With 207x (Introduction to Human Evolution) about a month away preparations have entered a frenzy mode. As it turns out, right after the class goes live, I will be speaking at Wellesley “Family and Friends” weekend about the intersection between online education, the liberal arts college experience, and human evolution. I will be sure to share more of my specific thoughts as the event gets closer.
…prior to the arrival of students, the beginning of school, and the traditional ramping up of Fall.
The Academy Fight Song, by Thomas Frank (The Baffler)
The coming of “academic capitalism” has been anticipated and praised for years; today it is here. Colleges and universities clamor greedily these days for pharmaceutical patents and ownership chunks of high-tech startups; they boast of being “entrepreneurial”; they have rationalized and outsourced countless aspects of their operations in the search for cash; they fight their workers nearly as ferociously as a nineteenth-century railroad baron; and the richest among them have turned their endowments into in-house hedge funds.
A large number of my colleagues in academia are passing this around…and for good reason.
Taphonomic comparison of bone modifications caused by wild and captive wolves (Canis lupus), by Nohemi Sala, Juan Luis Arsuaga, and Gary Haynes (Quarternary International, early view)
Abstract: This work presents data obtained from experiments conducted on wild and captive wolves. Actualism is a very useful tool for taphonomic studies, as it allows us to understand the behavior of fauna in the past. However, not many past experimental studies have dealt with wolves as taphonomic agents. The results of the study show that wolves modify animal carcasses in advanced stages that include fracturing the bones in order to consume the marrow. By comparing captive and wild wolves, we observe that captive wolves often modify ungulate carcasses to a greater degree than do wild wolves. Moreover, factors such as the size of the ungulate and the period of availability of the carcass influence the type and degree of bone alteration. Tooth mark dimensions also allow us to compare wolves with other large carnivores and reveal that wolves differ significantly from large felids and ursids, and they have more in common with hyenids.
One of the things I love about paleoanthropology is how readily it lends itself to cross-disciplinary work. Why should I care what wolves do to bones? Well…a small species of wolf (Canis etruscus) is one of the most common representatives in the Dmanisi faunal assemblage. Since Dmanisi was discovered, questions about site formation processes and accumulation vectors for the extraordinarily rich and well-preserved fossil assemblage have been raised. The site contains a lot of potential predator accumulators in addition to the canids, including hyaena, several species of large cats, smaller carnivores, and the hominins at the site. Being able to differentiate patterns of bone modification on fossils within the assemblage (e.g. canid vs. cat vs. hyaena) can reveal important aspects of how the site was being used during formative processes, and thereby potentially provide us with information about the temporal and spatial relationships of different materials found in the excavation, including the hominin fossils. Was part of the Dmanisi site a canid or hyaena den while the hominins were present in the environment? To address that question, you need to know what kinds of marks canids leave behind…
New evidence for early presence of hominids in North China (Ao, H., et al., Scientific Reports)
Abstract: The Nihewan Basin in North China has a rich source of Early Pleistocene Paleolithic sites. Here, we report a high-resolution magnetostratigraphic dating of the Shangshazui Paleolithic site that was found in the northeastern Nihewan Basin in 1972. The artifact layer is suggested to be located in the Matuyama reversed polarity chron just above the upper boundary of the Olduvai polarity subchron, yielding an estimated age of ca 1.7–1.6 Ma. This provides new evidence for hominid occupation in North China in the earliest Pleistocene. The earliest hominids are argued to have lived in a habitat of open grasslands mixed with patches of forests close to the bank of the Nihewan paleolake as indicated from faunal compositions. Hominid migrations to East Asia during the Early Pleistocene are suggested to be a consequence of increasing cooling and aridity in Africa and Eurasia.
The possibility of an early hominin presence in Northern China has been in the literature for more than a decade now, although the evidence has been limited to archaeological materials. This paper is another confirmation of that early presence on the basis of new dates, putting hominins in the area extremely early. An early presence of hominins in this region would be additional support that the technological and adaptive changes in early Homo really did open up a much greater range of habitats for hominins to exploit. The different kinds of seasonality, resource limitations, and ecological interactions of hominins ranging across a diverse range of areas of Eurasia, in addition to Africa, early in the Pleistocene poses interesting evolutionary questions and targets for research. The presence of hominins in Northern China in the Lower Pleistocene is also one of the reasons I was doing fieldwork in Eastern Kazakhstan earlier this summer….
And in honor of Seamus Heaney’s passing, the conclusion to his poem, “Digging”
The cold smell of potato mould, the squelch and slap
Of soggy peat, the curt cuts of an edge
Through living roots awaken in my head.
But I’ve no spade to follow men like them.Between my finger and my thumb
The squat pen rests.
I’ll dig with it.
*****
1. Nohemi Sala, Juan Luis Arsuaga, Gary Haynes, Taphonomic comparison of bone modifications caused by wild and captive wolves (Canis lupus), Quaternary International, Available online 30 August 2013, ISSN 1040-6182, http://dx.doi.org/10.1016/j.quaint.2013.08.017.
2. Ao, H., M. J. Dekkers, et al. (2013). “New evidence for early presence of hominids in North China.” Sci. Rep. 3. doi:10.1038/srep02403
The program for this November’s AAA meetings is beginning to come together. And while it is too late to submit a paper for this year’s meeting, it is not too late to consider attending (Chicago!).
For those with a biological anthropology focus, there looks to be a great lineup of sessions. Some of the highlights:
HUMAN EXPERIENCE in the GENOMIC /POST-GENOMIC AGE (12 talks)
Session organizer & Chair: Jada Benn Torres (University of Notre Dame)
Discussant: Alan Goodman (Hampshire College)
ENTANGLING THE BIOLOGICAL: STEPS TOWARD AN INTEGRATIVE ANTHROPOLOGY (14 talks)
Session organizers: Organizers: Katherine C. MacKinnon (Saint Louis University) and Agustin Fuentes (University of Notre Dame)
Session chairs: John Hawks (University of Wisconsin) and Katherine C. MacKinnon (Saint Louis University)
Discussants: Jonathan Marks (Univ. of North Carolina-Charlotte) and Julienne Rutherford (Univ. of Illinois-Chicago)
CAN THE FUTURE ESCAPE THE PAST: BIOSOCIAL FACTORS IN THE REPRODUCTION OF POVERTY (11 talks)
Organizers: Lawrence M Schell (Center for the Elmination of Minority Health Disparities, UNIVERSITY AT ALBANY, SUNY) and Thomas L Leatherman (University of Massachesetts)
Chairs: Lawrence M Schell (Center for the Elmination of Minority Health Disparities, UNIVERSITY AT ALBANY, SUNY)
CORRELATES OF POVERTY, DETERMINANTS OF PROSPERITY: REFINING CONCEPTS AND SORTING CAUSE FROM CONSEQUENCE USING ANTHROPOLOGICAL INSIGHTS (13 talks)
Organizers: Bram T Tucker (University of Georgia), Susan N Tanner (University of Georgia) and Jason A DeCaro (University of Alabama)
Chairs: Susan N Tanner (University of Georgia)
WHAT THE BONES TELL US: MODELS AND METHODS IN BIOARCHAEOLOGY AND SKELETAL BIOLOGY (12 talks)
Chair: Richard S. Meindl (Kent State University)
MOTHERS, MILKS, AND MEANING: INNOVATIONS IN STUDYING LACTATION, INFANT FEEDING, AND DEVELOPMENTAL ECOLOGY in HUMANS AND NONHUMAN PRIMATES
Organizers: Elizabeth A. Quinn (Washington University, St. Louis), Alyson Young (University of Florida)
Chair: Daniel Sellen (University of Toronto)
Discussants: Andrea S Wiley (Indiana University) and Penny Van Esterik (York University)
In addition, there will be small sessions on primatology, biocultural approaches to health, hominin evolution, forensic anthropology, and numerous other bio-relevant presentations.
I continue to meet biological anthropologist after biological anthropologist (this applies to archaeologists, too) who, while they do not terribly enjoy the atmosphere of the AAPA meetings (e.g. too busy, too intense), have never been to the AAAs. For us non-cultural/ling folks, the AAAs are actually a great place to have an intimate meetings experience in the midst of a very large anthropology conference.
Contrary to expectations generated by my absence from this space, I have not fallen off the planet. I have however been busy with a variety of projects, including an intensive filming schedule for my upcoming WellesleyX class (Introduction to Human Evolution) and several research projects which I will hopefully be blogging more about soon. The addition of a newborn to our house has also been a bit of a (wonderfully) disruptive element. (there was a little bit about submitting tenure materials over the summer, too…)
International student orientation begins today at Wellesley, however, which means the beginning of the semester is creeping over the horizon. As such, I should be returning to a more regular schedule here shortly. This semester is going to be an exciting one as I navigate the intersection between my on-campus students and (as of last check) more than 12,000 online students. The process of assembling the course over the past two months has been interesting and humbling, particularly in recognizing the challenges and decidedly different skill set associated with extensive filming. I consider myself very comfortable in front of a class or even a large conference audience*, but filming solo in front of a camera is not easy. I am fortunate to have a great video production team and from what I have seen, the final results will look great. But it is not easy.
It has its fun moments, though. One of the most enjoyable was filming in the Wellesley College library’s special collections last week. We were filming a short segment, placed early in the course, on the life of Darwin and the development of evolutionary theory. We are exceedingly privileged to own a 1st edition copy of On the Origin of Species (courtesy of a gift back in the early 1930s), which made for a wonderful backdrop for the lecture segment.
I am normally not much for the worship of historical objects (fossils are an obvious exception!), but I was surprised at how excited I was to flip through the pages. Alongside Darwin’s book I had a first edition of the two-volume collection put together by his grandfather, Erasmus Darwin, entitled Zoonomia: Or the laws of organic life, one of the important proto-evolutionary texts of the early 19th century.
Anyway…I just thought I would share.
I have been in radio blackout mode the past week busily getting materials ready for my tenure review. But I have also been deep in preparations for my Introduction to Human Evolution course coming up this Fall, which is notable because it is Wellesley’s first course in partnership with EdX. The course is featured on EdX’s front page today.
Full text of decision here (pdf), more thoughts from me later…
Background on Association for Molecular Pathology v. Myriad Genetics, Inc. (SCOTUSblog)
From the opinion (Justice Thomas writing for the unanimous decision, with Justice Scalia concurring, in part, and writing a concurring opinion):
“For the reasons that follow, we hold that a naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated, but that cDNA is patent eligible because it is not naturally occurring.” (p. 1)
“The central dispute among the panel members was whether the act of isolating DNA—separating a specific gene or sequence of nucleotides from the rest of the chromosome—is an inventive act that entitles the individual who first isolates it to a patent.” (p. 8)
“The rule against patents on naturally occurring things is not without limits, however, for “all inventions at some level embody, use, reflect, rest upon, or apply laws of nature, natural phenomena, or abstract ideas,” and “too broad an interpretation of this exclusionary principle could eviscerate patent law.” 566 U. S., at ___ (slip op., at 2). As we have recognized before, patent protection strikes a delicate balance between creating “incentives that lead to creation, invention, and discovery” and “imped[ing] the flow of information that might permit, indeed spur, invention.” Id., at ___ (slip op., at 23). We must apply this well-established standard to determine whether Myriad’s patents claim any “new and useful . . . composition of matter,” §101, or instead claim naturally occurring phenomena.” (p. 11)
“It is undisputed that Myriad did not create or alter any of the genetic information encoded in the BRCA1 and BRCA2 genes” (pp. 11-12)
“Many of Myriad’s patent descriptions simply detail the “iterative process” of discovery by which Myriad narrowed the possible locations for the gene sequences that it sought.” (p. 14)
“If the patents depended upon the creation of a unique molecule, then a would-be infringer could
arguably avoid at least Myriad’s patent claims on entire genes (such as claims 1 and 2 of the ’282 patent) by isolating a DNA sequence that included both the BRCA1 or BRCA2 gene and one additional nucleotide pair. Such a molecule would not be chemically identical to the molecule “invented” by Myriad. But Myriad obviously would resist that outcome because its claim is concerned primarily with
the information contained in the genetic sequence, not with the specific chemical composition of a particular molecule.” (p. 15)
“cDNA does not present the same obstacles to patentability as naturally occurring, isolated DNA segments.” (p. 16)
“cDNA retains the naturally occurring exons of DNA, but it is distinct from the DNA from which
it was derived. As a result, cDNA is not a “product of nature” and is patent eligible under §101” (p. 17)
And finally, Justice Scalia’s concurring opinion, in its entirety:
“I join the judgment of the Court, and all of its opinion except Part I–A and some portions of the rest of the opinion going into fine details of molecular biology. I am unable to affirm those details on my own knowledge or even my own belief. It suffices for me to affirm, having studied
the opinions below and the expert briefs presented here, that the portion of DNA isolated from its natural state sought to be patented is identical to that portion of the DNA in its natural state; and that complementary DNA (cDNA) is a synthetic creation not normally present in nature.” (p. 1)
Aaron Stutz, an associate professor of Anthropology at Oxford College, Emory University, has a wonderful new blog focused on biocultural evolution.
I have added it to the blogroll on the side (which needs to be updated further), but you should check it out.
The recent SCOTUS decision in the Maryland v. King case has produced a lot of interesting follow-up commentaries. A sampling of a few of them are linked below:
Panopticon, keep your eyes on the word (Ronald Collins, SCOTUSBlog)
DNA Fingerprinting as Routine Arrest Booking Procedure Upheld as Anticipated (Jennifer Wagner, Genomic Law Report)
Supreme Court Fails the Fourth Amendment Test (Barry Friedman, Slate)
The Coming California Sequels (Hank Greely, Stanford Law School)
A few thoughts on Maryland v King (Orin Kerr, The Volokh Conspiracy)
The dark side of DNA evidence (Jason Silverstein, The Nation)
A primary theme in many of these commentaries is the issue of privacy. To what extent do you as an individual have the right to keep your genetic profile (or, more accurately, CODIS profile in the Maryland v. King case) private?
Right on the heels of the Supreme Court decision came the even bigger story (based on media coverage) of the NSA data monitoring program, leaked by Edward Snowden, known as PRISM. Again, the central theme in the reporting and commentary on PRISM is the issue of privacy. To what extent do you, as an individual, have the right to engage in social behavior (phone calls, internet usage) unobserved?
In teaching about personal genomics this past Spring, personal privacy was a major issue my students read about and discussed. For nearly every student in the class it was one of their primary concerns either at the beginning of the class (based on their pre-conceived notion of genomics) or at the end of the class (brought on by readings outlining the challenges of maintaining genetic anonymity). What I want to bring up now is that for every student who brought up privacy as a concern, the perspective through which privacy was articulated was from the role of an individual. As I tried to convey to my students, from both a genetic and anthropological perspective, the concern with individual privacy, rather than a more collective valuing of privacy, is misguided.
The go-to example of genetic privacy that gets brought up by students is access to the genomic profile of high-profile public individuals. What if the American people knew in 1984 that Ronald Reagan was an APOE4[1] carrier and had a higher risk of developing Alzheimer’s (I don’t know, by the way, that Ronald Reagan was an APOE4 carrier…he quite possibly wasn’t)? What if Barack Obama, with a known history of smoking, released his genomic profile, enabling a clinical risk assessment[2] of his health prior to his election? Or what if someone got ahold of a stray hair from Senator Elizabeth Warren and tried to test the idea that she has Native American ancestry?
These are all interesting thought questions to consider, but I would argue they do little in furthering a practical stance on privacy. The reason is that in any of the above cases, if anyone was really motivated to take those steps, it would be nearly impossible to prevent such actions (though one could certainly critique the usefulness of whatever information was generated). The reason being that as an individual it is very hard to keep track of our DNA. We shed it throughout our life through hair, skin, feces, saliva (a fact which is very valuable for primatologists and other biologists). That all of the above individuals are public figures, who regularly engage with large crowds of people, merely adds to the challenge of maintaining anonymity against a concerted effort to reveal such data. Even if an individual were able to maintain their own secrecy, presumably through Osama Bin Laden like seclusion, it would be possible to get a pretty good sense of that individual’s DNA by getting access to the DNA of close relatives and imputing[3] the likely DNA of the individual in question. Indeed, this is a tool used by forensic geneticists to identify the remains of individuals who lack alternative identifying marks, such as mass burial victims or, in the example above, the positive genetic ID of Osama Bin Laden. Just as your DNA reveals important information about your relatives, their DNA can also be used to get a good sense of your genetic profile (much like a family medical history). One of the books we read in the class was Here is a Human Being, by Misha Angrist (@MishaAngrist), a recurring theme of which is the difficulty (and limited value) of maintaining genomic anonymity (and this was published well before last summer’s Gymrek, et al. [4] Science paper on re-identification of DNA profiles).
So is privacy a lost cause not worth guarding? No. Privacy is an important value and one that should be protected, even if the individual is not the primary locus of concern. The problem is not that an individual’s privacy might be compromised, but that whole groups of people might be passively (or actively) discriminated against based on identifiable and trackable information. This is where the NSA and Maryland v. King stories converge.
The fear should not be that you are being targeted for because you are person X (that is really difficult to prevent), but rather, you are being indiscriminately targeted because you are a person with trait Y. If someone wants your DNA, or if someone wants to spy on you, because of who you are, they probably can. But you shouldn’t be subject to discrimination just because you are an I1a1 mtDNA haplogroup carrier (my mtDNA haplogroup) or because you regularly make phone international phone calls to a particular part of the world.
Much of contemporary genomic research, much as the apparent NSA program, relies on a faith in “big data.” This is the idea that complex problems can be solved by using intensive computational methods utilizing vast amounts of data. This, interestingly, was a recurring theme in another text we read for our genomics seminar, The Decision Tree, by Thomas Goetz (@tgoetz). Big data, however, do not inherently make complex issues tractable. Those complex issues remain complex. The genetic and environmental architecture that underlies the development of cancer, or heart disease, or neurological conditions like Alzheimer’s, is complex. The limited gains in clinical approaches made by a decade of genome-wide association studies (GWAS) reflect not a failure of genomics so much as a reality of the complexity of these conditions. I am not a terrorism expert, but I would guess you can analogize the complexity of a terrorist (in terms of causation) to the complexity of a condition like heart disease. Big data make the identification of central tendencies in systems easier to identify, but they don’t increase the scope of central tendencies in complex patterns. Sometimes there is no easy solution. Just to use a recent example, the NSA wasn’t able to successfully identify the Tsarnaev brothers intentions despite a lot of prompting that could have pointed the agency in that direction.
There is a distinction I have tried to draw out repeatedly on this blog between the production of information and the production of knowledge. Since the human genome project, and particularly since the development of next-generation sequencing technologies, we have produced a VAST amount of genomic information (an increase of information more than an order of magnitude greater than Moore’s Law). And that information has certainly led to huge improvements to what we “know” about how the genome works and is organized, particularly at a structural level. But having the data is only the first step towards understanding the hows and whys of human phenotypic variation. Those data make it easy to draw lots of correlations and associations, which is what GWAS studies have done again and again, but they do not provide a magic solution to a complete understanding of cancer, or intelligence (if you want to define what intelligence is), or terrorism.
Complexity creates limits not only on what we know, but these ease with which we can develop new knowledge. From an individual privacy standpoint, this should be encouraging. There is only so much you can glean from looking at your DNA, much as I would guess there is only so much that can be gleaned by looking at your phone calls.
However, what can be done to a vastly greater degree is to classify you on the basis of a given set of genetic variants or, in the case of the NSA, social network patterns. From an anthropological genetic standpoint, this is where the real danger sits. The public, and often those of us in the field, still tend to think of individual genetic variants as good or bad. Angelina Jolie had a double-mastectomy because of her “flawed” BRCA1 gene. In some limited cases, this characterization may be correct, in the sense that a gene simply does not function. More often, what we are identifying as good or bad represent variations in how a gene functions and interacts with other genes and the environment in which it sits, something that makes a simple good/bad binary misleading. And yet…the appeal of such a binary classification makes it possible to suddenly identify groups of people who share to a greater or lesser frequency good or bad genes.
Another reference that students come back to again and again is the spectre of the eugenics movement and some kind of dystopian Gattaca-like future. The future is not going to be Gattaca (genes alone do not produce that degree of certainty). But it is worth probing the relationship between eugenics and genomic knowledge a little further. The really insidious part of the eugenics history, largely based in the US and UK (Germany was a great importer of American and British eugenics law), was how prevalent actively eugenicist ideas were within society. The notion that we should use hereditary knowledge to improve the human species was held by prominent writers, politicians and scientists on both the right and left end of the spectrum. And why not? Why not use the knowledge we have? In the case of the early 20th century eugenics movement, a reason not to was that the “knowledge” of that era regarding heredity was extremely limited. It was also mediated by existing societal structures that were sexist, racist, xenophobic and homophobic. 100 years later, on the tailwind of the human genome project, we certainly know a lot more about heredity. But knowing more does not mean we have a complete understanding of the topic or even an actionable understanding of the topic (and it also doesn’t mean our currently knowledge is any less mediated by existing social structures). Indeed, a complete understanding of the role of human heredity in shaping phenotypes requires vast exploration of variation on a case by case basis. Big data alone are not enough. Big data are good at making us think we know a lot, though, and that is a big problem (big data are also good at serving as a giant magnet for limited funding and resources).
*****
1. Poirier, et al. Apolipoprotein E polymorphism and Alzheimer’s disease, The Lancet, Volume 342, Issue 8873, 18 September 1993, Pages 697–699 DOI:http://dx.doi.org/10.1016/0140-6736(93)91705-Q
2. Ashely, et al. Clinical assessment incorporating a personal genome, The Lancet, Volume 375, Issue 9725, 1–7 May 2010, Pages 1525–1535 DOI:http://dx.doi.org/10.1016/S0140-6736(10)60452-7
3. Li, et al. Genetic Imputation. Annu. Rev. Genomics Hum. Genet. 2009.
10:387–406. DOI:10.1146/annurev.genom.9.081307.164242
4. Gymrek, et al. Identifying Personal Genomes by Surname Inference. Science 18 January 2013:
Vol. 339 no. 6117 pp. 321-324 DOI: 10.1126/science.1229566
This week’s NY Times “Room for Debate” segment is focused on gene patents. With a SCOTUS ruling expected any day on the issue in the Myriad case, this is something that will likely be in the news.
Check it out.
As summer begins, it is time to change the site banner. The old picture was of the Medieval/Bronze Age/Lower Paleolithic site of Dmanisi. The new image comes from my recent field trip to Kazakhstan, and features several members of our team surveying a terrace in the Charyn Canyon region. In the background are the majestic Tian Shan mountains, marking the border with Krygyzstan (south) and China (east).
The Charyn Canyon has a rich pre-history, some of which you can read about in this manuscript co-authored by two of our team members (Jean-Marc and Renato).
