john hawks weblog

paleoanthropology, genetics and evolution

open access

  • Agitating for open science

    Wed, 2011-09-07 20:13 -- John Hawks

    Cameron Neylon in New Scientist: "Time for total scientific openness".

    Above all, you should care because science thrives on new ideas and critical analysis, wherever they come from. Open science is better science. There will be growing pains as we figure out how best to enable that. But if we believe that science enriches society then we must accept that society can, and perhaps should, enrich our research. And that can only happen if it is open.

    Open science will not work unless it is better science. I think it will be better. I think the history in paleoanthropology shows very clearly that keeping results behind closed doors for years is not good enough. The results speak for themselves.

    We're already getting some incredible feedback on the Malapa Soft Tissue Project, and it has just gotten started. If you've got a lead and haven't written yet, why not?

    Tags: 
    open science
    open access
    metascience
    journals

  • Are apps the evil twins of e-books?

    Thu, 2011-09-01 23:31 -- John Hawks

    I really like e-books quite a lot. It's easy to take a device like the Kindle, load up books, and read them. It holds your place for you, and multiple devices can be synchronized so that you can pick up a different one and read from the same page you left. One of the things I like most is that the electronic files themselves are a very simple format. When devices change, these files are still going to work. They aren't very different from the basic HTML that your browser can read, and in fact converting from web authoring to e-book authoring is very natural.

    But there's a limit to what you can do with a very simple format. You can't present multimedia or interactive content without adding some complexity. Many people have started to incorporate book-like material with interactive content by packaging them as apps instead of e-books. The best-known example of this is an app called The Elements, half coffee-table book about the periodic table, half whiz-bang visualization of 3d objects.

    John Dupuis is a librarian who has been thinking a lot about the impermanence of apps: "On the evilness of the emerging ebook app ecosystem".

    In the longer term, it's not clear how apps such as The Elements could follow their owners to new platforms or new devices. Certainly the content for something like The Elements could have a very long lifetime, say even fifteen or twenty years. If you bought it today what do you think the likelihood is you'll be able to access it in that time frame. It's like if book publishers could make you use their proprietary glasses to read their books.

    I'm not sure how I feel about the issue but it's worth thinking about. Apps can be done for free, but if they need to be constantly updated they will introduce costs that tend to make them costly relative to e-books. Some app-like content can be done in a cross-platform way, for example with Flash or HTML5. I've worked to some extent with Wolfram's system for sharing interactive content, which they're trying to make more widespread. Hopefully a more open, e-book-like system for sharing interactive and media content on readers will emerge.

    Tags: 
    media
    open access
    e-books
    Synopsis: 
    Apps allow interactive content, but lock readers into a platform that may disappear.

  • Open access barriers

    Wed, 2011-08-31 11:16 -- John Hawks

    Richard Poynder discusses how Open Access policies may be perversely costing universities even more money, in the lead-in to an interview about the Wellcome Trust's support of open access publication: "The Open Access Interviews: Wellcome Trust’s Robert Kiley".

    If institutions now start to cancel their OA membership schemes (which some believe provide pretty poor value anyway), the question inevitably arises: in light of the continuing financial squeeze, who on earth is going to pay for the “dramatic growth of Open Access” — as some characterise it?

    I continue to maintain that price to the reader is only one barrier to accessibility.

    Many open access journals now fund their activities with upfront author fees, which are exorbitant to any author not on federal grant money. I'm not questioning that those journals use the money -- they've obviously been spending it. But it obviously can be done for much less, as some open access journals have no author fees at all.

    Many journals wrap their content in scripts and presentation -- often for the purpose of guiding readers to premium content -- provide content that is not easily read on multiple devices and put multiple clicks between a search and results.

    Barriers to readability and comprehension are more important than barriers to access. Most of the research being published each year is a giant slush pile, from which postdocs use search engines to pick out small nuggets of utility.

    Tags: 
    open access
    journals

  • Make journals work better

    Mon, 2011-08-29 17:51 -- John Hawks

    George Monbiot writes in the Guardian with some sobering statistics about academic publishing: "Academic publishers make Murdoch look like a socialist"

    The publishers claim that they have to charge these fees as a result of the costs of production and distribution, and that they add value (in Springer's words) because they "develop journal brands and maintain and improve the digital infrastructure which has revolutionised scientific communication in the past 15 years". But an analysis by Deutsche Bank reaches different conclusions. "We believe the publisher adds relatively little value to the publishing process … if the process really were as complex, costly and value-added as the publishers protest that it is, 40% margins wouldn't be available." Far from assisting the dissemination of research, the big publishers impede it, as their long turnaround times can delay the release of findings by a year or more.

    All of this money has gone into creating a publishing system that isn't even usable or accessible to the volunteer laborers that create the content. People who have good journal access at research universities (and I'm fortunate to be one of these) still have to burn minutes every time we access an article to go through the ridiculous paywalls. Then there's the crazy rigmarole of linking online discussion to these paywall-ridden papers.

    Could somebody please let Amazon take charge of this? They have a system that maintains content at varying levels of pay/free, recognizes its users across multiple devices, and presents text material in an easy-to-read format. Every research author can publish to the e-book format as easily as an export from a word processor. Let's suppose that editors charged for the service of managing peer review, at levels that vary with the prestige that they have earned. Some editors would charge a fee that enabled them to pay reviewers, some would be paid or subsidized by universities. Then authors could choose to pay for a prestigious editor, and recoup that cost by grants or charging per-access, again, possibly subsidized by libraries.

    The solution to the collective action problem isn't complaining about the journals, it's providing a solution that works better.

    UPDATE (2011-08-29): Noah Gray comments on Monbiot's article, sharing his perspective from inside Nature Publishing Group (but not speaking for the company). I thought he made a useful contribution, and contributed my own comment, including:

    Most of the participants in this process are uncompensated, or are at best compensated only indirectly. The indirect compensation at present is tightly linked to prestige: publishing, editing and reviewing for the right journals. Secrecy and control have been routes to reinforce prestige, as are the traditional methods of advertising, sponsorship and signing "big names" by giving preferred treatment. These methods are design flaws from the perspective of promoting good science, as they exclude by institution, by nationality, and by arbitrary tastes.

    Tags: 
    publishing
    open access
    journals

  • Mailbag: Textbook costs

    Fri, 2011-08-26 16:29 -- John Hawks

    Re: "Textbooks leaving students behind"

    Dr. Hawks,

    I am a long-time reader of your blog and a librarian at the University of South Florida. With interest, I read your comment of 8/24/11 concerning the high cost of textbooks for students and wanted to share some information.

    Here in the library we are taking it seriously and are leading an institution-wide effort to promote alternatives. There is some information concerning the library's Textbook Affordability Program (TAP) program at http://tap.usf.edu/. We've been encouraging faculty to develop open-access electronic textbooks (we will host them and assist with design/layout). We negotiated with the on-campus bookstore to donate copies of all textbooks with an expected user base exceeding 100 students to the library where we provide free access. We also have a VERY aggressive electronic book program that increasingly covers classroom needs. For context, our building holds 1.8 million physical volumes (the USF Library System holds 2.4 million) but our ebook collection is now approximately 600,000 volumes. Finally, we pay ~$140,000 to subscribe to a copyright clearance system that ensures that students no longer need to purchase expensive course packs and that faculty are protected as they try to help students.

    Thanks for mentioning this issue in your blog. I suspect that you caused some readers to consider solutions to this significant problem. And I appreciate your attention to such issues as peer review, the academic journal "ecosystem," and open-access.

    Cheers,

    Todd

    Todd Chavez
    Director, Academic Resources
    USF Libraries

    Thank you so much for writing with this! Yes, it's an awful problem, and my solution (write materials myself) obviously won't work for everyone. But maybe one step at a time we'll improve things.

    Tags: 
    teaching
    education
    metascience
    open access
    mailbag

  • Textbooks leaving students behind

    Wed, 2011-08-24 10:44 -- John Hawks

    The Chronicle of Higher Education reports on a survey of nearly 2000 undergraduate students on 13 varied college campuses:

    In the survey, released on Tuesday by the U.S. Public Interest Research Group, a nonprofit consumer-advocacy organization, seven in 10 college students said they had not purchased a textbook at least once because they had found the price too high. Many more respondents said they had purchased a book whose price was driven up by common textbook-publishing practices, such as frequent new editions or bundling with other products.

    I find that the textbook is consistently the source of the most complaints from students on end-of-semester evaluations. I'm committing to no longer use textbooks that cost more than $10. I will use open access when possible.

    Think that's impossible? I don't.

    UPDATE (2011-08-25): See also my mailbag entry from Todd Chavez.

    Tags: 
    teaching
    education
    open access

  • An academic journal copyright story

    Sat, 2011-08-20 08:30 -- John Hawks

    In a post from earlier this summer, info/library scientist Jeffrey Pomerantz describes his attempts to secure a less restrictive copyright agreement for a scholarly article in a special journal volume: "My copyfight".

    I have to stop again briefly here, to point out something very important. [Taylor and Francis] has — had all along — a License to Publish form. Why had Stacy not mentioned this before? This email exchange had, by this time, been going on for a month. Let’s give Stacy the benefit of the doubt: let’s assume that she was not being malicious, but that she simply did not know about this License to Publish form until she ran my version by T&F’s lawyers. This is a very significant piece of information for the rep to a journal (almost certainly more than one journal) to not possess. Which means that this is a very significant oversight on the part of T&F, not keeping their journal reps informed. The result of which was that the rep to a journal was unprepared for a situation in which the author demands a less-restrictive copyright agreement.

    That didn't have a happy ending. Pomerantz returned later to the topic, responding to reader suggestions, especially the point about institutional preprint repositories:

    Part of the point of OA publication is that the publication is freely accessible to the reader, but equally important is that it’s discoverable. Freely accessible without discoverability is, quite frankly, close to useless. The problem with most IRs is that they their contents are not discoverable through Google.

    They also don't solve the citation indexing problem. Why can't institutions manage something with academic papers that is so easily accomplished with blogs?

    Tags: 
    metascience
    journals
    open access

  • Open science radiocarbon databases

    Mon, 2011-05-16 04:23 -- John Hawks

    Last week I wrote a lot about the radiocarbon chronology of late Neandertals in Europe ("Neandertals didn't disappear before 40,000 years ago", "Neandertals of the North").

    For more information about the radiocarbon dates of late Mousterian, Châtelperronian and other industries in Europe, there are several database projects that have collated date estimates from sites across the continent. These are well summarized in a current open access paper in PaleoAnthropology by Francesco d'Errico and colleagues. [1] (direct PDF link) That paper announces an additional radiocarbon database, called PACEA, which is available as a zip version of an Excel spreadsheet, supplemental to the article (Link to ZIP file). The article discusses several other database projects as well, some of which have open download policies.

    The availability of the large database of date estimates is tremendously important for anyone attempting to make sense of the systematic errors possible for dates. For example, a plot of the data by d'Errico and colleagues shows immediately the downward bias of conventional radiocarbon dates compared to AMS dates.

    References

    1. D'Errico F, Banks WE, Vanhaeren M, Laroulandie V, Langlais M. PACEA Geo-Referenced Radiocarbon Database. PaleoAnthropology [Internet]. 2011;2011:1–12. Available from: http://dx.doi.org/10.4207/PA.2011.ART40
    Tags: 
    dating
    open science
    open access
    radiocarbon

  • Open science link

    Thu, 2011-05-12 07:08 -- John Hawks

    David Dobbs writes about the structural barriers to more open science: "Free Science, One Paper at a Time". Summing up a large collaboration on Alzheimer's research, he writes:

    The language used here — everything entering the public domain, the dismantling of silos, the parking of egos and IP padlocks — might have been lifted from an open-science manifesto. And even Big Science appreciated the outcome. To open-science advocates, this raises a good and somewhat obvious question: Why don’t we do science like this all the time?

    Part of the answer, strangely, is the very thing at the center of science: the paper. Once science’s main conduit, the paper has become its choke point.

    He discusses a number of new initiatives to assess researchers' activity in areas other than paper publishing, as well as strategies for post-publication review of research -- the kinds of incentives and technologies that might ease the paper publication bottleneck.

    Dobbs doesn't explicitly mention the high pressure to cram significant results into a single high-profile publication. I find this pressure in paleoanthropology to be worse than most other factors. Researchers hold up results so that they will have enough to get that Science or Nature publication. And then, the results are reported in a highly obfuscated way, because they are tacked into a supplement without much editing or review. The paper itself is usually all conclusions and discussion, with no discussion of methods. This allows some research groups to claim that a Science or Nature publication isn't a "real" publication of their results, because a more detailed monograph is necessary to report them fully.

    In other words, it's six different kinds of barrier to open science, all rolled up into one basic problem.

    Tags: 
    metascience
    open access
    journals
    open science

  • Opening up paleontology

    Mon, 2011-04-11 22:22 -- John Hawks

    Ewen Callaway writes in Nature News this week on open access science in paleontology: "Fossil data enter the web period". I write about this topic quite a lot. Me last year on the NSF data management requirements:

    I mean, seriously -- they're going to "put people on notice that they have to think about it"? Give me a break.

    Yeah, I'm a skeptic. Lots of entrenched interests oppose making paleontological data available to the public, and they've been acting as if the pressure for openness will just blow over.

    The sad part is that so far they've been right. Data access requirements were first mandated as part of NSF and NIH reporting by a Republican Congress, signed by Bill Clinton. We're now on our third administration, more than a dozen years later. I have been writing about these issues here for seven years, and I have seen very little progress toward making the primary research data available to the public. There's been a lot of talk, and regrettably little action in paleoanthropology.

    I wrote a long essay about this topic in 2005: "NSF and data access". I described many of the efforts to make data access more open and to encourage digital archiving as a routine part of NSF-funded projects. My concern:

    I do not think it would be overstating the problem to suggest that perhaps half the people teaching human evolution in four-year universities have never touched a cast of a Hadar fossil. I would be delighted to be proved wrong, but I don't think I am. Our field is educating students into a world in which A. afarensis is unknown in the laboratory and poorly represented in our textbooks. I'm not talking about new specimens, here, I'm talking about fossils that were found in the mid-1970's and monographed in 1982.

    Looking back at that essay, I have two reactions. I'm very proud of what I wrote. I think I captured that main points while giving much credit to the structural drawbacks of open access. But I must say that I'm depressed that the situation has not changed in six years.

    Callaway's article gives me some hope. He describes how paleontologists and morphologists have begun to put some teeth into data access policies. The motivation for the article is the change in policies of the Journal of Vertebrate Paleontology to require access to certain kinds of raw data:

    Propelled in part by data-sharing edicts from funding agencies such as the US National Science Foundation, the Journal of Vertebrate Paleontology announced in January that it would require authors to post raw data files on its website (A. Berta and P. M. Barrett J. Vert. Paleontol. 31, 1; 2011 ). It is also considering mandating storage in public repositories such as Morphobank. Meanwhile, the Paleontological Society in Boulder, Colorado, which publishes Paleobiology and the Journal of Paleontology, last month decided to archive data from its papers using a repository called Dryad. "My only concern is that archiving so far is an unfunded mandate," says Philip Gingerich, the society's president. "Archiving could easily consume an entire research budget."

    In the past (and continuing in many cases), paleontology has involved a huge fixed and ongoing investment in curation. Museums have been the repositories and guardians of fossils, the primary resources of paleontological science. Digital data does not end that responsibility, and in some senses may increase the resources needed to maintain collections. So Gingerich's point is an important one: data curation adds a large new expense, and many universities and museums are not up to the job, either because of a lack of funding or expertise.

    But seeing this as an "unfunded mandate" is, in my opinion, the wrong perspective. Data curation is necessary for good science. In paleontology, results depend on reconstruction and comparison, and this process cannot be understood without access to the primary data. Digital methods make this vastly easier and more rapid, while greatly reducing the wear and damage from repetitive inspection and measurement of original specimens. More eyes on more specimens make for better morphological work. When a journal makes data access a condition of publication, that's an enormously helpful step. It recognizes that data access supports the integrity of the science.

    Unfortunately, there is the problem of phallus-swinging behavior among paleontologists:

    Tensions between scientists who discover new fossils and those who analyse and synthesize their finds are not new, says Mike Benton, a vertebrate palaeontologist at the University of Bristol. For example, Jack Sepkoski of the University of Chicago, Illinois, who in the 1970s and 1980s studied mass extinctions in the global fossil record, faced criticisms for repurposing other scientists' field work. But, says Benton, "if you wanted to keep it secret, you shouldn't have published it".

    Guess what: if you wanted to keep it secret, you need to send back your grant money and permits, and go into the collectors' trade.

    Tags: 
    history of paleontology
    open access
    open science

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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.