Chaw joins poop in archaeology arsenal
Well, archaeology is set to receive a once-in-a-generation influx of interest from teenagers drawn to the allure of the past. I mean, from the new Indiana Jones movie, of course.
So what do they have to go and do? Discover a real life crystal skull? Sorry, kids. If you want to be an archaeologist, it's all bodily functions from here on out.
Tom Dillehay and colleagues (2008) report in this week's Science that they have found chewed-on seaweed "cud" from Monte Verde, dated to 14,000 calendar years BP. And that paper is right next to the final publication of the Paisley Caves coprolites from Oregon, also dating to slightly before 14,000 calendar years BP.
Both papers are pretty cool -- together they emphasize that these kinds of forensic evidence are becoming increasingly important in documenting the activities (and existence) of archaeological populations. After all, a person has to poop thousands of times during his life, but he has only one skeleton.
Dillehay and colleagues interpret their seaweeds as a specialized medicinal collection, based on the presence of non-edible species and species present at different times of the year. Here's a quote from Michael Balter's news piece on the find:
Back 14,000 years ago, Monte Verde was located about 90 kilometers east of the sandy Pacific coast and 15 kilometers north of a rocky-shored inland marine bay. Algae from both environments were recovered, including inedible species that are today used as medicines in Chile and elsewhere. Moreover, the algal species found are known to flourish at different times of the year, suggesting to Dillehay's team that the Monte Verdeans were intimately familiar with coastal resources--possibly because they had originally arrived in the region via that route. Erlandson agrees: "The variety of seaweeds implies a pretty deep knowledge of coastal ecosystems and a long history of exploiting them."
Well, that's pretty impressive, even if the seaweed were chewed up. And hey, my kids are much more interested in bodily functions than they are in crystal skulls. So maybe this will bring in new archaeologists after all!
References:
Balter M. 2008. Ancient algae suggest sea route for first Americans. Science 320:729. doi:10.1126/science.320.5877.729
Dillehay TD, Ramírez C, Pino M, Collins MB, Rossen J, Pino-Navarro JD. 2008. Monte Verde: Seaweed, food, medicine, and the peopling of South America. Science 320:784-786. doi:10.1126/science.1156533
Gilbert MTP and 12 others. DNA from pre-Clovis human coprolites in Oregon, North America. Science 320:786-789. doi:10.1126/science.1154116
Death, lye thou there
Since they first walked the planet, humans have either buried or burned their dead. Now a new option is generating interest -- dissolving bodies in lye and flushing the brownish, syrupy residue down the drain.
Generally, I'm most interested in the processes that give rise to dry bones. Particularly, dry bones that don't smell bad.
"Syrupy residue," on the other hand, is not really my thing. And I guess it's not really most people's thing:
Getting the public to accept a process that strikes some as ghastly may be the biggest challenge. Psychopaths and dictators have used acid or lye to torture or erase their victims, and legislation to make alkaline hydrolysis available to the public in New York state was branded "Hannibal Lecter's bill" in a play on the movie character's sadism.
The appeal seems to be that this generates fewer emissions than cremation -- think of it as an elaborate sort of carbon sequestration. And it has to be better than pouring embalming fluid down the drain.
UPDATE(2008/05/08): Miguel Capriles writes:
[J]ust a quick comment about your post "Death, lye thou there": the reference to the "syrupy residue" made me recollect one of John Aubrey's Brief Lives when he tells about the coffin of John Colet, broken after the Great Fire of London in 1666. Aubrey tells (in modern English, as I got it on Google Books in a version published in 1982 by Boydell & Brewer):Â
"After the conflagration, his monument being broken, his coffin, which was lead, was full of a liquor which conserved the body. Mr Wyld and Ralph Greatorex tasted it and 'twas of a kind of insipid taste, something of an ironish taste. The body felt, to the probe of a stick which they thrust into a chink, like brawn. The coffin was of lead and laid in the wall about two and a half feet above the surface of the floor."
Definitively it should be a lot nicer in the English Aubrey used.
And that, my friends, is why it is cool to have a blog. Because my readers have much better imaginations than mine.
Ooooh, they tasted it?!
Were ancient Africans divided into small, isolated bands?
Last week when I wrote about the study of African mtDNA variation by Behar and colleagues, I focused on the issue of population size. To me, that must be the first parameter that we try to estimate, because the simplest relevant model of population history -- the Wright-Fisher model -- is described by that single parameter: the number of individuals. If we are going to evaluate evidence for population structure, we first must deal with the question of size.
The claim in the press release is that the African population was divided into separate populations:
Doron Behar, Rambam Medical Center, Haifa, said: "We see strong evidence of ancient population splits beginning as early as 150,000 years ago, probably giving rise to separate populations localized to Eastern and Southern Africa. It was only around 40,000 years ago that they became part of a single pan-African population, reunited after as much as 100,000 years apart."
Is it true? Certainly that describes the model tested in the paper. But is it the right model? Is there evidence to justify that model as opposed to simpler alternatives?
A real population may be structured in many ways -- by age, by caste or class, by space. If we have samples that are taken from different geographic locations, as in this study, it is natural to test hypotheses about structuring across geography. That's what Behar and colleagues did: they tested a hypothesis of panmixia, or random mating across space.
Panmixia is the simplest model -- the null hypothesis -- about population structure. If everyone mates randomly, then there is no geographic structure. The population would be a single, unstructured gene pool. The paper refutes this model, demonstrating that people did not mate randomly across the geography of Africa during a certain period of time.
But the question is: which model do we adopt once we have refuted panmixia?
I rather like isolation-by-distance as a model for human population history. Isolation-by-distance (IBD) assumes that people travel some distance before they reproduce. It's a simple model -- the distance traveled may vary among individuals, but the variance in this value is the only parameter necessary to predict the structure of the population. IBD can explain quite a lot -- why people look like their neighbors, why intermediate populations on the map tend to look intermediate in allele frequencies, and why selected alleles take some time to disperse across space. It is generally consistent with what we know about hunter-gatherer demography. People tend to stay where they are, but a fairly large fraction move to marry into neighboring groups, and a smaller fraction go beyond the neighboring groups to marry further away. So I think this is the null hypothesis once panmixia is refuted. IBD is not a hypothesis of small, isolated bands -- it is a hypothesis of a geographically dispersed population with gene flow.
The Genographic Project has done more than any other single project to extend the sampling of human populations. The paper by Behar and colleagues is a testament to that -- they are able to work with a broader and deeper sampling of mitochondrial variation in Africa than has yet been available. This is a credit both to the ambitious goals of the project and to today's genetic technology, which has made it possible to sequence more whole mitochondrial genomes on the project's budget. It is a great example of how spending money can circumvent some theoretical problems.
Still, the Project likely wanted to maximize the effectiveness of its money, so it focused on sequencing only those variants that were underrepresented or rare in previous studies. From the Methods:
Samples were chosen to include the widest possible range of Hg L(xM,N) internal variation on the basis of the previously available sequence analysis of the mtDNA control region and are, therefore, biased toward rare variants. In addition, we attempted to focus on branches (e.g., L0d, L0k), populations (e.g., Khoisan), and geographic regions (e.g., Chad) for which the current data were scant. Last, we preferred to sequence variants that the current literature suggested to be rare or anecdotal in any given geographic region (e.g., L0k in the Near East).
Ummm... wait a minute. This is definitely not what you want to do if you're going to test hypotheses of population history. They have deliberately narrowed their sample in a way that distinguishes Khoisan from other peoples, and have excluded some proportion of variants already known to be common. We can predict, based on the sampling scheme alone, that Khoisan and other people ought to be more distinct that would be expected under a random sampling of each population, and certainly more so than expected under a random sampling of the African continent. This means that if the data were to reject IBD, we would have to examine whether that was because of the population history, or instead because of the sampling scheme.
Do the data reject IBD? Well, we don't actually know from the paper. The study employs an island model, in which Khoisan and all others are assumed to represent either one panmictic population or two isolated ones. They devised a test based on permuting the number of lineages that they inferred to have existed during past time intervals. An island model with isolation of two populations predicts that each will share some gene lineages lacking in the other -- so-called "private" haplotypes. In contrast, two samples taken from a single panmictic population would each have a small proportion of "private" haplotypes, as well as some number of common haplotypes shared by both samples.
So, the study (reasonably) tests the null hypothesis that the African mtDNA samples derive from a single panmictic population going back to the mtDNA coalescent. They estimate the date of this coalescent (based on their mutation rate model) as around 200,000 years ago, so this is a test of panmixia in Africa across this time period. They use a permutation test to evaluate the likelihood that some number of closely related lineages would all be private to the Khoisan population, under the hypothesis that they are randomly drawn from the African population as a whole. The lineages they examine are the ones they infer to have been present in the Khoisan population at various time intervals in the past -- again, based on their model of mutation rate. They can disprove panmixia across times after 100,000 years and before 80,000 years. Before this time, too few coalescent lineages are inferred to have existed to obtain a significant refutation of the test of panmixia. After 40,000 years, there are obvious shared lineages between Khoisan and other samples that could only have been shared by gene flow.
I worry that there is a bias in this test. The authors applied it only to a period of time earlier than the coalescence times of recent shared lineages, but after the diversification of the ancient lineages that are not shared. In other words, there appeared to be a gap in the coalescence times of shared haplogroups. Usually, you would correct the test for multiple comparisons not only across haplogroups, but also across time periods. Given that we are considering a range of 150,000 years, across which there is evidence for gene flow both early and late in that history, what is the significance of the fact that we see few shared lineages at intermediate times? That will be less significant than the values reported in the paper, but how much less it is difficult to predict.
In the end, what do the observations in the paper mean? In the simplest interpretation, either Africans were not random-mating after 100,000 years ago or regional selection differentiated southern and other African mtDNA pools.
Did ancient Africans live in two isolated groups? I wouldn't say that: the authors didn't test that hypothesis.
Did ancient Africans live in small bands scattered across the continent? Well, all ancient humans lived in small bands. The question of whether they were scattered is a question about the population size -- and as I showed last week, the population size during this period of time was not small. So we can imagine a population structure like recent historic hunter-gatherers -- with Africa possibly having something like the population size and structure of indigenous Australians.
What's the bottom line? The results are consistent with isolation-by-distance in ancient Africans. That model, followed by a subsequent global expansion, has been around for a long time. In 1993, Henry Harpending and colleagues called it the "Weak Garden of Eden" model: a geographically structured African population that underwent an expansion and dispersal to other regions. Certainly for the mitochondrial DNA, this seems to be the model that presently best fits the data.
What remains in question is how much of the subsequent spread of mtDNA was also reflected by spread of nuclear DNA haplotypes, and how much was induced by natural selection on mtDNA haplogroups. As I continue to write about population histories, we will meet this issue again.
References:
Behar DM, 14 others, and The Genographic Consortium (consortium again? Whoa). 2008. The dawn of human matrilineal diversity. Am J Hum Genet 82:1-11. doi:10.1016/j.ajhg.2008.04.002
Average diet versus extreme diet in robust australopithecines
I've followed the literature on early hominid diets from the beginning of the weblog. In 2005 I discussed Peter Ungar's analyses of dental occlusal morphology in A. afarensis versus Homo, concluding:
The contrast between Homo and A. afarensis is in the same direction as the contrast in occlusal morphology between primarily meat-eating carnivores like felids and canids as opposed to more omnivorous carnivores like bears. Another observation is that meat is a major food resource of chimpanzees, although this is hardly a fallback resource. Indeed, if meat eating was indeed an important component of the behavioral repertoire of early Homo, it probably is not fair to assert that the difference in diet between Homo and Australopithecus was primarily a difference in fallback resources. It may be true that australopithecines and early Homo overlapped in their food resources, particularly in plant species consumed. But considering the likely effectiveness of early humans as predators, I think it likely that the fallback foods of early humans--when hunting was ineffective--may well have been the preferred foods of australopithecines. And when australopithecines were forced to abandon their preferred foods by early humans, they were forced to fall back upon resources that either were common or were difficult for early Homo to exploit. The disappearance of early small-bodied Homo by around 1.6 million years ago, and the ultimate extinction of the robust australopithecines after a progressive increase in their molar sizes (Wood and Lieberman 2001) indicate that this fallback strategy could not be maintained in the face of increased hunting effectiveness by large-bodied Homo.
The concept of "fallback foods" has captured a large mindshare in explaining early hominid diets. The idea is that a species may depend on preferred, staple foods for most of the year, but adopt less preferred, "fallback" foods when their staple is not available -- for instance, during the dry season.
What can fallback foods explain about early hominids? For one thing, they could explain the difference between robust and non-robust australopithecines. We know from isotope data (reviewed in this 2005 post about Matt Sponheimer's work) that A. africanus and A. robustus had similar fractions of C3 and C4 plant source foods in their diets. Across the year, they may have eaten roughly the same mix of foods. A 2005 paper by Greg Laden and Richard Wrangham (discussed here) explored the idea of underground storage organs of plants, or tubers, as fallback foods for australopithecines. Later studies of isotope data using laser ablation of small segments of the enamel (discussed here) showed that diet proportions may have substantially varied across the time that teeth were developing -- possibly concordant with the idea of seasonal or longer-period fallback foods. An earlier analysis of dental microwear in the two hominids by Scott and colleagues (discussed here) came to a similar result: there was great variability in wear properties, especially within A. robustus, although the average in the two species showed a possibly greater fraction of brittle, hard foods consumed by the robust australopithecines.
So I've written about the topic a lot, and followed it closely.
Now, Peter Ungar, Frederick Grine and Mark Teaford have examined the wear properties of the molars of Australopithecus (Paranthropus) boisei. They find that -- unlike A. robustus -- none of the seven specimens showed any evidence of having eaten hard or brittle foods:
Comparisons with the extant baseline series suggest that none of the Paranthropus boisei individuals examined consumed extremely hard or extremely tough foods in the days before death. All of these specimens lacked the extremes of Asfc evinced by Lophocebus albigena and especially Cebus apella, both known to consume hard, brittle foods. Paranthropus boisei molars also lacked the extremes of epLsar seen in Trachypithecus cristata and Alouatta palliata, both known to consume tough leaves and stems. The P. boisei individuals examined evidently avoided such metabolically challenging foods, at least in the days before death. This is notably consistent with Walker's [23] early assertion that P. boisei microwear patterns resemble those of living frugivores, and differ from those of living grazers, leaf browsers, and bone feeders.
Comparisons with the South African hominins suggest that while Paranthropus boisei may have consumed foods with similar ranges of toughness as those eaten by Australopithecus africanus, the eastern African "robust" hominin did not eat harder and brittler foods than the South African "gracile" form. Further, the patterns for P. boisei and P. robustus are very different. Paranthropus robustus likely ate foods that were on average much harder and less tough than P. boisei. The differences in both central tendencies and ranges of variation suggest different feeding strategies, and by implication, that the two species of Paranthropus probably had markedly different diets or foraging strategies (Ungar et al. 2008, italics lost).
That is very interesting that A. robustus and A. boisei are so different in their microwear patterns. It makes me wonder whether there may have been substantial habitat variation in the use of hard foods -- maybe the extant A. robustus sample, mainly drawn from a small area of South Africa, had access to some food items that were rare or absent across the larger East African range of A. boisei. But if some A. boisei populations had also depended on such hard resources some of the time, you might expect that we would have found one, or at least a bit more variability. Yet the sampled specimens, drawn from a distance from Ethiopia to Tanzania and well over a half million years of time, are pretty uniform in their microwear, showing some variability in the anisotropy dimension (here, high values have mostly parallel striations, attributed to fibrous food consumption).
So we can return to the question: the major hominid competitor of A. boisei was Homo. Both lineages appeared in the period around 2.5 million years ago, and remained sympatric throughout the next million years. Some of the dynamics of that interaction must have involved diet (considering the different dietary adaptations of the two). We can speculate that A. boisei didn't get much meat, which would then be an important difference. But what else was A. boisei eating?
Meanwhile, the data are still consistent with the idea of fallback foods in A. robustus as a driver of dental morphology, but the story for A. boisei now seems less clear. With only seven specimens, there is almost certainly not enough data to test the hypothesis -- which after all predicts that the use of hard brittle foods may be rare. But that's not positive evidence either. Is there some other food that might explain the hyperrobust craniodental morphology?
References:
Ungar PS, Grine FE, Teaford MF (2008) Dental Microwear and Diet of the Plio-Pleistocene Hominin Paranthropus boisei. PLoS ONE 3(4): e2044. doi:10.1371/journal.pone.0002044
Is a new method going to "shake up" hominid phylogenetics?
No.
Oh, you know I can't manage a one-word post here. I can't get the paper yet -- now Nature has moved to the annoying press-release-long-before-paper-appears model! But I haven't read anything in the press yet that makes any sense. Most stories (and here) just seem to be press-release-regurges.
To me, this is the key passage:
The team goes back over the same well-known set of specimens, but uses a different approach to analyse it, focussing in particular on a set of fundamental yet long-term changes in skull shape.
They took digital 3D images of the casts of 17 hominid specimens as well as from a gorilla, chimpanzee and H. sapiens.
Well, that certainly sounds like the way we teach 100-level hominid phylogeny labs when we only have 17 casts. But it doesn't sound very much like the kind of careful character analysis that ought to go into a test of a phylogenetic hypothesis.
UPDATE(2008/05/06): More thoughts upon reading the paper here.
Animal metaphors of questionable taste, VIII
In an otherwise very interesting story about the mechanism of behavioral dimorphism in fruit fly mating:
The next stage was to find out how effective the artificially induced songs were as mating calls.
For this, the "Cyrano de Bergerac" test was applied.
Animal metaphors of questionable taste, VII
Not exactly a metaphor, but certainly of questionable taste in this story titled, "'Sex Pest' Seal Attacks Penguin":
Marion Island is the only place in the world where Antarctic fur seals are known to hunt king penguins on land, so the idea that the fur seal was trying to eat the object of its attention made sense.
"But then we realised that the seal's intentions were rather more amorous."
Did humans face extinction 70,000 years ago?
That was the headline of many of last week's stories about the paper by Behar and colleagues, drawing upon the Genographic Project African mitochondrial DNA (mtDNA) data. Here's a quote from the National Geographic Society's press release:
Previous studies have shown that while human populations had been quite small prior to the Late Stone Age, perhaps numbering fewer than 2,000 around 70,000 years ago, the expansion after this time led to the occupation of many previously uninhabited areas, including the world beyond Africa.
And here's project director Spencer Wells' quote in the same release:
Dr. Spencer Wells, National Geographic Explorer-in-Residence and Director of the Genographic Project, said: "This new study released today illustrates the extraordinary power of genetics to reveal insights into some of the key events in our species' history. Tiny bands of early humans, forced apart by harsh environmental conditions, coming back from the brink to reunite and populate the world. Truly an epic drama, written in our DNA."
Well, that certainly sounds dramatic. But is it true?
The paper itself does not provide any tests of the number of ancient humans indicated by the mtDNA phylogeny. The press release mentions "previous studies" that fix a small initial founding population for Africans, so I went looking through the paper to see which studies they had cited.
I found this passage, which seems relevant:
Different approaches were taken in the attempt to estimate the sub-Saharan Homo sapiens population size in different time frames.7
OK, that seems like what I want -- estimates of population size in different time frames in sub-Saharan Africa. So I looked up reference 7, and found this:
Hawks,J., Wang,E.T., Cochran,G.M., Harpending,H.C., and Moyzis,R.K. (2007). Recent acceleration of human adaptive evolution. Proc. Natl. Acad. Sci. USA 104, 20753-20758.
D'oh!
Now on the one hand, it is very gratifying to be recognized as an expert on the genetic demography of sub-Saharan Africa. I mean, we did work hard on that paper. But on the other hand, it seems like we might do a little better than that paper as an examination of the demographic history of sub-Saharan Africa.
And the current paper by Behar and colleagues provides exactly the right kind of information to get that more detailed demographic history. So I've put together some notes here on how we can discover whether there was a population bottleneck 70,000 years ago in Africa, using the mtDNA evidence. I'm setting aside for the moment the question of population structure -- the "isolation" story that was also made in the press release for the paper. Population structure and size are not independent of each other, and we will have to consider how they interacted in African prehistory. But the first issue should be size, because our interpretation of size is based on relatively simple aspects of genetic variation (at its simplest, the first moment), while testing hypotheses about population structure requires higher-order comparisons.
New Penn evolution exhibit, and the "Year of Evolution"
The University of Pennsylvania Museum of Archaeology and Anthropology has just opened a new exhibit on human evolution, titled "Surviving: The Body of Evidence." An online article by Janet Monge and Alan Mann explains the idea of the exhibit and its unique emphasis:
The genesis of the idea came from Alan Mann's realization that students seemed to understand the broad impact of evolutionary process if they could witness it for themselves in their own bodies and minds. In order to evoke this response in the context of the exhibit, we challenge visitors to try to understand and define what it means to be human -- to revel in the experience of humanness. We ask them to witness the evolutionary process and to contextualize the human experience. This part of the exhibit is peppered with over 200 touchable casts of both modern and extinct mammals and primates, including many of our human ancestors, our chimp relatives, and even comparisons to horses and whales.
Visitors are now ready to see evolutionary history in their own bodies. Using multimedia devices surrounding a massive model of a woman's body, they see themselves not as perfect or perfectible beings, but as animals dealing with the various medical dilemmas that characterize the shared human experience -- bad backs, difficult childbirths, teeth that do not fit in our jaws, as well as many other maladies that are best understood from an evolutionary perspective.
Janet very kindly sent me links to the exhibit's online components. This page discusses the "Year of Evolution," an observance involving many Philadelphia institutions leading up to Darwin's 200th birthday.
Meanwhile, the "Surviving" exhibit's online site provides an interactive overview of several of the exhibit's areas, short videos that present perspectives on human anatomy, and other multimedia compositions. A great introductory video starts with kids' perspectives on evolution and the future -- a nice way to contextualize the exhibit's importance for evolution education. Another multimedia piece presents four of the scientists crucial to building modern biology, and provides audio put into their own voices that describes some of their contributions. Educators may appreciate the inclusion of Rosalind Franklin and Mary Leakey along with the more stodgy-looking Linnaeus and Darwin.
I think it's a neat site to look at if you're thinking about planning projects for teaching evolutionary biology, or to share with students.
Should we want to live longer?
I've been lecturing about various genetic enhancement strategies in my genetics course the last two weeks. Today's lecture concerned clinical trials for gene therapy, but I have also talked about cloning, pharmacogenomics, genetic testing, GMO's and other aspects of biotechnology.
I ask my students to explore and engage with moral and ethical arguments. For example, we discussed whether there could be changes that would objectively be improvements in human biology. If so, are there moral or ethical objections that might apply to them? I don't think students are often asked to think in these ways, certainly not in basic science courses, so I am always interested to see where the conversation will go.
One of the topics last week was life extension. I can make a reasonable case that living longer (say, an average increase of 10 years) would be an objective improvement in human biology. The opposite case, dying 10 years earlier, seems like it would be an objective detriment.
I won't elaborate on my students' conversation along these lines -- that being limited to class -- but I wanted to give the story as a prologue, before linking to this op/ed by bioethicist Arthur Caplan, on the topic of life extension.
In this case Caplan does a good job expressing common sense (something not always true of Caplan's writing):
That said, arguments that we should not live a lot longer because we will grow decrepit are simply silly. No one proposes that we spend a lot of money on biomedical research to pursue a longer life of decrepitude and suffering. The idea behind radical life extension is that we live a decent quality of life for a lot longer. If all that is in store is frailty and mental decline, then the debate is over before it starts. But that is not what the debate is really about.
As for violating some natural limit if we live a lot longer -- what limit? We have already doubled our lifespan since the days of the Hittites, Israelites, Greeks, Babylonians and Egyptians, all of whom were lucky to make it to 35. Are we already living unnatural, and thus immoral, lifespans?
He also argues that it is not vain or indulgent to want to live longer, because others may wish you could live longer (children, grandchildren) even more than yourself. Those are good arguments, and it is hard to come up with a coherent argument against the idea that people should extending their lives if they want to do so (again, assuming that there is no unacceptable trade-off of increased pain and suffering).
UPDATE (2008/04/30): Arthur Caplan writes:
I would demur from the view expressed on your blog. I think all Caplan's writings are eminently sensible.
Heh. I think I've been just been served...
Arno Motulsky profile
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.
Francisco Ayala profile
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.
What have I been doing?
I spent much of the weekend digesting and writing notes on a couple of papers from last week, including the widely-reported Genographic Project paper on the mtDNA of Khoisan and other Africans.
After putting around 5000 words into it, I have decided this is becoming more of a research project than a blog post. It is now possible to build a much more interesting picture of the evolution of Africans continent-wide during the late Middle Stone Age.
This picture does not include many of the elements suggested in the press reports accompanying the paper. In particular, there is no evidence for the proposition that tens of thousands of years of droughts decimated humans down to a small number of tiny bands, which later reunited to conquer the earth. That account goes far outside the science presented in the AJHG paper by Behar and colleagues.
We are working in a wonderful time, when data from many different genetic projects are becoming available to examine the detailed pattern of evolution in parts of the world where archaeology and physical anthropology have been incomplete. But there has been a tendency by many geneticists to exaggerate the weaknesses of traditional artifactual and skeletal evidence. This is manifested in an unwillingness to approach multiple data sources with the idea that they must each be consistent with a single population history.
Since we have not only new genetic evidence, but also new fossil and archaeological evidence coming online, the time may have come for a new synthesis of the prehistory of Africa.
Jared Diamond on vengeance cycles
In the New Yorker, Jared Diamond writes a long article with an interesting personal account of revenge cycles in Highland New Guinea:
Hiring, supporting, and rewarding all those allies was a complex logistical operation. Daniel had to feed them during the actual days of combat, to arrange for houses in which they could sleep, and even, as he delicately phrased it, "to provide ladies for the warriors when they were homesick." Daniel estimated that, in the three years that it took him to get his revenge, he had to furnish about three hundred pigs. By custom, the pigs to be slaughtered during that long phase of preparation should be not one's own but, rather, stolen from the enemy clan. Yet Daniel had to be careful to steal only Ombal pigs and not to make the mistake of stealing pigs from other clans; otherwise, he would acquire new enemies.
Many students of anthropology may have seen videos of the large, showy, and ineffectual-seeming "public fights" between groups, and taken away the impression that such small-scale warfare could not be very dangerous. But in the context described by Diamond, this is only the surface of a deeper, more earnest pursuit:
Daniel emphasized the importance of distinguishing between long-range public fights and close-range private ones. He contemptuously described the former as a "small boys' game shoot." As he explained it to me, "Public battles are open not just to experienced fighters but also to new trainees, new allies hired to come and gain confidence, and fun-seekers. In a public battle, the fight-owners have the opportunity to see who really are the best marksmen, with the necessary experience to make quick but correct decisions." Such warriors are selected for the much more dangerous task of private fights, in which hired teams of stealth killers prepare ambushes. "That requires nerve, judgment, and presence of mind, to select the right target, and not to panic and shoot the first man who moves into a shootable position," he said. "Boys and young men are prone to make such mistakes and hence are excluded from the stealth parties."
At the outset of his essay, Diamond suggests that revenge cycles in small-scale societies are equivalents of the dehumanization induced by wars between states. I think this part of the essay is simplistic: he might have profitably explored the differences, the depth of which is suggested by the different psychological reactions that he mentions.
But the end, a personal account from a different culture, is much more evocative.
Peter Brown refutes Flores filling claim
Homo floresiensis describer Peter Brown has kindly sent me a link to his own website, where he lays out evidence against the claims for recent dental work on the LB1 specimen:
The left first mandibular molar of LB1, Homo floresiensis, is heavily worn. Most of the enamel has been removed from the occlusal surface. The remaining enamel forms a ridge on the buccal and lingual margins, and there is a thin platform of remaining enamel in the disto-lingual quadrant. The softer dentine is somewhat scooped out and has a flat white appearance. There is some adhering sediment on the occlusal surface. Absolutely no evidence of any dental work, temporary filling or anything else. The tooth wear and oral health of LB1 are in all respects typical of older palaeolithic and hunter/gatherer humans, and living apes, and distinct from the mesolithic and more recent human burials in the Holocene layers at Liang Bua.
Brown's discussion includes high resolution photos of the specimen, the 3-D CT reconstruction featured in the Scientific American web story, and CT slices taken through the middle of the left and right teeth. I didn't think the 3-D CT slice was quite right to establish that the tooth was normally worn without question, since it cut through the buccal cusps which are unaltered in any event, but it does show a pulp cavity of normal dimensions for that area.
The slice taken through the centers of the left teeth, although a bit fuzzy (again, characteristic of the CT resolution), is much less equivocal: it shows a normal pulp cavity of equivalent dimensions to the right side and no evidence of alteration or drilling.
That's enough to convince me.
The rest of Brown's description serves to support his experience in examining archaeological teeth, including some photos of worn teeth of various stages. Some of this description will be interesting to readers who may not be as familiar with dental remains (or for that matter to dentists who aren't that familiar with archaeological samples of teeth). I think that these comparisons are sufficient to show that the particular pattern of wear and breakage on the LB1 lower left M1 is a bit odd compared to normal wear. But given that the visible material is in fact dentine (a fact established by the CT), there's nothing else that is outside the scope of either premortem or postdepositional processes. Any single specimen is likely to have idiosyncrasies, and by now it is abundantly obvious that LB1 is no exception to this rule.
UPDATE (2008/04/23): Elizabeth Culotta has a nice story about the tooth online at ScienceNOW.
John Hawks Department of Anthropology
University of Wisconsin—Madison
Copyright © 2007 John Hawks