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User: John+Hawks

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  1. Re:Ardipithecus FAQ on Fossil Primate Ardipithecus Ramidus Described (Finally) · · Score: 1

    Thanks for the mod points everybody!

  2. Ardipithecus FAQ on Fossil Primate Ardipithecus Ramidus Described (Finally) · · Score: 5, Informative

    I have an FAQ up on my blog.

    It gives some of the story behind the news, and delves into the anatomy and implications for hominin origins. I'll be updating it as the day goes on to add more information.

  3. Umm...CSS? on Building Powerful and Robust Websites With Drupal 6 · · Score: 1

    You can move modules from one column to another to another to the footer. You can plug in any of a large variety of different modules and have them do exactly what they were designed for. You can make the blue bits a different color and up font sizes on your headers with awesome power.

    It's pretty easy to edit the CSS in the theme files and achieve whatever custom look you want. If you can do it on a static web page, you can get Drupal to output it. I'm in the process of converting a static website to Drupal, and I've had no problem replicating the look and feel of the current static page precisely.

    Now, if you're starting out without knowing any CSS or unwilling to customize a theme from the source, you are always going to be limited to the themes and options that someone else is kind enough to provide. But aside from there being more potential themes for some CMS engines (like Wordpress), I've not experienced any drawbacks in Drupal from the standpoint of page design.

  4. Re:Check Out the Sample Size on Humans Evolving 100 Times Faster Than Ever · · Score: 2, Informative

    The number of people sampled is more relevant when looking for smaller and smaller genetic changes -- things that presently are at very low frequency. In such cases we will miss rare things -- just like, if we sampled 270 Americans today, we would be pretty unlikely to find an NBA player in our sample, for instance. So that undersamples diversity.

    But we aren't looking at very rare things, we're looking at the most common ones -- things between 20 and 80 percent today. In this case, it's like measuring the mean -- if we measure 270 Americans, they are unlikely to be very far from the average height. Just in the same way, these people are unlikely to present unusual evidence of selection on very common alleles.

    Of course, we must keep in mind the limits -- if we identify selected things in these few populations, we are not seeing many things that may exist in other populations.

  5. Re:Not anymore on Humans Evolving 100 Times Faster Than Ever · · Score: 1

    Ah, perhaps everyone can (although tell that to those who can't), but so many don't. There is huge variation in fertility today. Selection doesn't care whether people are failing to reproduce because they died or for some other reason -- any genetic variations that correlate with reproduction will be selected.

    So I'm not so sanguine about the last 50 years: many of the genes impacting fertility have continued to change rapidly I expect. Still, our study wasn't looking at that time period; the genetic data don't allow it yet.

  6. Re:Prof. Hawks, is this evolution evenly distribut on Humans Evolving 100 Times Faster Than Ever · · Score: 3, Informative

    In terms of number of selected variants, the three populations in the HapMap are quite similar -- each has around 3000 new selected variants by our measures. Few of these are shared, because these recent things haven't had time to spread. Of the things that aren't shared, some of them probably have parallel phenotypic effects.

    For example, skin pigmentation genes causing lighter skin in Europeans are largely different from those in East Asians, even though they have the same general effect. Still, some specific effects, like hair pigmentation, may be quite different.

    Other genes respond to selection pressures that have historically been very different. Malaria is a huge source of selection in African populations historically, but it was much less important in Europeans, for example.

    As far as behavioral variations, the fact is that we don't know what most genetic changes may do. So we certainly can't say that some populations have undergone more or less behavioral change than others. Most of these changes are genetically very simple, so we're not looking at any kind of radically new changes in phenotype -- no growing antlers. The same would be true of any kind of behavioral changes under selection.

  7. Re:Bad Science on Humans Evolving 100 Times Faster Than Ever · · Score: 5, Informative

    Good comment.

    Here's the answer: natural selection takes initially rare mutations and magnifies them to large numbers, spreading them to most of the population rapidly. Our survey was looking at things between 20 and 80 percent frequency in living populations. That means that the average person has around half the new selected mutations, even though each mutation is very recent. As a result, genetically today's people really are radically different than the average person living 5,000 years ago -- it's within the last 5000 years we are seeing the most rapid change in frequency of these new alleles.

    This rapid evolutionary change has also been skeletal -- bodies really have changed during this time period. But the skeletal changes are just the tip of the iceberg -- most of the changes are metabolic, or pathogen-host interaction, or brain development -- things we will never see from the archaeological record.

  8. Re:Time scales on Humans Evolving 100 Times Faster Than Ever · · Score: 3, Interesting

    Progression of technology:

    Here's the thing: that change that makes it OK for you (and me) to wear eyeglasses releases us from selection to some extent against myopia. But by itself that would only cause a very slow, slow response -- mutations that harm vision won't increase quickly under drift alone. But any genes that are selected for other reasons and have the side effect of myopia may increase much more rapidly. These new selected variants are what we are finding, and they relate to many so-called "diseases" of civilization.

    All selection cares about is mortality and fertility. Within the past 200 years, mortality variation has reduced in many human populations. But fertility variation hasn't -- if anything, it may be increasing. So selection for disease resistance -- one of the largest sources in the last 10,000 years -- has probably reduced in importance. But selection on fertility -- things like sperm production, for example -- may still be increasing.

  9. Re:Evolving OR Mutating faster? on Humans Evolving 100 Times Faster Than Ever · · Score: 5, Informative

    The rate of mutations per genome has not changed, as far as we can tell. What is happening is that the overall larger number of people has generated more potential adaptive mutations, and these have been captured by selection. As a result, the neutral genetic changes in the population have slowed -- these being inversely proportional to population size. The very small fraction of mutations that are adaptive have caused rapid change by selection. Great question, I'll put it in the FAQ.

  10. Why these fossils are (or aren't) important on Missing Link Found Between Human Ancestors · · Score: 1

    The parent post asks such great questions. I have a post on my blog about the fossils and what they may show about the biogeography of early hominids.

    In response to the questions:

    • the evidence for a "missing link" is not very convincing -- it is only "missing" in the sense that fossils at the same time had not yet been found in Ethiopia
    • the idea of a link from Ardipithecus is convenient, since Tim White did find Ardipithecus
    • The fossils do not show any particular transitional features between Ardipithecus and Australopithecus, nor would we necessarily expect them to since Ardipithecus isn't very different from Australopithecus -- the story they are pushing is the location.
    • There are really only three partial sets of maxillary teeth, a part of a femur shaft, and some vertebrae and finger and toe bones. This isn't the next Lucy, in other words

    In any event, please read my blog for more information; I always update when new fossils are found!

    -John

  11. Swooping for feast on Ancestors of Homo Sapiens Hunted by Birds · · Score: 1
    RTFA... They didn't carry them off. They pierced the skull, circled waiting for death, then swooped back down to feast.

    The problem with that hypothesis is that it doesn't explain the accumulation of lots of eagle-eaten monkeys in a single cave. Transport does explain it, but then you have to figure out how they moved the hominid. I myself think that the swooping and eating hypothesis is more likely, but it isn't how the hypothesis came to be.

    --John
  12. Five pound toddlers on Ancestors of Homo Sapiens Hunted by Birds · · Score: 1
    The ancestor we are talking about was from two million years ago. It was a tree-swinging ape. The two year old probably weighed five pounds.

    Remember that chimpanzees and other apes develop faster than humans. Although the adults were a bit less in mass than living people (35 - 45 kg instead of 55 - 70), the toddlers would have been either about the same or slightly more for their age than living humans. My 2-year-olds are 30 pounds.

    --John
  13. Re:Those must have been BIG birds.... on Ancestors of Homo Sapiens Hunted by Birds · · Score: 3, Insightful
    ...because I don't think there is any bird alive today that doesn't fly away the minute we get anywhere near them, no matter how large. (okay, maybe an ostrich will fight us, but that is a BIG bird...)

    Certainly so, if it was big enough to carry the kid off -- we're talking about a 2-4 year old toddler -- it would have to be a LOTR-size eagle. Maybe Gandalf called in an airstrike?

    I think either an attack with damage inflicted at the site of attack, or an eagle who had later access to a carcass killed by another predator and carried off only the head would be more likely hypotheses.

    An earlier poster suggested that carrion birds might have been responsible, and I think that is a good idea as well.

    --John (My post is at my anthropology weblog, http://johnhawks.net/weblog)
  14. Old news, some doubt on Ancestors of Homo Sapiens Hunted by Birds · · Score: 4, Informative

    This story is mostly old news; the same researchers proposed it about ten years ago. The original idea was that the site where the skull was found (Taung) had a lot of young monkeys, which not only suggests predation, but also a relatively lightweight predator. Most of the other South African caves preserve larger adult specimens as well, which might have gotten in themselves or been carried (or dropped) by larger predators like leopards. It is a very tricky case to say that the accumulating agent at Taung must have been eagles, though, since it is much more likely that different predators and non-predation factors operated at different times for any given site.

    What they found that justified a new paper was damage inside the eye orbits of the specimen, which is one area where eagle talons damage their prey. It could be true, but on the other hand there is a lot of doubt. After all, eagles aren't the only predators that damage the eyes, and there are other ways that the bones may have accumulated, chiefly water transport, that might not require predation at all. As one of my colleagues put it, so many young primates die of disease or inadequate nutrition; the chances of this story is greater than zero, but how much?

    --John (my anthropology weblog is at http://johnhawks.net/weblog/)
  15. Orders of magnitude on A Unified Theory of Animal Locomotion · · Score: 1
    "From simple physics, based only on gravity, density and mass, you can explain within an order of magnitude many features of flying, swimming and running," added James Marden, professor of biology at Penn State. "It doesn't matter whether the animal has eight legs, four legs, two, even if it swims with no legs."

    I'm pretty sure that my own running speed is within an order of magnitude of almost anything with legs, regardless of its mass. That leaves a lot of biological interest within these simple physical parameters.

  16. No rare alleles in data on Scientists Complete Map of Human Genetic Variation · · Score: 4, Informative

    Actually, the HapMap is basically useless for "rare" genetic variants, because it intentionally is screening for common ones. Hence, it may actually be useful for common susceptibility alleles for heart disease or stroke but it isn't going to find the rare variants that affect only a few people.

    From my weblog:

    The HapMap is an incredible step forward in characterizing human genetic variation. It's a challenging dataset to work with, though. It's like an old map showing continent margins and little else -- we can see many of the common SNPs, but for most we have no idea which ones are functional or what they might do.
    --John
  17. Anthropologist FAQ on Flores on More Evidence For Hobbit Sized Species · · Score: 1
    For what it's worth, here's one anthropologist's take:
    It would not only have to be an australopithecine; it might have to be a DWARF AUSTRALOPITHECINE.
    Consider that the femur length of LB1 is just a millimeter shorter than Lucy and its body proportions are basically the same. Lucy (AL 288-1) is not only the most complete known australopithecine skeleton (barring STW 573, which is yet to be described), it has the smallest limbs. There are some individual bone fragments with smaller dimensions than Lucy's, but not very much smaller. At the same time, there are many larger specimens. Some of these, like the Sibilot radius KNM-ER 20419, are a whole lot larger.
    Now at Liang Bua, LB1 is nearly the biggest specimen. Brown et al. (2004) do report another radius from an older part of the deposit with an estimated length of 210mm. Again assuming the same brachial index, this would correspond to a humerus of 269mm, around an inch longer than LB1.
    But the other two adult long bones reported are the LB6 radius (157mm) and the LB8 tibia. At an estimated 216mm, this tibia is substantially shorter than the 235mm LB1 tibia. There is no comparably complete australopithecine femur, but if Lucy (missing around a third of the shaft) was around the same length as LB1, then LB8 would be shorter than any australopithecine.
    Even worse, it is shorter than all but one of 47 chimpanzee tibiae in my comparative data. That's really short.

    That and other questions answered on my FAQ about the Flores fossils.

    --John
  18. Hopefully substantive on Wild Gorillas Impress With Their Tools · · Score: 3, Interesting

    The interesting thing about gorillas is that they make tools quite readily in captivity, but hadn't yet been observed to use them in the wild. This would imply that their toolmaking facility was not actually a product of adaptation for toolmaking in their natural habitat.

    We could entertain a couple of hypotheses about this. Perhaps all apes share a common toolmaking ability shared from our common ancestors, which now is used in some lineages (humans, chimpanzees) but not extensively in others (gorillas). Or, which I think more likely, ape tool use draws upon other cognitive adaptations that are related to social learning and interactions, and actually using tools is a sometimes-beneficial side effect.

    In a related story this week, a group of experimenters found that chimpanzee social learning involves imitation of the techniques observed from other individuals, instead of merely copying the goals of those individuals. Chimps are conformists, in other words.

    From my weblog:

    Using this procedure, the experimenters introduced a device that would vend food to the chimpanzees. The device could be worked in either of two ways: by using a stick to lift a hook, or by using the same stick to poke a flap. The workings of the device inside are not visible from the outside, although both lifting and poking are always available to the chimpanzee using the device.
    The question is, when chimpanzees learn extractive foraging techniques, how much of the learning is direct imitation of the techniques they see others doing, and how much is emulative learning by individual experimentation?

    The results showed that even when the chimpanzees experimented with the apparatus themselves and learned both ways to get the food, they still tended to adopt the method that predominated in their group. I would guess that this trend toward learning the techniques in the group is important for learning social roles and interactions with other individuals.

    --John
  19. Switching fields may prove the shortage on NSF Reports No Geek Shortage · · Score: 5, Interesting

    Personally, I know many people in my field of science who are doing other things because of the lack of academic jobs. Big pharmaceuticals and other corporations can use people with graduate degrees in almost any kind of science, because they have the statistical and/or logical toolkits that can be applied to other work. So these folks would be counted as doing work "outside their field of training", and are doing so because of "greater financial opportunities".

    If anything, though, this doesn't mean there is a shortage of jobs for science and engineering degrees. It means that there are a shortage of people qualified to do trained statistics and problem-solving, and corporations are willing to pay a premium to raid surplus academics to get them.

    --John
  20. What was selected? on Researchers Say Human Brain is Still Evolving · · Score: 2, Informative

    One of my friends thinks a good candidate for selection would be avoidance of cities, since these were cholera-ridden population sinks for most of history. Maybe so.

    Really the reason to think that cognition is involved is that these same genes were selected repeatedly in primate and human evolution:

    Both genes underwent repeated adaptive subtitutions in the primate lineages leading to humans: these changes in Microcephalin were concentrated in the ancient hominoid ancestors of humans and chimpanzees; ASPM fixed a new adaptive substitution on average every 300,000 or so years since the human-chimpanzee common ancestor. Disease-causing alleles of both genes are associated with forms of microcephaly. The normal functions of neither have been characterized, although their effects in microcephaly would indicate that one important function is in early neural growth and differentiation. Thus, it is reasonable to think that they may have been involved in the evolution of brain size and structure in humans and other primates.

    I suppose it's possible they make you dumber. But then further experiments should show one way or the other.

    --John
  21. Re:Obviously... on Researchers Say Human Brain is Still Evolving · · Score: 1
    Eventually everyone writing on slashdot will be viewed as "monkeys" and religious fanatics of the future will proclaim that they did not evolve from these neanderthals.

    My god! I've traveled to the future! How long have I been asleep?!

  22. Re:Human evolution has STOPPED! on Researchers Say Human Brain is Still Evolving · · Score: 2, Informative

    Sure, some of the things that used to kill a lot of people don't so much anymore. People even survive and have kids with CF today.

    But selection requires only an incremental increase in reproduction. In a big population like ours, this increase can be as small as tenths or hundredths of a percent. This is so small that practically we will never measure it. Yet in a few thousand generations, this tiny reproductive effect will completely transform a population -- even a population of billions.

    That's the problem with predicting the future -- what will be important then, we can't observe happening today. But there is plenty of reason to think that things are happening now. From my weblog:

    Today, with 6 billion humans, every one-off mutation from the human consensus genome sequence occurs in dozens of people. Many multiple-off mutations occur in some people. In a larger population, selection is more potent, because genetic drift is weaker. This means that the advantageous variants of the next fifty millennia are already appearing in the world today, and may inevitably be selected. The global population is exploring the entire mutational space, many times over, and novel mutations are no longer likely to disappear so rapidly due to genetic drift. Any near variants that confer an advantage are already on the way to fixation. Many of these may lose their advantage once biomedical technology catches up to them. But others will be more subtle, more difficult to market in pharmaceutical form, and these will slowly, steadily increase.
    So if you want to have an effect, get out there and reproduce! --John
  23. Re:It's remarkable how wrong this is on Researchers Say Human Brain is Still Evolving · · Score: 5, Informative

    Well, it sure might look that way, but these genes strongly suggest that something related to cognition was under strong selection throughout history.

    One of the two genes, ASPM, appears to have come under selection only 5800 years ago; but it is now at around 20 percent, with a frequency of near 50 percent in some Near Eastern populations. Whatever this allele does, it had a selective advantage of more than 5 percent. They don't know it necessarily makes people smarter, but it's hard to think what else it might be.

    That's really the neat part; that it shows that this idea of "survival of the dumbest" is apparently not what has been happening. Instead, there is every reason to think we have been getting smarter.

    The submission doesn't mention the most problematic part: These alleles are high frequency in some populations, but absent or low frequency in others -- suggesting there may be adaptive differences in the brain among human populations. From my weblog post:

    Geneticists are increasingly finding genetic variants that affect behavior. Several of these variants are now known to vary in frequency in different human populations. These alleles are two; the 7r allele of the dopamine receptor D4 (DRD4) gene is another that influences ADD/ADHD susceptibility (Harpending and Cochran 2002). The selective structure underlying DRD4 variation may be frequency-dependent, with different alleles correlating with alternative behavioral strategies that pose greater or lesser advantages in some populations. It is not clear whether such a mechanism is true of ASPM and Microcephalin; the selected alleles have risen to such high frequencies in some populations that it seems they are not mere alternatives; they are unilaterally advantageous -- at least where they have become common already.
    --John
  24. Here's a mechanism: natural selection. on Modern Humans, Neanderthals Shared Earth for 1,000 Years · · Score: 1

    It's a common misconception that Neandertal mtDNA has proved that they went extinct. That is one interpretation of the data. Here's another:

    The real elephant under the rug of these papers (or as I've said elsewhere, the 800-pound gorilla) is natural selection. Both of the papers rely on the assumption that mtDNA is neutral. This is, in a sense, necessary to the papers' existence, since without this assumption mtDNA may be considered to be completely uninformative about the Neandertal problem. But there are good reasons to think that mtDNA has been under positive selection recently in human prehistory. Most notable among these reasons is the fact that human mtDNA violates every test of neutrality. Also suggestive is the limited mtDNA variation among the known Neandertal sequences--a suggestion that the positive selection that has affected human mtDNA recently may be just the most recent of several episodes throughout human evolution. Until papers like these take the issue of selection seriously, there is little chance of finding consensus on the Neandertal genetic problem.

    If they were under selection, Neandertal mtDNA would be gone, but some other genes might well remain. It's another hypothesis, but it may be demonstrated sooner than you think, since people are trying to reconstruct the Neandertal genome!

    --John
  25. Chatelperronian vs. Aurignacian on Modern Humans, Neanderthals Shared Earth for 1,000 Years · · Score: 5, Insightful

    There are two central issues. One is that the "Aurignacian" industry, which is proposed to have been made by modern humans, may not actually have been a single industry across Europe. In the current study, the "interleaving" of the two kinds of tools is documented by around 10 artifacts, out of 750 total.

    The other issue is that no fossil remains of modern humans have yet been found associated with early "Aurignacian" tools. We simply don't know who made them. Since they are not technically very different from the Neandertal-associated Chatelperronian, it is hard to say that there is a real cognitive difference represented by those tools, whoever made them.

    I have some pictures of the tools on my weblog post (John Hawks Anthropology Weblog), and conclude this:

    But when two pictures look like the ones above, and they are supposed to be typologically identifiable products of "modern humans" on the one hand, and "Neandertals" on the other -- well, it seems to me there needs to be a bit more than an edge of retouch behind that conclusion.

    --John