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paleoanthropology, genetics and evolution

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  • Eric Lander to co-direct Obama advisory council

    Sat, 2008-12-20 08:18 -- John Hawks

    Genome scientist Eric Lander has been appointed co-chair of Obama's Council of Advisors on Science and Technology:

    [Physicist John] Holdren also will direct the president's Council of Advisers on Science and Technology. Joining him as co-chairs will be Nobel Prize-winning scientist Harold Varmus, a former director of the National Institutes of Health, and Massachusetts Institute of Technology professor Eric Lander, a specialist in human genome research.

    ...

    Lander, who teaches at both MIT and Harvard, founded the Whitehead Institute-MIT Center for Genome Research in 1990, which became part of the Broad Institute in 2003. A leading researcher in the Human Genome Project, he and his colleagues are using the findings to explore the molecular mechanisms behind human disease.

    Relevant in view of upcoming policy on genetic information standards and government involvement in personal genomics.

  • Science from television drama

    Wed, 2008-12-17 08:56 -- John Hawks

    Wired has a story about the trend toward more television dramas with science content. Some may disagree that a show like CSI is especially science-related; notwithstanding the shots where a camera is being jammed up into a corpse orifice. But it seems obvious that the current crop of TV dramas uses science, like forensics, psychology, even math for goodness' sake, in a way that would have been unimaginable in the days of Murder, She Wrote and Crazy Like A Fox.

    Writer Hugh Hart attributes the trend to Michael Crichton:

    Why is real science so hot on prime time? Some of the credit goes to the late Michael Crichton. Ever since he introduced clinically correct doctor-speak to the airwaves with medical drama ER, story lines on science-heavy television shows have been bumping up references to astrophysics, neurobiology, quantum mechanics and other topics ripped from the headlines of obscure scholarly publications.

    The geek-friendly ER, which wraps its 15-year run in May, launched a spawn of pop culture/propellerhead crossovers that engage TV viewers' brainwaves even as they're being entertained by age-old soap-opera machinations. For an increasingly tech-savvy generation of couch potatoes, factually flimsy plot details simply don't pass muster.

    Well, I don't remember anything obvious pre-ER that presaged the trend. Definitely not Diagnosis: Murder territory. Maybe initially this was just the small-screen translation of Crichton's science fiction movie successes.

    Now some of the new science-y shows are just excuses for nerd humor -- witness, Big Bang Theory. And many of these shows, including some of my favorites, like House and Numb3rs, are ultimately driven by characters who are brilliant scientists themselves but have trouble relating to a group of more ordinary mortals. So there's the old unapproachable genius stereotype, where the genius has become the central character.

    Unless you're Lady Heather.

    But hey, at least the scientist has become the central character of these shows. It used to be that the scientist was some nebbishy middle-aged dude rescued by the hunky thirty-year-old hero. Now we haven't quite reached Doc Savage territory, but we're definitely moving up.

  • Rubik algorithm to Ph.D.

    Tue, 2008-12-16 23:26 -- John Hawks

    Bina Venkataraman tells the interesting story of Jessica Fridrich, who as a Czech teenager in 1981 developed the fastest algorithm for solving the Rubik's cube. It's one of those stories that takes you to briefly into the world of the fanatics who quest for sub-ten-second times. But there's a broader story, of the mind of a person who would solve the puzzle before ever handling one.

    After earning her master’s degree, she was building mathematical models of rock deformation at a mining institute when she was recruited by a professor from Binghamton who heard about her mastery of the cube and her grades at the Czech Technical University in Prague. After a brief meeting in which she described her cube algorithms, he asked her to apply for the doctoral program in systems sciences. She had no résumé, so she dashed one off on a typewriter just before the professor’s train left the station. A year later, she arrived in Binghamton, where she has lived ever since.

    Well, I'd recruit that one, too.

  • This year's gift: The vanity taxon

    Wed, 2008-12-10 15:39 -- John Hawks

    Scientific American reports on a taxonomic auction by Purdue University:

    Naming your kid after you is one thing. But imagine if an entire species were named for you.

    This week, Purdue University is auctioning off the rights to name seven newly discovered bats and two turtles, the Associated Press is reporting. The winners — who will shell out a minimum of $250,000 for at least one of the bats, a Purdue spokesman told ScientificAmerican.com — can link their own name or that of a pal to the animal’s scientific name.

    "Unlike naming a building or something like that, this is much more permanent. This will last as long as we have our society," John Bickham, who co-discovered the nine species, told the AP.

    I don't think there's anything wrong in principle with selling the naming rights to your new species. Heck, I'd be happy to name a new species after a donor, if I had either. I don't even think there's anything wrong with consistently adopting a splitter's viewpoint on new species, keeping in mind that you have many donors and other people that you might honor with your work.

    But it seems to me there is a truth-in-advertising problem here. Species names are not eternal. They are hypotheses. We re-evaluate the relations between living populations and fossil populations all the time. The scientific community ignores ("sinks") taxonomic names that they come to believe are synonymous with existing taxa. So there is an obvious question: what are you really paying for, if you bid on naming rights for a species?

    Naturally, it will depend on the investigators. Are they credible? Do they have a good record in the practice of taxonomy?

    In the end, you're taking a bet: A bet against future discoveries. A bet that today's knowledge is the best there will be, at least where taxonomy is concerned. A bet that today's fashion won't reverse itself -- where the fashion is to recognize lots and lots of species, which helps to promote conservation goals tied to Endangered Species status.

    Well, I suppose we can say that the people who would splurge for more than $250,000 for a name don't really care if the name sticks. They probably want something else -- let's say, a story. That might include a motive to fund research on bats (in this case) or some other group of organisms, or just to fund conservation work generally. Or it might just be a line at a cocktail party -- hey, my wife has a species named after her. Or in the case of a recent taxon sale, good advertising for a casino.

    But maybe the people who bid on species naming rights ought to be made aware that it is a bet. Not eternal glory, just a chance at it.

    (via Sandwalk)

  • The tuition Singularity

    Mon, 2008-12-01 21:31 -- John Hawks

    The Singularity is a future time when, in theory, the pace of technological change becomes so great that we cannot predict the course of future developments of human society. The prediction of such a time was made by Vernor Vinge, and others, popularized by Ray Kurzweil. The basic idea is that technological progress is occurring now at an exponential rate. For example, the number of transistors on commercial microprocessors doubles every 18 months or so (that's called "Moore's Law" after Intel founder Gordon Moore).

    Exponential growth is a constant relative growth. When we chart an exponential growth process against time, we find that the rate of absolute change naturally proceeds to an "inflection point" at which the change becomes arbitrarily fast. If these changes do not meet some natural limit, they may be interpreted as a Singularity -- a point at which the apparent effects of changes in human terms becomes fundamentally different than before.

    Universities help to accumulate knowledge, and fulfill an educational role as they bring knowledge to a broader public. For this, students pay tuition. Our monetary system has its own exponential growth process -- the rate of inflation, at which a given amount of money purchases less and less value over time. University tuition has been increasing over the past twenty years or more at a rate much three or more times that of inflation. It is clear that at the historic rate of compounding, the tuition bills for U.S. universities are approaching a singularity.

    Exponential growth may continue quite a while into the future for technological development. But it cannot proceed indefinitely for tuition dollars. Compared to other economic needs, people can only spend a finite proportion on higher education. A story in Inside Higher Ed profiles the coming tuition crunch, discussing a recent report on college affordability:

    In recent years, the report notes, increases in public university tuition have not been used to improve the quality of instruction and other services, but to offset the declines in the relative share of support coming from state appropriations. Looking ahead, the report sees affordability issues created by shifting demographics, in which more of the potential student body will be coming from disadvantaged groups with lower family incomes. Further, based on current government projections, the report suggests that the share of family income required to pay tuition and fees (even after discounting is applied for institutional or other aid) is likely to get too large for many families

    Presently the tuition at private research universities is nearly 60 percent of the average family income; at public research universities it is over 11 percent. Over the next 30 years, private tuition will increase to nearly 100 percent of the average family income and public tuition to nearly 30 percent. Those projections seem unduly optimistic to me, considering recent rates of tuition increase and the cost structures of public universities.

    Four times the annual family income is a generous home price; homes are generally supported by long-term loans paid over 15 or 30 years, which together with property taxes make up more than 30 percent of the average family income. Long-term student loans have become a larger proportion of private debt. As the proportion of people seeking higher education increases, it is implausible to suppose that a high proportion will see a net increase in family income large enough to justify the expense.

    The question naturally arises: what does the student attain from a university that justifies an expenditure of several hundred dollars a week (in 2008 dollars)? The current average monthly tuition cost of a public university is over $700 a month. This adds up to more than $45 per hour of direct instruction.

    I don't think that university tuition will reach a singularity after all. What it will reach is a Malthusian limit, at which students find alternate means of obtaining credentials often enough that further tuition increases yield diminishing returns. For the universities, this won't very likely be pretty. Government intervention, in the form of tuition supplements or tax credits, may delay this crisis by distributing the cost of education across a broader population than the students and their families. But the fundamentals seem pretty obvious, particularly given the increasing effectiveness of distance learning technologies.

    What will happen to university instruction? One can hope it will become more dedicated to outcomes. If you're a parent of school-age children, consider this:

    While many students (and their tuition-paying parents) believe that attending a high quality college will yield higher incomes in post-graduate life, the report says that there is little objective data on the relationships between attending certain colleges and subsequent economic success. “No university can legitimately claim that their students learn more than do students graduating from competing universities,” the report says.

    High cost private colleges may have benefits for some students, but those benefits do not include reliably larger incomes.

    And there is this:

    The report suggests that public universities are unusual economic organizations in American society in that their costs are so integrated, or “bundled.” The same professors may perform research (either with or without major outside support), teach (either undergraduates and/or graduate students) and offer service to their institutions, disciplines or society. At a community college, the report says, faculty time is clearly instructional. But measuring the costs of undergraduate education at a research university may be “very difficult,” and that, in turn, may make cost control “nearly impossible,” the report says. While the report acknowledges that “unbundling” is easier said than done, it urges public universities to consider how costs can be separated for closer examination. And it notes that competitors to public universities — such as for-profit higher education, which has moved into areas once dominated by public universities — have no such difficulty.

    This is the biggest complication when comparing tuition costs. At a public research university, professors are generally expected to devote far more time and effort to research than to instruction. This is not universal or uniform, but as an example I spend more than four times as much effort on research, professional service and public dissemination of knowledge as I do on direct instruction, grading, and class preparation. These activities make me a better teacher, and provide my students with learning opportunities that they would not otherwise have. But they vastly complicate the task of quantifying the costs of education.

    Even so, research effort is hardly the cost breaker of university education. My salary has increased rather more slowly than inflation (keeping in mind that some components of my total cost of employment, notably health insurance, have grown faster). Meanwhile tuition has sped along at a much higher rate. That money isn't going into instruction, but it's not going into research, either.

  • Restoration

    Tue, 2008-10-28 13:21 -- John Hawks

    I found myself touched by this story about the restoration of Raphael's "Madonna of the Goldfinch." And glad that some people make it their life's work to preserve and restore the past:

    "I am just a technician," the chief restorer of the project said with humility. "But, yes, I think I probably know this painting almost better than Raphael. He looked at it, sure, but all these years I have been looking at it with a microscope."

    She lifted the painting out of a wooden box with the confidence of someone who has done it many times -- like a mechanic changing a tire -- but then gently positioned it at the center of an easel with the love of a mother adjusting her child's scarf on a winter day.

    "To think of it, I have spent more time with him than with my daughter," said Riitano, a 30-year veteran of restoration.

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  • A "Spore" review in Science

    Thu, 2008-10-23 17:33 -- John Hawks

    John Bohannon ("The Gonzo Scientist") gives the videogame "Spore" a flunking grade. He sits down four scientists, including Niles Eldredge, to play the game. Surprise! It's a game, not science!

    All species reproduce sexually in Spore. That must have posed quite a challenge for the development team's kiddy police. I can't fault them on this count because the compromise solution made me laugh out loud. Once you return to the nest and hit the "call mate" button, another of your species approaches with a flurry of Valentine hearts. What follows is a soft-porn vision of how cartoon characters come to be. Easy-listening lounge music pipes in as the pair coo and gyrate in slow circles, never touching, before one of them suddenly squats on the nest and--from no apparent orifice--pops out an egg.

    OK, that passage was just hilarious. But the rest of the review makes the scientists look like total whiners. For example:

    "Clearly, the only thing that determines an organism's morphology in Spore is what the player thinks looks cool," he said. (Before Electronic Arts began filtering it, the Sporepedia was filled with creatures designed to resemble human genitalia.) "And even that doesn't matter because you're ultimately forced to evolve into a terrestrial vertebrate with sentience, which is completely teleological. That's not real science," says Gregory. The "goal" of evolution is not to produce walking, talking vertebrates, because the process is undirected and unintelligent.

    Dude, it's a game. If the game includes progress, it's playable for longer. If it allows players to choose, it's playable repeatedly. Yes, it's kind of cool when the Magic School Bus visits real life dinosaurs, but you don't need to watch it more than once. If I lay out for a computer game, I want to design my own creatures. And forget the idea (floated by Eldredge) that you should pay some developmental "cost" for changing your body plan. Haven't these people ever played a role playing game? If big changes cost anything, players would just waste a lot of time getting the points to make the big changes! That's not fun, it's tedium.

    Ooh, ooh! Or we could get some Chinese gold farmers to do it for us! Now that's exactly what we want our kids doing, making a buck by selling their Spore points to their classmates. Maybe the nerdy kids can snootily tell them how anti-evolutionary they are.

    I haven't played Spore. But in my day, I loved to play Civilization. Sure, it had only the barest relationship to real culture history. Yes, it depended on obsolete concepts of cultural evolution and overly simplistic concepts of knowledge generation. And yes, it was totally lame that the computer players never honored treaties, that a Bronze Age phalanx could, on occasion, shoot down a stealth bomber, and other stupid things (some addressed in later versions of the game).

    I still think references to Civilization are among the best ways to get students to understand how anthropology differs from fiction. But in Bohannan's assessment, Spore fails to meet the scientific content of Civilization:

    In the game Civilization, for example, you learn a great deal about the history of ancient cultures through a series of pop-up mini-articles. When you stick a limb on your creature, wouldn't it be nice to have an optional pop-up window that explains the real (and fascinating) science behind limb evolution?

    Well, since the pop-up mini-articles are sort of ludicrous, I have a hard time believing this is going to be an improvement. Maybe what we really need is some Spore blogs?

    Don't get me wrong -- I'm not saying go buy this game for your kids, cause I really don't know. From the descriptions, it seems like the game is really trying to do too much. I mean really, from unicellular organism to interstellar civilization? It's going to be hard to do one of those well, much less all the levels in between.

    But wow does this review fail to tell me anything I would want to know! It's like I can imagine someone reading the entire thing with a William F. Buckley voice. The idea that Spore isn't science is a dumb one to be pushing. It's not science. It's a game. What we want to know is whether it's a good game.

    (OK, yes, I admit it would be entertaining to hear the words "Pimp my ride" in a William F. Buckley accent. Now, there's an idea for a game.)

    Meanwhile, an accompanying story describes a real outrage: Some of the scientists who appeared in a National Geographic Channel program about the game feel they were tricked by the film's producers.

    [Cliff] Tabin, along with Neil Shubin, a paleontologist at the University of Chicago in Illinois, and Michael Levine, a geneticist at the University of California, Berkeley, sent Science identical e-mails from the film's producers inviting them to take part. The e-mail describes the documentary as an investigation of "recent discoveries in evolutionary science" with no mention of Spore or Wright. "I thought I was being interviewed for a documentary about evolutionary biology," says Shubin, who appears to be playing the game in the film. "They didn't mention Spore until we were in the middle of [the interview]. … I sat there with Will Wright as he fiddled with it," he says. "I don't endorse video games, particularly one that claims to be about evolution."

    That's bad faith on the part of the producers. Similar tactics were used by producers of Expelled!, the anti-evolution documentary that hit theaters earlier this year, to lure evolutionary biologists into appearances in the film. That just leaves a bad taste in my mouth. I've had great experiences working with documentary producers, and I really appreciate the work they do putting science in front of the public in an interesting way. But it is essential to be up front about the topics likely to be covered in a documentary, and how the interviewees fit into a story line.

    National Geographic provided this quote for Bohannon's article:

    Ellen Stanley, National Geographic's communications vice president, says there was no intent to mislead the participants. "Our producers were transparent with all of the scientists," she says. The production of such a documentary takes "several months" she adds, and "the idea for the film evolves during that process."

    It may be true that the idea for a film evolves over time. But when producers plan who they are going to interview, they already have talked to many people, and have a good idea of what the interviews will say. They begin their shoot with a tentative script. Productions do not waste time or money unnecessarily, and while things can change during editing, they are not arbitrary.

    My advice: If you are asked to be in a documentary film, you can ask to see the producer's outline. Ask who else they are interviewing, and what those people are expected to contribute to the topic. You want to be prepared for the best things to say in your short time on camera, including likely responses to the arguments other scientists will be making. Spend as much time preparing as you would for a research paper. You wouldn't submit a paper to a journal that you hadn't looked at before; why would you appear in a documentary that you know nothing about?

    None of that advice can protect you from outright fraud, but in the final assessment you have to ask yourself: Is the benefit of communicating my opinion to a broader audience worth the risk, as I understand it? Personally, if I were Electronic Arts and National Geographic, I'd be offering to set up a travel fund for graduate students in each of these scientists' labs.

  • Prince Valiant encounters Neandertals?

    Wed, 2008-10-08 08:14 -- John Hawks

    I don't have a picture, but this week Prince Valiant seems to have encountered a band of Neandertals. At least, they look just like Neandertals that Charles Knight might have painted. Except they're wearing swamp-walking snow shoes and helping drive away a giant octopus with their tiny arrows.

    We'll find out more next week...

    UPDATE (2008-10-10): A reader very kindly sent a link to the online strip (P.S. If you're that reader, my e-mails to you are bouncing). Here are the Neandertals:

    Neandertals emerging from the mist, from Prince Valiant

    See what I mean? Compare:

    Neandertal display at old Field Museum
  • Terry Pratchett describes his Alzheimer's

    Tue, 2008-10-07 18:51 -- John Hawks

    I know many readers are fans of Terry Pratchett, as I am. He has a long, heartfelt article about his experiences with PCA, a type of early-onset Alzheimer's. An excerpt:

    When in Paradise Lost Milton’s Satan stood in the pit of hell and raged at heaven, he was merely a trifle miffed compared to how I felt that day. I felt totally alone, with the world receding from me in every direction and you could have used my anger to weld steel.

    Only my family and the fact I had fans in the medical profession, who gave me useful advice, got me through that moment. I feel very sorry for, and angry on behalf of, the people who don’t have the easy ride I had.

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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.