john hawks weblog

paleoanthropology, genetics and evolution

Malaria death toll estimate rises

Fri, 2012-02-03 07:42 -- John Hawks

Notable, from the Guardian: "Malaria kills twice as many people as previously thought, research finds".

The study demolishes conventional thinking on malaria – that almost all the deaths are in babies and small children under the age of five. The study found that 42% were in older children and adults.

"You learn in medical school that people exposed to malaria as children develop immunity and rarely die from malaria as adults," said Murray, IHME director and the study's lead author. "What we have found in hospital records, death records, surveys and other sources shows that just is not the case."

It will take some figuring to work out what that means relative to births in areas where malaria is endemic, but we can add to the higher death toll the clear long-term costs of malaria even to its survivors.

American Anthropological Association keeps it from the people

Thu, 2012-02-02 16:34 -- John Hawks

Last month, the White House Office of Science and Technology Policy solicited comments concerning open access publication policies for federally funded research. I submitted a comment to a related solicitation, concerning open access to data from federally funded research ("Public interests in data from federally funded research"). But the open access publication comments are also interesting to me, and the OSTP has just released the full list of comments to the public ("Public Access to Scholarly Publications: Public Comment").

Included in the list is a comment written on behalf of the American Anthropological Association by its executive director, William E. Davis, III (PDF of comment). The letter is a defense of closed-access journal policies, and includes many statements that I view as disputable.

For example, Davis addressed the embargo period for open access to journal articles. The NIH access policy allows this embargo period for journals to restrict exclusive access to subscribers for 12 months after publication.

First, after twelve months much of the content in many STM fields is old news. An embargo period of 12 months often has little effect on the financial models upon which publishing in STM fields is based. In anthropology, however, where over 90 percent of downloads occur after 12 months from the date of publication and the cited half-life of our quarterly journals is over 10 years, a 12 month embargo period does nothing to hep protect our subscriptions.

May I offer an alternative view of this problem? I suggest that the closed access policy has contributed to the irrelevance of AAA journals. Nobody outside the AAA membership notices when papers of note are published there. The AAA journals, including American Anthropologist have effectively cut themselves off from the rest of the academic world. The "half-life" is high not because new papers are steadily building more citations, but instead because their impact is anommalously slight compared to papers from 50 years ago.

Instead of making its journals more rich and relevant, the AAA leaches vampire-like its past icons. Instead of giving libraries reasons to support its efforts, the Association depends on its university-based members to argue with their libraries' acquisitions staff to keep the journals despite their poor impact.

Others have focused on this passage in the letter, which is particularly grating:

We know of no research that demonstrates a problem with the existing system for making the content of scholarly journals available to those who might benefit from it. In a recent article published in the Journal of the Medical Library Association, authors Philip Davis and William Walters conducted a literature review and concluded that "...recent studies provide little evidence to support the idea that there is a crisis in access to the scholarly literature." A separate earlier study found that 93% of the researchers surveyed reported easy access to original research articles in journals. This study surveyed 3,800 researchers and evaluated their access to 18,000 journals. It is worth keeping mind [sic] that this same study found that 62% of these scholars enjoyed easy access to data sets, data models, and the research compendium of other scholars. AAA independently corroborated these results in a survey about anthropological information with its members, who reported in February 2009 very high levels of access to peer-reviewed journals and scholarly monographs.

I think the most appropriate response to this passage is parody. Consider: "We know of no research that demonstrates a problem with the existing system of providing health care information to indigenous peoples.... A study of indigenous people covered by health plans found that 93% of them enjoy easy access to such information."

The American Anthropological Association over the past several years has shaped policies that keep peer-reviewed AAA publications accessible only by members and large institutional subscribers. Past and ongoing journal issues are walled within the Association's "AnthroSource" archive, available with association membership or to institutional subscribers for a hefty fee.

In 2007, when the AAA more than doubled the institutional subscription prices for its flagship journals, I ran some numbers on open access publication. Even using high-end price schemes, it was clear that open access electronic journals could be provided free worldwide for an annual cost of $10 per AAA member. That would represent a substantial cut in the cost of society membership, considering the current membership dues include a hefty subscription subsidy. Instead of moving toward an open access model of publication, the Association chose to provide its publisher partner (Wiley) with the opportunity to market AnthroSource and association-sponsored journals to libraries. For this, the Association receives some income, printing, and bit-moving services. Not too impressive, considering the low actual bit-moving requirements for these journals.

Overall, the AAA statement is a defense of their current policies and an argument against being required by federal policies to release any content to the public. I believe it does matter. Anthropologists have increasingly been courted by NIH funding programs directed toward "ethical and social impacts" of biomedical research. Skimming the acknowledgements section of the American Anthropologist today will not find many references to NIH, but other federal funding programs are prominently represented. Anthropological research has always been supported by the public, both as funders and participants. The AAA has kept its head low until now, but if federal policies shift any further, they will find themselves subject to the embargo or other open access requirements.

I am disappointed that AAA does not step forward into the lead on this issue. Public access to research results is the right direction for anthropological research. Davis is obviously wrong to write that "easy access to original research articles in journals" is available to the communities affected by anthropological research. Surely the legacy of distrust left by past elitism by anthropologists are evident to everyone?

It is inevitable that we will move in the direction of greater and more open access to our research. The only question is whether today's institutions will be the ones to make the transition possible, or whether we will replace them with new ones. New journals and organizations springing up to support effective online communication and collaboration are very compelling for young academics looking for a more vibrant research community. Maybe the AAA's final transmogrification will be to Archie Bunkerhood.

More voices on this issue:

Daniel Lende: "American Anthropological Association Takes Public Stand against Open Access"

Doug's Archaeology: "American Anthropology Association FAIL!!!! This Time on an Epic Scale"

Dienekes Pontikos: "The American Anthropological Association opposes open science"

Savage Minds: "News: AAA Response about Public Access to Scholarly Publications", and "How do we mobilize anthropologists to support open access?"

Denisova in the news

Mon, 2012-01-30 23:45 -- John Hawks

Hey, I'm in the New York Times today!

"DNA Turning Human Story Into a Tell-All"

It's a story about the Denisova genome and its possible relationships to recent human populations. We have been concentrating here on the Neandertals for the last few months, but I did get some analyses run on Denisova last week (thanks in large part to my grad student, Aaron Sams, who lifted over the genome from the old to new genetic map coordinates). I'll share some of those results soon.

Open science interview

Mon, 2012-01-30 10:46 -- John Hawks

NPR's Science Friday interviewed open science advocate Michael Nielsen last week: "Can science be done without secrecy?" I like the headline.

FLATOW: Why are scientists the last ones to get in on this?

NIELSEN: Well, it's kind of funny. I mean, they certainly helped bring us the Web back in the early '90s. Unfortunately, they're pretty bought into doing things in the standard way, the way they've done them for centuries, which is you do your work in the lab, you get all your results, you write them up in a paper and possibly several years later, it all appears for your colleagues to digest at that point.

And, you know, that's a great system if you're back in the 1600 or 1700s, but today we've got better tools, but people still haven't adopted them.

It's a long, thoughtful interview. I want to point to a later part also:

FLATOW: Mm-hmm. Is it - do you find that there is resistance to the way - to changing the way, the old way, of things being done? Are older scientists resistant to change and becoming part of this process?

NIELSEN: I'm not so sure I'd say resistance so much as it's just difficult to see how to cause a large-scale change. How do you get everybody simultaneously to adopt the new way of doing things? And so some people will kind of throw up their hands and say, well, it just can't be done. Probably the people actually get that the most from, scientists who are sort of in their mid-career. They're doing post docs or they're at the end of their graduate studies. And while they're subject to the system, they don't really feel like there's very much they can do to change it. When I talk to younger scientists, they're often very enthusiastic. And sometimes, when I talk to much more senior scientists, because they feel like they have some power to actually change the system, they can actually be quite enthusiastic.

Some thoughts on this later. For now, let me point again to my "Public interests in data from federally funded research."

Low-velocity spatter from the Neandertal palette

Sat, 2012-01-28 16:43 -- John Hawks

Paleolithic archaeology is the home of some of the best forensic work anywhere. I've often written about impressive analyses of stable isotopes, microscopic starch grains, phytoliths, and wear traces on artifacts. Among these, some of the most detailed studies involve the use of pigments by ancient people. Out of these, last week's paper by Wil Roebroeks and colleagues [1] really stands out by wringing every drop of information out of an ancient archaeological horizon.

I wrote last fall about the pigment "workshop" at Blombos, South Africa, which is around 100,000 years old ("Blombos pigment workshop"). And some time ago I wrote extensively about pigment use among Mousterian-era Neandertals ("Pigment use and symbolic behavior in the Neandertals"). These kinds of studies face many challenges. If a mineral pigment has been used by ancient people, it will often exist in a site only in tiny pieces. At best, some accumulation of the mineral pigment might give an indication of intentional use by ancient people. In this case, the material was scattered in a dozen or so tiny droplets over a diameter of 15 meters.

Mineral pigments have uses other than decoration. Sometimes they were used as part of a formula to make glue, which we can find still adhering to the back end of stone points. Ochre may also have been used in the process of softening animal hides. These uses were reviewed by Lyn Wadley [2], who has done more than anyone to uncover the ways MSA people processed ochre in South Africa. Pigments were used by humans as early as 200,000 years ago in Africa, and earlier than 100,000 years ago in West Asia (Skhul and Qafzeh [3]) and Europe.

The new study by Roebroeks and colleagues extends the time of pigment use in Europe to earlier than 200-250,000 years ago, which is newsworthy. It is notable that this time is early enough to suggest that the common ancestral population of European and African archaic humans may have also used pigment (or have been capable of learning to use it given the right cultural or ecological conditions). But to me, much more interesting is the way the red ochre was discovered in the archaeological site, and the experimental replication of the process by which it was deposited.

In the course of the archeological excavations, one of the sites, site C (excavated between 1981 and 1983), yielded 15 small concentrates of red material, with maximum size of 0.2–0.9 cm and 0.1–0.3 cm thick, with sharp boundaries to the sedimentary matrix (Figs. 1 and 2). The contrast in color between the bright- red concentrates and the yellowish-brown (Munsell soil color 2.5Y5/3) to grayish-olive (5Y5/3) sediment was striking (Fig. 2), facilitating recovery of these small, friable pieces at this site, excavated over an area of 264 m2 (Fig. 3). Although the red material has been interpreted as hematite (15, 23), these finds did not play a role in the history of ochre use, even though Maastricht-Belvédère became one of the flagship sites of Middle Paleolithic archeology, reviewed extensively in numerous textbooks (24).

These hematite features are pictured in several ways in the article and supplement. They are tiny: here is one of them, on a piece of sediment that was removed in total from the site:

Red ochre droplet from Roebroeks et al 2012 supplement

Detail of Figure S4 from Roebroeks et al. 2012 supplement, showing red hematite concentration upon sediment fragment removed from site.

It is simply remarkable to me that this excavation in the early 1980s uncovered an ancient sediment horizon using such great care that these tiny patches of red ochre were found. All were only a few millimeters in size. They were highly visible against the surrounding sediment, which helps to confirm that they don't belong there. Other aspects of the archaeology were likewise carried out meticulously. For example, the paper presents two refits of flakes and cores taken from the site, demonstrating that primary reduction of stone artifacts happened there with some products taken away from the site.

The paper notes the lack of hematite in local contexts where people might have found it, arguing that it must have been imported from a distance of at least 40 km from a natural source. The archaeological presence of contemporary tools taken in the opposite direction toward that hematite source helps support this argument. Forty kilometers isn't terribly far for hunter-gatherers, but it is interesting.

The experimental aspect of the paper is only sketched out in the text, and is described much more fully and illustrated in the supplement. Roebroeks and colleagues, looking at the small patches scattered across a diameter of 15 meters, guessed that they were a low-velocity spatter dropped from some kind of liquid. So they set out to reproduce it:

We hypothesize that the best explanation is that the fine hematite material was originally concentrated in a liquid solution, and that blobs of this ochre-rich substance became embedded in the sediments during use of the liquid,spilled on the soil surface. To test this interpretation, we performed an experiment to observe the impact of drops of a hematite-rich liquid on the site C sediment (SI Text). Despite the limitations of this experiment, the similarity of the experimentally produced concentrates to the archeological concentrates at both macroscopic and microscopic levels is remarkable (SI Text) and lend support to our interpretation of how the material entered the sediment.

The experiments are illustrated very nicely in the supplementary information for the paper. Here's one of the photos:

Red ochre droplet experiment, figure S10, B from Roebroeks et al 2012

Figure S10b from the supplement of Roebroeks et al. 2012. Original caption: "(A and B) Experimental hematite dots created on a 'smoothed' dry surface (50-cm height, 0.3-cm drops). The concentrates are within small craters produced during impact of the drops on the dry sediment."

Their "hematite liquid" consisted of ground mineral combined with rainwater, "launched" from a height of a half meter. Sounds like something that should be for sale in a natural cosmetics store.

What were these ancient people doing with liquid ochre? Good question. Given the unique care of excavation, the local context in which the mineral is highly visible in the fine sediment, I wonder how many other instances of similar deposits may have been lost over the years. It is sometimes excruciating to wait for results from an archaeological discovery, but the extremely slow and careful excavation methods do obtain results that could not be gotten any other way.

I was privileged to see some details from another excavation this week, where even greater care is being taken. It's totally remarkable some of the things that are out there waiting to be found.


References

Orangutan loris capture and meat-eating

Fri, 2012-01-20 16:38 -- John Hawks

Madeleine Hardus and colleagues [1] describe long-term observations of hunting by Sumatran orangutans.

The paper is straightforward in its description of the hunting observations: They hunt slow lorises, the practice is rare, it occurs at times when their other preferred foods are scarce, some individuals hunt but most don't, and food sharing among individuals other than mother-infant pairs wasn't observed. This isn't the first time hunting has been reported by wild orangutans, what it does is report a longer-term observation of one hunting female, tying this case to earlier observations.

I'm pointing to the paper because it includes some discussion about the requirements of meat eating for early hominins. These orangutans take a long time to chew up a slow lorus.

Orangutans used more than twice the amount of time (160.9 g/h) to eat the same amount of meat than chimpanzees (348 g/h) (Wrangham 2009; Wrangham and Conklin-Brittain 2003). Other chimpanzee data shows that this species is able to consume meat at much higher rates, i.e., 1.9±1.2 kg/h (Gilby 2006). This difference between orangutans and chimpanzees may suggest that higher sociality in chimpan- zees influences intake rates, where individuals are surrounded by conspecifics when eating meat, and where meat is a highly preferred food item and stealing occurs (Boesch and Boesch 1989; Goodall 1986; Stanford 1999).

I'll point out that orangutans may make a better model for early hominin jaw mechanics than chimpanzees do, because the sizes of jaw musculature and teeth are more comparable. Neither orangutans nor australopithecines have teeth that look well-made for reducing fibrous, tough meat into smaller pieces. Recent humans have been able to cook meat, which reduces its mechanical resistance to chewing. Early hominins didn't cook, so getting some high fraction of their caloric requirements from meat (even if only seasonally) might have taken a lot of time.

According to orangutan data (ingestion rate of 185 kcal/h), Australopithecus africanus would have had to chew for ca. 2 h to achieve 25% of these caloric requirements purely from meat (Table III, orangutans×A. africanus), while achieving the remaining 75% of its caloric requirements from food sources with faster chewing/intake rates, e.g., leaves or insects. This constitutes a considerable period of the day for orangutans, which spend ca. 6 h/d feeding (Morrogh-Bernard et al. 2009), and does not include the time necessary for the collection of vertebrate prey.

That sounds like a lot of chewing time, but it's not an insuperable barrier. The isotopic values for A. africanus and A. robustus suggest the possibility of up to 25% meat consumption, although they may have gotten C4 plant input by several different food sources (e.g., corms, edible stems, aquatic animals) as well as meat. Altogether, the chewing time analysis shuts off one line of argument that early hominins would have faced extreme constraints preventing them from moving to a more meat-intensive diet before the control and routine use of fire.


References

The thrifty brainotype

Wed, 2012-01-18 23:58 -- John Hawks

Andy Clark, a philosopher of the mind, has entered a useful essay in the NY Times online commentary section: "Do thrifty brains make better minds?"

"Thrifty" in the headline refers to efficiency of information processing. That's a departure from the standard anthropological version of the story, in which "expensive brains" are optimized for energy efficiency. These ideas are not mutually exclusive: a strategy toward bit-saving might well reduce the neural overhead, so to speak. But a brain that follows a strategy of greatest information efficiency might in some respects be more energetically expensive. More important, an evolutionary process that results in a brain with high information efficiency might follow a very different pathway than a process that would give rise to high energy efficiency.

Clark considers the philosophical implications of this "thrifty" model of neural processing, particularly as applied to the relative roles of perception and cognition:

All this, if true, has much more than merely engineering significance. For it suggests that perception may best be seen as what has sometimes been described as a process of “controlled hallucination” (Ramesh Jain) in which we (or rather, various parts of our brains) try to predict what is out there, using the incoming signal more as a means of tuning and nuancing the predictions rather than as a rich (and bandwidth-costly) encoding of the state of the world. This in turn underlines the surprising extent to which the structure of our expectations (both conscious and non-conscious) may quite literally be determining much of what we see, hear and feel.

Clark does not really touch on the evolutionary constraints that affected brain evolution. He discusses perception and cognition as related engineering problems for which efficient information encoding is the principal constraint. From this point of view, certain well-known perceptual illusions (he uses the "hollow-face illusion" as an example) make great sense.

It may be more useful to rephrase the headline. Thrifty brains may not make better minds, but they do yield a certain kind of mind. There are some things about which it is better not to be fooled. In a world where the brain evolved under natural selection, we should expect some kinds of perception to be more subject to mental abbreviation and shorthand than others. Illusions give us not only insight into how our brains work, but also how they evolved.

Meanwhile, human minds include much information that will not be found in other primates. This includes at least one modality of information (language) not found elsewhere in nature. It seems unlikely that our brains should have been optimized for processing this kind of information in the limited time available. The kinds of tricks visual perception uses to make visual processing more efficient may be analogous to "verbal illusions" in language processing, and maybe there is some evidence there about the pathway taken by language evolution. For a new perceptual modality to come into our population de novo, bootstrapping itself in every growing child, I expect that many steps along that pathway were determined by limitations and constraints.

What we perceive today as elegant, natural selection created as simply as gravity creates a river. The water will flow downhill, every other parameter is free.

"Journals seem noticeably less important than 10 years ago."

Mon, 2012-01-16 16:56 -- John Hawks

As ScienceOnline2012 gets underway later this week, the New York Times is running an article about open science: "Cracking open the scientific process". The article spends many paragraphs promoting a social networking startup for scientists called ResearchGate, which honestly strikes me as having a not-very-useful approach to openness. For example:

Dr. Rajiv Gupta, a radiology instructor who supervised Dr. Madisch at Harvard and was one of ResearchGate’s first investors, called it “a great site for serious research and research collaboration,” adding that he hoped it would never be contaminated “with pop culture and chit-chat.”

I doubt that a walled garden where scientists share their reprints is the wave of the future. The "answering questions" aspect of the site seems similar to the Faculty of 1000 and similar concepts. Such sites aim to make social sharing into a virtue for scientists by credentialing them. On the other hand, if a social network for science can succeed in filtering out politics, that might be worth paying for.

There are many other things in the article. One thing that shocked me: The open access fee for Nature Communications is really $5000. Holy cow. For $5000 I could pay someone to sit in a coffee shop all day and hand-type the contents of my article into personalized e-mails to everyone who reads it. What the heck is that about?

Aleut origins and relationships

Sun, 2012-01-15 22:59 -- John Hawks

Michael Balter last week had a news article in Science reviewing archaeological and genetic research into the origins and relationships of Aleut populations [1]. The topic has a rich combination of historical and contemporary approaches.

Recent genetic work confirms the distinction: Mitochondrial DNA (mtDNA) from 69 of Hrdlička's skeletons showed that Neo-Aleuts, like most modern Aleuts, descend from a common ancestor that carried genetic markers known as haplogroup D, according to recent work by University of Utah geneticist Dennis O'Rourke. But most Paleo-Aleuts were members of haplogroup A, as are most groups now living in Arctic North America.

Hrdlička argued that the Neo-Aleut populations came from the Alaskan mainland and replaced the Paleo-Aleuts. But Coltrain and others have found that the newcomers in fact coexisted with the original settlers. “The long-headed Paleo-Aleuts were still very much around” for several hundred more years, says anthropologist Richard Davis of Bryn Mawr College in Pennsylvania. About two-thirds of living Aleuts belong to haplogroup D and one-third to haplogroup A, according to work by Crawford and his co-workers, and they are presumed to be the result of admixture between Paleos and Neos. Crawford's research with modern Aleuts also suggests that they carry some Paleo-Aleut DNA, because their ancestors branched off from other Arctic peoples about 13,000 years ago—long before they colonized the islands, perhaps when they were still in Asia or Beringia.

Such a great case, where today's scientists can draw upon Hrdlička's models of population history. Still, what I think we are seeing today is only halfway through a revolution in studying human population interactions. In this case, mtDNA haplogroup frequencies are fairly informative -- similar to the situation in the Neolithic of Europe. But as we move to whole-genome approaches, it will be possible to attain a much more refined understanding of the relationships and pattern of mixture between what look like distinct groups. Likewise, the distinction between long-headed and broad-headed populations radically oversimplifies what is possible from craniometric comparisons. The biggest limit on craniometrics and genetics is the availability of relevant comparative samples from other early Beringian and American populations. This situation is getting better for genetics, and anthropologists continue to find ways to expand our understanding of New World peopling. The Aleuts are not only an interesting group for their own distinctive history; their ancestry may give them a store of the variability that was present in Eastern Beringia before people moved further south into North America.

The Aleutian islands are a microcosm of the human habitation of other, larger areas of the world. In my opinion, we aren't going to get the big areas right until we have approaches that work well in cases like this one.


References

  1. Balter M. 2012. The Peopling of the Aleutians. Science 335:158 - 161.

Steno: not just for stratigraphy

Sun, 2012-01-15 13:19 -- John Hawks

Matthew Cobb, guest-blogging at Why Evolution Is True, gives an appreciation of Nicholas Steno's contributions to biology: "Google’s doodle: women have eggs".

‘The testicles of women are analogous to the ovary’: in other words, women have eggs. This amazing statement – almost a throwaway comment in a brief section on sharks – was the start of our modern understanding of both human reproduction, and on the essential unity of the animal kingdom.

Cobb is the author of Generation: The Seventeenth-Century Scientists Who Unraveled the Secrets of Sex, Life, and Growth, which goes through this interesting chapter in the history of science, with names like Steno, Swammerdam, Leeuwenhoek all interconnected with each other.

Synthetic biology explainer

Sat, 2012-01-14 14:47 -- John Hawks

Nice piece on synthetic biology by Adam Rutherford:

But Freckles is a long way from normal. She is an extraordinary creation, an animal that could not have existed at any point in history before the 21st century. She is all goat, but she has something extra in every one of her cells: Freckles is also part spider.

UPDATE (2012-01-14): A knowledgeable reader writes:

Ah, journalists! What do transgenic animals have to do with synthetic biology? Absolutely nothing, in fact. And the hyperbole fails, too. If the protein was human instead of arachnid (as is the with many cows now), that goat would be part human then? Which would then mean that a lot of bacterial, insect and mouse cells I grow in the lab are part human, too! Woo-hoo! Meet Dima Klenchin, a synthetic biologist...

And Venter Institute's bacterium is not a synthetic life by any stretch of imagination and neither is anything else described in the article (modifying microorganisms for industrial production is about two decades old news). In fact, "synthetic biology" seems to be simply a new buzz word to get funding easier. You see, "transgenic organisms" is getting too routine and stale from the funding point of view and "nanotechnology" too has been overused to the point of losing much of its buzz power as well. So pharmacology is now "chemical biology" and gene engineering is now "synthetic biology".

As for the truly synthetic life, we are finding that it is a very hard going. Everyone would be enormously impressed by a single brand new enzyme or a metabolic pathway (no aping from existing prototypes in nature). Alas, even that turns out to be easier said than done. But fear not - all those computer scientists and physicists will soon, veeeery soon, come to the rescue. :-)

I thought it was a fun article but your points are well taken. I think that there is a faction who are trying to "define down" the term synthetic biology so it applies to everything from recombinant DNA upward. Venter obviously hasn't helped matters by trying to lower the bar for an artificial life form.

But maintaining any useful distinction may become impossible anyway if molecular machines can be made to interact in any useful way with endogenous genomes. Of course if they make spider silk comes straight out the goat's udder it would be more awesome than tomacco!

The Mayflower criminal registry

Fri, 2012-01-13 22:25 -- John Hawks

Of some interest with respect to DNA databases and privacy concerns: "DNA links 1991 killing to Colonial-era family".

The DNA sample was taken in the death of 16-year-old Sarah Yarborough, who was killed on her high school campus in Federal Way, Washington, in December 1991. The King County Sheriff's Office has circulated two composite sketches of a possible suspect -- a man in his 20s at the time with shoulder-length blonde or light brown hair -- but had been unable to put a name to the sketch.

In December, though, the department sent the DNA profile to California-based forensic consultant Colleen Fitzpatrick. Fitzpatrick compared the profile to others in genealogy databases and found the closest match was to the family of Robert Fuller, who settled in Salem, Massachusetts, in 1630 and had relatives who came over before him on the Mayflower.

This is a Y chromosome match based on the genealogical research of people who may be completely unknown to the "suspect". Fitzpatrick offers that a Y-chromosome match may be expected to share a surname, which is probative in the forensic situation. Obviously there are many possible scenarios in which such information will not lead to discovery of a suspect: the chance of non-acknowledged paternity events across 200 years is very high. I don't view the result as strongly actionable, but I do think it raises important questions about the future of genealogy databases.

We are near the time when whole-genome sequencing will make this kind of identification much more likely because unique genetic matches to 3rd and 4th degree relatives will be plausible. Finding a handful of rare mutations shared between a crime scene sample and an individual in a whole-gneome database would be a strong indication of a relationship. It's possible that the databases for whole genomes will grow faster than the technology will allow reliable whole-genome sequencing from a crime scene sample. So in this case, the issues with database use may be primary.

It would be an interesting exercise to estimate the fraction of unknown samples from crime scene Y chromosome and mtDNA that could be matched to a 10th-degree relative in the Genographic (or any other large) dataset.

Public interests in data from federally funded research

Thu, 2012-01-12 20:20 -- John Hawks

I submitted the following essay in response to the Request for Information on Public Access to Digital Data Resulting from Federally Funded Research from the National Science and Technology Council's Interagency Working Group on Digital Data.

This RFI is not the same as the current bill before Congress ("Open access op/ed in NY Times"), which would restrict public access to research articles based on federally funded research. Research articles are a very important issue, but I hope that the access to digital data will not be overshadowed by the attention to published results. As a paleoanthropologist, I believe that access to digital data from federally funded research projects is a fundamentally important issue, as I remark below.

Introduction

The United States provides grant funding to scientists through many federal programs. This funding advances work of public interest that might not happen without federal assistance.

The creation of scientific knowledge may serve the public interest directly by enabling useful inventions or supplying actionable information on issues of public importance. A funded project may also serve the public interest indirectly, by (1) finding negative results that prevent wasted effort or public harm; (2) building the scientific infrastructure that enables future discoveries and advances; (3) training new and established scientists in effective research techniques; (4) enhancing international cooperation and public/private partnerships.

Congress and the Executive Branch have recognized that access to the published results of scientific research is not sufficient to advance the direct and indirect public interests served by federally funded projects. Facilitating the indirect benefits of research is a major aim of federal agencies' "Broader Impacts" and data access rules. These policies have been a qualified success since their implementation, limited mainly by the exceptions carved out by programs and agencies to avoid requiring certain kinds of data to be reported along with research reports.

I argue that open public access to digital data should be a requirement for all federally funded scientific research. Digital data can be maintained by federal agencies as a part of the reporting requirement of federal grant funding. Doing so will advance the interest of the public and ensure that today's science generates a continuing heritage of research excellence.

Data access and transparency

Transparency is essential to public trust. Scientific conclusions are formed by observation and replication, and for this process to be transparent, all data must be available for independent inspection. The possibility of such inspection should not be limited to qualified researchers, because the very existence of special access requirements blocks transparency of the scientific process.

Changing technology has shifted the public's expectations about transparency. Digital technology enables most research data to be shared rapidly and at low cost. If data are produced in digital form, and digital data can be shared at low cost, researchers and agencies cannot credibly claim that the difficulty of reproducing and disseminating data is a sufficient reason to restrict access. Where no competing interest argues for restricted access (such as human subjects protections), a lack of access to digital data itself can now be a compelling reason for public distrust.

Therefore, federally funded researchers should release digital data to the public by default. Federal agencies should facilitate this public reporting by requiring digital data to be supplied as part of final project reporting.

Data access has a well-established record of success

The recent history of human genetics demonstrates that open access to data has unforeseen benefits that can spawn innovation, support more effective education, and catalyze new discovery. In genetics, both federal and journal policies require release of data; raw data from federally funded projects are often available as they are generated, long before publication.

My own laboratory has no federal research funding to date, but is actively engaged in research using data from federally funded projects. Today my laboratory trains undergraduate students in genetics with new data from ongoing federally funded genetic projects such as the 1000 Genomes Project. We use open access data from archaic human genomes to investigate the variation of ancient people and their relationships to living humans. This kind of work would be impractical without clearly established open data access policy.

The open access to data from the Human Genome Project facilitated the rapid development of microarrays that are now used on a broad scale in human genetics to investigate the genetic correlates of human health and disease. Access to data from these studies has enabled other scientists to independently replicate many genetic associations. More important, meta-analysis of such data has shown that many associations cannot be replicated, while also showing some cases in which nonsignificant results across different samples give rise to a significant finding when pooling those samples. Access to negative results and raw data is necessary, in other words, to establish the facts in subsequent research. This goes beyond access to published research results and requires open access to unpublished digital data.

Intellectual property protections and data access

Research data are somewhat distinct from the intellectual property issues relating to research publications. Some kinds of data do not meet the standard of originality necessary for copyright protection, such as sequence data, CT or MRI data, or data from measurement instruments. For raw data from instruments, there is no intellectual property reason why federal agency should not maintain an open archive for the public.

Much research data is unquestionably subject to copyright protection, such as lab notebooks, written descriptions, photographs, and original reconstructions. Yet there is still a substantial public and scientific interest in inspecting such data. For example, photographic documentation of archaeological sites and specimens are of particular scientific value and are today routinely produced by digital technologies and stored in digital form. Some primary digital records are unique products that cannot be recreated at another time and place: for example, in situ photographs of specimens, photographs and records of sites before excavation, and digital reconstructions. The scientific record would be incomplete without such contributions, and maintaining an archive of such data over the long term is a difficult task for a single investigator, beyond the scope of a grant term.

In cases where it is impracticable to obtain Creative Commons or other open licenses to such content, a funding agency should at a minimum require that a copy of all such archival information be deposited along with the final project report and a limited-use non-commercial license permitting electronic dissemination of these materials to the public as part of the report.

Metadata and data access

Many have noted that raw data may be useless in the absence of additional information about how the data were obtained. Such information is known as "metadata". Researchers generate instrumental data using particular instrument settings and recording standards. They gather observational data under particular research protocols. These standards are may change quickly as instrumentation, technology, and scientific results themselves demand new practices.

Some scientists note the problem of incompatible metadata, using it as an argument against to delay the establishment of open public access to data. In their view, the public are likely to misunderstand or misuse scientific data where metadata are not clearly indicated. Meta-analyses combining data from multiple research projects are an important secondary use of digital data, and such meta-analyses are impossible when data cannot be reconciled into common observational or instrumental frameworks. Performing original work with data collected in heterogeneous contexts is a research speciality of its own, and is itself sometimes targeted by federal grants.

However, meta-analysis is only one purpose of data access. Transparency, replicability, and education are central public interests that do not require the reconciliation of data collection methods from multiple studies. They require only clear description of the methods under which data were obtained. At a minimum, final research reports on federally funded projects must describe the standards of data collection with sufficient detail to allow independent replication, including all unpublished results and data.

Successes of data access in paleoanthropology

I am an anthropologist, and am most familiar with the scientific data relating to human evolution. These data include genetic observations on living and skeletal samples of humans. They also include fossil and archaeological evidence such as photographs, CT scans, isotopic records, anatomical measurements and descriptions.

For many years, nearly all genetic data resulting from federally funded research have been made available for public download. Much genetic data generated by non-federally funded research programs, including foreign and domestic institutes, has also been free for public download. These data have resulted in a massive acceleration of research on recent human evolution and human origins. They have also led to unexpected discoveries and a burgeoning contribution of other disciplines to understanding our evolution.

Data from radiocarbon dating and other isotopic sampling has also been made available to the public. Human occupation sites are among the best sources of evidence about past climates. The investment of federal resources in human evolution research has generated a temporal record that is now essential to studying changes in the faunal and plant compositions of past environments. Free access to records has enabled stronger calibration of radiocarbon dates, the development of a more secure chronology, and a more highly replicable scientific record correlating different regions of the world. Our understanding of such events changes is vastly stronger when data are made public.

Institutions and data access in paleoanthropology

By contrast, CT scans and photographs pertaining to human origins are typically not made freely accessible to the public. The United States funding agencies are not the only parties with an interest in such data. In particular, museums and institutes that curate specimens often permit data collection under agreements that restrict the dissemination of the resulting data. Such agreements may be equated to "non-disclosure agreements" with respect to scientific data.

An institution has a legitimate interest in controlling the public use of images and access to curated materials. Nevertheless, the lack of access to digital data results in reduplication of effort, overapplication of destructive sampling and measurement techniques, and unnecessary handling of precious and fragile specimens. Where it is practical, the United States should facilitate agreements with institutions that allow the release of digital data produced by public funding. Where release is not possible, funding should be granted only for those activities that will result in the release of data under a limited-use non-commercial license. Non-disclosure of data from instruments such as CT scanners, electron microscopes, or mass spectrometers is incompatible with scientific replication.

Scientific careers and data access in paleoanthropology

The economy of federal funding for scientific production sometimes leads to perverse incentives for high-ranking researchers that prevent public access to research data. Some scientists believe that their own future research will require exclusive access to data. Others want to impede research achievements by their academic rivals, or to maintain prestige and future funding opportunities.

Scientific data in some areas may constitute "trade secrets" until they are protected by patents. Even in noncommercial research, federally funded scientists sometimes claim exclusive ownership over data that they plan to use in future research. In my own field of paleoanthropology, data secrecy supports a clandestine "quid pro quo" economy among researchers, in which established researchers and institutions allow furtive looks at unpublished data, to support and consolidate their power and influence.

This is a game that the United States should simply decline to play. When federal research supports scientific results that are not subject to independent replication, it betrays the public interest in science.

Established collaborations and centers of scientific research will always exert a strong influence upon the future of science, irrespective of federal data access policies. But established players should not use federal funding to construct barriers to open inquiry.

Conclusion

Open public access to data is one indication that a research project is following scientific principles. Making digital data available to the public would be good practice for any researcher, irrespective of funding source. Data access mitigates the risk that negative data will be unreported. Data access facilitates broader stewardship of research projects, in particular where collaborations create data that are distributed across many institutions. Data access and reporting standards enable other researchers to fill in for those who cannot complete scientific project due to health or other personal reasons.

Federal grant agencies already have successful repositories for many kinds of digital data. Such data are shared with the public at minimal cost relative to the overall budget for federal research grants. Supporting digital data repositories has itself been an important granting aim for several federal agencies and continues to be an active part of scientific infrastructure. Limiting such repositories for the exclusive use of a small cadre of researchers is enormously wasteful of resources, when they can be opened to an interested public for a small incremental cost.

The public has repeatedly invented surprising uses for digital data that can complement or enhance the scientific record. But much more important, open access to digital data serves the scientific values of transparency and independent replication, essential to maintaining public trust and investment in the research enterprise.

Body donation is a weighty matter

Thu, 2012-01-12 16:42 -- John Hawks

Barbara King gives a shout-out to the Forensic Anthropology Center at the University of Tennessee ("Cremation, burial, or Body Farm?").

Twenty-two years ago, Dr. William M. Bass founded the Body Farm, or, as it's properly known, the University of Tennessee's Forensic Anthropology Center (UTFAC). Today it's a leader in a field populated by programs it inspired, as a newspaper article last week informed me.

Last week a science news story went around that medical schools don't want to accept obese body donations ("Nobody wants a chubby corpse"). The embalming makes them too heavy for the dissection tables, the story went, and medical students are supposed to learn "normal" anatomy, not "abnormal" obese people.

What America are these anatomy programs living in?

At any rate, my first thought was that forensic anthropology programs would be happy to get a broad representation of donated remains. Many of the qualities that have been developed to distinguish sex and age from the skeleton depend on samples donated 80 years ago or more. Today's weightier population differs -- bone size, robusticity, and age-related changes all vary with body mass. Doing good forensics on today's population takes a more updated sample, of the sort that continues to be built beneath the Tennessee football stadium.

Open access op/ed in NY Times

Tue, 2012-01-10 23:43 -- John Hawks

Molecular biologist Michael Eisen, writing in the New York Times: "Research bought, then paid for".

THROUGH the National Institutes of Health, American taxpayers have long supported research directed at understanding and treating human disease. Since 2009, the results of that research have been available free of charge on the National Library of Medicine’s Web site, allowing the public (patients and physicians, students and teachers) to read about the discoveries their tax dollars paid for.

But a bill introduced in the House of Representatives last month threatens to cripple this site. The Research Works Act would forbid the N.I.H. to require, as it now does, that its grantees provide copies of the papers they publish in peer-reviewed journals to the library.

Three years ago, a similar bill was introduced into Congress and did not proceed into law ("Congress to repeal open access science provisions?"). Today's NIH repository and the data access provisions of NSF grants were established by acts of Congress in the late 1990s. In my opinion, the agencies have in many areas gotten away with the bare minimum of compliance with these regulations. Worse, far from strengthening open access to publications and data, some in Congress want to reverse them. The current effort owes much to lobbying by academic publishers, and large campaign donations from officers and employees of those publishers to key Congressmen. Eisen shares more information on his blog ( "Elsevier-funded NY Congresswoman Carolyn Maloney Wants to Deny Americans Access to Taxpayer Funded Research").

Again, public comment on access to federally funded research ends this Thursday, January 12.

Max-Planck-Weizmann

Tue, 2012-01-10 08:50 -- John Hawks

A reader tipped me off to this Michael Balter news item: "New German-Israeli Center Will Research Archaeology and Anthropology".

The new Max Planck Weizmann Center for Integrative Archaeology and Anthropology, as it will be called, won't have a new building. Instead, the money will fund up to 10 postdocs or graduate students in each city, says anthropologist Jean-Jacques Hublin of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. It will also support equipment and infrastructure such as the rental of additional lab space in Leipzig and the kitting out of existing space at the Weizmann Institute. Hublin and archaeologist Steve Weiner of the Kimmel Center for Archaeological Science at the Weizmann will co-direct the new center.

Looks like an ambitious cooperation between two strong institutes.

Stature estimates for Sima de los Huesos

Tue, 2012-01-10 00:44 -- John Hawks

José-Miguel Carretero and colleagues [1] report on the lengths of long bones from Sima de los Huesos, Spain. I've long been hoping this research would come out, because we've gotten interested in the pattern of body size as an aspect of evolution in early Homo.

Sima de los Huesos is the single largest sample of fossil Homo, and Carretero and colleagues include 27 mostly complete long bones in their sample. That's around a dozen fewer than the entire sample of Neandertal long bones. This one site has more long bones than the rest of the Early and Middle Pleistocene combined.

Here are the tibiae, for example:

Tibiae from Sima de los Huesos

Complete tibiae from Sima de los Huesos, from Carretero et al. [1], figure 2.

The paper shows that the Sima hominins averaged a bit taller than Neandertals for most of the long bones.

That conclusion isn't quite as simple as it might look, because the sample of male Neandertal femora actually average 3 mm longer than the Sima de los Huesos femora. Both samples have more than double the number of males as females, so the male comparison draws on a much larger sample size. The Neandertal male femoral sample is biased a bit high by the inclusion of both left and right femora from Amud, the tallest of the Neandertal skeletons. The tibia sample gives a substantially shorter stature for Neandertal males, both because Amud isn't there, and because the limb proportions of Neandertals have short tibiae relative to their femora.

That's the problem of using stature estimates instead of simple bone lengths: Nothing's simple. Fossil samples impose some limits on the kind of analyses we can undertake. Carretero and colleagues address stature both because of its biological relevance and because estimating stature is the most reasonable way we can incorporate different long bones into a single size comparison. But considering stature introduces some problems of estimation. We can't be sure how many individuals are represented by the long bones. We can determine a minimum: Six right tibiae came from a minimum of six bodies, for example. But if two arm bones and a leg bone all came from the same skeleton, that individual will be represented three times within this sample, and we don't have a way to exclude that possibility. Worse, estimating stature requires a regression drawn from some population, but that population may have different proportions than the fossils. In this case, Neandertals and the Sima de los Huesos samples probably have different crural indices, the ratio of the length of the tibia to the length of the femur. So statures estimated from these bone lengths based on some recent human population will have systematic biases due to the different proportions in the fossil populations.

Carretero and colleagues note that most of the bones (humerus, radius, tibia) have shorter average statures in the Neandertal sample compared to the Sima de los Huesos sample. The femora and ulnae are longer in the male Neandertals. All the bones that can be compared are shorter in the female Neandertals than the female Sima de los Huesos individuals. It's probably a good bet that the Sima people were a bit taller than Neandertals. Still, the tall West Asian Amud skeleton points to the possibility of variation among Neandertals from different regions.

The differences between Neandertals and the Sima de los Huesos sample are quite small compared to the much taller statures attributed to modern humans from West Asia (Skhul and Qafzeh). These skeletons are more ancient than most of the Neandertal sample, but at 100,000 years old, much later than the other skeletal samples included in the paper including Sima de los Huesos. The authors make a strong point of this, suggesting that tall stature is a fundamentally new feature of the evolution of modern humans (which they equate with "early H. sapiens"):

As we have shown here, ‘medium height’ and ‘above-medium height’ people seem to characterize the primitive Homo biotype, while a ‘very tall’ body characterizes the derived biotype. The heights proposed for all fossil human species, except early H. sapiens, seem to average around 165–170 cm, although tall individuals exist within all samples (e.g., Amud 1, Kabwe and Jinniushan). It is only the first H. sapiens that are consistently and dramatically taller. Therefore, the evolution of stature (and perhaps also body size and shape) in humans seems to have been characterized by a long period of stasis during which the primitive body plan shared by the different Homo species varied rather little in stature throughout the Pleistocene, until the rapid appearance 200 ka of a new species with a new biotype, the ‘light’ H. sapiens.

The paper's broad assertion is that Early and Middle Pleistocene humans everywhere in the world shared the same basic body plan, with stature around 165-170 cm (for males) and relatively broad pelves. The reference to modern humans as "light" concerns the relatively narrower pelvis of recent humans.

I have no disagreement about the issue of pelvic breadth, although it deserves a separate review. But the stature of the Skhul-Qafzeh sample is neither very extreme nor is it typical of other Late Pleistocene or Holocene modern human samples. I will reprint a quote from my 2007 post about the statures of the Dmanisi hominins ("News flash: Dmanisi hominids were not short"):

Pretty and colleagues (1998) studied an archaeological sample of Aboriginal Australians from the Murray River region. Using stature estimation methods for the tibia, femur and humerus, they found that males in their sample (n=55) had an average stature of 166 cm and females (n=40) an average of around 153 cm. Wells (1952) reported a mean for !Khu (Northern Bushmen) males of 158 cm and females of 148 cm, both with standard deviations around 5 cm. Ruff (2000) puts the average stature of males at Pecos Pueblo at 161.2 cm with a range from 155 to 168 cm. In the KNM-WT 15000 monograph, Ruff and Walker (1993) report the average stature of African population samples, excluding Pygmies, as 162.3 cm. And although it is common knowledge that the Early Upper Paleolithic people of Europe were tall, the average male stature in the Late Upper Paleolithic was around 166 cm, and the average female stature around 153 cm (Formicola and Giannecchini 1999) -- virtually the same as Australians.

The Skhul and Qafzeh people were indeed tall relative to these other human samples, with male skeletal elements yielding stature estimates from 170-190 cm. The average stature of American men today is 176 cm. Holliday [2] showed that early Upper Paleolithic males had an average stature around 170 cm. According to Carretero and colleagues, the average Sima de los Huesos adult male had a stature around 168-170 cm. And as they note, taller individuals with stature estimates of 180 cm or more are present in the Early and Middle Pleistocene sample -- most notably the large Kabwe tibia, but we can also mention KNM-ER 1808 and KNM-ER 736 from the Early Pleistocene of Kenya.

I disagree with the paper's suggestion that modern humans represent a new pattern of tall stature compared to earlier humans. I propose instead as a null hypothesis that human stature has not changed systematically since the Early Pleistocene.

That doesn't mean human stature hasn't evolved. Human populations today are variable in stature, and they were in the recent past. We have pygmy populations with statures that average 150 cm or less in males, and peoples with statures that average close to 180 cm. Tall and short-statured populations today live in nearly every region, or did so in early Holocene times. Some of the variation in stature among populations is nutritional, some is additive, and both sources of variation appear to have emerged repeatedly in different contexts in recent human evolution.

I suggest that pattern of variability would also have been present in earlier populations of humans. The differences between Neandertals and early Upper Paleolithic Europeans and the Skhul-Qafzeh sample were substantial but do not exceed the differences among recent human populations. The human stature adaptation is variable within a relatively broad niche, and has been so for nearly 2 million years.


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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.