john hawks weblog

paleoanthropology, genetics and evolution

open access

  • Public access to federally funded research

    Sat, 2009-12-12 11:39 -- John Hawks

    The Obama Administration's Office of Science and Technology Policy is running a forum on public access to federally funded research. There seem to be ongoing events and commentary on this topic, and I'll just point people to the initial call for comments on the OSTP blog.

    The background question is whether other federal agencies (such as NSF) should enact policies similar to the NIH public access after one year condition. The comments so far seem to be running in favor of total public access to federally funded research results, which would be my position also.

    I think in this case it may be more productive to wait for a more formal opportunity to register opinions, as "blog comments" on a government website may have limited impact. But I like the way the "forum" seems to be going.

  • The trouble about Kenyanthropus and Ardi

    Thu, 2009-12-10 15:32 -- John Hawks

    There are three skulls from putative "hominins" that date to 3.5 million years or earlier. Every one of these skulls is known now from extensive reconstruction or correction for distortion in the original.

    By itself, the extensive reconstruction might not be a problem. But as Tim White has repeatedly shown, the specialists on these crania actively and vociferously disagree about the basic anatomy due to problems reconstructing them. White's ongoing dispute about the skull of KNM-WT 40000 is a matter of public record, both in his initial 2003 article on the skull, and in Michael Balter's description of the recent Royal Society meeting*:

    When the talk was thrown open for discussion, White took the microphone and began firing questions at Spoor about the degree of variation of the cheekbone position among specimens of A. afarensis and other hominin species. “We took that into account,” Spoor responded, “and I just showed you a graph” about it. “I didn’t ask you whether you took it into account; I asked you what it was,” White said. Spoor, clearly frustrated, told the audience that he had no vested interest in this debate. At that point, the session chair interrupted and invited everyone to break for coffee, but Spoor and White continued to debate between themselves for the next half-hour.

    If KNM-WT 40000 were the worst case, that would be bad enough. But Ardi's skull has required reconstruction even more extensive than would be required for the Kenyanthropus holotype.

    In their description of the Ardipithecus skull, Suwa and colleagues (2009) mainly present metrics taken from the CT reconstruction. The publication strikes me as remarkable in that it includes few photographs of the original fossil, and only one or two of the photos are in standard anatomical orientation. A substantial part of the CT reconstruction is based on a second individual (ARA-VP 1/500), of which no photographs are provided. For this, readers may refer back to the single rather poor photo in the 1994 description. Anatomical comparisons in the present paper are limited to visualizations of the CT reconstruction.

    As I've written elsewhere, I think that Suwa and colleagues did a remarkable piece of reconstruction. But it is non-replicable. The CT-reconstruction is a composite of two specimens that includes mirror-imaged parts. A tremendous amount of work went into it, but without access to the component parts, it isn't possible to test or verify the assumptions underlying the present model.

    Another striking thing about the Ardipithecus skull description is the lack of anatomical comparisons with relevant samples. I mentioned above that most of the figures involve metric comparisons -- many of them scaled to the cube root of endocranial volume -- which of course can only be taken on a small fraction of early hominin crania. That leaves out the most relevant specimens in the Hadar sample, including all the cranial specimens from AL 333. It leaves out most of the Sterkfontein collection.

    And it brings us back -- again! -- to Kenyanthropus. Reading back through the paper, it's hard for me to believe that reviewers allowed Suwa and colleagues to publish on Ardi's skull without including any comparisons with KNM-WT 40000. It's the earliest complete skull of an undoubted hominin.

    They're entitled to their opinion that the skull is distorted. I agree. But you can still compare most of its nonmetric features and put some reasonable bounds on its metrics. I mean, they included OH 5, for goodness sake -- which has nothing whatever to do with hominin origins. Including the comparisons wouldn't have changed much about the paper, although I'll point out that there's at least one derived feature of later hominins that KNM-WT 40000 and ARA-VP 1/500 both lack, and which isn't noted either by Suwa and colleagues (2009) or in the table presented by White and colleagues (2009).

    So what should we do? We can't see the scans, no independent reconstructions are possible, and the people who can see the scans refuse to present comparisons of these three skulls that together represent the supposed origin of the hominin lineage.

    AAAARRRRGGHHHH!

    We need to set up multiple sets of independent reconstructors having a replicable go at these skulls. These are the three earliest hominin skulls. Every one of them is crushed in some weird way. It would be a credit to the science to document their reconstruction in nauseating monograph-level detail. They're scans, for goodness' sake -- there's absolutely no argument that access should be limited for any reason.

    If I were running this, I would set up a graduate seminar devoted to putting them together, split among four universities, with results to be reported in a session at the meetings and monographically by e-publication. The issue is not whether we can obtain an exact representation of the original anatomy. The issue is whether we can reject hypotheses about that anatomy. Testing hypotheses requires us to survey the range of possible reconstructions and how they relate to the range of anatomical variation in living and extinct analogs. The more reconstructions, the better the testability.

    At the moment, that testability isn't there. I trust the anatomical expertise of the people who made the models, but they're just single models with no assessment of the range of error. I've written about the importance of open access for these reconstructions already ("Open access and fossil reconstruction"). The points here just amplify that theme.

    * As an aside, I wonder if the title of the Royal Society meeting ("The First 4 Million Years of Human Evolution") contemplated the possibility that there may have been only 4 million years of human evolution in total?

  • Open access and fossil reconstruction

    Thu, 2009-10-08 14:30 -- John Hawks

    I would love to be able to say that the Ardipithecus pelvic and cranial reconstructions were open access.

    The reconstruction of fragmentary fossils has in the past been more of an art than a science. An anatomical expert can eliminate some possible morphological configurations based on the remains themselves. But for many, she has only her knowledge of variation in extant species as a reference. The bones she has studied might or might not be representative of anatomical variations; variations within extant taxa might or might not be relevant to ancient species. Working with casts of a fragile specimen is fraught with problems. Missing parts or uncertain joins in the fossil material can be shored up with plasticine, but to other scientists these This process poses obvious drawbacks: the resulting reconstruction may present the appearance of features that are in fact completely sculpted out of clay.

    I describe this as an “art” for one important reason: there are many barriers to replicating a reconstruction. The reconstruction ends up including the quirks of other specimens used as reference material, may have fragments misplaced due to uncertain identifications.

    The pelvic reconstruction of Sts 14 is one example of how the implicit assumptions of a reconstruction can affect the interpretation of a fossil. After its discovery in 1947, John Robinson reconstructed the distorted ox coxae and partial sacrum with a rounded pelvic inlet, more or less like humans. After the discovery of Lucy’s pelvis (AL 288-1), it was clear that A. afarensis had a very broad pelvis, flattened from front to back — different from Sts 14’s apparently rounded pelvic shape. The original reconstruction of Sts 14 was revisited in the 1990’s, when it was found that a flatter, more Lucy-like shape is consistent with the specimen’s anatomy (Abitbol1995). The point is not that Robinson’s reconstruction was wrong — any reconstruction will be wrong in some details. Nor is the point that the reconstruction was not replicable in principle – at any time, anybody could have sawn apart a few casts of Sts 14 into the component bones, and then built them back in a different shape. The point is that replicating the reconstruction would have been expensive and difficult, so for forty years nobody made the effort.

    With digital scanning, all the expense and difficulty go into producing the initial scans. After that, the only limit on testing a model reconstruction is the time that someone is willing to spend studying the anatomy.

    In principle, this is wonderful. A whole team of researchers can easily share digital models, working on the specimen with an explicitly shared referent. The digital model can be instantly transported anywhere in the world, allowing direct comparisons with original material housed in museums. The existence of such virtual 3-d images of fossil and model allows independent scholars to apply their own models, testing a model’s assumptions without needing to handle and possibly damage the original specimens.

    But many of these benefits of the technology depend on scholars being able to access the scans. Today they can’t.

    I’m hopeful that in the future we’ll be able to make full use of the technology — not only enabling a single reconstruction, but multiple reconstructions and widespread comparison of digital models.

  • Whoa, who stole the data?

    Sat, 2009-10-03 10:59 -- John Hawks

    OK, as you know I do this thing where I read the supplementary information in papers. I hate doing it; think they should put the stuff in the actual paper where it belongs, but well, that's life, right?

    Sooooo...I'm reading through the 73 pages of Supplementary Information for the Ardipithecus dental paper...

    Supplementary table S1 from Suwa et al. 2009

    Now let me just explain what's going on here. This is a spreadsheet of all the dental specimens they studied, and all the dental elements that they could measure. And they've entered an "m" in the table if they could measure the specimen, and an "f" if it was too fragmentary to measure. Fair enough.

    But wait a minute. There aren't any measurements. IT'S A DATA TABLE WITHOUT ANY DATA.

    What kind of rinky-dink journal is this?

    They give us descriptive statistics for each tooth, and print the canine measurements necessary to replicate their sex assignment bootstrap program, but they include no other measurements and no plots of measurements that aren't multiplied or divided by others.

    I understand why the authors don't want the numbers published. There's nothing you can do to compare individuals in the dataset to other samples of fossils. The summary statistics are enough to compare species with A. ramidus tooth by tooth, but not enough to study the relation of different teeth to each other. Some of the authors must want to do this themselves.

    What I don't understand is the journal. I mean, it's like some kind of government agent blacked out all the information. It's not like anyone can say it's appropriate to hold the data for a monograph -- there are SEVENTY-THREE PAGES here. It's not even like many of them are secret -- the ones discovered by 1994 have the measurements reported in White and colleagues' 1994 paper. In the current supplement, much of the information presented is valuable, and includes multiples of many of the measurements. I'd expect that any journal would include the measurements, and routinely require it when I edit papers. That way, other scientists can use the data in comparisons of their own samples, and outsiders can replicate the study's conclusions.

    Don't get me started on the scans....

  • Mailbag: Ardipithecus

    Thu, 2009-10-01 21:33 -- John Hawks

    thanks for your pellucid ardipithecus blognote--it was enormously helpful in digesting the reports.

    i was astounded though by the 15 year study "under wraps"--it reminds me of the dead sea scroll scholars who hoarded the scraps for decades
    to prevent other scholars from getting any credit for scholarly efforts.

    given technological advances are very accurate casts of the materials found available for other scholars to examine?

    Someday I think they will be. I'm very hopeful about this now.

    There are bright spots. The NESPOS project stands out as one making data avaiable to qualified researchers. The Kenya National Museums has done very well getting casts of recent fossil discoveries out there for sale. There are others. At the same time, there are many fossils where neither scans nor casts can be had at any price. Unless, of course, you are friends with the right people.

    One of the things the Ardipithecus work shows its that it is now possible to use CT technology along with primary specimen preparation and reconstruction. With plaster, glue and plasticine, reconstruction was potentially destructive to the fossils, so repeated attempts at reconstruction were not made. Now, anyone can attempt a new reconstruction, using different comparative data or models, and replicate or alter all the decisions made in the reconstruction process. I think that's very exciting, because it makes the process of anatomical interpretation a real science.

    But unless people have the scans, they can't replicate the science. That means access is not just a convenience or courtesy, it is essential. Without access, it's not science, it's authority.

    So I'm hopeful. I think people are beginning to understand the value of access, and that only a few interests -- powerful, but few -- are holding it back.

  • What can you learn for free

    Sat, 2009-09-05 11:30 -- John Hawks

    I'm all in favor of self-educating -- most of my genetics I learned on my own. So I was interested to see what you can really learn from free online sources like MIT Open Courseware, in an article by Josh Dean, "How Much Can You Really Learn With a Free Online Education?"

    I got that long-dormant lost-in-class feeling that triggers notebook doodles and clock watching, and I started to dread "going." And so, in a departure lounge at Miami International Airport, around the time Lewin said, "We now come to a much more difficult part, and that is multiplication of vectors," I decided to drop the class.

    I wonder what the internal impact of the program is -- what difference does it make when you're enrolled in a course, to have all the lectures of the course (albeit, from a past semester) online? Personally, I don't like doing the same thing in my courses every time I teach them. If I had an online lecture set, I'd probably expect students to listen to those in their free time, and add a bunch of additional content to my lectures.

    "You know where we're heading with this," says Shigeru Miyagawa, who believes that OCW has enriched current students and faculty, enhanced MIT's reputation as an institution at the forefront of innovation, and provided an invaluable opportunity to show off its smarts to those prospective geniuses that top schools fight for. "You can already see it. You" -- here he means an institution -- "can't afford not to do OCW. I foresee that in five years, all major institutions will be opening courses to let the world see what they do. It's a no-brainer, right?"

    Well, there is a downside. MIT doesn't offer human evolution.

    Muwahahahahahaha!

  • Academic publishing notes

    Tue, 2009-09-01 08:30 -- John Hawks

    On academic publishing, Jason Hoyt:

    This past February, I was on a panel discussion at the annual NFAIS conference, a popular forum for academic publishers. The conference theme was on digital natives in science. At one point I was asked (rather rudely) by a rep from a major publisher what exactly the new business model should look like for publishers in an Open Access world. My first thought was, “I don’t care if you find one or not. I’m here to advance science, not your bottom line.”

    ...and Zoë Corbin in the Times Higher Education:

    [Sir John] Sulston argues that the use of journal metrics is not only a flimsy guarantee of the best work (his prize-winning discovery was never published in a top journal), but he also believes that the system puts pressure on scientists to act in ways that adversely affect science - from claiming work is more novel than it actually is to over-hyping, over-interpreting and prematurely publishing it, splitting publications to get more credits and, in extreme situations, even committing fraud.

    The system also creates what he characterises as an "inefficient treadmill" of resubmissions to the journal hierarchy. The whole process ropes in many more reviewers than necessary, reduces the time available for research, places a heavier burden on peer review and delays the communication of important results.

    It's an increasing problem in Britain:

    The pressure to publish in top journals has increased even further with the recent announcement by the Higher Education Funding Council for England that citations will be available for use by panels to help them judge the quality of academics' output in the new research excellence framework. As academics strive to increase their citation counts, it seems likely that the new system will only serve to intensify the publish-or-perish mentality.

    Just keeping track. I think it's more an evolution than a revolution that's coming -- today's system is financially similar to 1980, but structurally very different. The development of trust in new findings has changed as the volume of work has changed. It has gotten easier to ignore things, for better and for worse.

    (via Bora)

  • Free the trees

    Wed, 2009-07-01 05:30 -- John Hawks

    Further drawbacks of databases in anthropology, after my post mentioning the issues. I'll point to Martin Rundkvist's discussion of "Open Source Dendrochronology":

    Dendrochronology has a serious organisational problem that impedes its development as a scientific discipline and tends to compromise its results. This is the problem of proprietary data. When a person or organisation has made a reference curve, then in many cases they will not publish it. They will keep it as an in-house trade secret and offer their paid services as dendrochronologists. This means that dendrochronology becomes a black box into which customers stick samples, and out of which dates come, but only the owner of the black box can evaluate the process going on inside. This is of course a deeply unscientific state of things. And regardless of the scientific issue, I am one of those who feel that if dendro reference curves are produced with public funding, then they should be published on-line as a public resource.

    He details work being done by a dedicated crew of amateurs, to replicate and sometimes expose errors in published chronologies, just by using open source principles.

  • Congress to repeal open access science provisions?

    Sat, 2009-02-14 14:18 -- John Hawks

    Putting science back in its proper place, Congress has taken up a bill to eliminate the requirement that publicly-funded research be freely accessible by the public. Open access watchdog Peter Suber writes:

    The Fair Copyright Act ... would repeal the OA policy at the NIH and prevent similar OA policies at any federal agency. The bill has been referred to the House Judiciary Committee, where Conyers is Chairman, and where he has consolidated his power since last year by abolishing the Subcommittee on Courts, the Internet, and Intellectual Property. The Judiciary Committee does not specialize in science, science policy, or science funding, but copyright.

    The premise of the bill, urged by the publishing lobby, is that the NIH policy somehow violates copyright law. The premise is false and cynical. If the NIH policy violated copyrights, or permitted the violation of copyrights, publishers wouldn't have to back this bill to amend US copyright law. Instead, they'd be in court where they'd already have a remedy.

    I think the existing policy is not nearly as open as it should be. The free availability of most NIH-funded research after a year is very important; even scientists at most institutions may not have immediate access to research findings, since journal subscriptions have become so high. But even aside from the way that open access may improve the quality of research, I think it is essential that science remain an open process, with results open to the public.

    Two years ago, I wrote about the problems of open access in paleoanthropology:

    Most papers about new fossils are supported by data from scanning. A small proportion of these scans have been made available to paying professionals, or soon will be. Most are locked away, with no long-term prospect of ever being distributed. Today, none are openly available. Not a single scan of a hominid fossil can be obtained in the open, free of charge.

    ...[T]oday paleoanthropology faces a real credibility problem. A substantial majority in most of the world's countries believes that we are lying about human evolution. In the few nations that are exceptions, a substantial minority holds the same belief: human evolution is false. The human fossil record has been fabulated.

    On Thursday, I had the privilege of doing an hour-long show on Wisconsin Public Radio, broadcasted statewide, about Darwin. It was a great experience, and I appreciated the chance to talk about the record of human evolution as well as Darwin's importance today. But it should be no surprise that one caller questioned the truth of the evidence about our evolution, claiming that scientists had proven that no transitional fossils exist.

    I'm very fortunate in my topic. To answer this question I can immediately draw upon the rich hominid fossil record. And on Thursday, I was able to point to the newly sequenced 3 billion base pairs of the Neandertal genome.

    But there's one important difference between those two kinds of evidence. Later this year, the Neandertal genome will be entirely public, so that anyone in the world with an Internet connection can download and examine it. Not so with the hominid fossil record. I can't point the public to any comparable source of raw information. With the Neandertal genome, by next year we may see high school science fair projects on Neandertal evolution. But do you think those kids will ever have a CT scan to work with?

    Even on the more limited topic of open access publishing, more progress is needed. Some of the costs of making publications open access are now covered by grants, but not enough. Ultimately, open access depends on this funding. Scientists who do not have grant support may apply to have publication fees waived, but we need to be expanding public funding and requirements for open access publication, not contracting them.

    A lot of scientists out there don't like the existing policy and want to roll it back. They would rather not have to make their data public. They have worked through conferences and meetings in the funding agencies to limit the impact of the current open access requirement.

    Now, it looks possible that Congress will do the rolling back for them. That's at the behest of scientific publishers' interests, naturally. Public open access to the products of the public's money is nowhere near as important as Congress' open access to lobbyists' money.

    (via Slashdot)

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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.