: 
    A new memo from the Obama administration alerts my interest in data access.

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