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paleoanthropology, genetics and evolution

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  • A reason for practical genomic education

    Fri, 2011-11-04 21:41 -- John Hawks

    Photo credit: Graham Stanley on Flickr, creative commons.

    The New York Times devotes a long article to understanding why such a high fraction of students who begin science, technology, engineering and math (STEM) majors drop out of them in their second and third years of college.

    The National Science Board, a public advisory body, warned in the mid-1980s that students were losing sight of why they wanted to be scientists and engineers in the first place. Research confirmed in the 1990s that students learn more by grappling with open-ended problems, like creating a computer game or designing an alternative energy system, than listening to lectures. While the National Science Foundation went on to finance pilot courses that employed interactive projects, when the money dried up, so did most of the courses. Lecture classes are far cheaper to produce, and top professors are focused on bringing in research grants, not teaching undergraduates.

    I have an interesting experience with this problem. Getting students engaged with skeletal biology is really easy, because they can get started learning practical information really fast. This is a common pathway for students to enter biological anthropology. In genetics, in contrast, is has historically been harder to devise practical early experiences. First genetics courses are very much based on theory and memorization. Students who get onto a lab bench early are likely to stay very engaged. But many areas of biology today are most productively learned in other ways than the bench.

    I've been putting undergraduate students directly into bioinformatics, getting them working with data and presenting theory as it becomes useful to the project. This has been a really positive experience so far, and there are just countless opportunities today to get students working with the sea of data coming from next-generation sequencing projects. But there's not really much support at hand for developing these practical experiences for students -- that's something that hasn't changed since the eighties. Very hard to envision scaling up to a broader set of undergraduates, because a lot of supervision is necessary for these experiences.

    The article discusses piecemeal solutions, and more widespread ones adopted by some engineering schools for retaining first and second year students. Taking students who start out interested and engaged with science, and then treating the subject as "sink or swim", is a waste of everyone's time.

    The irony is that everyone already treats lab experiences as the only serious training for STEM students in many fields. Professors already bring undergraduate students into labs and spend time (and their graduate students' and postdocs' time) training them in lab experiences. They just use the lecture classes as an expensive and time-consuming IQ test to filter those students. But this has a real cost: Instead of developing expertise within the undergraduates, which might get some real work done, and at least allow senior students to train younger cohorts, they learn techniques only a year or two before they depart.

    Synopsis: 
    A NY Times article explores the causes for STEM dropouts
  • A story behind Manis

    Tue, 2011-11-01 23:15 -- John Hawks

    A couple of weeks ago, I pointed to new research dating a mastodon kill site from Manis, Washington, to around 13,800 years ago ("Bone of the victim mastodon"). Today I ran across an interesting article in the Seattle Times that profiles the archaeologist who discovered the site, Carl Gustafson, and discusses why the Manis site became a focus of academic debate: "WSU prof was right: Mastodon weapon was older than thought, scientists say".

    What sets the story apart from the typical "maverick scientist against the establishment" theme is the candid admission that disseminating results is the standard by which we have to judge archaeology.

    Quentin Mackie, at the University of Victoria's Department of Anthropology, agreed the Clovis-first model most likely subjected Gustafson's site to unfair critiques. But over the years Gustafson, too, didn't share his results in a great number of high-profile journals.

    "I just think Carl was hiding his light under a bushel," Mackie said. "I respect what Carl did. He poured countless hours into documenting the site. But for the rest of us, we rely on publication of results in peer-reviewed journals, and I don't think his evidence was presented in a way that was persuasive enough. And I hate to say that."

    Gustafson concedes his output could have been greater.

    "I probably should have published more," Gustafson said. "But I had so much. I didn't know how to take all this information and make a story out of it."

    If you want your science to make an impact, you have to write more and write promptly. Science needs the details to get in front of more eyes.

  • This is anthropology

    Thu, 2011-10-13 21:25 -- John Hawks

    With reference to my story earlier this week ("Florida: Anthropologists not wanted"), the students at the University of South Florida have put together something that is roughly three hundred and twelve times more effective than any organizational response so far.

    My apologies if the embedded Prezi causes problems for your system. I hope they'll follow up by adding a YouTube version also (not hard, just run the Prezi and add audio track). Remember when I wrote that young anthropologists are making their own brand?

  • Florida: Anthropologists not wanted

    Tue, 2011-10-11 21:26 -- John Hawks

    Last week I linked to my essay, "What's wrong with anthropology?" My theme was that anthropology has been a failure over the past two decades at engaging with policymakers and the public, and that the field can only look forward to decline unless we take immediate action to improve this situation.

    Well...today the governor of Florida, Rick Scott, gave a convincing proof of my thesis on a radio program:

    We don’t need a lot more anthropologists in the state. It’s a great degree if people want to get it, but we don’t need them here. I want to spend our dollars giving people science, technology, engineering, and math degrees. That’s what our kids need to focus all their time and attention on, those types of degrees, so when they get out of school, they can get a job.

    And in the Herald-Tribune:

    “I got accused of not liking anthropologists the other day,” Scott said. “But just think about it, how many more jobs do think there are for anthropologists in the state?

    “Do you want to use your tax dollars to educate more people who can’t get jobs in anthropology? I don’t. I want to make sure that we spend our dollars where people can get jobs when they get out.”

    Daniel Lende has a roundup of stories and responses by anthropologists. It's very difficult to come up with a rapid and effective reply from an organization or department, so I understand these aren't as punchy as they might be. Still, it seems to me a vastly more effective response would describe the economic impact of anthropologists in Florida, the dollar amounts of federal and private grants they bring to Florida universities, their role as custodians of natural and cultural history, and their history of engagement with indigenous and immigrant peoples in the state.

    Oh, and the major associations could mention that the state will not be considered for national meetings. The AAA meeting in particular drives millions of dollars of direct and indirect revenue to its host city.

    Florida anthropologists have a great opportunity moving forward to get attention for their work in public engagement. The attention of the press will never be directed as closely to the value of anthropology within the state.

    UPDATE (2011-10-12): According to the AP and Tampa Bay Online, Governor Scott's daughter took a degree in anthropology. Let me just say, that reinforces the message. We can't even communicate the importance of our field to the parents of our students!

  • What's wrong with anthropology?

    Wed, 2011-10-05 23:31 -- John Hawks

    Anthropologies is an online project organized by Ryan Anderson that brings together voices reflecting the state of the discipline today. The current volume has the theme, "Anthropology with purpose". My essay has riled a lot of people already: "What's wrong with anthropology?"

    Academic anthropology in America is complacent, at a time when budgets are falling, academic departments are being closed, and a larger and larger number of people have become skeptical of the value of science. It's time for an intervention.

    We must change not only for practical reasons but for moral reasons as well. Anthropological research depends on the cooperation, interest and goodwill of many communities, both today and in the past. People do not donate their cooperation lightly. Wherever anthropologists do their work, they are lucky to have the help of these communities of people. Whether biological, archaeological, or cultural, our research relies on unique resources that in many cases cannot be duplicated. We bring these things to light, for the broader appreciation and education of the rest of humanity.

    Having our work read by twenty people is an not acceptable communication strategy. Failure to share results broadly betrays the cooperation of the communities who enable our research.

    I argue for three strategies:

    1. Embrace new forms: use technology to change the way we publish our work.

    2. Defend good science, acknowledging anthropology's unique place.

    3. Empower our students: leverage the incredible value of fieldwork by requiring translational work from the beginning.

    A section from this last:

    Making our students more competitive for non-academic careers does not mean turning our back on what we already do well. Our students learn how to think in ways that other students don't. Fieldwork gives our students tremendous advantages that most industry professionals can only look on with envy.

    We should reinforce those essential experiences and make them greater opportunities for engagement. Why are anthropology students going into the field without contracts to write weekly or monthly about their work? Why do our professional associations do not support themselves by becoming clearinghouses for ongoing field reports? Where are the workshops and press kits that will enable our young researchers to build ties to media and communities outside their institutions?

    I've served up some real red meat in this one, and I've been so heartened to see the growing comment stream. A sample:

    I did an honors thesis on applying an empirical methodology to an ethnographically documented phenomenon that won a university-wide social science prize. I was the kind of promising student which anthropology as a field should be trying to retain – someone with ideas, creativity, and able to produce original research early. While an undergrad, I had every intention of continuing on in anthropology. However, after graduating and sitting down to figure out where to apply to graduate school, I discovered that getting a degree in cognitive anthropology would be a pretty horrible life plan if I wanted to have a career based on my graduate training ... From what is now an outsider perspective, the AAA ditching science in its mission statement suggests to me that I made the right decision. Anthropology has already lost intellectual territory to other disciplines, seemingly without a fight.

    Some great names have already chimed in, and I hope that many more will take the opportunity to join the conversation.

    Synopsis: 
    I link to my essay in Anthropologies, which calls for greater engagement by anthropologists.
  • How to blog for your lab

    Sun, 2011-10-02 17:07 -- John Hawks

    Christie Wilcox makes a case that every lab should be doing science outreach on social media: "Social media for scientists Part 1: It's our job, and Part 2: You do have time. Her rationale is worth spreading:

    Yes, part of the solution to this problem is to invest in better education. But even assuming we do that, we are ignoring the millions of Americans who are no longer in school. We can make the next generation more scientifically literate, but we have to consider the current generations, too. Adults over age of 35 never learned about stem cells, nanotechnology or climate change in school, so they depend on the media to learn what they need to know. These are the people who vote. They are the ones whose taxes pay for scientific funding. We need to reach out to them, and to do that we need their trust.

    I'm not sure social media are necessarily the best way for most labs to make an impact on the public. You may do better working with other institutions, or by going into a collective with other labs. I know that one great way to increase your lab's profile is to get your department or program to set up a group blog, where the lab's home page is one contributor along with other labs. Two new posts a month, as Wilcox suggests, is a good start for a single lab but won't drive much interest; weekly or biweekly posts by a group of five labs would build much more attention.

  • Will monographs arise from the dead, or eat our brains?

    Sat, 2011-10-01 21:26 -- John Hawks

    Inside Higher Ed reviews and interviews an author who argues that the scholarly monograph shackles academics to an obsolete model of communication:

    So it is strategic that Kathleen Fitzpatrick, director of scholarly communication at the Modern Language Association and a professor of media studies at Pomona College, invokes the living dead early to illustrate her argument in Planned Obsolescence: Publishing, Technology, and the Future of the Academy (NYU Press). The scholarly press book, she writes, “is no longer a viable mode of communication … [yet] it is, in many fields, still required in order to get tenure. If anything, the scholarly monograph isn’t dead; it is undead."

    I agree with this thesis in part. Sixty-dollar monographs are going the way of the thylacine. Locking scholarly content in the tall stacks of university libraries doesn't disseminate it. Peer review no longer improves work to the extent that it's worth locking it up in response. It is ridiculous for anyone to judge the quality of a young scholar's work by the imprint of a "prestigious" academic press. Tenure committees have simply delegated their responsibilities to editors, and the editors do a poor job.

    But I disagree that the scholarly monograph is dead. Personally, I expect monographs to undergo a renaissance as more academics adopt e-publishing. Academic presses affiliated with universities should be going all-digital, and should start massively promoting their back catalogs as e-books at fire-sale prices. The smart ones will take the opportunity to change their agenda, competing to publish new books by a new generation of scholars who are building a broad readership both inside and outside academia. There's no reason why we need to constrain our scholarship to books so boring that nobody wants to read them. Tomorrow's scholars should be engaging with a much broader public than university presses have historically cultivated.

    The stumbling block is that these books still must serve as a guide to the academic quality of young scholars' work. On this count, Fitzpatrick provides some useful ideas about how to build quality scholarship under a more collaborative model:

    The way to make this work, Fitzpatrick says, is to change the currency of scholarly communications from paper to credit. Instead of rewarding faculty for getting a lot of paper published, universities should consider how helpful tenure candidates have been in parsing other people’s articles written and helping others refine their ideas, she says. Journals could help out with this by creating “trust metrics” that cede more weight to academics who consistently give constructive feedback. They could also encourage frequent, thoughtful reviews by making them prerequisites for publishing one’s own work — thus attracting the sort of critical mass of reviewers that Fitzpatrick argues is necessary for successful peer-to-peer review (and which some previous high-profile experiments with the model failed to get).

    Under such a system, faculty members could glide to tenure on the wings of their reputations as positive contributors to the advancement of knowledge in their field — a metric the current “publish-or-perish” model does not adequately represent, Fitzpatrick says. “Little in graduate school or on the tenure track inculcates helpfulness,” she writes, “and in fact much militates against it.”

    Obviously I think this model would be better than our current one. Still, I worry about the actual assignment of credit. Quite frankly, all my writing here has done wonders for my influence, but has had a substantial drawback: Many of my ideas are used by other scholars without credit or citation. We compete for research support, and in that competition I get no credit or acknowledgement whatsoever for any contributions I make. That's a cost I've been willing to pay for what I do, but if we expect more young academics to share their ideas broadly, we're going to need to change the culture of research funding to recognize their contributions appropriately.

    My favorite part of the interview is the last question, which asked Fitzpatrick to give advice about new models of publication to a junior faculty member, librarian, and university provost, respectively.

    Finally, to the provost: understand that scholarly communication is a core responsibility of the university – so fundamental to the university mission, in fact, that it must be thought of as part of the institution’s infrastructure, not as a revenue center. And every university must develop some kind of plan for scholarly communication. If you leave disseminating the work of your faculty exclusively to corporate publishers, corporations will profit from it at your institution’s expense. Instead, invest in the structures that will get your faculty’s work into broader circulation – not least because those structures will help you make clear to the concerned public why the university continues to matter today.

    I'm going to append to this post the first link to my entry in the Anthropologies project: "What's wrong with anthropology?" where I discuss my own perspective on these problems. Needless to say, I think things need to change. I expect the change in scholarly communication to be highly specific to each academic field, as what works for cultural anthropology will not be the same as what works for genetics or English. But new approaches will be digital, and that means a university may find much more ability to support multiple approaches than is possible with print. The tools to support varied forms are already available, if universities would support and extend them, they could capture much of the need for academic communication.

    Synopsis: 
    Making academic writing relevant means abandoning the monograph, says a specialist.
  • An arsenical profile

    Wed, 2011-09-28 08:51 -- John Hawks

    Popular Science writer Tom Clynes gives us a long profile of Felisa Wolfe-Simon, who became a lightning rod for criticism after she authored an article claiming some bacteria were using arsenic in the place of phosphorus in their DNA ("Scientist in a Strange Land"). I've been following the story as it has become a case where traditional methods of peer review have conflicted with more open approaches to science.

    This article tells a story that hasn't come out fully before, while emphasizing repeatedly the reasons why many have criticized the approach to the media by Wolfe-Simon and NASA's role in hyping the findings.

    Wolfe-Simon says that “otherworldly” is the word that came to mind when she first visited the lake in 2009 on a grant from NASA’s Astrobiology Institute. She was there with several other researchers, including Ronald Oremland, a senior scientist with the U.S. Geological Survey in Menlo Park who has studied the biogeochemistry of Mono Lake for 30 years. The two had met at a conference in 2006. “She was always persistent,” Oremland says. “She kept on talking about arsenic substituting for phosphorus. Every two years, her argument became a little more complicated and a little more compelling. Finally, I said, ‘Look, I don’t think this is going to work, but it might. Come on out to the lake—what have we got to lose?’ ”

    Now, for the first time since last summer, Wolfe-Simon has returned, not to do fieldwork but to pretend to do it for the benefit of a two-part Nova television documentary that will air this fall when NASA launches its Mars Science Laboratory, a mission to determine the habitability of the Red Planet and to search for chemical signatures of life. The video crew has flown in from London for what will turn out to be a one-day shoot.

    I just don't get why NASA and NOVA are continuing to present this to the public instead of getting to the bottom of it as quickly as possible. I would be in my lab constantly until I knew the answer, or I wouldn't feel like I could tell the story honestly to anyone. It is difficult for a young scientist to turn down the kinds of invitations Wolfe-Simon has received, but I think the whole situation is poisonous. In the article, she worries that her career in science may be over (she's been dismissed from Oremland's lab), and in my opinion her mentors and funders bear a lot of responsibility for the series of public relations mistakes.

  • Can Watson navigate the medical literature?

    Wed, 2011-09-21 08:30 -- John Hawks

    Last week, Computerworld reported that IBM's famous "Watson" supercomputer is moving to its next challenge: prescribing cancer treatments for the WellPoint health plan.

    For example, Watson's analytics technology, used with Nuance's voice and clinical language understanding software, could help a physician consider all related texts, reference materials, prior cases, and latest knowledge in journals and medical literature when treating an illness. The analysis could quickly help physicians determine the best options for diagnosis and treatment.

    "There are breathtaking advances in medical science and clinical knowledge [but] this clinical information is not always used in the care of patients," said Dr. Sam Nussbaum, WellPoint's Chief Medical Officer, in a statement.

    Looks to me like a first step to removing humans from the decision-making chain. A.I., the ultimate bureaucrat. Plus, it can beat Ken Jennings on Jeopardy!

    It occurs to me that the current medical literature is really poorly suited for AI trawling, in many ways. The data and results are obfuscated in many ways, and there's a strong publication bias toward positive results. Someone asked me just today about why open science is interesting to many of us, and the positive results bias struck me as a really important aspect. When you are keeping an open notebook, the negative results are right there along with the positives. Open notebook science might be better for AI-enhanced treatment plans. In any event, a more standard form of result reporting would be helpful. Why can't anyone run their own meta-analysis anytime she chooses?

  • Malapa conversation on NPR

    Sat, 2011-09-10 13:22 -- John Hawks

    The "Science Friday" NPR show with Ira Flatow did an interview with Lee Berger and Bernard Wood yesterday about Australopithecus sediba. The transcript is now online: "Examining Ancient Fossils for Clues to Human Origins", or you can also get the audio.

    This is a nice interview with a lot of detail. I especially like the later part where Berger promotes the importance of getting more researchers into field discoveries.

    Remember, that this was recovered right in the middle of the most explored area, probably, in the continent of Africa - for these very fossils, lying on the surface so easy a nine-year-old could find it. And there - Africa is a big continent. It is unexplored. The rest of the world's a big place, and we need to get more exploration and find more fossils. And I think that that is a clarion call at sediba rings out, that I think Bernard was alluding to as well.

    Oh, and there's this:

    We are allowing scientists to examine this material, published and unpublished, anything we find. Any bona fide scientist can come to our labs and examine, whether we published it or not. So we're attempting an open access experiment. We've casts available. You, today, could go to the Smithsonian Museum or the American Museum of Natural History and see casts of the material that we published in Science today. They've been in those institutions for months and months and months, available to any scientists who wanted to look at them.

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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.