john hawks weblog

paleoanthropology, genetics and evolution

Hawks lectures at the University of Alabama, December 6 and 7

Sun, 2012-12-02 17:05 -- John Hawks

I will be traveling south this week to give a pair of lectures at the University of Alabama. On Thursday night, I will be giving a lecture in the ALLELE (ALabama LEctures on Life’s Evolution) seminar series. The lecture will be in the Biology Building Auditorium (room 127) at 7:30 pm. This is a big public lecture, and if you're in the area, I encourage you to come.

The title is "Neandertime: How Ancient Genomes are Transforming our Past and Present". I'll be reviewing the science of Neandertals and Denisovans, some of the work we've been doing here in our research group on these ancient people, and how ancient genomes are beginning to yield new insights about the biology of living people.

Biology building at the University of Alabama

The Biology building at the University of Alabama. Borrowed from the Alabama website, until I get there to take my own picture!

The ALLELE lectures are really one of the premier lecture series in biology, anywhere in the world. For some perspective, Christopher Lynn reviewed last year's ALLELE lectures in a post on EvoS, with a great list of wonderful speakers. It's really humbling for me to be included on this year's list, along with two other prominent scientists and a humanist engaged with evolutionary biology including Edward O. Wilson, Bruce MacFadden and Joe Carroll. The interdisciplinary evolution perspective is something we try to promote here at the University of Wisconsin-Madison, because it's a great way to explore commonalities and threads of connections that deepen others' engagement in our evolutionary history.

On Friday afternoon, I'll be giving a smaller lecture for the Anthropology Department, on human evolution during the Holocene. That lecture is at 3:00 pm in ten Hoor Hall, room 22.

If you're a reader in the area, I hope to meet you there!

An interview with trade science authors of 2012

Sun, 2012-12-02 15:17 -- John Hawks

The Guardian hosted a conversation among several authors with new trade books on science last year, including Steven Pinker, Brian Greene, James Gleick, Joshua Foer and Lone Frank: "Science writing: how do you make complex issues accessible and readable?" They share many experiences and insights about the need to make scientific concepts clear to a general audience.

I liked this answer from Steven Pinker about the limits of analogy in science writing:

Analogy is enormously powerful. In fact, one could argue that we understand everything except for the physical world of falling objects by analogy. If you look at our language it's almost all metaphorical. But, there is a difference between literary metaphor and scientific analogy, and that is in a literary metaphor the more connections there are between the figure of speech and the thing in the world the richer and more wonderful it is, and in the scientific analogy if there are too many ways in which you can relate the analogy to the world, that makes it a bad analogy, not a good one. Analogies have to be chosen and explained carefully. You've got to point the reader to the correspondence, point for point between the thing in the world you're explaining in terms of your analogy. To be whipsawed between one analogy and other so you don't know what point is doing the work, that's what can make an analogy misleading.

Also, this response from Joshua Foer is provocative:

What you're supposed to be doing in a science book or popular article is distilling, finding what is essential and communicating that. That's not just an act of storytelling, it's an act of thinking and it requires a kind of clarity of communication that not just the scientists but academics in general have moved away from and I think it makes them think less clearly.

I agree with that. The act of writing here on the blog generally clarifies my thinking and makes me a better analyst. The beauty of blogging is that writing more about a topic really does build a better conceptual understanding of it, even if you are writing for nonspecialists. What I find frustrating is that I don't have time to write about everything I'd like to understand better!

Hiding above the dinosaurs

Sun, 2012-12-02 13:00 -- John Hawks

The early bin at PNAS has a cool, short paper by Yongjie Wang and colleagues, which matches a ginkgo tree with its insect mimic [1]. The cool part is that both of them lived during the Jurassic. I'm quoting a passage from the discussion that adds some more context to the fossils in this case:

This association joins a previously published instance of leaf mimesis from the same deposit by another group of insects, the Neuroptera, whereby two species of saucrosmyline lacewings were mimetic, although only their forewings resembled particular cycadophyte leaves (9). The association of J. ginkgofolia and the Ginkgoitesleaves of Y. capituliformis considerably extend this phenomenon. More importantly, it adds a more finely tuned example of leaf mimesis wherein the entire insect body participates in the de- ception. This mimicry would necessitate a quantum increase in the coordination and integration of somatic development to achieve replication of a leaf model in size, shape, surface texture, and probably behavioral control of motion, sufficient to either deceive a potential predator or prey item. This similarity only could occur during an interval wherein the multilobed ginkgoa- lean leaf (the model) was present in sufficient numbers to con- tinue the deception. In any event, Y. capituliformis became extinct during the Jurassic–Cretaceous boundary (19), as possibly did its mimic, J. ginkgofolia, significantly before the initial appearance of angiosperms during the mid Early Cretaceous. The interpretations of these two different examples of leaf mimesis can provide unusual insight (2, 16) into a preangiospermous world of elevated counterdefensive plant–insect associations such as leaf mimesis.

The artist's reconstruction of the mimic insect upon a prehistoric ginkgo branch is one of the coolest pieces of paleoart I've seen. I hope they don't mind me spreading this, it's a wonderful image:

Hangingfly mimic of Jurassic ginkgo, artist's reconstruction, from Wang et al. 2012

Figure 3G from Wang et al. 2012. Original caption: "(G) Artist’s reconstruction of J. ginkgofolia mimetic on Ginkgoites leaves of Y. capituliformis."

Breathtaking. As the text above indicates, this isn't the only known mimic from the same formation, but it is truly interesting to see this kind of association long before the intricate insect-plant mutualistic relationships that accompanied the rise of the angiosperm plants.


References

Cutting room floors

Sat, 2012-12-01 01:07 -- John Hawks

Reading items on my desktop, I found a rant I had written a while back. I generally don't post rants, but a decent amount of time has passed...

I'm totally irritated this morning because we turned on a cable channel where they were showing a documentary about Neandertals from only a few years ago. It's a clutch of talking heads telling stories about what Neandertal life "must have been like", accompanied by actors dressed in skins and clay brow ridges. The difference between the "modern" and "Neandertal" actors is whether the skins have been stripped of fur. If you've seen any human evolution documentaries in the last decade, you know the genre.

Walking caveman shows are hardly anything new, and I've been in a few that have been pretty good. So why am I particularly irritated?

This particular program was such a waste. The producers assembled a fair group of scientists to comment on the Neandertals and clearly spent a lot of money on the production. But then they encouraged those scientists to go way beyond the science. And the scientists went along for the ride.

Here's a hint: When you're talking about the differences between Neandertal and modern human spiritual beliefs, you've gone beyond the science.

Earlier this week, I saw a link on Twitter from a chemist sick of spending time on interviews with journalists: "Another interview makes the cutting room floor".

Yes I wanted to be interviewed because its been drummed into me over 20 years that the public understanding of science is pathetic and we scientists have to do a better job communicating to the masses etc.. Now if you filter the scientists through journalists does that make us better communicators? I think in the pre blog days that was the only way to go but some scientists are cracking communicators and have huge audiences. Not me. My work has a couple of journals and magazines that would likely cover something I might do. The potential for my work to reach a broader audience by contributing to an interview is the “bait”. We scientists are lured hook, line and sinker every time. Bigger audience, equals more citations, more citations equals success, funding and respect. I should go further and say that we try to highlight the work because our collaborators and co-authors also benefit from the exposure.

His complaint is related to tuberculosis research, not bad caveman outfits. But I thought about his concerns when I was watching the program this morning. So many scientists want to help tell good stories about their research, hoping it will make some difference -- a difference to their profile, a difference to public understanding, a difference to their status in the field. It's a mix of selfish and altruistic motivations, a complicated mix.

We can't tell stories alone. But we need to tell our stories, not the stories that writers feed to us.

Moonies of Bethesda

Fri, 2012-11-30 16:22 -- John Hawks

Highly recommended for Friday: Michael Eisen on "Is the NIH a cult?"

The NIH has several national indoctrination programs, but the most dangerous and effective is something known as the “Training Grant”. These NIH cells, found on most university campuses across the country and always led by an established “grantee”, prey on impressionable youths just out of college and eager to shed the structure of their parents’ worlds. The NIH takes them under its wing and gives them a generous personal stipend and a structured program of research and experimentation. They dangle the carrot of one day becoming a “grantee”, but they do not tell them about the lonely, grueling years to come, or that only a handful of them will actually make it to the point where they are even allowed to submit their first application for membership. By the time they are done with this program, most have drunk the NIH Kool Aid, and can think of nothing they want more than to become a grantee. And those who do not feel they have sunk too much of their time and energy into these first steps along the grantee path to give up.

The "charismatic leader" section is not to be missed.

Stone tools on the moon

Thu, 2012-11-29 21:46 -- John Hawks

Moon rock is expensive here on Earth, but on the moon it's as cheap as dirt. So maybe future moon colonists could make stuff out of it using 3-d printing technology?

Typically, lasers use 300 to 400 watts to melt conductive metals. But the moon material was more similar to ceramics — Bandyopadhyay’s area of expertise. He had used that material for 3-D printing through selective laser sintering, where a powder is fused with intensely focused pulses of light, layer by layer, to form a specific object. He knew that throwing metal-specific levels of power at an insulator like this would only cause most of the energy to be absorbed, and the molten material to lose viscosity.

“If you go higher, then what will happen is you will go from honey to water, and then what happens?” says Bandyopadhyay. “It flows so much that you cannot make a part. So you need to have, you know, high enough to melt, but low enough not to overflow, basically. That’s the challenge.”

Now imagining casts made from lunar regolith.

I hate the idea of having to depend on tools made from an inferior material, when slightly greater expense and more time could transport metals from the asteroid belt. Oh, wait a minute - that's the basic tradeoff of Oldowan technology in Africa, isn't it?

Martian will

Wed, 2012-11-28 15:46 -- John Hawks

Adam Mann in Wired covers Elon Musk's ideas about putting people on Mars: "Elon Musk Wants to Build 80,000-Person Mars Colony".

That first flight would be expensive and risky but “once there are regular Mars flights, you can get the cost down to half a million dollars for someone to move to Mars,” Musk told Space.com. ”Then I think there are enough people who would buy that to have it be a reasonable business case.” Musk added that he sees the future 80,000-person colony as a public-private enterprise costing roughly $36 billion.

I'm right now finishing an essay about the constraints on human colonization of space, so to see this topic developing in the news again is a good thing.

Bigfoot DNA?

Mon, 2012-11-26 09:57 -- John Hawks

A press release claims the recovery of Sasquatch DNA:

“Sasquatch nuclear DNA is incredibly novel and not at all what we had expected. While it has human nuclear DNA within its genome, there are also distinctly non-human, non-archaic hominin, and non-ape sequences. We describe it as a mosaic of human and novel non-human sequence. Further study is needed and is ongoing to better characterize and understand Sasquatch nuclear DNA.”

This has been developing for a while. Until I see the data, I am withholding judgment.

One benefit of the world of genetics as opposed to traditional anthropology: The original sequence data must be made available to the public. No data, no discovery.

Micro-RNA 941

Sun, 2012-11-25 19:39 -- John Hawks

John Timmer covers the story of miR-941, a micro-RNA that may influence the expression of genes in human brains, and which appears to have taken on a novel role in our lineage compared to other primates:

Looking at the region in the human genome that contains miR-941 showed it's an area with a series of repeats of the same sequence, arranged in tandem. Chimps and macaques have similar sequences, but the duplications aren't arranged in a way that allows the production of a hairpin structure. Somewhere after we split off from chimps 6 million years ago, a rearrangement in the area (an event that's common in areas with duplicated sequences) created the human form of miR-941. It was already in place a million years ago, when the Denisovan population branched off.

But the rearrangements didn't end there, as there have been a series of duplications that created as many as 11 extra copies of miR-941 (the numbers vary in different populations, but average is about six or seven copies in most). The extra copies should help ensure it's expressed at higher levels than it would be otherwise.

The research was carried out by Hai Yang Hu and colleagues [1] in an open access paper ("Evolution of the human-specific microRNA miR-941". It deserves a bit more attention than I can give it at the moment, as it is one of a series of recent papers demonstrating human-specific duplications that affect gene expression. It is one of the first cases in which RNA structure and function have been investigated in an ancient genome. The number of copies of miR-941 varies substantially both within and among human populations.

This passage from the paper is provocative:

Humans display both increased longevity and increased occurrence of certain forms of cancer compared with both chimpanzees and macaques39. It is, therefore, appealing to speculate that emergence of miR-941 enhanced the maintenance of adult stem cell populations, thus supporting longer human lifespan, but rendering human cells more prone to malignant transformation. The role of miR-941 in the regulation of insulin signaling adds support to this notion. The insulin-signaling pathway was consistently implicated in lifespan regulation in many species, including humans. Notably, experimentally verified targets of miR-941 within this pathway include genes directly shown to be involved in lifespan extension in model organisms: IRS1, PPARGC1A and FOXO140 (ref. 40). Furthermore, FOXO1 was linked to extended human longevity.

Still, I am skeptical of the idea that this molecule had a strong effect on the human phenotype. The greater the network of genes influenced by this micro-RNA, the less likely a massive up-regulation or down-regulation will have a simple phenotypic effect. Most genes that were duplicated or deleted during our evolutionary history probably were free to change because of a lack of fitness effect. Maybe this micro-RNA is an exception -- with a new effect on the human lineage, and extensive variation in copy number within humans. But it seems more likely to me that the variation in miR-941 dosage leads to a minor phenotypic effect across the network of affected genes, not a major directional effect.


References

Quote: Jerry Pournelle on science writing

Sun, 2012-11-25 15:46 -- John Hawks

Jerry Pournelle, in A Step Farther Out ($2.99 on Kindle):

Science writers have a problem; how much detail do we include, and how technical can we get? After all, our first purpose is to entertain; if we can't do that, there's no point in writing a column or article for the general public. On the other hand, there's buried in most of us a frustrated teacher: we want the readers to understand and even to be able to work these things out for themselves.

Einstein and Taung: two brains collide

Wed, 2012-11-21 13:03 -- John Hawks

Dean Falk has a new article in the journal Brain, in which she and collaborators uncover the details within historical photographs of Albert Einstein's brain [1]. The brain was sectioned after Einstein's death and samples have been studied by several researchers over the years, including Falk. The research was recently covered by the TV program NOVA ScienceNOW, which is being rebroadcast this week.

I wanted to point to the article by Falk and colleagues because it includes a brief discussion of the lunate sulcus -- one of the most persistently pernicious topics in paleoneurology.

The terminology for sulci of the human occipital lobe, in particular, has been influenced by an erroneous historical claim that human brains manifest a so-called lunate sulcus that is homologous to the Affenspalte (‘ape sulcus’) that forms the rostral boundary of the primary visual cortex [Brodmann area (BA) 17] on the lateral surface of the brain in apes and some monkeys (Smith, 1904, 1925). However, BA 17 of humans may, or may not, extend onto the external surface of the occipital lobe. When it does, its rostral border is located far posterior to the normal position for ape brains and is rarely bordered by a sulcus (Allen et al., 2006). Despite the fact that recent gross morphological and cytoarchitectural studies refute the assertion that humans have a lunate sulcus that is homologous with the Affenspalte (Allen et al., 2006; see Falk, 2012 for a discussion of the evolutionary implications), contemporary authors continue to use a variety of criteria to identify different sulci as so-called lunate sulci in humans (Duvernoy et al., 1999; Iaria and Petrides, 2007). The classical terminology used by Connolly (1950) for the occipital lobe is also grounded on the mistaken notion that humans have lunate sulci that are homologous to those of apes. For example, Connolly (1950) identifies a prelunate sulcus, which we identify with its modern name of the lateral occipital sulcus (Table 1). For these reasons, we do not recognize a lunate sulcus in Einstein’s brain.

The long-running argument over the possible location of the lunate sulcus in the endocast of the Taung fossil hominin was a heated debate for more than 20 years in paleoanthropology. For Falk, the end of the story is that the sulcal patterns in human and other primate brains in this region are not homologous -- making it problematic to recognize either in the fossil endocasts of early hominins. I'm sure it isn't over, but I find it inspiring to see the evolutionary record make an appearance in this consideration of the brain of a very famous scientist.


References

Hooton's complexity

Wed, 2012-11-21 12:37 -- John Hawks

Eugene Giles has an article in the new Yearbook of Physical Anthropology that will be of great historical interest to many in the field: "Two faces of Earnest A. Hooton" [1]. Hooton was a central character in physical anthropology, and ultimately his students would come to populate most of the positions in physical anthropology in the United States. It is often said that every student who learns osteology in American schools today is fundamentally taking Hooton's course in the subject. He was born in Wisconsin and received his Ph.D. here at the University of Wisconsin, in classics, after a time in the U.K. as a Rhodes Scholar. In other words, he was scientific royalty. Unlike most, he took that status and became a public intellectual of substantial note, publishing popular articles throughout his lifetime on the topics of evolution, race, and eugenics.

Giles has accumulated a rich record of biographical details about Hooton, who was a complex figure. I might describe him as embodying the apotheosis of racial science -- dividing up human groups by an involved scheme of "major" and "minor" races, he attempted to categorize human variation into types purported to represent historical connections among peoples. It is not enough to say that this was typical of physical anthropology, because up until 1950 or so, this simply was physical anthropology. Hooton's students were the first generation to really take an alternative approach, and most of them did so only after a substantial period working with racial categories in a nineteenth-century framework.

Giles approaches crucial questions: Can a racial scientist be a non-racist? Could one be a eugenicist and yet oppose the doctrine of "race hygiene"? Hooton is such an interesting figure because he, more than anyone, stood at the center of established race science during the 1920's and 1930's.

By 1930, Hooton made it clear he believed something had to be done about what he saw as our increasing lack of biological fitness. “[I]n spite of the infinitesimal quantity of our knowledge [of their genetic bases], we are completely justified in urging that measures be taken to prevent the insane and the mentally defective from reproducing. Segregation and sterilization of the unfit ought to be promoted by scientists and by instructed laymen” (Hooton,1930b:103). But at the same time, he goes on to warn that “we have no data which justify the raising of racial issues as a part of eugenics propaganda. We know nothing at all about inherent superiorities or inferiorities of the several races and the many nationalities. If eugenics is to be made the vehicle of bigoted race prejudice, it must be ditched… To me, eugenics in the United States represents too much ill-considered talk and too little careful scientific research” (Hooton,1930b:103). Those in the eugenics movement in the United States who were in fact displaying “bigoted race prejudice” became role models for German “racial hygienists” before Hitler's ascension in 1933 and admirers afterward, for a while (Kühl,1994).

Giles is in the end a defender of Hooton, in opposition to recent public presentations (in particular the "Understanding Race" project by the American Anthropological Association) which Giles sees as having tarnished Hooton's scientific reputation.

For another view of Hooton, Jon Marks returns to blogging: "A Rootin' Tootin' Blog Post". Marks is writing in partial reaction (or addendum) to Giles, accentuating the negative. Marks acknowledges that Hooton was a complicated character -- speaking out against some of the worst instances of scientific racism, but ultimately rooted himself in a typological scheme of human classification that was losing its value.

Anyway, back to Hooton. His ideas about race, and about human biology generally, certainly weren’t the worst ones around at the time, but that’s faint praise. I think my biggest problem with Hooton, since it’s hard to know exactly what he did believe at any point in time, is that he did not use his position as an authority to confront and repudiate the worst elements of racial science in America. He went after the Germans, which was safe, and although he tried to differentiate his racial science from theirs, he ultimately was not very successful, because his physical anthropology was in fact only subtly different from theirs.

However, Marks adds a number of quotes and historical cases in which Hooton presents a less sympathetic side. It is clear that if words are actions, Hooton's record is complicated.

Hooton's racial typological scheme was just as complicated as his position in the history of science. I'm interested in the theory as well as the social impacts of the theory, and this is a great case in the history of science where social change and changes in scientific theories were linked. Like Ptolemaic epicycles, Hooton's classification was an attempt to shoehorn the growing data on human diversity into a theoretical scheme that was losing its value. His typology was full of dozens of "minor races" as variants of the "major" three. Yet the scheme of clinal variation that would come to dominate in postwar anthropology left much unexplained.

I think the Copernican revolution is in some ways a good analogy -- replacing epicycles with heliocentric orbits was in the long run the correct choice, but circular orbits as predicted by Copernicus did not fit the data as well as the overly complicated Ptolemaic scheme. In astronomy, this problem was solved by Kepler and elliptical orbits. But the transition from the geocentric to heliocentric view wasn't easy, with many heavyweight holdouts for a long time, and hybrid systems like Tycho Brahe's geo-heliocentric model.

In human biology, clines were indeed more correct as a description of the pattern of variation. As Hooton and his contemporaries began to appreciate, typological races would have to be endlessly subdivided to adequately account for variation. Any typological theory is weighed down by this complexity.

But the clinal perspective is not as simple as generally presented -- clines of variation in humans are not random, nor equally distributed, and some human populations really have undergone long periods of very low gene flow from others. The advent of genetics in the 1950s promised to make human classification simple -- as simple as blood type frequencies. In fact over time genetics has reinforced the complexity of our history as a polytypic species.

So Hooton, a representative of the Old Guard as his students began to pursue a new kind of human classification, is tremendously interesting. I recommend Giles' entire article, and will be looking forward to seeing more.


References

  1. Giles E. Two faces of Earnest A. Hooton. Am J Phys Anthropol. 2012;149 Suppl 55:105-13.

Shirky essay on online courses

Tue, 2012-11-20 23:27 -- John Hawks

Clay Shirky reflects on the nature of college education and the potential disruptive nature of online courses: "Napster, Udacity and the Academy". For those who don't remember, Napster was a highly disruptive factor for the recording industry during the late 1990s-early 2000s: a way for millions of college students to download free music instead of paying for CDs at $17.00 and up.

Higher education is now being disrupted; our MP3 is the massive open online course (or MOOC), and our Napster is Udacity, the education startup.

We have several advantages over the recording industry, of course. We are decentralized and mostly non-profit. We employ lots of smart people. We have previous examples to learn from, and our core competence is learning from the past. And armed with these advantages, we’re probably going to screw this up as badly as the music people did.

...

Cheap graduate students let a college lower the cost of teaching the sections while continuing to produce lectures as an artisanal product, from scratch, on site, real time. The minute you try to explain exactly why we do it this way, though, the setup starts to seem a little bizarre. What would it be like to teach at a university where a you could only assign books you yourself had written? Where you could only ask your students to read journal articles written by your fellow faculty members? Ridiculous. Unimaginable.

I bolded the phrase with "artisanal" because it is so evocative. Lecture is theater. A great lecture can capture and hold attention better than any video. Yet, lecture is not the perfect medium for many subjects. Certainly not mine. Paleoanthropology and genetics demand multimedia.

For me, the most impactful part of Shirky's essay is the conclusion, in which he turns to the low quality of some existing massively online open courses (MOOCs). He recounts the case of a math professor who enrolled in Sebastian Thrun's statistics course, finding the content and course generally poor. The full story is recounted by the anonymous math professor's blog, "Udacity Statistics 101". Shirky reviews the rest of the story, in which Thrun quickly responds to some of the criticisms and the math professor admits that colleagues at his own institution have similar pedagogical problems. The point: University courses are often flawed and rarely fixed.

Open systems are open. For people used to dealing with institutions that go out of their way to hide their flaws, this makes these systems look terrible at first. But anyone who has watched a piece of open source software improve, or remembers the Britannica people throwing tantrums about Wikipedia, has seen how blistering public criticism makes open systems better. And once you imagine educating a thousand people in a single class, it becomes clear that open courses, even in their nascent state, will be able to raise quality and improve certification faster than traditional institutions can lower cost or increase enrollment.

University courses are hidden behind closed doors, and the only audience -- undergraduate students -- are very poorly positioned to judge the quality of information they receive. We all have stories of lecturers who go on and on, semester after semester, giving students the same set of erroneous facts. Can open online courses take advantage of the bazaar instead of the cathedral?

Pardis Sabeti profile

Tue, 2012-11-20 20:46 -- John Hawks

Smithsonian is running a profile of geneticist Pardis Sabeti, written by Seth Mnookin: "Pardis Sabeti, the Rollerblading Rock Star Scientist of Harvard".

It was a radical approach: Instead of using existing tools to analyze new data, she was trying to develop new tools to use on available data. When she was at Oxford, “Everybody thought what I was trying to look for was dumb,” Sabeti says. “It seemed as if I was just going to go nowhere. I know everyone has a hard time at some point when they’re in graduate school, but I was on the higher end of the hard time early on in my PhD.”

Sabeti's work identifying recent positive selection on genetic data served as an essential foundation to much later work, including our own work on the Holocene acceleration of these positively selected variants.

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Quote: H.G. Wells on lacunar reading

Tue, 2012-11-20 20:21 -- John Hawks

From the preface of Mankind in the Making, by H. G. Wells:

It is a work that the writer admits he has undertaken primarily for his own mental comfort. He is remarkably not qualified to assume an authoritative tone in these matters, and he is acutely aware of the many defects in detailed knowledge, in temper, and in training these papers collectively display. He is aware that at such points, for example, as the reference to authorities in the chapter on the biological problem, and to books in the educational chapter, the lacunar quality of his reading and knowledge is only too evident; to fill in and complete his design—notably in the fourth paper—he has had quite frankly to jerry-build here and there. Nevertheless, he ventures to publish this book.

Mankind in the unmaking

Tue, 2012-11-20 19:59 -- John Hawks

Annalee Newitz gives a worthwhile etymological lesson: "Think twice before using “mankind” to mean “all humanity,” say scholars".

In modern English, man is used very infrequently as an autohyponym. Possibly that's because it's become too confusing to use "man" — it's hard to know what it means in any given context when we have no word like wæpenmann that refers exclusively to males. But we do have the words "person" and "human" that clearly refer to both sexes, so those have eclipsed "man" when speaking about everyone.

More at the link. "Mankind" used to be very common in paleoanthropology, most notably in the title of W.W. Howells' Mankind in the Making: The Story of Human Evolution, last published in 1967. Howells cribbed his title from H. G. Wells, whose own Mankind in the Making came out in 1909. It's available for free on the Kindle, or from Project Gutenberg in multiple formats. A name with a long pedigree, that we simply don't use anymore. Star Trek was a few years behind science when it gave up the "no man has gone before".

I guess that popular culture is usually recycling the science of a decade ago. We've just gotten to where popular culture treatments of human evolution suffer through a volcanic winter, and where Neandertals are extinct. Guess that makes a fertile ground for rewriting over the next decade!

Don't sound like a kook

Mon, 2012-11-19 10:52 -- John Hawks

Larry Moran describes a lecture by Michael Behe, an advocate of intelligent design arguments: "Michael Behe in Toronto, Part 1". Moran didn't care for the lecture. I wanted to react to this comment:

This is one of the distinguishing characteristics of kooks. If you have to defend your views by pointing out that many great scientific ideas were initially rejected by the scientific community then you've already lost the battle. No legitimate scientist does this.

Some scientists unfortunately do do this. Especially in paleoanthropology. As in, "They all scoffed at Dart, too". Or, "They all said Neandertals were just pathological modern humans, too". Yes, former paleoanthropologists faced challenges in having their ideas accepted. It is the nature of science. It doesn't follow that your ideas are correct.

I think paleoanthropologists should take Moran's words seriously. Great scientists overcome challenges. Kooky scientists try to make their own trivial challenges sound like the great intellectual battles of history.

Early Stone Age hafted spear points from South Africa

Sat, 2012-11-17 02:57 -- John Hawks

This week in Science, Jayne Wilkins and colleagues report on part of the lithic assemblage from Kathu Pan, South Africa, which includes 210 points [1]. The paper reports that these are the earliest known hafted points in the world, predating the previous record by more than 200,000 years.

The minireview of the spear literature:

By ~780 ka, hominins were regularly killing large game, based on evidence of repeated in situ processing of complete carcasses of fallow deer at Gesher Benot Ya’kov in Israel (4). At the English site of Boxgrove, a horse scapula with a semicircular perforation is consistent with spear-aided hunting by ~500 ka (5). Wooden spears dating to ~400 ka have been found in association with butchered horses at Schöningen, Germany (6). Hafted spear tips appear to be common in the MSA and Middle Paleolithic (MP) sites of Europe and Africa after ~300 ka (7–20).

This is a very short paper, and it sets out two problems: demonstrating that the points really are 500,000 years old, and demonstrating that they really were used as spear tips. The first is fairly straightforward as a function of the stratigraphy at the site and some ESR/U-series dating of faunal teeth. Possibly a broader issue is the identification of the assemblage as Fauresmith, which has been poorly defined in the literature and sometimes means different things. It is more or less indicative of assemblages based on large cutting tools (such as handaxes), with an increased fraction of flake core production and some MSA-like elements. Andy Herries published a good review of the Fauresmith issue and its chronology last year [2]. He wrote this with respect to Kathu Pan:

Previous dating of the site was based on elephant fossils that were more evolved than those from Olduvai Bed IV [62]. This simply gave the site an age of 417 ka may lend weight to the Fauresmith at Wonderwerk also being in this time range or at least older than 182 ka as suggested by Chazan and Horwitz [147] unless it occurred for over 200 ka in the region and was being produced contemporarily with the MSA.

Fauresmith at some other sites in southern Africa, including Wonderwerk Cave, is apparently younger, less than 300,000 years ago. The entire range is coincident in time with the Early-Middle Stone Age transition in the Kapthurin Formation sites in Kenya, which makes these "transitional" assemblages really representative of a long-term pattern of variability and change. The marker of MSA industries as opposed to Early Stone Age is the MSA's reliance upon prepared core reduction techniques. Yet, prepared core techniques (like the Levallois technique) appear much, much earlier. One marker of the MSA, as reviewed by Herries [2] (citing McBrearty and others) is the appearance of projectile point technology:

Mcbrearty [22] also suggests that the fundamental change from the ESA to the MSA is the end of LCTs and a shift to projectile point technology. Of course, it should be noted that Acheulian bearing hominins in Europe were utilising an entirely wooden projectile technology for hunting as shown by the occurrence of the Schöningen spears at either ~400 (MIS 11 [157]) or ~310 ka (MIS 9d-e; [168]) but were seemingly still disarticulating their kill with LCTs. Whether a similar wooden projectile technology was being used by hominins in Africa is almost impossible to tell given the almost complete lack of preservation of such organic remains in most MSA sites. The exceptions are two wooden tools from Floor 1 at Kalambo Falls in Zambia [30, 56] and one from Florisbad in South Africa [13]. Other sites where large pieces of wood have been recovered include the Acheulian sites of Amanzi Springs [73] and Gesher Benot Ya'aqov [169]. Despite the discovery of significant amounts of wood from these deposits, no tools have been noted. The Kalambo falls tools are reminiscent in some ways of the European “spears” and are associated with large well-formed cleavers from the Acheulian bearing Floor 2, below the Sangoan. Given their context these wood tools might be older than those from Europe and might point to a wooden projectile point technology in the late Acheulian, complimenting the earlier LCT technology. At most sites, the only clue would be in finding injury patterns on faunal remains indicative of such activities. In a similar vein, the co-occurrence of LCTs and projectile point technology in the Sangoan and Fauresmith may reflect similar activity patterns, or as McBrearty [22] suggests that the mix of technologies may, in fact, represent different hominins using different technologies at the same time in the same regions of Africa.

This brings us to the current paper, which pushes the appearance of projectile points back well before the clear appearance of the MSA. So is the evidence solid?

Triangular stone flakes may look on the surface like spear points, but that doesn't necessarily mean they were used that way. Triangular flakes are useful cutting tools, and actually preferred as cutting tools in some archaeological contexts.

Springbok used in experimental archaeology

The springbok spear test. Figure S6D from Wilkins et al. 2012

I think the authors did a nice job of finding multiple ways to test the use of these points as spear tips. They examined edge wear to show that on these artifacts it is differentially concentrated near the tip. They shot a bunch of experimentally-produced tips into springbok carcasses, showing the pattern of wear that comes from use on a hafted spear, and this pattern matches the archaeological points. Furthermore, they show that experimental use of the points as cutting tools yields a different wear pattern, as does postdepositional damage to the artifacts. They find that some of the points are modified on the base, suggesting hafting, but do not report any evidence of glue or base wear that would have come from the wooden spear. A clever part of their analysis concerns the symmetry of the points. They expected that as a cutting tools is blunted and resharpened, the shape of the overall tool will become skewed, so smaller points should be less symmetrical. The archaeological points show the opposite pattern, with smaller points just as symmetrical as the large ones. The sizes of the points fall within the range of ethnographic and MSA spear points, not smaller projectiles such as arrows or atlatl darts.

So all in all, these look like good spear tips. This seems like yet another case where a more intensive investigation of the African record has shown that supposedly "advanced" toolmaking techniques were mastered by Middle Pleistocene humans. With some of the other techniques -- such as blade production -- people seem to show an effervescent pattern. A handful of sites show an early occurrence of the technique but no clear tradition carrying the early innovation into later time periods. Maybe hafting is another such case, a relatively complex innovation that was repeatedly reinvented, with people repeatedly falling back to the simpler option (in this case, sharpened wood spears without points).

The archaeological record may be giving us a signal of the importance of communication and knowledge accumulation relative to innovation in our prehistory. But to be clear about this will require a fuller record, with fewer blank spots.


References

Chimpanzee microbiome variation is like ours

Tue, 2012-11-13 23:55 -- John Hawks

A new paper by Andrew Moeller and colleagues surveys the variation in species composition of gut microbiomes in the chimpanzees from Gombe, Tanzania [1]. They found that chimpanzees have a very similar pattern of variation to that found in human populations. Here's their mini-review of the human variation in "enterotypes":

The gut microbial communities in contemporary populations of humans have been partitioned into three clusters, termed ‘enterotypes’, each of which is characterized by a distinct set of overrepresented bacterial genera. Whereas initially no relationship was detected between enterotypes and specific features of the host (such as age, health status, body morphotype, provenance or gender), recent work has revealed associations between enterotype and long-term diet: the Bacteroides-dominant enterotype is prevalent in individuals whose diets are high in animal fat and protein, whereas the Prevotella-dominant enterotype prevails in individuals with high-carbohydrate diets.

A microbiome is a multispecies community, in which each kind of bacteria has its own distinctive metabolic role. The entire bacterial is made up of different proportions of each bacterial genus. The "enterotypes" discussed here are defined by variation in the proportions of different bacterial genera.

A visual depiction from the paper helps to show the three enterotypes in humans and chimpanzees. Each is characterized in a principal components plot, which reduces the proportions of dozens of bacterial types into two dimensions. This reduction is possible because the bacterial communities have covariance among species abundances -- when Dialister is common for example, Ruminococcus also tends to be common. The consistent association of some of the bacterial genera suggests that the community as a whole is regulated by the host gut and immune system factors.

Bacterial enterotypes, after Moeller et al 2012

Figure 1 from Moeller et al. 2012. Original caption: "(a) Assortment of gut microbial communities into enterotypes in chimpanzees and humans. Shown are BCA visualizations of enterotypes (coloured ellipses), as identified by PAM clustering, with black dots representing abundance distributions of bacterial genera from an individual host and numbered white rectangles marking the centre of each enterotype. Panel (right) showing human gut enterotypes modifed from Arumugam et al.1 Bacterial taxa uniquely overrepresented in the corresponding chimpanzee and human enterotypes are listed. (b) Relative abundances of the three bacterial taxa that are principally responsible for the separation of chimpanzee enterotypes. Shown are means, ranges and first and third quartiles. Colour coding of enterotypes follows that in (a)."

The chimpanzees have the same associations among bacterial species as humans, which suggests that the ecology within the chimpanzee gut is regulated by similar factors. The paper makes it clear that the bacterial communities of chimpanzees and humans, despite the consistent similarity of enterotypes, do differ in many ways. There are some bacterial species that are common in chimpanzees that are rare in humans, or that are overrepresented in one chimpanzee enterotype without being similarly represented in the human equivalent. The paper does not provide evidence that the chimpanzee and human microbiomes have remained static from our common ancestors. Instead, it shows that there may be ecological factors or feedbacks that keep the variability within a trimodal dynamic.

Another interesting aspect of the paper is that the bacterial enterotypes of chimpanzees are not stable within individuals. The authors examined the microbiomes in 2000, 2001, and 2008, finding that every individual changed from one enterotype to another during that period of time. The Gombe community did not change in a directional way, and no obvious factors explain the changes in enterotypes for individuals:

As observed in humans, there is no obvious association between chimpanzee enterotype and host genetics or geography. When sampled in 2000, the siblings, Sandi and Shelton, and their mother, Sparrow, each possessed different enterotypes, and their enterotypes changed, and still differed, in later samplings. Meanwhile, three chimpanzees that are not all members of the same family or same geographic community (Darbee, Gremlin and Kris) harboured the same enterotypes at each of the three time points sampled. In humans, diet is likely to be a major contributor to a host’s enterotype2. As the availability of different foodstuffs in Gombe can fluctuate seasonally15, 16, diet may also influence the possession of certain chimpanzee enterotypes. However, we found no consistent association between enterotype and the season in which a host was sampled. Furthermore, all three enterotypes were present during each wet season when foods were abundant and the diets among the chimpanzee hosts were the most homogenous.

All in all, I think this is a really fascinating study. The microbiome reveals something previously hidden, which may be important to dietary adaptations or immunity in hominoids generally. We might naturally assume that human microbiomes are products of very recent dietary innovations and rapid bacterial adaptation -- particularly among human agriculturalists. The chimpanzees may be showing that the important dynamics are much older than agriculture.


References

AAA Meetings watch

Tue, 2012-11-13 16:54 -- John Hawks

I will be at the American Anthropological Association meetings in San Francisco for the rest of the week. If you're an anthropologist, I hope to see you there! Remember you can tweet me @johnhawks and I'll be following some of the sessions while tweeting on the #aaa2012 hashtag.

I will be participating in an exciting podium session on Saturday afternoon, organized by Jamie Clark and Adam Van Arsdale. Adam has a list of the talks in the session, which includes some really great young anthropologists from cultural, archaeological, and biological perspectives.

Here's my abstract, which is a pretty strong statement of where I think the biological species concept applies to archaic humans:

Neandertal Genetics: Drawing a New Boundary for Humanity

John Hawks (University of Wisconsin-Madison)

Genetic information from ancient skeletons has transformed our understanding of human origins. For more than 160 years, anthropologists defined humanity in contrast to the Neandertals. Now it is clear that the genealogical ties between living people include Neandertals and other archaic humans within our biological species. An accounting of the shared genetic ancestry in humans worldwide and the ancient Neandertal and Denisova genomes helps to show the pattern of population structure in the Middle Pleistocene populations that gave rise to modern humans. Our species included variations that no longer exist today, while our evolution within the last 100,000 years has been a process of amalgamation and rejoining of populations that were once much more different. As we redraw our genealogical boundaries to recognize this pattern of relationships and evolution, we are beginning to discover the way that the present traits of humans around the world emerged in a variable population.

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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.