john hawks weblog

paleoanthropology, genetics and evolution

The North African Neandertal descendants

Thu, 2012-10-18 16:25 -- John Hawks

A new paper by Federico Sánchez-Quinto and colleagues reports on comparisons of North African population samples with the Neandertal DNA project data [1]. The paper shows that North African populations also carry a substantial trace of Neandertal ancestry, like living populations outside of Africa, much more than populations of sub-Saharan Africa.

One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.

The interesting aspect of the paper is that the authors attempted to separate the ancestry of North African samples into a pre-Neolithic indigenous African component, and a residual component that represents more recent gene flow into North Africa, from all sources. The historic movement into North Africa has been fairly cosmopolitan, involving sub-Saharan Africans, Arabs, Medieval Europeans, Romans, Carthaginians and many other peoples. Sánchez-Quinto and colleagues used the ADMIXTURE program to try to sort out a pre-Neolithic indigenous component and analyze that specifically for Neandertal similarity.

Unsurprisingly, the fraction of estimated sub-Saharan African ancestry in each population sample was inversely correlated with the estimated Neandertal ancestry. That is, the more a population looks like sub-Saharan Africans, the less Neandertal it has.

Here's what's surprising: When they sorted out parts of the genome in Tunisians that ADMIXTURE determines to be most likely from pre-Neolithic North Africans, they found these parts of the genome had more Neandertal ancestry than typical of the CEU sample of northern European ancestry. Is it possible that ancient North Africans had more Neandertal similarity than today's Europeans?

Sánchez-Quinto and colleagues suggest that the Neandertal ancestry in this population came in Upper Paleolithic times from the Near East. That is possible, or some of the Neandertal similarity may reflect ancient African population structure. Really I think we will have to do a finer analysis of chromosome blocks to examine the subset of shared Neandertal derived alleles that reflect introgression versus incomplete sorting from the ancestral African population. It will be very interesting to examine more closely the mixture of population history within Egypt, through which most Near Eastern pre-Neolithic population movement must have come.

The authors note that the distribution of Neandertal similarity outside Africa increases with distance from Africa.

A previous study [26] observed that the similarity to Neandertals increases with distance from Africa and suggested this could be explained by SNP ascertainment bias plus a strong genetic drift in East Asian populations. Nonetheless more complex, population-biased, ascertainment schemes might have additional effects (i.e bottlenecks), but these are not expected to significantly increase the rate of false positives in admixture tests [31]. The Tunisian population has been reported to be a genetic isolate [17] so it is plausible that part of the signal detected is actually due to genetic drift. However, this should not affect the other North African groups in our study. Finally, given that SNP arrays are based on common alleles and probably the relevant admixture information is encoded within the rare and very rare alleles, the potential bias, if anything, will underestimate ancient hominid admixture signals, as shown in previous studies [2],[3].

This pattern was also observed by Meyer and colleagues earlier this year [2], and I discussed it in my post on that paper ("Denisova at high coverage"). Both papers note that ascertainment bias may contribute to this pattern. I added that Meyer and colleagues had assumed that genes found in sub-Saharan African populations could not have come from Neandertals, which greatly biased their estimates against Europe and West Asia, considering historical and prehistoric gene flow across the Sahara and along the Indian Ocean coast. So I'm not yet accepting the relative numbers of Neandertal ancestry from different populations, as we don't know that they have all come from consistent assumptions. In particular, an elevated amount of Neandertal ancestry in China -- this paper puts it almost as double the amount of Neandertal ancestry in northern Europeans -- is unlikely. There is no pattern of bottlenecks that can give rise to that excess without additional population mixture, and hard to see where such population mixture would have happened without also affecting the ancestors of Europeans. Instead, we have some work to do in reducing the biases on these comparisons.


References

When Hollywood and paleoanthropology intersect

Wed, 2012-10-17 13:07 -- John Hawks

In a world, lost before time, lived an ancient race of tiny people... "'Hobbit' Lawyers Threaten 'Age of the Hobbits' Movie (Exclusive)".

The word “Hobbits” has referred only to Bilbo Baggins and his bretheren since the Tolkien novel was first published in 1937, right? Not so, argues Asylum, whose lawyers have told New Line that the word is fair game because the Hobbits featured in Age of the Hobbits refer instead to an early hominid species.

"Age of the Hobbits is about the real-life human subspecies, Homo Floresiensis, discovered in 2003 in Indonesia which have been uniformly referred to as 'Hobbits' in the scientific community," a rep for The Asylum tells THR in a statement. "As such, the use of the term 'Hobbits' is protected under the legal doctrines of nominal and traditional fair use. Indeed, a simple Google search of Hobbits and archaeology reveals dozens of articles containing the term "Hobbit(s)" in the title."

Yes, that's what paleoanthropology is really for: Making the world safe for B movie producers.

Quote: Bérubé and the Boas Bowl

Mon, 2012-10-15 15:12 -- John Hawks

Michael Bérubé writes in the Chronicle of Higher Education: "Why I Resigned the Paterno Chair", with a discussion of academics versus athletics. I'm linking because of this:

The day thousands of alumni cheer "We are Penn State" in celebration of the fact that the anthropology department is No. 1 nationally (having defeated Duke in the prestigious Boas Bowl) will be the day we know we've changed the culture in Happy Valley.

Somehow I don't see it happening, although a Boas Bowl would be entertaining.

Composite tools

Sun, 2012-10-14 21:26 -- John Hawks

What if you took flaked stone implements, scanned them in three dimensions, designed specially fitted accessories, which you then printed with a 3-d printer and assembled into a composite? "modern stone + flint tools by ami drach + dov ganchrow".

through a method of three-dimensionally scanning and printing, the ancient artifacts are digitally outfitted with custom-designed handles, encapsulating the rugged forms in a perfectly enclosed case. by juxtaposing the polarities of the manufacturing processes in computer generated forms, an intersection of material technologies and functionality coincide on a tangible scale.

These are elegant and well-designed, truly art. Still, despite the fancy fabrication, the concept itself was known to the Neandertals.

(via Neatorama)

Panda gestion

Sun, 2012-10-14 20:25 -- John Hawks

Here's a story that showed up in my feed this morning: "Prehistoric man ate panda, claims scientist".

Wei Guangbiao said prehistoric man ate the bears in what is now part of the city of Chongqing in south-west China.

Wei, head of the Institute of Three Gorges Paleoanthropology at a Chongqing museum, said excavated panda fossils "showed that pandas were once slashed to death by man".

This really wouldn't be very surprising, as occasional evidence of human predation or consumption of other carnivores, including bears in Europe, goes way back.

Liveblog of ScienceNOW on Neandertals, Dikika

Wed, 2012-10-10 22:09 -- John Hawks

Now watching the NOVA ScienceNOW about "What makes us human".

9:06: "The idea of another species of humans sharing our cities isn't that far-fetched. 30,000 years ago, there were at least four different kinds of humans sharing the earth, including the Neandertals"

The introduction to Neandertals isn't bad, although I really don't like it when people say "the ones who stayed in Africa became us" -- that minimizes the contribution of other people, and glosses over the possibility that some ancient Africans didn't become "us", or were among the ancestors of some Africans but not all.

9:08: "Daniel Lieberman from Harvard looks for answers in the way human heads evolved" -- Lieberman: "What makes you different from Neandertals is basically above the neck."

9:09: Now Pogue is showing himself in a makeup studio being made into a Neandertal character. Back to Lieberman explaining how the Neandertal head is different from ours. It's really interesting to hear him describe this, because the description is completely typological -- there's no conception here of variation within Neandertals or within humans.

9:11: OK, the makeup transformation is complete. I don't want to cast aspersions on the artists, but the result doesn't compete with the makeup jobs on Face/Off.

Pogue goes walking down a city street. I don't see anybody noticing..but of course there's a cameraman following him around.

9:13: Differences in the shape of the brain. Lieberman "wouldn't bet his mortgage" on human brains being better than Neandertals.

Now Pogue is presenting several just-so stories about why we were superior to Neandertals. He dismisses these as "speculation" and starts talking about the Neandertal genome. We see a Max Planck scientist grinding up some bone with a Dremel tool.

9:15: Yay, Ed Green!

Green: "They had sex, they had descendants, we find this trace in our DNA today. Amazing."

9:18: This is the fourth show I know of where they have a presenter get their DNA sampled to find the Neandertal fraction. It's really cool that they are getting this news out there.

Green shows Pogue a part of chromosome 12 where he has a Neandertal nucleotide. They're showing a laptop screen with a slot machine-like display of nucleotides. I suppose it was really a blank screen and they did it in post-production. Either that, or I have to get the slot machine DNA typing program!

9:20: "We may not see Neandertals among us, but they are still here, within us."

Still walking down the street. An older lady seems to have decided Pogue is some kind of freak.

Oh, no! An animated Neandertal in drag! She/he is putting on makeup (this is about the shells and pigments associated with Neandertals). I have only this to say: Through the Wormhole has way better short animations than ScienceNOW.

Whew, that was over quick. Now he's on to the origin of language.

9:22: It's Dave Frayer! He's got a suitcase with skulls inside. Man, it would be cool if it were like the one in Pulp Fiction!

OK, well, it's cooler to have one with skulls inside, I guess.

Going through Homo erectus brain size. A symmetrical stone tool becomes a way to look into the cognitive abilities of early Homo.

9:26: On to Dietrich Stout, who is discussing the pathways in the brain used for stone tools. He works with Bruce Bradley, expert stone knapper, who is giving Pogue a lesson in toolmaking.

With toolmaking we're looking at complex, sequential thought. Bradley: "Because what are we looking at with language, it's complex sequential thought"

9:29: Now Cynthia Thompson, who is looking at people with brain injuries that lead to aphasia. "Agrammatic aphasia patients share a common characteristic: damage to the left hemisphere of the brain, which contains an area called Broca's area...does Broca's area have anything to do with stone toolmaking?"

9:31: Going into a scanner, where people are watching stone toolmaking via a projector, on the argument that watching an activity and doing the activity involve the same brain area. "Watching the video of simple choppers resulted in mild activity in Broca's area, but watching the video of making a handaxe caused four times as much activity"

9:34: A short interlude on babies learning language.

9:35: Looking at babies learning to laugh. Gina Mireault is studying babies smiling and laughing. "What we found with these very young babies, is that when we tell parents to make their babies laugh, they do some very outrageous things. Laughter is irresistible"

9:37: Now at the Cincinnati Zoo to see if animals laugh. Pogue tickles a penguin -- "he's laughing" -- "no, that's the noise they make when they want to breed"

Pogue is really talented at this part, he totally commits himself to being silly in the name of science.

Marina Davila-Ross is studying primate laughter. They are at the Stuttgart Zoo with gorillas. She collected sounds from all the great apes being tickled. Super cool audiogram images of the laughter sounds going from most distant -- orangutans -- to humans across the phylogenetic tree. Gorillas always use the same kind of panting laughter, as a part of horseplay.

9:42: Now with psychologist Michael Owren, looking at acoustic models of laughter sounds in people.

9:43: Pogue asks a great question: "How did that make me have more babies?" The program gives an answer (for laughter and social relationships) but it's great that they edited it to emphasize this question.

9:44: Zeray Alemseged in Ethiopia: "I went to start the first Ethiopian-led project in paleoanthropology ever, but it wasn't easy". The show gives a great short biography of Alemseged. This is an awesome segment.

9:48: Now at Dikika. They do a great job illustrating the discovery of the skeleton.

9:50: Don Johanson discussing how we "did not instantly become human".

9:51: "Day after day, for six years, Zeray chipped away at the piece of stone." They're comparing the Selam teeth to apes and humans, inferring its age and pattern of development. The show has him at a computer with Fred Spoor examining CT data.

9:53: Describing the hoopla that arose upon the publication of the Dikika skeleton. This has been a great 12-minute segment on Alemseged.

9:55: And that's the program. Very well done, a range of segments that go together very naturally. They really did save the best for last, but really everyone in the program did a great job.

A Neandertal mortuary in Spain?

Tue, 2012-10-09 19:53 -- John Hawks

El Pais has a fascinating story about the Paleolithic sites in the Lozoya river valley: "A Neanderthal trove in Madrid".

It was on the floor of Des-Cubierta that the Neanderthal must have placed the dead body of a small child aged two-and-a-half to three years old. They placed two slabs of stone and an aurochs horn on top, and set the body on fire. [Enrique] Baquedano explains that they found some of the child's teeth - they call it a little girl, although they have no scientific evidence of its gender - as well as a piece of coal that turned up just a few days ago and which will enable precise dating. "Complete burials, with a clear structure that allows [researchers] to reconstruct behaviors, is a very rare thing in any part of the world," says [Juan-Luis] Arsuaga, who is also co-director of the excavations at the major prehistoric site of Atapuerca.

This one sounds like an incredible context, if it really is as described.

Arsuaga is author of The Neanderthal's Necklace.

Why do scientists follow fads instead of acting like proper skeptics?

Tue, 2012-10-09 00:07 -- John Hawks

I had a question tonight from a reader who is a student at a university somewhere else. Without going into the details, this student was in a seminar where her colleagues were all espousing a position that has been for some time a fad in paleoanthropology. My correspondent did exactly what any good student should do: she found the relevant literature, which seemed to contradict the faddish seminarians.

What to do? Well, I mean besides flashing the hawk signal.

How could these seemingly earnest students have slavishly adopted the fad as their own? Did some professor mislead them?

I thought of that question when I was reading a post by Jeremy Fox: "Can the phylogenetic community ecology bandwagon be stopped or steered? A case study of contrarian ecology". Fox is writing about a particular branch of ecology, in which a growing group of researchers have been using phylogenetic methods to study the factors that determine the species composition of ecological communities. For the details of the methodology and substance of Fox's critique, you'll have to read the whole post.

The interesting part is the literature analysis. Fox notes the publication two years ago of a strong critique of the fad methodology, published in the leading field-specific journal. It makes a unique case study in citation practices:

Even if you don’t agree with M&L’s critique, I hope you’ll agree that this is an interesting case study of a contrarian attempt to stop or steer an ongoing bandwagon. You have a situation where lots of people are pursuing a particular question using a particular approach. But then someone well-known publishes a serious, easy-to-understand critique of that approach in a very prominent venue, and suggests an alternative approach. What happens next?

He discovers that much research plodded along as if no critique had ever been published. The most common kind of citation for the critique is in papers about totally different aspects of ecology, citing the paper as a review. Specialists within the relatively narrow area of the critique have shunted it aside. As Fox concludes, a paper can't stop a bandwagon. It can't even redirect one.

This isn't entirely a fair comparison, considering that research already underway may be hard to alter in response to critical research. Doubtless the researchers on this bandwagon can defend their preferred approach. Still, they should cite and take seriously a prominent methodological criticism.

As for my correspondent, I wrote back:

The quote you pulled is a very good one. I'm afraid you've discovered an inconvenient truth about academics: very few of them are good scholars who read and take seriously the primary literature.

Scientists are supposed to act like proper skeptics, but certain ideas seem to run away with them. I think that failure to read is the biggest reason why bandwagons get going. I've seen it so many times: Instead of engaging with a critical paper, an entire crowd of scientists cite some lame -- and often wrong -- secondary description of the paper. They take the incorrect description because it's short, because it accords with their prior conceptions, and most importantly because reviewers don't demand accuracy.

Oh, about that hawk signal -- one of my other readers today noticed that I am also a superhero. No, really -- if you're a long-time reader, you will no doubt remember:

Yep, I deliver a mighty lecture, an' pack a mighty punch.

UPDATE (2012-10-09): Jeremy Fox writes:

Just saw your discussion of my recent post on the phylogenetic community ecology bandwagon and pushback against it. Glad you liked the post. I don't know that I'm quite as pessimistic as you about the effect Mayfield and Levine, or anyone, to affect the ultimate course of that bandwagon. I think it's still fairly early days, and it's promising that some folks are already publishing papers based on Mayfield & Levine's ideas.

I thought you might be interested in a recent paper that a commenter on the post pointed out to me, and which I'm embarrassed to admit I hadn't seen. It's a review of 17 high profile papers that were subsequently rebutted, asking how often the rebuttals were cited and how they affected the citation patterns of the rebutted papers.

http://www.esajournals.org/doi/pdf/10.1890/ES10-00142.1 (it's open-access)

If anything, the review suggests that Mayfield and Levine is an unusually *high impact* rebuttal. Most rebuttals seem to have very little impact. Which is indeed a rather depressing conclusion. I'm planning a follow-up post on this paper as soon as I can carve out some time.

Quote: Ashley-Montagu and his zingers

Mon, 2012-10-08 22:04 -- John Hawks

Ashley Montagu is a unique character from the history of anthropology. I ran across an essay of his yesterday, which I found entertaining for its many zingers. It's entitled, "A cursory examination of the relations between physical and social anthropology", and while it has a four-field (well, two-field) tenor, it's far from complementary of his contemporaries [1].

As for the effects of social anthropology upon physical anthropology, I am not aware that there have ever been any; yet, as we shall see, not only have physical anthropologists a great deal to learn from the findings of social anthropologists, but we shall also see that unless they make certain of these findings part of their methodological procedures, much of their labor is likely to prove abortive. The same may be said of social anthropologists in relation to the findings of physical anthropology. Each division in its many branches has been so intent upon pegging out its claims that the peggers seem almost to have lost sight of one mother for the number of the pegs. In a science such as anthropology, which covers so wide and so complex a range of phenomena, this is not altogether surprising; but the pioneering stage is over and it is time that the peggers began to take some cognisance of the larger purposes of their activities.

I already tweeted that first line (my emphasis). What a classic!

On craniometrics:

In the past physical anthropologists have been content merely to philander upon the outskirts of these subjects, their chief occupation, being the production of a sort of calculated confusion with calipers wrought upon unoffending crania. The measurement of long series of crania has now been proceeding for more than 100 years as the main pastime of numerous workers, but with the exception of the work done within relatively recent years, it would be difficult to conceive of any work more useless or more barren of results than this.

The final paragraph of the essay expresses an early version of Ashley-Montagu's later concern with race and social justice:

The world would be immensely the poorer for the dissolution of all cultural differences between peoples. There is one belief, however, which is an essential article of faith and practise of many peoples, expressed in the notion: “We are the best, all others are our inferiors; they must be kept in their proper place.” I deem it among the most important tasks of the anthropologist to make available the evidence which may eventually prove to all mankind whether any people has, or has ever had, any justification for such a belief other than an hypertrophied sense of its own importance and the wishful mythology they have devised to support them in this belief. Only when the combined labors of physical and social anthropologists have laid bare the true meaning and value of such beliefs will anthropology have justified its claim to be called the science of man.


References

  1. Ashley-Montagu MF. A cursory examination of the relations between physical and social anthropology. American Journal of Physical Anthropology. 1940;26(1):41 - 61.

"Productively stupid"

Mon, 2012-10-08 09:20 -- John Hawks

I was passed an essay today from 2008, by Martin Schwartz in the Journal of Cell Science: "The importance of stupidity in scientific research" [1].

Second, we don’t do a good enough job of teaching our students how to be productively stupid – that is, if we don’t feel stupid it means we’re not really trying. I’m not talking about ‘relative stupidity’, in which the other students in the class actually read the material, think about it and ace the exam, whereas you don’t. I’m also not talking about bright people who might be working in areas that don’t match their talents. Science involves confronting our ‘absolute stupidity’. That kind of stupidity is an existential fact, inherent in our efforts to push our way into the unknown. Preliminary and thesis exams have the right idea when the faculty committee pushes until the student starts getting the answers wrong or gives up and says, ‘I don’t know’. The point of the exam isn’t to see if the student gets all the answers right. If they do, it’s the faculty who failed the exam. The point is to identify the student’s weaknesses, partly to see where they need to invest some effort and partly to see whether the student’s knowledge fails at a sufficiently high level that they are ready to take on a research project.

The essay is tone-deaf in interesting ways. Schwartz begins by recounting a chance meeting with a female former classmate, now a successful attorney, who dropped out of graduate school because "after a couple of years of feeling stupid every day, she was ready to do something else." Instead of investigating further how her experience as a woman might differ from his, Schwartz reflects that everyone should feel stupid in graduate school. Likewise, he makes a great show of the overwhelming difficulty of science, without describing the support of colleagues. He describes, in other words, a certain kind of ideal that most science careers do not (and probably should not) match.


References

Quote: Paleolithic religion as sex mysticism

Sun, 2012-10-07 13:39 -- John Hawks

I ran across a 1940 paper by George Barton, a specialist on Near Eastern religious tradition, during the course of researching a paper I'm writing. The paper is entitled, "The Palaeolithic origins of religion" [1], and it has one of the most incredible abstracts I've ever seen:

The burials and the art of the Aurignacian period show that men then worshipped a mother goddess, and this worship can be traced back to Mousterian times, when Neanderthal man flourished. The same art shows that women reverenced the erect phallus. These are the only objects that they seem to have considered divine. There is reason to believe that the part of a father in procreation was not yet known. The worship was not a fertility-cult in the later sense. No privacy existed; men and women knew the details of each others' physical forms. Men saw women miraculously produce children. Like the male animals, they had from instinct coitus with her. Orgasm give them the divinest thrills they knew. It was to them like the later bacchic ecstasy of intoxication. Women became their goddesses. Probably they did not generalize more than the dog, but each was devoted to his mistress. Women obtained a similar mystic ecstasy from the experience. She did not deify man, but the erect phallus. The heart of religion is a mystic thrill, uplift or satisfaction. Creeds, rituals, and conduct are all subordinate to this. Palæolithic religion was, then, sex-mysticism. The psychologic unity of the race made it universal as its survivals in the historic period prove. This is the real origin of religion. It was not begotten by fear (Lucretius), nor by animism (Tylor), nor by ancestor worship (Herbert Spencer), nor by the mysterium tremendum (Otto), but by the mysterium feminium -a mysterium tremendum indeed, but scarcely that which Otto contemplated. In adult life we forget the umbilical cord and the nursing; similarly religion has now almost everywhere left far behind its biological beginnings.

They just don't write them like that anymore.

The article fits perfectly as an illustration of the excesses of using prehistoric evidence from archaeology as a strut for interpreting the evolution of behavior, which is why I'm citing it. The article as a whole is less foolish-sounding than the abstract, rooted in exposition of the archaeological record of "ritual" then known. These aspects of the archaeological record were often wishful thinking, but that wasn't Barton's fault.


References

  1. Barton GA. The Palæolithic Beginnings of Religion-An Interpretation. Proceedings of the American Philosophical Society [Internet]. 1940;82:pp. 131-149. Available from: http://www.jstor.org/stable/985012

New RSS feed address

Fri, 2012-10-05 13:54 -- John Hawks

If you follow my RSS feed, you will have noticed the duplication of posts over the past few weeks. Thanks to the many readers who have written to ask about the problem.

This problem has been uniquely difficult for me to track down. Behind the scenes, I've been managing a server crossgrade to a new hosting company, and some changes to the infrastructure of the site. As I often do, I have also been experimenting with some new functionality and features for the site. So it has been tough to figure out which of the many changes may have caused the RSS problem.

The simplest solution for the problem is to provide a new feed address: http://johnhawks.net/rss.xml . I apologize for the inconvenience of making a new bookmark, but at this point the irritation of duplicated entries is probably causing some readers to drop their bookmark anyway.

Meanwhile, I have redirected the basic http://johnhawks.net to go to the blog front page. The original http://johnhawks.net/weblog will continue to work also, and I have no plans to change that.

Thanks again for reading. Also, thanks to readers who have been hitting those Amazon links and sending tip jar donations, which enable me to continue serving the site independently.

Tags: 

The cost of sequencing

Thu, 2012-10-04 20:45 -- John Hawks

In all the stories about the lowering cost of DNA sequencing, this NY Times contribution has to be the most heartbreaking: "Infant DNA Tests Speed Diagnosis of Rare Diseases". Yes, I know it doesn't sound like a heartbreaking headline, but the article is about end-of-life decisions for infants with undiagnosable congenital disorders.

Although genetic causes for the diseases were found in three of the four babies, the diseases had no treatments — except for surgery for the brothers — and that baby was the only one who survived.

The biggest surprise for Dr. Kingsmore, though, was that the families greatly valued having a diagnosis.

When a baby has a mysterious disease, he said, the family often embarks on a terrifying diagnostic odyssey. “Test after test is performed,” he said. “Some tests are invasive; the child is suffering. The child is getting worse and worse — most spend their entire lives in the hospital, and there is no answer.”

Just knowing the answer can be a comfort. “Providing a definitive diagnosis somehow brings closure,” Dr. Kingsmore said. “It is something they can name.”

Sequencing today is still quite expensive, and interpretation still is usually uncertain. These factors make some skeptics question whether whole-genome sequencing will ever find effective clinical applications.

The article describes a proof-of-concept study in which rapid whole-genome sequencing was applied to clinical pediatric cases, in some cases retrospectively. That area of medicine puts the question of cost and benefits of sequencing in a very different light: A day in newborn intensive care can cost $8000, at present the testing costs $13,500. Accurate information about a fatal genetic disorder can help parents and doctors call off heroic efforts, prevent extraneous and sometimes painful forms of non-genetic testing, and assure them that they have done everything possible for a child.

This is the hard edge of personalized genomics. It's not about whether you should cut back on LDL to lower your long-term cardiac risk. It's about when to end care of babies with no treatment options.

Quote: Jerison on animal intelligence

Thu, 2012-10-04 14:20 -- John Hawks

Harry Jerison, famous researcher of brain sizes across classes and orders of animals, commented on the relation of "encephalization" to the intelligence of animals by considering the problem one of multidimensional optimization [1]:

The insight is that comparable amounts of intelligence in different species may not (and normally would not) reflect comparable kinds of intelligence. Many and various intelligences (in the plural) must have evolved in conjunction with evolving environments and with brains and behaviours adapted to those environments.

That intelligences would be of various kinds is almost an axiom of evolutionary analysis, since adaptations evolve in the contexts of the environments in which they are effective, and species never occupy identical niches. The evolution of neural and sensorimotor adaptations provides many fine examples of uniqueness of species. The visual systems of deer and wolf, for example, may be similar in many ways, for example, in the structure of the sensory cells, neural networks of the retina, and the central nervous pathways and centres. Yet these systems are significantly different: the deer, like most ungulate 'prey' species, probably has panoramic vision whereas the wolf's visual field is more nearly like the primate's proscenium stage. The visual system encumbers significant amounts of nervous tissues and, thus, contributes to brain size and measured encephalization. Neural machinery associated with the sensory systems and motor control systems as a group determines a large fraction of the mass of the whole brain. Equality of encephalization of deer and wolf, thus, implies that the neural control systems for the specialized adaptations, though different in the two species, sum to approximately equal amounts relative to body size.


References

  1. Jerison HJ. Animal intelligence as encephalization. Philos Trans R Soc Lond B Biol Sci. 1985;308(1135):21-35.

Fearfully genetic

Wed, 2012-10-03 20:45 -- John Hawks

Holly Dunsworth comments on an NPR report on personal genomics: "Be afraid of fear, not personal genomics".

And the same fear that I'm trying to mitigate through education is the same fear that some journalists and ethicists seem to be perpetuating if not creating.

In my experience, if you're informed, you're likely to appreciate biological complexity rather than cling to genetic determinism. If you're informed, you understand the positive and negative consequences and aspects of personal genomics. If you're informed, you don't get lured into personal genomics for all the wrong reasons.

My favorite part of the post is her comment where she notes that the NPR piece devotes more space to describing the movie GATTACA than it does to the actual science. Here's a hint: When your fictional analogy takes more words than reality, you're doing it wrong.

Anthropocentric aliens

Tue, 2012-10-02 10:12 -- John Hawks

Steve Silberman provides an in-depth interview of Lee Billings, in the middle of writing a book about the discovery of extrasolar planets: "Five Billion Years of Solitude: Lee Billings on the Science of Reaching the Stars".

I do think humans are motivated to daydream about extraterrestrial intelligence, and, to put a finer point on it, extraterrestrial “people.” They are motivated to dream about beings very much like them, things tantalizingly exotic but not so alien as to be totally incomprehensible and discomforting. Maybe those imagined beings have more appendages or sense organs, different body plans and surface coverings, but they typically possess qualities we recognize within ourselves: They are sentient, they have language, they use tools, they are curious explorers, they are biological, they are mortal — just like humans. Perhaps that’s a collective failure of imagination, because it’s certainly not very easy to envision intelligent aliens that are entirely divergent from our own anthropocentric preconceptions. Or perhaps it’s more diagnostic of the human need for context, affirmation, and familiarity. Why are people fascinated by their distorted reflections in funhouse mirrors? Maybe it’s because when they recognize their warped image, at a subconscious level that recognition reinforces their actual true appearance and identity.

A Neandertal research report

Mon, 2012-10-01 10:15 -- John Hawks

Rebecca Wragg Sykes went to the European Society for Human Evolution meetings last week and reports on some of the Neandertal-related research presentations: "ESHE 2012 Meeting Report: Neanderthal Edition!".

Predictably there were some disputes during questions for papers, mainly regarding issues surrounding the dating of the industries termed "transitional": the Chatelperronian in SW France and also some Spanish sites following a talk by Zilhao et al.. Despite an embargo on new results from the Grotte de Rennes at Arcy sur Cure, France, Talamo et al. presented new chronological data from the site of Les Cottes, one of the only sites in Europe with a complete and defined sequence of the different archaeological cultures from late Middle Palaeolithic, Chatelperronian and Aurignacian- the earliest Upper Palaeolithic...

Much more of interest.

Enmeshed in technology

Mon, 2012-10-01 00:03 -- John Hawks

Anthropology and technology combine in a Sarah Bakewell piece about the most recent Channel swimmer, Karen Throsby: "Man is a work in progress, constantly adding technology". Purists pooh-pooh anyone who swims the Channel in a wetsuit.

Throsby's contribution was to remind us that even something as elementally "human" as marathon swimming involves many artificial techniques: gaining weight, acclimatising to the cold, monitoring one's psychology, and developing new micro-senses – an awareness of tiny differences in water temperature, a heightened kinetic sense of the body's balance and position, and so on. It means self-transformation, and is filled with "uncountable, mundane bodily technologies". Channel swimmers use rubber caps, sunblock, Vaseline to prevent chafing, sleek swimsuits and energy-boosting snacks. They are accompanied by boats with GPS.

I can't believe there are Channel-swimming purists. I mean, if they brought back Annette Kellerman, they'd still find a woman in a full-body suit.

Annette Kellerman, from Wikimedia Commons

Annette Kellerman, from Wikimedia Commons

Of course the technology that accompanies the body is only one aspect of Channel swimming. The technology inside the head is even more essential; a product of training, pacing, knowledge about risks and methods, contingency plans and logistics. I often use Channel crossing swimmers as an example of human potential, an incredible achievement for a primate body made possible by a human brain.

Teeth and teaching

Sun, 2012-09-30 14:21 -- John Hawks

Razib Khan has a short but worthwhile post about dental health and heritability: "The moral measure of bad teeth".

As someone who is quite conscious of the power of genetics, I was quite taken aback by this blind spot. I realized that not only did I attribute my own rather fortunate dental health (so far) to my personal behaviors, but, I had long suspected those with dental issues of less than optimal habits. Obviously environment (e.g., high sugar diet) does matter. But apparently a great deal of the variation in the trait is heritable.

Tooth pathologies are a great example of heritability, because they provide a discrete character (cavities or no cavities) with an age-dependent component, a meristic (how many cavities) component, and several well-characterized environmental components. They're wonderfully multifactorial -- unlike, say, obesity, which is usually understood only along a single factor dimension. Plus, teaching students about this stuff actually helps them address their own health needs, as well as those of their future children.

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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.