profile

The "Careers" section of Science is running a profile of two young scientists working in field paleontology, Faysal Bibi and Jean-Renaud Boisserie. It's a long article with lots of nice details about starting a career in the field.

Earlier [in 2002], while visiting family in the United Arab Emirates, Bibi saw an opportunity to have his own excavation team when he found himself standing at the top of a fossil-rich hill in the island of Shuweihat in the Abu Dhabi emirate. "There were fossils everywhere, and I remember I pretty much lost my head in the excitement," Bibi says. He read a 1999 monograph written by Peter Whybrow and Andrew Hill on the Abu Dhabi fossil site White had loaned him for the journey. The paleontologists who had worked on the site previously had abandoned it, so Bibi then applied for funding from the Abu Dhabi government to start his own dig. As soon as his first field season with White in Ethiopia ended, "I was back in Abu Dhabi with two friends from UC Berkeley to find some fossils from the Abu Dhabi Baynunah sites," he says. "That experience really taught me the value of just taking opportunities, as and when they come, and not self-doubting too much."

The two are connected through their history of work in the Middle Awash collections; the article is a good illustration of the dependence of so many field projects on young scientists, training while working to build our understanding of the sites. Not everyone who does valuable work gets recognized, even with authorship, so it's good to see some attention paid to those not at the top of the marquee.

The long delay before the publication of the Ardi work was not a problem for Boisserie. "When you want to [present] something with a lot of details, with [a] general analysis of the environment, it takes a lot of time," he says. "When you are part of a project like that, you have your own research you conduct and you can publish other things ... that are faster." Today, his CV lists 36 publications, including descriptions of large mammals in the Ardi sites and of another important hominid called Toumaï Sahelanthropus tchadensis, which was found in Chad. His work also reports the discovery of new hippo species in Chad, the Middle Awash, and other places, and the study of the origins and relationships of Hippopotamidae. "I'm not just relying on these major papers with hominid description to be able to build my CV," he says.

Two important lessons for those wanting to break into field paleontology: Don't expect to work on the hominins, and do spread yourself around, at your own expense if necessary, to work on multiple sites with different teams.

I ran across an interview between Anna Plutinski and population geneticist Warren Ewens.

I cannot say enough about Ewens' book, Mathematical Population Genetics. If you can work through it, you can do population genetics. It doesn't cover every au courant topic, but those will change next week anyway. And it's on Kindle now. Which I suppose probably looks pretty good on the DX, assuming the math displays well -- the book's format is just the right size for it.

Anyway, this interview from 2004 was probably conducted around the time the book was released. It covers pretty much the gamut of his career. I have to select some part to quote for you, so I'll select the passage that would be most likely to come out of my own math in my genetics class:

WE: Of course there is a strong possibility that the neutral theory is assumed not because it is appropriate but because the math of that theory is so very simple compared to the math applying for any selective theory.

AP: Can I follow that up? Do you think that that has lead to models of phylogenetic change that is not very well supported by the evidence?

WE: I think that that is quite possible. However, here we enter into another question. In mathematical population genetics theory you know from the very start that you are making big simplifying assumptions. You are in a very different position from a physicist, who might believe that his mathematical models describe reality exactly. No sensible population geneticist would make any claim along those lines. He or she is forced to simplify, because reality is so complicated that you don’t know it in any detail, and even if you did know it and used math describing it faithfully, the analysis would be impossible to carry through. So simplification is unavoidable. I do not know whether the use of the neutral theory is too much of a simplification and has lead us to incorrect and distorted views about the true evolutionary tree, it’s shape and dimensions, but I suspect that there has been quite a significant distortion.

There is much more at the link, some history of association testing, genetic draft, a lot on Ewens sampling theory, and a touch about his work here in Madison.

The Freakonomics blog has a long question-and-answer with Anne Wojcicki, of 23andMe. It's interesting to see how she takes reader questions -- many of the answers are what you'd expect a company management type to give, but a few are enlightening.

I'll quote the last Q and A, because it is the most striking:

Q. How does all the snickering from genetic counselors about your site make you feel? Seriously, can you guys come to my medical school and defend yourselves, because they’re really dragging your name through the mud? Doctors aren’t willing to have anything to do with the site, but there have got to be some cases where the predictive power of the results you get is really high. — Joel

What a question! "How does all the snickering...make you feel?" How can you answer that? "I pity them as they cling to their dying creed." "I feel great joy because soon we will crush them!" "It makes me throw up a little in my mouth."

Oh, well, naturally Wojcicki's answer is more diplomatic:

A. While many doctors support 23andMe, individual empowerment application with respect to health information has sometimes been a protracted process in parts of the medical community. Earlier in the 20th century, cancer diagnoses were not shared with patients. Over-the-counter pregnancy tests and anonymous HIV tests both faced numerous hurdles before they got to the public. And with the arrival of the Internet, many doctors bemoaned the kind of information their patients now have access to (at times perhaps with good reason).

Nonetheless, history has come to show that these developments have improved people’s knowledge of themselves allowing them to be more involved in their personal health care. It is now hard to imagine a world where a patient would not receive her diagnosis, have easy access to pregnancy or HIV tests, or have access to the world’s vast online health information.

We believe that genetic information will follow the same course. ...

That continues with a couple of examples.

Right now is an uncertain time, with lots of companies attempting new models of business relationships based on genetic information. So far, genetic information is minimally useful, even in an actuarial sense across thousands of people. 23andMe has found creative ways to market genetic information, and continues to explore new approaches.

Consider Dan MacArthur's post yesterday, "23andMe offers free genome scans to 4,500 senior athletes, seeking genetic fountain of youth". That's verging on the "free credit report" business model -- give us your info, we'll use it in our research and be able to advertise things to you (say, genealogy) that you might like. It's creative -- no doubt accounting for any "snickering" that genetic counselors might be doing. But this isn't genetic counseling. There aren't many genetic counselors who will go near phenotypes with heritabilities as low as cardiovascular disease or obesity. 23andMe is pitching a kind of armchair research participation, which can only be practical by making the information delivery highly automated (by that snicker-inducing website).

Free credit report. You input your name, taxpayer ID, and other information, a computer mines its database and gives you a number with supporting records. Then, you get additional information keyed to that number, informing you about issues related to your number and records. Plus, you're marketed additional products based on your record and personal information -- or signed up for a "credit protection" service with a monthly fee. The value of the business depends on the ability to sell advertising placement or additional services, which is enabled by the middle step -- the narrative of non-personalized information, connected to the personalized record. It's like a create-your-own-story book, except the computer turns the pages for you.

Is personalized genomics any different? Well, there are a few problems.

1. Credit scores really do matter to financial planning. So far, consumer genetic information doesn't help medical decision-making.

2. Credit scores are actionable -- people can do something about errors, if they know about them. There's nothing you can do to change your genes.

3. There are critical times, planned relatively long beforehand, when the information is valuable -- chiefly before large purchases like houses or cars. Not so with genetics -- you won't know when the information might become useful, and there may be no critical moment where you need to know.

4. Oh, and credit records are already accumulated by three large companies, who are required to make them available by request. If you want to get genetic information, you have to take cheek swabs from people -- nobody's doing that for you, yet.

The genetics company must make some accommodations then -- developing the database requires some loss-leading and investment; the "continuing surveillance" of your record can be given as a free benefit of a large initial fee instead of a subscription that pays the free initial report. Late night television advertising won't (presumably) work for genetics (although, there are loads of "male enhancement" ads...) -- but maybe social networking will?

Well, anyway, I found this an entertaining exercise...it's late though, so I'll have to stop.

Software publisher O'Reilly is running an interview with David Dooling, data chief of the Genome Sequencing Center at Washington University: "Sequencing a genome a week". If you want a little background on the current challenges in genomics, the history of genome sequencing technologies, and the infrastructure that allows modern bioinformatics, it's a really nice interview. Dooling is a speaker at the upcoming Open Source Convention (OSCON).

A sample:

James Turner: It sounds like there are a lot of informatics challenges with genomic data. There's the computational challenge of doing the sequence, which you mentioned. There's a challenge of managing the resulting data and finding meaning in it. And then there's the challenge of applying that understanding to a larger population. First of all, did I miss any of the challenges? And second of all, what are the unique problems in each set of those?

David Dooling: Well, let me talk a little bit about each of the ones you did mention, and maybe that'll bring up some that you didn't. So as far as just analyzing the data and generating the data, that is computationally intensive because essentially what you're getting off of these new instruments is pictures, images. And you need to apply algorithms to detect features in those images and then translate those features accounting for different vagaries of chemistry, and then resulting in a sequence, a series of basic Gs, As, Cs and Ts, the building blocks of DNA. Once you have that information, there's a whole host of secondary analysis, or analysis of biological relevance if you want to think of it that way, that need to happen, and those are project-specific. So for some sorts of projects, for example a cancer project, you would want to find all of the ways that the DNA that you sequenced differs from the reference and then take -- for the tumor, let's say. And then for the normal, do the same thing. And then for all of those variants, find out which ones are unique to the tumor genome as compared to the normal genome.

It's not an interview about biology; it's about technology and how people are working to enable us to test more and more detailed biological questions.

Michael Balter writes in this week's Science about the artistic reconstruction of ancient fossil hominins. The occasion for the article seems to be John Gurche's preparations for fleshing out the new Hall of Human Origins at the National Museum of Natural History:

In the morning, Gurche would pack up the heads in crates and drive them to the Smithsonian Institution in Washington, D.C., where they will be displayed next year in the National Museum of Natural History's new Hall of Human Origins. The result, says Richard Potts, head of the Smithsonian's Human Origins Program, will be a chance for museum visitors to "look into the eyes of our ancestors." It will also be another job done for Gurche, one of an elite group of paleoartists (see sidebar, p. 139), who combine cutting-edge research and exquisite artistry to bring hominins back to life in museum displays, magazines, and documentaries.

The article goes through some of the scientific background and artistic choices made in reconstructions. The most interesting to me is to see the way that different contemporary artists choose to represent the same fossils -- Balter's article illustrates Daynès' and Gurche's reconstructions of the Liang Bua 1 hominid as a good example -- the two differ radically in hair, pigmentation, nose form, and attitude. That's a big reason why I think more representations are much better for the science -- if we start to really focus in on one reconstruction, it has the potential to cloud our thinking. Looking at two images of the same fossil really helps to clarify the interpretive effort that goes into them.

A sidebar to the article profiles the training of paleo-artists Gurche, Elizabeth Daynès and Adrie and Alfons Kennis. Want to reconstruct hominins in three dimensions? There seem to be two routes: start with dissections and work your way up, or start with an art background and work your way down.

References:

Balter M. 2009. Bringing hominins back to life. Science 325:136-139. doi:10.1126/science.325_136

The NY Times profiles Southwest archaeologist Steve Lekson, "Scientist Tries to Connect Migration Dots of Ancient Southwest":

“Steve is possibly the best writer in Southwest archaeology,” said David Phillips, curator of archaeology at the Maxwell Museum of Anthropology at the University of New Mexico. “Our academic writing has this inherent gift of taking something interesting and making it dull and boring. And Steve doesn’t have that problem. He thinks outside the box, and the rest of us comb through his ideas.”

“Having said all that,” Dr. Phillips added, “I personally think that the Chaco meridian is a crock.”

Lekson has a new book coming out, History of the Ancient Southwest, which updates his "Chaco meridian" idea along with many other elements of Southwest archaeology. It seems to me that this is an interesting case study in the power of archaeology to test ideological versus ecological hypotheses -- that in a complex society with long-term occupations and stylistic elements for comparison.

But whenever you're talking about a hypothesis involving ideological causation, there's a tremendous potential for confirmation bias:

“Anyone can take any position and find evidence,” Dr. Phillips said. “Done properly, science means that you stop yourself and figure out what the opposite is — the null hypothesis — and you prove the null hypothesis couldn’t possibly be true. By process of elimination, your desired outcome becomes more plausible. This gets back to Karl Popper. You can only falsify.”

But Dr. Lekson insists that archaeology can advance only by pushing beyond the Popperian ideal, trying to make sense of all the data with plausible accounts of what was happening historically in the ancient Southwest.

“We were trained to treat ancient Pueblo societies like cultures in laboratory petri dishes,” he recently wrote. “Sprinkle the right amount of rainfall on the proper soil and up popped pueblos.” What has been neglected, he says, is an appreciation for the unquantifiable.

What they're talking about is different prior assumptions. How close to a meridian do sites have to be to confirm or reject the hypothesis that they're plotted on the meridian? How much can they overlap before they reject the hypothesis of mass relocation? It depends how committed you are to the idea to begin with -- and that depends on your prior expectations about the role of ideological and ecological forces on complex societies.

As for myself, I'm never surprised when a complicated scenario falls close to the mark. It's the simple ones that get my attention.

On the intersection of science and art, the NY Times profiles former astronaut Alan Bean, who for nearly thirty years has painted what he experienced in spaceflight:

Critical attention has eluded Mr. Bean, 77, though he has developed, largely through word of mouth, a following among private collectors who pay up to $175,000 for one of his works. In July, the Smithsonian Air and Space Museum in Washington will mount a show of 45 of his works and will release a book of reproductions of his paintings. He has high hopes that the 40th anniversary of the moon landing may lure critics to take a look at his work.

I'm used to drawing and painting an entirely different kind of lifeless body. But the Moon poses unique challenges:

“People talk about nature being beautiful, and it is, but it’s not harmonized like a painting,” he said. “If Monet painted what he saw, we wouldn’t celebrate him today. He painted a little of what he saw but then he painted mostly the way he felt about it.”

Yet Mr. Bean’s methods still reflect his scientific side. He builds a scale model of every scene he paints, and uses a klieg light to simulate the sun and to get the shadows right. He works out the angle of the light and the positions of the people with mathematical precision. He wants the details to be historically correct.

The story doesn't cover the artistic side of NASA, and thereby may leave the impression that Bean is more of an anomaly than he really is. An immense attention to scientific illustration accompanied the development of the space program, as photorealistic renderings of space (and very early on, animated computer graphics) were an important part of spreading the science to the public. Bean's approach is, of course, very different and helps to extend the tradition outside the technical aspects into the humanistic sphere.

On the occasion of the Lucy exhibit going to New York, Donald McNeil, Jr., profiles artist and reconstructor Viktor Deak. Deak's 78-foot mural of human evolution is part of the exhibit.

The article gives a nice short picture of Deak, what it takes to be trained as a paleo artist (hint: lots of anatomy), and his working environment. Deak's website has photos of a lot of his work. I especially like the way McNeil's article describes the artist-scientist interaction:

Picasso never had to explain that his mistresses weren’t actually cubic, but Mr. Deak has taken grief over as little as a flexed knee. One academic critic who saw his Lucy mural publicly boasted that he himself “had the good fortune to examine Lucy when she was in Donald C. Johanson’s lab in Cleveland, and I can assure you that the anatomy of the lower back, hips, feet and knee and ankle joints all provide clear evidence that those early hominids stood just as erect as we do.”

Mr. Deak replied on the same Web site that he knew perfectly well that Lucy could stand up, but he had depicted her crouching because she was pulling away from a predator — the viewer. She was, he explained, protecting the baby in her arms and about to run off.

I just think that's classic. The scientist (and you know you can guess who) wants an iconography. The specimen is its features, and the artistic representation should lay those features out for the viewer. It's like having all the stigmata in the right places on a crucifix -- the wounds tell the story. The artist, on the other hand, wants to express the individual beyond the features, a story to be conveyed by posture and gesture. It's a conflict -- with many stories to tell, only a few can make it into a museum display.

The New York Times' Claudia Dreifus interviews anthropologist Polly Wiessner, known for her pathbreaking work on Hxaro exchange among the !Kung and other social networks in small-scale societies.

Q. WHY ARE THESE NETWORKS WORTH STUDYING?

A. I think they are a clue to how modern humans moved out of Africa around 45,000 years ago. Unless these migrants had support systems in a founding group and could maintain ties with them, it probably wouldn’t have been possible to keep pushing into unknown territory.

It only took modern humans some 5,000 years to move out of Africa, cross Eurasia and end up in Australia. I think that the invention of social networks — the storing of relationships for a time when you will need them — is what facilitated this expansion.

The interview trends from here into the impact of Facebook on today's social networks, and the changes technology may bring to the Kalahari.

The New York Times has an interview with primatologist Richard Wrangham, who's promoting a new book, "Catching Fire: How Cooking Made Us Human.

The austrolopithicines, the predecessors of our prehuman ancestors, lived in savannahs with dry uplands. They would often have encountered natural fires and food improved by those fires. Moreover, we know from cut marks on old bones that our distant ancestor Homo habilis ate meat. They certainly made hammers from stones, which they may have used to tenderize it. We know that sparks fly when you hammer stone. It’s reasonable to imagine that our ancestors ate food warmed by the fires they ignited when they prepared their meat.

Now, once you had communal fires and cooking and a higher-calorie diet, the social world of our ancestors changed, too. Once individuals were drawn to a specific attractive location that had a fire, they spent a lot of time around it together. This was clearly a very different system from wandering around chimpanzee-style, sleeping wherever you wanted, always able to leave a group if there was any kind of social conflict.

Wrangham's hypothesis falls into a long tradition in paleoanthropology -- the "umbrella hypothesis", a term coined by John Langdon (1997). In Wrangham's version, cooking was the fundamental change from which most of the other changes in early Homo can be derived. Other well-known umbrella hypotheses include the "expensive tissue" hypothesis, the aquatic ape hypothesis, and the "killer ape" hypothesis.

An umbrella hypothesis isn't necessarily false just because it relies on a single cause. Hey, maybe cooking really did cause all that other stuff. Many well-respected scientific theories started out as umbrella hypotheses, like continental drift, or the K-T impact hypothesis.

But an umbrella hypothesis can be difficult to test because its supporters may draw in many facts that are explained equally well by other causes, or worse may be irrelevant. Take for example the argument that a fire provides an attractive location for social interactions. That is certainly true in many recent human hunter-gatherers. But food-sharing hominids may have had home bases attractive for social interactions without fire. And ethnographic hunter-gatherers really do leave groups because of social conflicts. They are much freer to move than male chimpanzees are, and this freedom to move has nothing obvious to do with cooking.

Anyway, I'm looking forward to reading Wrangham's book -- not because I think I'll agree with it, but because it can be so useful to line up the facts in different ways.

UPDATE (2009-04-21): A reader asks if I could add some more detail -- what do I really think about cooking/diet change/brain evolution? That's a tall order; it will take a while to write it up but I'm happy to do it.

Especially since I've come to think something completely counter-intuitive. The brain of early Homo erectus didn't grow relative to body size. If anything, it shrank.

References:

Langdon JH. 1997. Umbrella hypotheses and parsimony in human evolution: a critique of the Aquatic Ape Hypothesis. J Hum Evol 33:479-494. doi:10.1006/jhev.1997.0146

A local Knoxville paper did a story last month on anthropologist Bill Bass. Bass is probably best-known for his efforts to establish the "Facility," otherwise known as the "Body Farm". In recent years, he has been involved in writing a series of best-selling crime novels. So now, he's a celebrity anthropologist:

“At the University of Kansas, I had a doctoral student, Bob Gilbert, who was wondering if females age the same as men,” Bass says. “Well, nobody knows. Cadaver populations are notorious for having people in the older ranges. You get old and crotchety and drive your friends away, when you die, your body ends up in the anatomy department. A young person dies, the family buries them. We had very little data dealing with younger individuals, excepting the skeletal remains of American prisoners who had died in North Korean prison camps. How do you get these things? I had been working with a number of pathologists in the country on various little things and I started asking if, when they did an autopsy on a young female, would they save the pubic synthesis [sic, should be "symphysis"] for Bob Gilbert? One who did, fortunately, was Jerry Francisco in Tennessee. When UT decides they want to hire me, Jerry asked if I would be the forensic pathologist for the Tennessee State Medical Examiners System.

“He notified the 95 Tennessee county medical examiners that they had me on staff, and the bodies started coming in. The first 10 I got had maggots. I didn’t know about maggots. Kansas had twice the amount of land as Tennessee, and half the people, so the chances people smelling a body and finding it while it still had maggots was pretty small back there. I looked in the literature for more about maggots, and there wasn’t much. So I went to the UT dean and said, ‘I need some land to put dead bodies on.’ He picks up the phone and I started with a former sow barn on the ag campus.”

It's a very nice profile, good for forwarding to people interested in forensic anthropology.

A reader forwards this article from the Washington Post:

In a dim hallway in the Smithsonian's Museum of Natural History, anthropologist David Hunt opens a dingy green cabinet and pulls out a drawer full of human bones.

"This," he says, "is Grover Krantz."

If you're an anthropologist, that's all you will need to see to follow the link and read the whole thing. If not, you may need a little more:

"Grover kept a lot of stuff," he says. "These are his baby teeth."

Or:

Working at the Berkeley museum, Krantz broke his big toe in a particularly memorable manner: He dropped the Dead Sea Scrolls on it.

Click the link. You know you want to. And you'll find a sweet story of a misunderstood anthropologist, the dog he loved, and a death spent teaching.

Oh, and Bigfoot, too.

Alan Boyle, who writes the "Cosmic Log" feature for MSNBC, has a long interview with Don Johanson. It's a nice read, which touches on many paleoanthropological topics as well as Johanson's soon-to-be-released book with Kate Wong, Lucy's Legacy: The Quest for Human Origins:

Cosmic Log: What do you think? Would [this museum exhibit] blow Darwin's mind?

Johanson: Well, first of all, there are a couple of things that would trickle through his mind immediately. One of them is the fact that Lucy is sort of an amalgam: long arms, small brain, but yet bipedal. ... One of the things that Darwin stressed in his model of human evolution was the acquisition of upright walking. We still think that may be the first distinguishing feature that separated us from a common ancestor with the chimps. He would be gratified to see that.

But he would be mostly gratified when he read that Lucy was 3.2 million years old - because that was one of the things that Darwin struggled with, almost more than anything. We all face it today: We need more time, we need more time. For example, you're taking an exam as an undergraduate, and it's time to turn in the exam. But Darwin really meant it: He needed time, and that really bugged him. The world had to be old for all this to have happened for him. So, how gratified would he be that his predictions turned out to be correct?

Honestly, that was my first reaction to an article that includes relatively neutral grey-background shots of Pinker from several angles. Way to go, dude!

The article is Pinker's insider's account of the Personal Genome Project, and is larded with some ongoing results in human behavioral genetics. Both should interest those who have been following technology and human genetics. Earlier this week, I posted about Sharon Begley's reaction to Pinker's last Edge essay; I thought the short section cited probably didn't reflect the full nuance of Pinker's views (for instance, as expressed in The Blank Slate). Today's essay in the NY Times Magazine does a better job of describing the science, along with its possible benefits and risks:

Though the 20th century saw horrific genocides inspired by Nazi pseudoscience about genetics and race, it also saw horrific genocides inspired by Marxist pseudoscience about the malleability of human nature. The real threat to humanity comes from totalizing ideologies and the denial of human rights, rather than a curiosity about nature and nurture. Today it is the humane democracies of Scandinavia that are hotbeds of research in behavioral genetics, and two of the groups who were historically most victimized by racial pseudoscience — Jews and African-Americans — are among the most avid consumers of information about their genes.

Pinker describes the current state of what behavior geneticists know (most things are heritable, shared familial environment accounts for little variation) and what they don't know (which genes account for any of the heritable variation). Given this state of knowledge, the results from direct-to-consumer genetic testing seem to approach the trivial -- and are notable for their exceptions more than their rules:

Direct-to-consumer companies are sometimes accused of peddling “recreational genetics,” and there’s no denying the horoscopelike fascination of learning about genes that predict your traits. Who wouldn’t be flattered to learn that he has two genes associated with higher I.Q. and one linked to a taste for novelty? It is also strangely validating to learn that I have genes for traits that I already know I have, like light skin and blue eyes. Then there are the genes for traits that seem plausible enough but make the wrong prediction about how I live my life, like my genes for tasting the bitterness in broccoli, beer and brussels sprouts (I consume them all), for lactose-intolerance (I seem to tolerate ice cream just fine) and for fast-twitch muscle fibers (I prefer hiking and cycling to basketball and squash). I also have genes that are nothing to brag about (like average memory performance and lower efficiency at learning from errors), ones whose meanings are a bit baffling (like a gene that gives me “typical odds” for having red hair, which I don’t have), and ones whose predictions are flat-out wrong (like a high risk of baldness).

The second half of the essay focuses on Pinker's own experiences with gene testing and the constraints of behavior genetics. In particular, he discusses the observation that so far the genes found to be significantly correlated with behavioral traits like IQ explain only a very tiny fraction of the heritable variation in large populations -- he calls this "Geno's Paradox". We've plumbed the depths -- as noted here on other occasions -- and if there were any genes explaining large fractions of the variation, we would have found them by now. The observation is easily explained -- the heritable variation is explained by rare alleles or small effects across hundreds or thousands of genes. But this solution means that genome-wide tests will not be good predictors of such traits in the foreseeable future.

With that result prominently in mind, what is the point of all this genome sequencing? Pinker makes the point that the Personal Genome Project is not about predicting phenotypes, it's about research. The participants want to help find new pathways by which genes affect phenotypes. Recording the whole genomes of a well-studied set of people, whose phenotypes have been recorded in more-or-less excruciating detail, is the way to get data for this process. Conceivably, if influential alleles really are rare in the population, we will continue to get valuable data as we expand the set of such public genomes into the hundreds of thousands.

There are many good analogies in the essay. I especially like Pinker's distinction between an person's physical state and the mental state of other individuals who may know genetic information about that person. The conclusion of the essay conveys an important point: Even if the genome were destiny, it's pretty unlikely that any particular gene would explain it:

It’s our essentialist mind-set that makes the cheek swab feel as if it is somehow a deeper, truer, more authentic test of the child’s ability. It’s not that the mind-set is utterly misguided. Our genomes truly are a fundamental part of us. They are what make us human, including the distinctively human ability to learn and create culture. They account for at least half of what makes us different from our neighbors. And though we can change both inherited and acquired traits, changing the inherited ones is usually harder. It is a question of the most perspicuous level of analysis at which to understand a complex phenomenon. You can’t understand the stock market by studying a single trader, or a movie by putting a DVD under a microscope. The fallacy is not in thinking that the entire genome matters, but in thinking that an individual gene will matter, at least in a way that is large and intelligible enough for us to care about.

Well, I've pulled several quotes, but it's a very long essay -- 8000 words. So it's hard to give an impression of the whole thing. I think it will make great reading for the students of my course in genetics. Of course, the printed PDF doesn't include Pinker's legs...

The New Yorker has a fascinating article about Irene Pepperberg and the way people are grieving over her deceased parrot, Alex:

In Wheaton, she quietly worked the crowd into a pleasurable state of shared outrage. At one point, she said that colleagues had admonished her, "Birds can't do what you say he can do. They just don't have the brainpower." Linnea Faris, a woman from Michigan who was wearing a "Remember Alex" T-shirt, shook her head in disbelief. Faris told me, "My husband doesn't really understand it. I can't fully explain it myself. But I've spent hours crying over that damn bird." She went on, "People used to think birds weren't intelligent. Well, they used to think women weren't intelligent, either. They talked about the smaller circumference of our skulls as though it made us inferior to men! You know what? They were wrong on both counts."

The article gives a bit of historical background to studies of intelligence in animals, from Descartes and Darwin through C. Lloyd Morgan and B. F. Skinner. Oh, and the obligatory "Clever Hans" story.

Also, a lot of more current research on animal intelligence, including crows. I liked this part about a smart crow named Betty, which seems to solve problems that other crows have trouble with:

Though some crows, like Betty, cracked the challenge quickly, others took many tries; still others never mastered it. Watching videos of Betty on Kacelnik's Web site, I noticed that she seemed to have a particularly focussed and alert way about her. Even Kacelnik, who is loath to anthropomorphize, confessed to me, "An element of our finding that still puzzles me is that while Betty was not chosen or treated in any special way, she was different. She showed a readiness to coöperate and solve problems that none of the other animals in our study have replicated. We have no idea why."

And to my mind, the saddest statement in the whole article, which echoes a conversation I was having yesterday:

"Irene's work could not really have been planned ahead, as nobody knew what was possible. . . . Alex's development as a unique animal accompanied Irene's as a unique scientist. Hers is not a career trajectory one would advise to young scientists--it's too risky."

It shouldn't have been viewed as risky at all! The worst that could happen is a confirmation of the previous biases against significant learning capacity. But there was nothing in theory that didn't permit what turned out to be the case, and plenty of anecdotal evidence in support. When Darwin cited correspondences with animal breeders in support of the idea of heritable variation, that's good science, reaching out to the edges of what people knew about heredity. Pepperberg began to reach out to the edges of what people know about animal learning.

Frankly, I admire her (and her assistants) the most for their ability to run through the incredible degree of repetition necessary to test these kinds of learning with the parrots. One passage in the article notes that Pepperberg collaborated with an autism researcher on the effects of similar teaching methods (with some success). It's a good comparison in terms of the required patience, also. I think that few researchers are really cut out for the kind of work that Pepperberg does, and that may contribute to some lack of understanding of the results and their limits.

This is a great profile of Alan Mann, on the occasion of the new human evolution exhibit at the University of Pennsylvania Museum of Archaeology and Anthropology:

Describing himself as an evolutionary biologist and a physical anthropologist, Mann remembers that when he began teaching at Penn in 1969, he thought "human evolution was one of the most im portant subjects going." But his students didn't always share his enthusiasm. "So I began thinking about how to make this information not only interesting but also personally important, so they could learn something about themselves that would be useful."

Calling on what he knew about how teeth have changed over time, he asked his students about their own experiences with wisdom teeth and crowded teeth. "Our ancestors had much bigger faces and jaws, with plenty of room for third molars," he says. "But as our faces have evolved, they've become much smaller. They've literally moved under our braincases and the dental arch has shortened. There's no longer room for the third molars" a situation Mann describes as a consequence, or "scar" of evolution.

The article goes though a number of other examples, all fitting the theme of the exhibit. But I especially liked this passage about creationism and evolution:

"Look," he says. "I have been studying human evolution for 40 years. I have traveled around the world. I have handled just about every human fossil, every relic of our evolution. I know them to be genuine. I know that they represent the development of our own kind from creatures who had many resemblances to apes but were not apes, and over time, I see a system of change that can be marked in the record of geology and in dating processes that show that over time, our kind evolved into who we are.

"When I say this to a creationist who has never handled a fossil, who doesn't really have my experience, and they suggest that this is wrong, that I don't know what I'm talking about, I am distressed. It's not to me a proper way of debate."

I pulled the quote for the headline of the post, because it has such a resonance for those of us who study the human fossil record.

It seems to be biomedical profile week in the NY Times, so in addition to the profile of Francisco Ayala, Claudia Dreifus presents a profile of Arno Motulsky. Known for his early work on enzyme interactions, he is now credited for essential ideas leading to pharmacogenomics.

Q. YOUR OBSERVATION IN 1957 ABOUT THE INTERACTIONS BETWEEN THE ENZYMES PRODUCED BY GENES AND SOME DRUGS -- DOES IT PLEASE YOU TO SEE HOW IMPORTANT IT HAS BECOME?

A. Yes, because at first the idea was not well accepted. I remember going to an important pharmaceutical executive and I said, "I found a new way to find out about drug reactions." And he kissed me off: "Drug reactions?"

Things also moved slowly for a long time because it was hard to test for this. But now, with the new DNA testing, you can do many things faster and better. And with the modern computerized genomics, you can even test for reactions to many different enzymes, all at the same time.

On the other hand, I think the promise of pharmacogenetics is sometimes overhyped. There are people who think we'll be able to solve almost everything with an individualized prescription. We need more research, which will be expensive.

It's a short interview, but includes some interesting biographical details.

Cornelia Dean writes a long profile of Francisco Ayala in today's Science Times. The occasion is the publication of his new book, Darwin's Gift to Science and Religion.

Dr. Ayala gives about 50 talks a year, he said in a recent interview in New York, a day after he delivered the inaugural Louis Levine-Gabriella de Beer lecture in genetics at City College. (He had spoken the day before, at North Carolina State University, on the evolution of morality, and spoke two days later at McGill University in Toronto, where his subject was Darwinism and religion.)

Because of his eminence -- he is a member of the National Academy of Sciences, a former president of the American Association for the Advancement of Science and a winner of the National Medal of Science -- Dr. Ayala "has a bully pulpit," said Eugenie Scott, who heads the National Center for Science Education, a group that advocates for the teaching of evolution and against creationism in public schools. "When Francisco speaks, people listen."

Ayala is a fascinating person to talk to, and his vines make some of the best wine I've ever had. The article is a nice portrait of his current work.

The sad part of this story is that nobody cares about the identity of the other guy:

The mystery surrounding the skulls began in 1826, 21 years after [Friedrich] Schiller died in Weimar, when the local mayor had 23 skulls retrieved from a mass grave in which the poet was buried. Many eminent people at that time were buried in mass graves.

The mayor identified the largest skull as Schiller's and it was brought to the home of his contemporary Goethe, who wrote a poem about it, according to German scholar Albrecht Schoene.

In 1911, another skull was disinterred from the mass grave which researchers claimed was the real one. A long debate amongst academics, historians, medics and anthropologists about the identity of the skulls ensued.

So, naturally, they're digging up his relatives and plan to sample their DNA for a match.

I suppose it's a real advance when we go beyond testing live people who are purporting to be long-dead celebrities, against the live relatives, and move on to testing dead skeletons that people purport to be celebrities against dead relatives. How long can it be before we establish a catalog of dead celebrities' DNA profiles?

Yves Coppens and colleagues have found a frontal bone, and a bit more, in Mongolia. They do not report a date for the specimen beyond Late Pleistocene; it comes from a pit dug for gold mining. The site is north of Zhoukoudian and other northern Chinese sites by several hundred kilometers, and is approximately the same latitude (though further east) as Okladnikov Cave (discussed in my interview with Mica Glantz). The place is called Salkhit.

They describe the anatomy of the specimen: it has a complete supraorbital torus, thicker in the superciliary area than laterally; a slight frontal keel, and an overall sloping profile. In other words, it looks to be generally archaic in morphology. Their metrical comparisons put it generally with Middle Pleistocene crania like Zhoukoudian, Steinheim, and Petralona.

(via Paleoanthro)

References:

Coppens Y, Tseveendorj D, Demeter F, Turbat T, Giscard P-H. 2008. Discovery of an archaic Homo sapiens skullcap in Northeast Mongolia. Compte Rendus Palévol (in press) doi:10.1016/j.crpv.2007.12.004

Amy Harmon profiles Dan Stoicescu, a Swiss-living millionaire who has become the first paying customer of the genome-sequencing company, Knome.

Mr. Stoicescu said he worried about being seen as self-indulgent (though he donates much more each year to philanthropic causes), egotistical (for obvious reasons) or stupid (the cost of the technology, he knows, is dropping so fast that he would have certainly paid much less by waiting a few months).

But he agreed to be identified to help persuade others to participate. With only four complete human genome sequences announced by scientists around the world -- along with the Human Genome Project, which finished assembling a genome drawn from several individuals at a cost of about $300 million in 2003 -- each new one stands to add considerably to the collective knowledge.

"I view it as a kind of sponsorship," he said. "In a way you can also be part of this adventure, which I believe is going to change a lot of things."

"Sponsorship" seems like a good way to look at it, as long as they don't start including companies' names in the sequence, like "Pepsi" on a high school scoreboard!

Amy Harmon brings several patients' stories to this article, "Fear of insurance trouble leads many to shun or hide DNA tests."

In some cases, doctors say, patients who could make more informed health care decisions if they learned whether they had inherited an elevated risk of diseases like breast and colon cancer refuse to do so because of the potentially dire economic consequences.

Others enter a kind of genetic underground, spending hundreds or thousands of dollars of their own money for DNA tests that an insurer would otherwise cover, so as to avoid scrutiny. Those who do find out they are likely or certain to develop a particular genetic condition often beg doctors not to mention it in their records.

Some, like Ms. Grove, try to manage their own care without confiding in medical professionals. And even doctors who recommend DNA testing to their patients warn them that they could face genetic discrimination from employers or insurers.

According to the article, many people are choosing to pay out of pocket for genetic tests to avoid insurance or medical involvement. If this precedent becomes more common -- people paying for single-disorder tests -- then companies that offer genome-wide SNP typing may have an easy time growing their market.

This one I hadn't heard about:

When the Equal Employment Opportunities Commission sued the Burlington Northern Santa Fe Railway for secretly testing the blood of employees who had filed compensation claims for carpal-tunnel syndrome in an effort to discover a genetic cause for the symptoms, the case was settled out of court in 2002.

That is creepy.

It seems likely that the insurance risk fear will be addressed soon by legislation:

The Genetic Information Nondiscrimination Act, which passed the House of Representatives by a wide margin last year, would prohibit insurers from using genetic information to deny benefits or raise premiums for both group and individual policies. (It is already illegal to exclude individuals from a group plan because of their genetic profile.) The bill would also bar employers from collecting genetic information or using it to make decisions about hiring, firing or compensation. But it has yet to reach the Senate floor.

The article deals with both kinds of fears -- the fear of insurance consequences, and the fear of testing itself. It ends with a woman who feared being tested for the BRCA1 mutation so much that she chose surgery to remove her ovaries. Before a double mastectomy, she had the testing anyway -- and learned that she did not carry the risk allele after all.

UPDATE (2008-02-24): Hsien-Hsien Lei picks up the story also, and adds a perspective from Britain:

Two years ago, Cancerbackup found in a survey of regional genetics centers that waiting time for appointments to receive a BRCA genetic test can be as long as nine months with a further wait of 1 to 2 years for results. In some ways, this could be construed as discrimination in that other forms of testing are probably taken more seriously and performed more speedily.

She also provides a raft of links to other blogs that have posted on the Harmon story.

Identical twins may be genetically different due to somatic variations, and a new study by Bruder and colleagues finds that large deletions contribute to some of that difference:

The exploration of copy-number variation (CNV), notably of somatic cells, is an understudied aspect of genome biology. Any differences in the genetic makeup between twins derived from the same zygote represent an irrefutable example of somatic mosaicism. We studied 19 pairs of monozygotic twins with either concordant or discordant phenotype by using two platforms for genome-wide CNV analyses and showed that CNVs exist within pairs in both groups. These findings have an impact on our views of genotypic and phenotypic diversity in monozygotic twins and suggest that CNV analysis in phenotypically discordant monozygotic twins may provide a powerful tool for identifying disease-predisposition loci. Our results also imply that caution should be exercised when interpreting disease causality of de novo CNVs found in patients based on analysis of a single tissue in routine disease-related DNA diagnostics (Bruder et al. 2008:1).

If this is a large source of phenotypic discordance between twins -- that is, one twin gets a disease and the other doesn't because of a non-shared somatic CNV -- then our estimates of the heritability of phenotypes based on MZ-DZ twin comparisons will all be too low. This research group is involved in finding genetic risk factors for Parkinson's disease, and they think somatic SNVs are a promising avenue to explain phenotypic discordance where one twin has Parkinson's and the other does not.

But their study cannot say (because of a lack of power) that phenotypically discordant MZ twins have CNVs that explain the discordance. It's possible that most of the CNVs they observe have no phenotypic effect.

MZ twins represent an excellent focus for such studies [of somatic CNVs] because any genotypic difference between twins derived from the same zygote highlights an irrefutable case of somatic variation. It is likely that the confirmed CNVs shown here represent only the "tip of an iceberg" of all CNVs that are actually present in the studied twins. The notion of somatic variation being more far more common than previously assumed agrees well with our other, recent results showing CNVs between normal, fully-differentiated tissues within an individual human subject (Bruder et al. 2008:4).

This does raise an important question. CNVs are a newly-understood component of human genetic variation, for example in the current paper by Jakobsson and colleagues (2008). But if people often exhibit CNV mosaicism, then some of the rare variants in global samples may be somatic mutations that do not occur in the gene pool of their respective populations. And if there are "hotspots" of CNV mutations, then multiple people might show somatic mutations for the same
variant. It's probably a rare event, but given how little we know about the evolution of CNVs, it might be nice to know how rare.

References:

Bruder CEG and 21 others. 2008. Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles. Am J Hum Genet 82:1-9. doi:10.1016/j.ajhg.2007.12.011

Jakobsson M and 23 others. 2008. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451:998-1003. doi:10.1038/nature06742

Another thing I didn't expect to see today: DeCode Genetics went looking through James Watson's genome sequence for evidence he is secretly black:

A new analysis of Dr. Watson's genome shows that he has 16 times the number of genes considered to be of African origin than the average white European does -- about the same amount of African DNA that would show up if one great-grandparent were African, said Kari Stefansson, the chief executive of deCODE Genetics of Iceland, which did the analysis.

...

Dr. Stefansson's company is one of several marketing genome scans that promise to reveal anyone's genetic propensities for disease, origins and more, for a price. Dr. Watson had already placed his own genome information online, as has another genetics pioneer, J. Craig Venter. Dr. Stefansson said he simply ran the data through his company's analytical system.

Dr. Stefansson said that because his company had not produced the original data, "I am reluctant, personally, to make much of the analysis." He added, however, that "on my face, it would elicit smiles."

I find this incredibly strange. Not that Watson may have a mixed ancestry -- ultimately, everyone's ancestry is mixed.

No, I find it strange that the leader of one of the major genetics firms in the world is cheerily showing one of the worst possible abuses of personal genomics, in the most high-profile way possible! I find it just flabbergasting.

Sure, you can argue that Watson deserves the abuse he's gotten, and that his genetic ancestry is legitimately related to the story about his race comments. I don't agree, but there's a sense to which all this couldn't happen to a better person.

But the entire reason why many people think public genomics is a bad idea revolves around privacy and informed consent. People want to believe that their genes won't be used against them -- that information about risk alleles won't be used to deny employment or insurance, for example. Information about one's ancestry clearly falls in that category: most people want to keep such information private.

Informed consent is a problem in public genomics because your genes are not only yours -- they are also the genes of your parents, children, and other relatives. When you make your gene sequence public, you are taking with it information about your kin, who may not want such information out there. At present, they have no way of stopping you -- they have to live with your decisions. Which has created ticklish situations: a number of anonymous sperm donors have been tracked down by their children, using the donors' relatives' DNA sequences available from genealogy testing services.

If you want to advance the field, then you want to find ways to build confidence that genomic data won't lead to these "gotcha" moments.

I mean, what is the purpose really of spreading a news story that Watson may be 1/16 African, without adding the context of how common this degree of genetic mixture has been in American history in particular, and between populations generally? Why would a geneticist working with humans not realize the ethical problem? It has exactly the same salacious quality as a story about a political candidate's ancestry -- remember the story about former senator George Allen's Jewish mother? I can't believe that a credible researcher would want to bring this to genomics.

Maybe this is a play to discredit public genomics and advance the idea of some kind of data security system. From Stefansson's quotes, it seems possible he is trying to make his company look good and other ideas, like George Church's sequencing project, look bad.

But somehow I doubt it was that closely thought out. Probably their zeal to "get" Watson carried them away, to the detriment of the field.

Michael Balter wrote a nice "Scientist at Work" profile of paleoneurologist Ralph Holloway.

Ralph is one of my real idols in the field, so it's a pleasure to read this. Of course it begins with the hobbit, but Balter devotes much of the piece to explaining the lunate sulcus controversy of the 1980's and 1990's.

I think that Balter really captures the most important aspect of Holloway's scientific work with this:

Most notably, during his 43 years at Columbia, Dr. Holloway has argued that hominid brains began to evolve important anatomical alterations several million years ago, when they were ape-size and had yet to undergo the striking expansion often seen as humanity's hallmark.

We humans are rightly proud of our big brains. But most anthropologists now agree with Dr. Holloway that increases in size alone cannot explain advanced human cognition. There have also been structural changes that distinguish the brain of Homo sapiens from those of our hominid ancestors, as well as those of close cousins like the chimpanzee.

The lunate sulcus story illustrates this point quite well, but far more important (and less controversial) has been Holloway's identification of an enlarged Broca's area in the KNM-ER 1470 endocast. Only recently has imaging analysis been able to flesh out some of the internal ways that brain reorganization has characterized primate and human evolution. But the external manifestations on endocasts were a leading indicator -- and remain the only direct source of evidence about brain function from fossils.

There's much more to say than this, but start with the profile!