john hawks weblog

paleoanthropology, genetics and evolution

technology

  • 3D printing, faster, please

    Wed, 2011-10-12 20:51 -- John Hawks

    Casts!

    Origo is still in the prototype phase, but its creators have openly discussed some of the ultimate specs on their Twitter feed and Facebook page, as well as on their main site. We should expect the 3D printer to have a USB port, wireless connectivity, a price around $800, and it will use 3Dtin as its design software. Peels tells me that the printer will be able to produce objects about the size of a “large mug or medium jar.” Depending on complexity, Origo should be able to give kids a small object (like a ring) in a manner of minutes, but larger objects (like a detailed baseball) could take a few hours. Material costs for 3D printing are high (say $40 to $400 a kilo for plastic!) but Peels really wants to bring this down to something very reasonable.

    Please, please, please, I would gladly go to a license-for-unlimited casts model. Open access would be better. I just want the flexibility to shuffle the major casts into multiple lab stations, build kits to send around to schools, and not worry about things breaking. It's just not quite there, yet, either in price or simplicity.

  • The box isn't nearly as big, either

    Wed, 2011-10-05 23:20 -- John Hawks

    I saw this: "India launches Aakash tablet computer priced at $35" on Slashdot, which notes:

    The Aakash computer runs Android 2.2 (Froyo), has a 7-inch touch screen, 256MB of RAM, 32GB expandable memory slot, two USB ports, and weighs in at only 350 grams.

    I just want to note that 21 years ago I bought my first computer for $1700. It came with 2MB or RAM and 40MB of hard disk, 1 serial and 1 parallel port, and it weighed roughly 35 pounds. I know many readers can tell much scarier ghost stories about early computers, but those stats just struck me.

  • 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?

  • The new wired physical anthropologists

    Tue, 2011-05-17 08:32 -- John Hawks

    Katy Meyers, graduate student in anthropology at Michigan State, has posted at the Chronicle of Higher Education her experience "hacking" the AAPA meetings in Minneapolis: "Using Twitter and QR Codes at Conferences".

    Prior to the conference even starting, I had been active on the twitter backchannel for the conference found at #aapa2011. About a week before the conference started, a number of more well known physical anthropologists started using this specific hashtag, and I made sure that I was ‘in’ on the conversation. Throughout the conference, those of us who could get access to internet or were lucky enough to have 3G were actively tweeting on the channel about the sessions we were attending, the posters to drop by, and the various activities to check out. At the AAPA, there are about 3 to 5 concurrent presentation sessions and a poster session running throughout. By having this backchannel, those of us attending one are able to get the highlights of the other sessions. While I primarily attended sessions on bioarchaeology and digital databases, I have a general idea of the main discussions that were occurring in the primatology and paleoanthropology talks because of the twitter backchannel.

    She also discusses the QR code on her poster, which led to a good number of people accessing her work online. We tried this with Marc Kissel's poster this year, just putting a PDF version online with a QR code on the poster, and I think it worked quite well. With some more time, we'd have come up with a Prezi version of the poster.

    The interesting thing to watch is the way that this backchannel is emerging, sort of a subculture within the field. The "internetness" of it all isn't really generational -- there are lots of full professors who maintain really active Facebook relationships, for instance. But something about the backchannel definitely is a generational thing. I can't be positive, but I might have been the oldest active tweeter at the meetings. It can be so tremendously useful as a follower of the Twitter feed, because many of the active tweeters are science writers and specialists who are really good at picking out the interesting points from a talk.

    I expect we'll see more QR codes in the future -- I for one am going to start putting them into talks. Conference presentations take too much work to let them expire after a weekend; we should leverage that work into a stronger, more lasting and more interactive form.

  • Stone age selectivity

    Sat, 2011-05-14 08:30 -- John Hawks

    I'm pointing this morning to a nice recent post by Brigid Gallagher, discussing the importance of raw material and processing steps for stone age technology: "Working With Stone, Connecting the Past".

    She writes from New Zealand, where toolmakers were working with a choice between ground stone and flaking techniques. Here's a short excerpt on wastage:

    An interesting aside to this that I like having witnessed many examples when I worked at the Auckland Museum, is when pounamu adzes break in the making. Instead of being able to quickly turn out a modified artefact, the original tool may be turned into a completely new artefact, such is the desire not to waste the stone This is often evident in the hei tiki. Along the base edge of many historic and prehistoric tiki examples, a short bevelled edge can be seen, where the pounamu was originally intended as an adze. It broke in the making, and was changed from a adze perform to a hei tiki.

    Technology is not merely a series of steps, it is a way of organizing behavior. The flowchart can trigger a totally different cascade of actions than the stereotype or ideal. Flexibility of procedure coupled with a flexible choice of procedures makes the relation of intention and material very complex.

    Tags: 
  • Monkey numerical distractions

    Fri, 2011-04-15 08:20 -- John Hawks

    This study has been out for a few weeks, and I've been meaning to put up a short comment about it: "Representational format determines numerical competence in monkeys", by Vanessa Schmitt and Julia Fischer [1]. The abstract:

    A range of animal species possess an evolutionarily ancient system for representing number, which provides the foundation for simple arithmetical operations such as addition and numerical comparisons. Surprisingly, non-human primates tested in ecologically, highly valid quantity discrimination tasks using edible items often show a relatively low performance, suggesting that stimulus salience interferes with rational decision making. Here we show that quantity discrimination was indeed significantly enhanced when monkeys were tested with inedible items compared with food items (84 versus 69% correct). More importantly, when monkeys were tested with food, but rewarded with other food items, the accuracy was equally high (86%). The results indicate that the internal representation of the stimuli, not their physical quality, determined performance. Reward replacement apparently facilitated representation of the food items as signifiers for other foods, which in turn supported a higher acuity in decision making.

    This seems so obvious in retrospect. An experimenter has to provide some kind of motivation or there will be no experiment. Providing food rewards in psychology tests on animals will conflate numerical cognition with food, rewards, and motivation. I'm surprised that a simple substitution of inedible items turned out to be so successful in relaxing this cognitive bias.

    As I'm thinking about the "numbers as technology" theme, I keep returning to the idea that most interesting technologies are cobbled together from heterogeneous parts. Cognitive technology is no exception. In this experiment, we see the interference between the food/reward aspects of cognition and the representation of number. To have an effective practice of number as applied to food items, an individual would have to overcome this interference.

    We might tinker with the system in different ways -- for example, we could set up a new system of behavioral rewards or we could change neurotransmitter regulation to decrease food salience. What is the dividing line between technical and natural solutions? Imagine a pill that improves monkey math by inhibiting dopamine receptors. The same inhibition might emerge by mutations to dopamine receptors -- a natural tweak that alters the threshold of technical interventions. A new reward system might seem purely technical -- in the experiment, it worked to substitute different kinds of food treats in different contexts. But then, "different" is itself a function of perception, which can be changed by changing visual and olfactory receptors. "Technical" is a matter of arranging heterogeneous things in such a way that their natural course of action achieves a desired end.


    References

  • Did humans colonize the northern latitudes without fire?

    Mon, 2011-03-14 20:47 -- John Hawks

    Wil Roebroeks and Paola Villa [1] review the evidence for human control and use of fire in the archaeology of Europe during the Middle Pleistocene (130,000-780,000 years ago) and earlier. They observe that no evidence of human-controlled fire occurs in Europe before 400,000 years ago. This raises a puzzle: How did humans occupy the northern part of Europe without fire?

    The argument about the antiquity of fire is not new. There is very early evidence of fire at Swartkrans, Koobi Fora, and Chesowanja, which includes burned bones and heated artifacts, along with clay nodules that show evidence of heating as high as 400 degrees Celsius. The criticism of these early finds (reviewed by James [2]) centers around the difficulty of distinguishing human-made fire from natural bush fires. The association of the fire with artifacts can be readily explained: archaeologists only look for evidence of fire where they already have artifacts. The remaining question is whether artifacts or bones have been heated to temperatures hotter than those possible in bush fires, thereby providing evidence of human involvement. Burned bone from Swartkrans at least did reach such temperatures, seemingly unlikely without human involvement given their presence in the cave. I tend to think that humans did control fire early in some cases.

    Roebroeks and Villa do not dispute possible earlier evidence of fire, but claim that it was not habitual. Or to put it another way, some early humans may have used fire, but many or most did not do so. The lack of fire seems particularly surprising in the northern latitudes of Europe, where sites like Happisburgh (and Pakefield) show evidence of human habitation in the late Lower Pleistocene. Their review of the early sites is really worth reading and impressively compact. Nonetheless, I can't quote it in full; it's just too much text to extract. After a discussion of the earliest archaeological occurrences, they turn to the long sequences from Arago and Gran Dolina, where we really should expect to see some evidence of fire if people were using it.

    Arago and Gran Dolina contain long sequences and large quantities of lithic and faunal remains, subjected to taphonomic analyses (34–36). Their settings are comparable to the ones that, in later times, have often provided strong evidence of fire, such as Bau de l’Aubesier, Grotte XVI, and Lazaret in France; Bolomor Cave in Spain (Dataset S1); and Middle Paleolithic/Middle Stone age caves in Israel and in South Africa. Traces of fire have been found in the upper part of the sequence at Arago, in layers younger than 350 ka. No charcoal, no burnt bones, nor any other evidence of fire have been reported from any of the assemblages from the lower levels (dated to MIS 10–14). No charred bones or heated artifacts have been reported from the Gran Dolina sequence (TD4– TD10). Rare charcoal particles have been found in thin sections of the TD6 sediments, but these sediments originate from the exterior of the cave, and there is evidence of low-energy transport (37); thus, the charcoal may not be in situ. However, the high density of human, faunal, and lithic remains as well as their state of preservation and refitting studies (38, 39) clearly indicate an occupation in situ with little postdepositional disturbance. The absence of any heated material from the long sequences of Gran Dolina and Arago, both documenting hominin occupations over several hundred thousand years (36, 40), is striking. This is a strong pattern, which can be tested by future work at other hominin habitation sites. We suggest that the European record displays a strong signal, in the sense that, from ~400 to 300 ka ago, many proxies indicate a habitual use of fire, but from the preceding 700 ka of hominin presence in Europe, we have no evidence for fire use.

    One thing that really impressed me visiting Roc de Marsal last summer was that the site preserves a long archaeological sequence in which some levels are densely packed with charcoal and the remains of hearths, and at least one well-defined layer, with abundant evidence of tools and debitage, just has hardly any evidence of fire at all. These were Neandertals, not Middle Pleistocene Homo, and they managed to get by without leaving any clear evidence of fire even though many Neandertal populations clearly did control and use fire extensively, including at this very site at other times.

    There really were people living in the Pleistocene of Europe who didn't use fire very much, at least as evidenced by relatively long cultural deposits in well-stratified rock shelters and caves. Unfavorable preservation can explain the lack of charcoal or hearths at some sites, but not all of them. If we don't have a single good instance of fire in Europe before 400,000 years ago, people may well have done without it.

    The authors' review of fire evidence after 400,000 years ago in Europe is also very useful, and they include supplementary data table with fuller information and references for all the sites they discuss. It is impressive just how much evidence has accumulated over the years, and Roebroeks and Villa have doggedly tracked it down. They conclude that Neandertals had essentially the same degree of control of fire as Upper Paleolithic humans, and consider the use of fire as a processing step in the manufacture of complex tools:

    A recent study provides evidence of early modern humans at the site of Pinnacle Point in Southern Africa regular use of heat treatment to increase the quality and efficiency of their stone tool manufacture process 164 ka ago (13). The authors infer that the technology required a novel association between fire, its heat, and a structural change in stone with consequent flaking benefits that demanded “an elevated cognitive ability.” They also suggest that, when these early modern humans moved into Eurasia, their ability to alter and improve available raw material may have been a behavioral advantage in their encounters with the Neandertals. However, this interpretation ignores that Neandertals used fire as an engineering tool to synthesize birch bark pitch tens of thousands of years before some modern humans at Pinnacle Point decided to put their stone raw material in it. In more general terms, a greater control and more extensive use of fire is sometimes (12) seen as one of the behavioral innovations that emerged in Africa among modern humans and favored the spread of modern humans throughout the world. As stressed by Daniau et al. (52), if extensive fire use for ecosystem management were indeed a component of the modern human technical and cognitive package, one would expect to find major disturbances in the natural biomass burning variability associated with and after the colonization of Eurasia by modern humans. In their study of microcharcoal particles from two deep-sea cores off of Iberia and France, spanning the 70- to 10-ka period of biomass burning, the authors did not recover any sign that Upper Paleolithic humans made any difference: either Neandertals and modern humans did not affect the natural fire regime, or they did so in comparable ways.

    I do think the silcrete processing is interesting, but so is the pitch processing. For that matter, the possibility of fire-hardening in the Schoeningen spears would be a case of deliberate production of a complex tool using fire (complex, in that the fire-processing adds a step).

    Gesher Benot Ya'aqov, in Israel dating to around 800,000 years ago, is a highly compelling site in terms of evidence of fire. There are distinct hearth areas that correlate with archaeological scatter and have burned nut hulls and other foodstuffs. While Roebroeks and Villa express skepticism about the earlier evidence from Africa (specifically pointing to the high likelihood of bush fire as an explanation), they do accept Gesher Benot Ya'aqov as a likely fire location, while discussing the strength of the evidence. It's not such a high threshold to set; it seems like other sites should be able to meet it if fire was common.

    Personally, I am quite ready to accept that fire was invented many times by Lower Pleistocene humans and may have occurred in some regions of the world ephemerally. The maintenance of this tradition may have been a challenge that these early humans couldn't meet over long spans of time. This view does imply that the advantages of fire, including cooking, were not a typical part of the repertoire of Early Paleolithic people. But that would be consistent with what we understand of traditions in other species of primates; where one population may be pursuing complex and apparently valuable extractive foraging that another population lacks, despite otherwise being ecologically similar.


    References

    1. Roebroeks W, and Villa P. 2011. On the earliest evidence for habitual use of fire in Europe. Proceedings of the National Academy of Sciences [Internet] 108:5209–5214. Available from: http://dx.doi.org/10.1073/pnas.1018116108
    2. James SR. 1989. Hominid use of fire in the {Lower} and {Middle Pleistocene}: a review of the evidence. Current Anthropology 30:1–26.
    Synopsis: 
    Wil Roebroeks and Paola Villa claim the archaeological record doesn't provide evidence for systematic fire use in Europe before 400,000 years ago.
  • Number as cognitive technology

    Tue, 2011-03-08 21:00 -- John Hawks

    Archaeologists often define technology in terms of material products. People make stuff, and that stuff is technology.

    But there's another way to think about the stuff we make: in terms of the information we need to make it. Technology is know-how, it's skill. It's something we learn how to do. Manufacturing may have physical side effects, but it's the cognitive software that lies at the heart of technology.

    This usage is true to the etymology of the word, "technology":

    from Gk. tekhno-, combining form of tekhne "art, skill, craft, method, system," probably from PIE base *tek- "shape, make" (cf. Skt. taksan "carpenter," L. texere "to weave;" see texture).

    I mention this because, if we take this perspective on technology, then some "technology" may never be instantiated in material -- it may reside purely in the mind. That is the contention that Michael Frank and colleagues made in a 2008 paper about speakers of a language that does not have cardinal numbers above two [1]. Frank and colleagues set out to find whether this curious lack of number words causes Pirahã speakers to deal with numbers in experimental contexts differently from speakers of other languages.

    The results showed that Pirahã speakers could complete number matching tasks, using strategies that were also widespread among non-Pirahã speakers in other contexts.

    A total lack of exact quantity language did not prevent the Pirahã from accurately performing a task which relied on the exact numerical equivalence of large sets. This evidence argues against the strong Whorfian claim that language for number creates the concept of exact quantity (and correspondingly, that without language for number, any task requiring an exact match would be impossible). Instead, the case of Pirahã suggests that languages that can express large, exact cardinalities have a more modest effect on the cognition of their speakers: They allow the speakers to remember and compare information about cardinalities accurately across space, time, and changes in modality. Visual and auditory short-term memory are highly limited in their capacity and temporal extent (Baddeley, 1987). However, the use of a discrete, symbolic encoding to represent complex and noisy perceptual stimuli allows speakers to remember or align quantity information with much higher accuracy than they can by using their sensory short-term memory. Thus, numbers may be better thought of as an invention: A cognitive technology for representing, storing, and manipulating the exact cardinalities of sets.

    At the moment, my twins are making great strides in math, at least compared to their skills six months ago. Then, their mastery of number depended on counting objects, which they tracked using fingers and toes. When they got to higher numbers, they would carry out operations by envisioning imaginary fingers and toes in their heads. Now, they have learned several different strategies to break up numbers and regroup or double them, allowing them to easily add and subtract two-digit numbers.

    It's pretty cool to see it unfold, but it's essentially based on learning a technology of number. Numbers can be patterned to accomplish addition and subtraction in many ways, and with some practice and memorization, kids can attain a very rapid pace of solving problems. It's something that most of us have in their schooling somewhere, and there's nothing magical about it -- we just have to learn some algorithms and practice them.

    The Pirahã are different from speakers of other languages with more cardinal numbers, because they do not have that particular shorthand. It's a significant aid to number processing, because words and concepts provide ways to escape the limits on human short-term memory. Frank and colleagues connect this research on number to other aspects of language and cognition:

    Where does this leave the Whorf hypothesis, the claim that speakers of different languages see the world in radically different ways? Our results do not support the strongest Whorfian claim. However, they are consistent with several recent results in the domains of color ([Gilbert et al., 2006], [Uchikawa and Shinoda, 1996] and [Winawer et al., 2007]) and navigation (Hermer-Vazquez, Spelke, & Katsnelson, 1999). In each of these domains, language appears to add a second, preferred route for encoding and processing information. In the case of color, language enables faster performance in search, better discrimination, and better memory when target colors can be distinguished from distractors by a term in the participant’s language. However, verbal interference – which presumably blocks access to linguistic routes for encoding – eliminates this gain in performance, suggesting that the underlying perceptual representations remain unmodified. Likewise in the case of navigation: The use of particular linguistic devices allows (though does not require, see e.g., Li & Gleitman, 2002) efficient compressive navigational strategies. But again, under verbal interference these strategies are not accessible and participants navigate using strategies available to infants and non-human animals.

    I would have written more subtle things about the Whorf hypothesis, and maybe I will some other time.

    I very much like the idea that language itself provides the gears of a cognitive technology -- I think that is a very powerful one that we should apply more broadly in the past. It is misleading to see minimal stone tools, or the organic tools of other primates, as the simplest basis of technology. Technology begins with habits of mind, developed as strategies to better process regularities in the social environment. The powerful thing about language is that it gets in from outside. Children encounter regularities that have already taken hold in experienced minds. As I discussed last week ("Language bootstrapping the brain"), the process of language learning can proceed surprisingly well within brains with very different structural equipment.

    One other observation of interest: Color and number words were "technologies" that were acquired surprisingly well by Alex the grey parrot. Talk about a very different kind of brain!


    References

  • Jebel Faya and early-stage reduction

    Sat, 2011-01-29 21:58 -- John Hawks

    Simon Armitage and colleagues [1] describe archaeological remains from Jebel Faya, in the United Arab Emirates. The assemblages come from a rock shelter in the mountain, which is around 100 km south of the Straits of Hormuz, entry to the Persian Gulf. Below Bronze Age and later remains, are three Paleolithic units. The oldest (assemblage C in the paper) is dated by OSL to the last interglacial, around 125,000 years ago. My comments here are more note-like than usual; this topic opens a window into some work we've been recently doing.

    The authors' main conclusion is that the oldest assemblage displays technical similarities to East African archaeological assemblages, which are not present in the archaeology of the Levant either before or after this time. We have to dig into the supplementary material to the paper to get a good account of the technical similarities:

    Technologically, this assemblage has general links to East Africa (S3 S4) while showing none of the technological traits characteristic in the contemporaneous Levantine Mousterian (S5). As in the early Middle Stone Age (MSA) of East Africa, Assemblage C exhibits three profoundly different reduction strategies: bifacial, volumetric blade, and radial Levallois. This combination is unknown in the Levant after about 200 ka, where there is no bifacial reduction and the Levallois method is largely limited to unidirectional converging. The latter produced large numbers of Levallois points, which are absent from Assemblage C.

    For a layman's description of the result from coauthor Anthony Marks, I can recommend Katherine Harmon's account at Scientific American's website.

    I like the observation, but I think we should be cautious about it. The basic idea is that African assemblages display three different strategies early in the reduction sequence, none of which are evident in Levantine assemblages of equivalent age.

    Reduction sequences and conservatism

    Yesterday I talked over this concept with my graduate student Marc Kissel. I find it very interesting that the authors focused on initial reduction stages as elements of technical similarity. They thereby assume much about the cultural transmission of the reduction sequence.

    It seems reasonable that the initial steps of a reduction sequence -- from quarrying through early core shaping -- should be conservative. Early stages necessarily constrain the later steps toward finished tool production, so that a skilled toolmaker who wants to carry out the later stages of a reduction sequence has first to get the early steps right.

    Paradoxically a naive learner may be ill-equipped to attend to the importance of these first steps, compared to later steps where the preform is more readily identifiable by its physical configuration. Within a social group, the early steps of reduction may well be carried out by other people, including less-skilled artificers. The best toolmaker may go to the quarry himself, but often he may call on someone less skilled to carry out the initial reduction, or may be forced to work with partially exhausted cores from earlier attempts.

    I'm willing to hazard a guess that the social learning that enables tool manufacture would exert a bias toward low error rates early in the reduction sequence. We can consider a biological analogy -- early embryonic development is more strongly conserved across taxa (and phyla) than later development. Changing something early in a developmental sequence may make later events impossible. If I'm right, the argument by Armitage and colleagues should have some force -- finding that the early stages of the reduction sequence are shared among sites should be a better indicator of relationship than most archaeological indicators.

    But Armitage and colleagues' conclusion has force just to the extent that we accept two proposals: (1) that we understand the technical variation in the Levant, and (2) that independent development of the early-stage reduction strategies in the Jebel Faya assemblage is unlikely.

    These proposals hang together. The Levant is richly documented across the period before and after the last interglacial, moreso after OIS 6 (around 130,000 years ago) than before. These assemblages were directed toward convergent removal of Levallois points. I'm not immediately in a position to discuss the variation within these assemblages, but the question strikes me as crucial. Although the archaeological record from this area is relatively dense, like all places it samples only a small fraction of the actual groups that must have existed at the time -- to use a genetic comparison, the record has high coverage over a very small fraction of the regional behaviorome.

    Was independent invention of these early-stage reduction strategies likely? The answer depends on whether a particular early-stage reduction strategy is merely rare in the large Levantine sample, or entirely absent. If such a strategy (in this case, foliate reduction) occurs at all, we can infer that its invention was possible, if not likely. With assemblage C at Jebel Faya, we are considering the cultural tradition represented by 500 artifacts. If we treated these as a random sample of the Levantine record, they are exceedingly unusual, no doubt. But random sampling across an entire record isn't the correct comparison; we want some equivalent sampling of the cultural information in terms of time and space.

    The paper's conclusion that Jebel Faya represents an incursion of African-derived technical traditions into the Arabian peninsula depends on these assertions. I don't have strong feelings about them, but I think we should work to get a better statistical understanding about the issue. I am singularly unimpressed when archaeologists assert that one assemblage "resembles" another on purely typological grounds. Typological similarities may result from many constraints other than cultural information, and rare appearances actually carry a lot of information about them.

    Out of Africa early

    Now, what about this "southern route" business? I say it's a year behind the times. The entire reason for the "southern route" hypothesis was to explain how Africans could have left Africa 70,000 years ago without being stopped by Neandertals in the Levant. Sail them around the southern coast of Asia, and you can get them early into SE Asia and Australia without mixing with those darned Neandertals.

    We obviously don't need to rule out Neandertal interbreeding anymore. We know it happened, most likely in West Asia. Putting Africans into the Levant during the last interglacial isn't a bug, it's a feature. We need contact between moderns and Neandertals in this area to explain the genetic data.

    The dates may seem like more of a stumbling block. If we accept that a major out-of-Africa movement was underway by 70,000 years ago, we are going to have a hard time explaining why the Levant seems to have been entirely uninfluenced by it.

    But a 70,000-year-long chronology, based on estimates of mtDNA haplogroup divergences, is already out of kilter with the majority of evidence. Nuclear DNA suggests a substantially longer timescale, which would derive non-African and sub-Saharan populations from common ancestors before 140,000 years ago. Depending on the amount of mixture among these populations and the mutation rate we adopt, these populations may have begun to differentiate very early in the Middle Stone Age.

    It's hard to account for the diversity of people outside of Africa with a short migration timescale. People outside Africa are around 20 percent more inbred than sub-Saharan Africans, but they don't look like they underwent any sudden severe bottleneck. Even accounting for the mixture with archaic people like Neandertals and Denisovans, much of the variation of Middle Pleistocene humans (still present in Africa) just didn't get into non-Africans.

    I would propose a movement of MSA Africans into West Asia before the last interglacial as a model that provides a good fit to these data. An early movement followed by long interactions in this limited area would explain so much of the population structure and morphological variation of MSA Africans wasn't represented in the people who peopled Eurasia. A substantial delay between the initial entrance into West Asia and the dispersal to Europe and the rest of Asia would explain why the later archaeological transitions in those regions have no sign of immediate technical or cultural links to the MSA. It would also explain why the initial "modern" humans outside Africa share few if any derived morphological features with Africans after 100,000 years ago.

    The anatomy of the Skhul and Qafzeh samples suggests that an African incursion into the Near East did occur before 100,000 years ago. Many paleoanthropologists have supposed that this early incursion did not persist, even locally. The later Levantine sample includes individuals with more Neandertal resemblances, chiefly Amud and Kebara. But each of the later specimens shares several traits with early modern humans from Skhul or Qafzeh. Indeed there is no clear constellation of derived traits that sorts the Skhul-Qafzeh sample cleanly from Tabun 1 and the later Levantine specimens. I just don't think this skeletal record poses any problem for the idea of a long interaction of populations in this area -- especially if we extend the focus from the Levant into the Arabian peninsula and Persian Gulf region.

    The strongest reason to suppose that an African incursion was extinguished is not the skeletal record but instead the mtDNA timescale. I can refer readers to the paper by Endicott and colleagues [2], which discusses a range of mutation rate estimates and their effects on the origin of macrohaplogroups M and N, the key ancestral non-African lineages. Current estimates unanimously suggest that these clades originated within the last 75,000 years. By itself, this would suggest that the mtDNA common ancestors of non-Africans and sub-Saharan African populations diverged shortly before that time.

    I keep coming back to this, because the mtDNA just seems so out of line with the autosomal and X-chromosome picture. I regard this as a serious sticking point and hesitate to just wave it away. As I suggested to Charles Choi, the resolution may involve a time of isolation outside Africa during which the ancestors of non-Africans lost heterozygosity (and became enriched for the later mtDNA clades M and N). Or maybe we just have the mtDNA clock wrong -- the large revisions of the Neandertal-human mtDNA divergence in the light of developing evidence don't inspire confidence about the timing of internal nodes to the human mtDNA tree.

    The early archaeological assemblage from Jebel Faya strikes me as consistent with a model of early dispersal from Africa, but not especially good evidence for it. The outstanding question is whether the early reduction strategy is a behavioral trait that provides good evidence about biological relationships. I see the logic but think that it is tenuous.

    The model obviously is relevant to the question of an early presence of African-derived modern humans in India. If we combine the presence of an African-derived population in eastern Arabia with the large exposed Persian Gulf region during the last interglacial, this begins to look like a large habitable region with easy land connections to the Indus River valley. But the Indian subcontinent would potentially have been home to a very large population of ancient humans. I doubt that an occupation across the large area of West Asia plus the Indian subcontinent would have enabled the substantial reduction of heterozygosity that we see in present-day non-Africans.


    References

    Synopsis: 
    A 125,000-year-old site on the Arabian peninsula presents similarities with African MSA sites.
  • Genomes too cheap to meter

    Wed, 2011-01-12 00:03 -- John Hawks

    Matthew Herper is a science and medicine contributing writer at Forbes.com. He has just written a series of posts themed as "Gene Week", focusing on advances in genomics. One of the most provocative, "Why You Can’t Have Your $1,000 Genome", focuses on the hidden costs of interpretation and high-coverage necessary for clinical use of genome data.

    His argument is that even if the cost of sequencing a low-coverage genome goes to $1000, the true cost of using the data will remain much higher:

    Great buzzword, but it may never happen, especially not any time soon and especially not at a cost of $1,000. Research costs for sequencing a human genome may drop that low very soon, but that doesn’t include paying the doctors or the cost of information technology to process the data. Research genomes are not accurate enough for medical use. Getting better accuracy requires sequencing the DNA more times, which drives the cost back up. I’d think if we’re talking about actual medical use, $10,000 is a more accurate number. Certainly, it is not going to drop below the $2,000 level for a magnetic resonance imaging scan. And once the technology is in use, I think it is possible that the costs will go back up.

    Daniel MacArthur replied to this argument, "Why you CAN have your $1000 genome - so long as you learn what to do with it".

    None of this is simple, but it will become easier with time. As the retail costs of sequencing drops, a substantial niche will develop for innovators providing affordable, intuitive, accurate interpretation tools (embryonic versions already exist: see, for instance, Promethease or Enlis Genomics). Open-source academic software built for large-scale sequencing projects will be adapted for use by non-specialists. The increasing availability of large-scale computing power (for instance, via Amazon EC2), coupled with this intuitive software, will make even compute-intensive analyses available to the educated, motivated lay-person.

    MacArthur sketches out a genome interpretation landscape in which professionals and tinkerers support a community of genome hobbyists. This landscape is already taking shape thanks to MacArthur and many others (even me), and it's a solid prediction that this kind of human genomics will become more and more important, using open access tools to investigate history and phenotype prediction.

    Herper has a reply and consideration of the two posts, Herper "Debating The $1,000 Genome". In it, he notes the comments of several professionals that the $1,000 number itself is not an important fact, it is the availability of sequencing within that order of magnitude.

    The inevitability of the $1000 genome has already made it irrelevant. We should expect a $1000 genome announcement this year. This will be hype, because the real $1000 genomes won't be here until...next year! Before the end of 2014, whole genome sequences at 4x coverage will cross the $100 mark. I think there's a good chance they will be less than $50 at that time.

    Based on numbers I've seen, those numbers are around six months optimistic. Geneticists are already planning projects anticipating $100 genomes -- some suggest that the next big project should be a "Million Genomes", because there isn't any sense bothering with a hundred thousand.

    It helps to realize what is driving the rapid reduction in price. The "next-gen" approaches have shared many basic assumptions (e.g., in situ amplification) but have not thus far been stymied by bottlenecks caused by patent overlaps because they have progressed along semi-independent pathways. As the technology moves to long single-strand approaches, multiple approaches still seem viable, although we are awaiting a solid demonstration of these methods at higher throughput. Price is not the only factor differentiating startups -- sequence quality and ease of sample prep are very important. But major research institutions justify new equipment by runtime and amortized acquisition costs, over years. A new sequencer needs to run enough this year not only to pay its overhead, but to pay the opportunity costs of a five-fold cheaper sequencer next year. As long as progress along multiple trajectories is possible, tech startups will continue the rapid reduction in per-genome price -- because price is the most visible way of differentiating their offerings and extending the sequencing market.

    This cannot continue indefinitely: at some point there may remain only one viable path to faster or cheaper sequencing. Or one company may be able to make startups more difficult by cornering the essential patents along multiple development trajectories.

    There are two fundamental questions:

    1. Where's the bottom? Cells replicate DNA fairly slowly, and they don't transmit the resulting data in a form that computers can read. Today, rapid sequencing depends on running massively parallel reactions, exploiting imaging electronics and computers and far from the limit of either (which themselves continue to increase in capacity subject to Moore's Law). We may be surprisingly close to a portable sequencing device the size and expense of a film camera.

    But the bottom of the market depends may depend less on supply and more on demand. Maybe human genomes will be clinical necessities, or maybe they will remain niche diagnostic data. In either case, there's an upper limit. We'll never need much more medical sequencing than we have people.

    Genomics cannot work on the microcomputer model. Computer companies sell new equipment to people and companies who already have lots of last-generation equipment. Genomics cannot work on that model: once you have your genome sequence in the cloud, you won't need it again. By itself, this business model stabilizes at fairly expensive prices. As long as you need to bill a technician and maintain highly regulated records, your service costs will be very high. That leaves little incentive for lowering the sequencing cost. It's like the genomics DMV -- when was the last time your state gave you a technology rebate on vehicle registration?

    Future cost reductions must depend on applications of massive sequencing in agriculture, genetic engineering and synthetic DNA. Those areas can support a different business model, one that can operate on an annual basis. They create potentially a much larger, decentralized global market, like the market that supported the development of microcomputers.

    The problem is developing the applied genetics -- the "killer app" to take advantage of the cheaper technology. And that brings us to...

    2. Where's the utility? The reduction in cost is happening despite the fact we don't really know why genomes will be useful. Both Herper and MacArthur agree that one obstacle to clinical use of genomic data will be annotating and interpreting the sequences. This problem generalizes to applications far beyond clinical contexts. How do we use genomes to do anything interesting or useful?

    At the margins, of course, we know what to do with a genome. Look for damaging mutations. This is a straightforward empirical challenge -- find out how alterations to particular nucleotides would affect phenotypes, both by themselves and in combination with common variants elsewhere in the genome. Annotation and interpretation will require us to have genomes from millions of people and expression data from hundreds of thousands of human tissue samples and animal models.

    Every other use of genomic information poses similar challenges. Do we want to use genomes to place individuals in a genealogical context? We need to work out the genealogical trees for loci genome-wide and find the historical causes for correlations within these trees. Want to use genomes to predict the response of old-growth forests to rainfall fluctuations? Testing 10,000 dead blackbirds for causal factors? Same story -- gene variants, microclimates, and functional networks.

    There will be an expensive, professional class of genome interpretation. In medicine, these will be clinicians or clinical assistants of some kind. In applied genetics, these will be research geneticists and postdocs. If you want a personalized genealogical consultation, a gut microbiome assessment of your beef cattle, or a read on that speck of black mildew in the basement, there will be a consultant for you. Like today's IT consultants, these genome consultants' knowledge, skills, and price structures will vary. They may offer knowledge of the latest discoveries, a crew of paid tinkerers, or the comfort of hand-holding, but mostly they're adding value to the software.

    Off-the-shelf software may always be a step behind the state of the art in genome interpretation, but it will always be cheap. Today you can compare your genome to cataloged SNP-phenotype associations for free, or you can pay $5 a month to 23andMe for a more user-friendly interface and non-expert information presentation. I expect HMO's to incorporate similar information applications as they embrace genomics, just as most are currently moving to patient-accessible charting software. Last year's research information will always be cheap, and for most purposes it will be good enough.

    Put these things together, and personal genomics today is where personal computing was in 1973. We haven't yet had an Altair, much less an Apple 2. But it's almost in reach. Quasi-professional hobbyists can cobble together data using primitive tools, and carry out the same analyses as postdocs. Sequencing costs falling by an order of magnitude every other year. The state of the art in interpretation totally free for the trained, with applied genomics and synthetic biology as growing industries. Genomes may not be literally too cheap to meter, but they'll certainly be, as George Church has suggested, free with additional purchase.

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