john hawks weblog

paleoanthropology, genetics and evolution

Are MOOCs technical or practical?

Tue, 2013-04-09 12:42 -- John Hawks

All the NY Times columnists will be writing about MOOCs before long, I suspect. Today it was David Brooks' turn: "The Practical University". His argument is that digital technology allows much more efficient transmission of "technical" know-how than do classrooms in big buildings, but "practical" know-how cannot be taught without real hands-on training.

The problem is that as online education becomes more pervasive, universities can no longer primarily be in the business of transmitting technical knowledge. Online offerings from distant, star professors will just be too efficient. As Ben Nelson of Minerva University points out, a school cannot charge students $40,000 and then turn around and offer them online courses that they can get free or nearly free. That business model simply does not work. There will be no such thing as a MOOC university.

Nelson believes that universities will end up effectively telling students: “Take the following online courses over the summer or over a certain period, and then, when you’re done, you will come to campus and that’s when our job will begin.” If Nelson is right, then universities in the future will spend much less time transmitting technical knowledge and much more time transmitting practical knowledge.

Like many NY Times columns about education, this one reads like a paid advertisement -- in this case for Minerva University. That doesn't mean that it's wrong, but I don't think the practical-technical distinction holds. In anthropology, for example, it is possible for us to use digital tools to bring much more of the experience of the field to students than we can accomplish in the classroom. I also think the "technical-practical" distinction breaks down when considering laboratory work.

I think a basic rule of thumb is to ask whether the analogy works for sports. In sports, we have broadcast events seen by millions, and coaching clinics that scale down to individuals. It takes lots of experience and practice to perform a sport well..and it also takes some experience and practice to watch a sport well. But watching and playing are not the same kinds of activity. They can enhance each other, feed back on each other, and both can contribute to broader appreciation. And digital tools can help with both of them -- they're just different digital tools.

Math for biology

Mon, 2013-04-08 00:36 -- John Hawks

Edward O. Wilson, in the Wall Street Journal writes: "Great Scientist ≠ Good at Math".

For many young people who aspire to be scientists, the great bugbear is mathematics. Without advanced math, how can you do serious work in the sciences? Well, I have a professional secret to share: Many of the most successful scientists in the world today are mathematically no more than semiliterate.

Wilson takes himself as the canonical model. Razib Khan comments somewhat critically ("Does one need math for a career in science?"). I think that field biology requires working diligently and independently in the field in a way that some kinds of science do not, and personal qualities that set successful fieldworkers apart are pretty much orthogonal to math skill.

Notes on a broken science funding system

Sun, 2013-04-07 13:14 -- John Hawks

A jeremiad from Henry Bourne: "Writing on the wall" [1].

Competition drives scientific discovery, but too much competition for scarce resources can block progress, and has done so. Thus, the growing flood of grant applications surpasses growth in NIH dollars, reduces the proportion of grants that are funded, and renders peer review increasingly arbitrary because a project ranked in the 20th percentile is often no less meritorious than one ranked in the 10th percentile (Berg, 2013).

Another problem is that we now have a ‘holding tank' of postdoctoral scholars that is overflowing with bright young scientists who are indentured to greying lab chiefs and are thus unable to break new ground as independent researchers (Bourne, 2012). The worst consequence, but harder to quantify, is that scientists avoid risky, creative projects in favour of ‘sure things’ more likely to be funded by conservative reviewers (Nicholson and Ioannidis, 2012).

Probably most people who have thought about these problems recognize the fundamental catch-22 represented by centralized funding of science. It would be more efficient of time, training, and human capital of all kinds to simply pick a limited number of "winners" early in their careers, provide adequate funding to a relatively small number of institutes, and turn excess talent away at the door. But large institutes often breed groupthink and complacency. There is no accurate indicator of "talent" that would allow selection of those who will achieve great scientific findings from the vast pool of undergraduates. And forcing people to compete every so often does provide a mechanism for cutting out deadwood. That is to say, the likeliest alternative to the current system has lots of obvious problems.

Yet as Bourne and many others say, granting agencies have become the main drivers of groupthink and complacency, we have set up a system where talented creative people are actively turned away from science careers, and no "deadwood" is ever actually cut out of the system because networks of greyhairs protect each other zealously.

I want to draw attention to the comment section of the essay, which has a series of thoughtful exchanges. This passage from Bourne deserves to be front-paged:

A more vexing and crucial problem is that even the faculty who agree with me remain silent and virtually inert. They worry constantly about difficulties getting grants funded, and (correctly) feel pressured to spend most of their time writing grant applications, scrambling to support students and postdocs, and wrangling with prestigious journals. These pressures combine with habituation (in earlier years) to a friendlier funding climate to impose a devastating inertia.

My instinct is that we need to democratize the process of science. A wider group of researchers should have power, not just a stake in the results.


References

  1. Bourne HR. The writing on the wall. eLife. 2013;2:e00642 - e00642.

Templeton on modern human origins

Sun, 2013-04-07 00:33 -- John Hawks

Alan Templeton has written a popular article in Genetic Engineering and Biotechnology News about his work on the biogeography of modern human origins: "Revolutionizing the 'Out of Africa' Story".

However, the mitochondrial evolutionary history was also compatible with the multiregional model. Indeed, there has never been a genetic dataset or analysis that favored the replacement model over alternatives in a statistically significant fashion (Templeton, 2007). Nevertheless, the replacement model became the standard model of human evolution through the 1990s onward.

Now that ancient DNA studies offer direct confirmation of the MLNCA inference that there was admixture, this major controversy in human evolution can now be regarded as settled—at least, as settled as any scientific debate can be.

This is such a neat time for those of us interested in modern human origins, as ancient DNA and whole genome data from living people are changing things so markedly. Looking at the approaches from the last decade through this lens makes it clear how older analyses never excluded the point where we now find ourselves. Likewise, to predict where we may be ten years from now, we have to imagine the full range of scenarios that are not excluded by today's data.

Massive courses: massive opportunity or massive problem?

Sat, 2013-04-06 11:42 -- John Hawks

Dan Ariely is an economist at Duke University who has been teaching a massive open online course on behavioral economics to 140,000 students, titled "A Beginner's Guide to Irrational Behavior". He recently sat down with the PBS NewsHour to answer questions and share perspectives about the MOOC: "The Plusses and Pitfalls of Teaching Online". It is a long piece with many useful parts, here's a sample:

there's a great deal of room for variance once you have over 140,000 students in a class. There's a substantial probability that at least some students will be engaged, knowledgeable, thoughtful, and passionate about the class. And indeed, the discussion boards for my online class show just this -- a select group of students truly stand out as motivated individuals who are taking the content seriously and thinking critically about how ideas can be developed and applied to the real world.

In this regard, the diversity of backgrounds is also a huge benefit in online classes that are available internationally. We hear from students of different ages from around the globe who have so much to contribute. And they not only contribute by sharing their perspectives with their professor and teaching staff, but also with their fellow students.

Ariely also discusses some of the negatives of a very large student sample: the greater likelihood of disgruntled students looking to draw attention in a public forum, for example.

This is a really concern for me as I prepare my course, "Human Evolution: Past and Future" (which I announced here earlier this week). A fraction of my students may have goals that include promoting creationist or fringe ideas, for example.

We are working on some strategies in both the design of the course and the materials that will help to focus students of all backgrounds on the science, while hitting their learning level appropriately. That aspect of the course will really be an important target of our assessment and research efforts. Can we engage this diverse audience productively, increasing science and evolution literacy while stemming possible attempts to derail the process?

Sahelanthropus brain

Fri, 2013-04-05 23:13 -- John Hawks

Kate Wong has been reporting from the Paleoanthropology Society meetings in Honolulu. Today she describes a presentation about the endocast shape of the Toumaï skull, Sahelanthropus tchadensis: "Brain Shape Confirms Controversial Fossil as Oldest Human Ancestor".

Toumaï has been claimed to be the earliest member of the hominin lineage, although I and some other paleoanthropologists have disagreed with this interpretation.

The resulting virtual reconstruction of the endocast reveals that Toumaï had a cranial capacity of 378 cubic centimeters—consistent with earlier estimates. This puts it within the range of chimp cranial capacity. In comparison, modern humans have brains around three times larger than that. But though Toumaï’s brain was apelike in its small size, it was apparently homininlike in other ways. In a presentation given on April 2 at the annual meeting of the Paleoanthropology Society, Bienvenu reported that the endocast shows strongly posteriorly projecting occipital lobes, a tilted brainstem, and a laterally expanded prefrontal cortex, among other hominin brain characteristics.

A "laterally expanded prefrontal cortex" has been a recurring argument for changes in brain organization in hominin endocasts across a range of geological ages. Understanding when and how this area really changed in our evolution will be very useful.

Anthropology's online ecology

Fri, 2013-04-05 10:19 -- John Hawks

Jason Antrosio has composed a short report on the "Anthropology Blogosphere 2013 – Ecology of Online Anthropology". I appreciate his kind words about my work here, and love how he has connected the new media activity of many prominent anthropologists, the move to open access by Cultural Anthropology, and the increased activity of social media networks dedicated to connecting anthropologists. It really is an ecology with many niches for people to increase their engagement and connections across fields.

What should be the shape of the science journal landscape?

Tue, 2013-04-02 23:12 -- John Hawks

Michael Eisen, one of the founders of the Public Library of Science, has thought a lot about how to make the system of scientific publishing better. He has posted the text of a presentation he recently gave, which explains many of the current problems with access and curation: "The Past, Present and Future of Scholarly Publishing". In this passage, he suggests a different system that would obviate the problems finding appropriate research among the 10,000 different journals of the current publishing environment:

So what would be better? The outlines of an ideal system are simple to spell out. There should be no journal hierarchy, only broad journals like PLOS ONE. When papers are submitted to these journals, they should be immediately made available for free online – clearly marked to indicate that they have not yet been reviewed, but there to be used by people in the field capable of deciding on their own if the work is sound and important.

The journal would then organize a different type of peer review, in which experts in the field were asked if the paper is technically sound – as we currently do at PLOS ONE – but also what kinds of scientists would find this paper interesting, and how important should it be to them. This assessment would then be attached to the paper – there for everyone to see and use as they saw fit, whether it be to find papers, assess the contributions of the authors, or whatever.

This simple process would capture all of the value in the current peer review system while shedding most of its flaws. It would get papers out fast to people most able to build on them, but would provide everyone else with a way to know which papers are relevant to them and a guide to their quality and import.

So far, this kind of value-added curation is not happening very much with PLoS ONE. I'm an associate editor and I still can't keep track of all the research in the journal relevant to me. But even though I have access to many paywall journals through my university library, I still love the ease of just clicking on a link to a PLoS article. It just works, no library proxy, no password, just text. Creative Commons text and graphics, that I can freely comment and reuse. The way science should be.

Centuries of grant writing

Tue, 2013-04-02 15:40 -- John Hawks

Jenny Rohn has an article on the wasted effort into failed grant writing, which is so full of good paragraphs it's hard to figure out which one to snip: "Show me the money: Grantwriting is taking over science". Here's one:

There is some evidence that having the vast majority of scientists spend the vast majority of their time writing grants instead of doing and thinking science might be a tad inefficient, and not, perhaps, the best way to get science done. A recent correspondence in Nature about the Australian system, for example, reported that collectively, in 2012, researchers spent "more than five centuries' worth of time" writing or revising grants for the major funding scheme; as only 20.5% were successful, this account for a staggering four centuries' worth of wasted time.

I suppose if we looked at the U.S. we'd be talking about the geological timescale.

Announcing my MOOC, Human Evolution: Past and Future

Mon, 2013-04-01 15:54 -- John Hawks

I have begun a project that may change the way we teach and communicate the science of human evolution. Starting in January, 2014, I will be offering a massive open online course titled, "Human Evolution: Past and Future".

This course and all its materials will be open and free for anyone, anywhere in the world. As of this moment, more than 6500 people have already signed up for the course. The course is still more than nine months away, and I'll be developing materials across the entire time up through January.

Developing this course is a huge investment for me. My institution, the University of Wisconsin-Madison, is making it possible -- but at the same time I'm actively seeking out partnerships and sponsors. I'll be documenting the development process here on the blog, and in a series of presentations and publications as I go. Massive open online courses (MOOCs) have begun to change the way universities approach online education, and the course will be a research platform as well as an educational experience.

What will be new in this course:

Expert interviews. I'll be assembling and curating a series of filmed interviews with experts in paleoanthropology to talk about their work. Why should students hear me describe other people's work, when I can engage the scientists themselves? I've already begun these interviews, and will be adding more than thirty by the time the course begins.

Mini-documentaries. To the extent possible, I'll be virtually taking students to the field, into the laboratory, and giving first-hand experiences with the materials of human evolution. That means many of my video presentations will be much more like short documentary productions than lectures. My priority is making the real materials as available as possible.

Guided laboratories. We'll be exploring genome data, providing some excellent virtual laboratories with the fossil evidence, and running experiments with evolutionary change.

Participatory science. With a worldwide group of thousands of students, we'll be giving people the opportunity to participate in some real research. Some will be as simple as massive measurements of body proportions. Others will be more involved, leading us to...

Looking to the future. The course title is "Human Evolution: Past and Future." To me, the path of our evolution in the past is closely tied to where our species may be going. To that end, the course will be looking at the next hundred, thousand and ten thousand years of our evolution. I'll be interviewing people who are thinking about the impact of technology on our future evolution, and students will come up with their own scenarios based on a strong understanding of the forces that shaped human evolution in the past.

I'm doing this because human evolution is important. The effects of the past shape who we are today, our health and choices, our societies and imaginations. Anthropology can engage people in their own lives and experience. The MOOC technology platform has such potential for innovating new forms of education, I am eager to bring human evolution into that space.

And who wouldn't jump at the opportunity to reach tens of thousands of people looking for information about our evolution? Some people really don't like the word, MOOC. All I have to say is, I got used to "blog", so why not another strange word? This is a natural extension to what I've been doing for nine years here on my blog: curating and writing reactions to the best research in paleoanthropology. In this project, I'll be able to bring people virtually out to the field, and let experts tell about their findings in their own words.

What you can do:

Sign up for the course. I encourage everybody to sign up! You don't have to finish a MOOC, or even watch all the materials, to get a lot out of it. My MOOC will allow you to "choose your own adventure" to the maximum extent possible. If you want a strong module on ancient diets, you can get that by itself, or together with my best materials on Neandertal genetics and post-agricultural evolution.

Look for your opportunity to help. I'm working on several partnerships for this course, and the most important one is with you. With a worldwide group of students, many from developing economies, I cannot assign a traditional textbook. I need a free version of everything written for the students in the course, and that means I'll be providing the text myself. I'll be providing some opportunities to help support this important cause, which will impact students everywhere.

Adopt the materials. We're putting a lot of work into the materials for the course. A lot of professionals are donating time to be interviewed, and are allowing me to use photos and other materials to make a really high-quality presentation. I want to get these high-quality materials into as many classrooms as possible. If you're teaching human evolution in a college or high school setting, look out for additional information on how to use materials and develop curriculum that works in your context!

I learned a lot from my experiment last year putting lectures online from my regular course. I am putting those insights together with discoveries from other MOOC experiments to create new ways for students to network with each other and with ongoing science. This is just the initial announcement. As the summer progresses, I'll be giving you more background about how I'm producing the course, along with sample materials and some chances to participate. I'm looking forward to the experiment, and I hope you will follow on the journey.

Riparo Mezzena and the Neandertal transition

Sun, 2013-03-31 00:38 -- John Hawks

A paper by Silvana Condemi and colleagues examines the anatomy of a partial mandible from Riparo Mezzena, Italy [1]. The mandible is a relatively late Neandertal specimen by its archaeological association and mtDNA sequence. As the introduction to the paper notes, the identities of skeletal specimens in the timespan from 45,000 to 30,000 years ago across Europe have been shifting along with radiocarbon ages and further analyses of fragmentary specimens. In this case, like other late Neandertals, the specimen bears a chin:

This study of the Mezzena mandible shows that the chin region is similar to that of other late Neanderthals which display a much more modern morphology with an incipient mental trigone (e.g. Spy 1, Saint Césaire). In our view, this change in morphology among late Neanderthals reopens the debate on the "more modern like" morphology of late Neanderthals and can lend support to the hypothesis of a certain degree of continuity with AMHs or a possible interbreeding with them.

The paper concludes that the Mezzena mandible lies morphologically amid the sample of modern humans from Upper Paleolithic and Levantine Middle Paleolithic contexts, even when compared to Neandertals like Saint Césaire or La Ferrassie 1 that have relatively vertical mandibular symphyses.

I prefer not to play the game, "is it a Neandertal?", "is it a modern human?" If we had a sample of well-dated relatively complete specimens across the period from 45,000 to 30,000 years ago, we could test the hypothesis that two populations (earlier Neandertals and later "modern" humans) were genetically well-differentiated from each other. We don't have that sample.

In my view, we shouldn't assume more than we know, which is that both the frequencies and combination of traits of earlier Neandertals are much more strongly present in Mousterian-associated specimens than in other, mostly later, industries. I don't yet see a reason to exclude the hypothesis that this pattern reflects both evolution and migration into Europe. And as I wrote last year, the late Neandertals may represent both evolution and migration into Europe from a central Asian or West Asian source population [2].

One effect of genetic sequences has been to demonstrate that anthropologists' morphological distinctions among Neandertals don't match the groupings we would make along purely genetic lines. I considered this problem in my paper last year, "Dynamics of genetic and morphological variability within Neandertals" (open access, PDF) [2]. Jim Ahern and colleagues (including me) have showed that the Vindija G3 Neandertals have morphological features that are not typical of classic Neandertals, and that are significantly different in the modern human direction [3], [4]. Here's what I wrote last year:

The discussion of genetic diversity among these Neandertals has not yet attempted to reconcile their genealogical arrangement with morphological classification schemes. The later Western European Neandertals that share a close mtDNA genealogical connection (Vindija-Feldhofer-El Sidrón) are not synonymous with "classic Neandertals". The well-known classic Neandertals include specimens such as La Chapelle-aux-Saints (France), La Ferrassie 1, Monte Circeo 1 (Guattari) as well as Feldhofer 1. This classic Neandertal sample includes specimens earlier than 70,000 years old and some as recent as 45,000 years ago. The classic Neandertals flank both the earlier and later sides of the 50,000-year-ago dispersal of Neandertals proposed by Dalen and colleagues (Dalen et al., 2012).

Meanwhile, the clade that connects late European Neandertal mtDNA into a tight cluster includes great morphological diversity. The two Vindija mtDNA sequences included by Dalén and colleagues (Dalen et al., 2012) are both from layer G3 of the site, perhaps 40,000 years old. Both are derived from postcranial fragments without diagnostic morphological traits. The other material from G3 includes cranial, mandibular and dental remains that are not synonymous with classic Neandertal morphology (Ahern, 2004). These late Neandertals from Vindija display less pronounced morphology than classic Neandertals and lack traits that are common in the earlier classic Neandertals (Smith, 1992). These specimens are connected to Feldhofer and El Sidrón not only by mtDNA relationships but also their very low nuclear DNA diversification. If the Vindija specimens can be lumped together in mtDNA and nuclear DNA diversity with the remains from El Sidrón and Feldhofer, it seems possible that traditional morphological groupings will fail to capture real biological differences among Neandertal populations.

Riparo Mezzena adds further to this pattern. I would note that this looks at the moment like the specimen most likely to give rise to an Italian Neandertal whole genome. As we begin to examine the data from the Denisova Neandertal specimen ("A new high-coverage Neandertal genome"), the population genetics of later Neandertals will come more and more into focus.

Steven Churchill and Fred Smith wrote a review of the initial Upper Paleolithic skeletal record several years ago [5] that still remains the best single summary of the remains from this time period. What strikes you in this review is the overall fragmentary nature of the record. That review is already out of date in some respects, as a number of specimens have been moved into or out of this period by radiocarbon revisions, and the archaeological conception of "early Aurignacian" has substantially changed.

There really ought to be an equivalent review for the latest Neandertals. I think that the sample has become more complex and confusing as we have developed a better idea of the genetics.


References

Privacy, family history, and genomes

Sat, 2013-03-30 23:52 -- John Hawks

Razib Khan comments on the ethics of making your genome public without the consent of your family: "On genetic privacy".

For example, if you have one of the high penetrance BRCA mutations, you may not want to expose your family’s information for pragmatic reasons. But my question would be: why do people talk about their highly heritable illnesses in public forums already? I’ve seen media profiles of women with a BRCA mutation, with female relatives. By talking about this they’re exposing their family’s genetic information implicitly. Therefore, I suspect many of the pragmatic concerns are moot, because though there is privacy in regards to health information, there isn’t a taboo about discussing one’s health status in public.

Many people diagnosed with highly heritable disorders don't make their diagnoses public. Many talk publicly only after consulting with relatives. There may not be a taboo against discussing health information, but there is certainly no expectation that health diagnoses are public information. Many people believe that their family's health is nobody else's business and act accordingly.

Still, this is an important point. Why do we perceive it as being more invasive to sequence a genome than to take a family medical history?

The family history point suggests that there is no ethical standard. You do not have an expectation of privacy about your relatives' medical conditions.

Alfred, possibly not under a car park

Fri, 2013-03-29 21:08 -- John Hawks

So after they found the bones of Richard III under a parking lot, now everybody is apparently going crazy to dig up bones under parking lots, churchyards, unmarked graves, wherever.

Now we hear that churches and institutions that have bones under their parking lots are digging them up to prevent forensic anthropologists from doing it first: 'Alfred the Great' bones exhumed from unmarked grave".

His body was first buried near Winchester Cathedral, moved at least once there, then moved again to Hyde Abbey in a great procession in 1110. As in Leicester, that church was destroyed in the dissolution of the monasteries, and his remains too were assumed to lie under a modern car park which had previously been the site of a prison. In 1999 there was great excitement when archaeologists found the foundations of abbey buildings, and then human bone – but it proved to be that of an elderly woman who had suffered from painful arthritis.

Here, they have a body from an unmarked grave in a cemetery that they believe to be Alfred's. They've dug it up as a prophylactic against digging it up. Or something.

Does England have any parking lots without bodies under them? Can the ghosts of medieval monarchs turn your Lancia into another Christine? Is there any chance that these bones won't be subjected to forensic study leading to another TV show?

By the way, the most interesting use of genetics here would be to get a whole genome and make an estimate of the proportion of ancestry of common Britons that come from the royal family 1000 years ago...

Everyday genomes

Fri, 2013-03-29 20:46 -- John Hawks

From the Guardian, a pause to consider how ordinary complete genome analysis has become: "Genome research: discovery as an everyday event".

When the Human Genome Project was completed in April 2003, it was hailed as biology's equivalent of the moon landing. Ten years on, what began as costly, painstaking and uncertain science has become commonplace.

Researchers now have the entire genomes of more than 4,000 species – pathogens such as salmonella, leprosy and tuberculosis, parasites such as the malaria plasmodium, insects such as the fruit fly and the malarial mosquito, crops such as maize, the grape and the golden delicious apple, mammals such as the dog, the African elephant, the laboratory mouse and the chimpanzee. One consortium is comparing the genetic texts of a thousand human beings; another is assembling all the variations that might explain differing susceptibilities to disease, and differing responses to the same drugs; a third is using inherited markers to build up a detailed picture of the great journey of homosapiens [sic] out of Africa 70,000 years ago to colonise almost the entire world.

It is glorious, because it means that we can now do comparative science instead of "big science" on genomes. There's a whole lot of opportunity for those of us who concentrate on statistical and analytical methods of comparing populations, instead of single genomes. And it will become more and more possible to do good work with new data, as new data become cheaper and cheaper to obtain.

Meanwhile, I'm tired of "the great journey out of Africa". Clue to writers: Most of our species was still in Africa, where the majority of humans still lived some 20,000 years ago. When those genetic markers are doing a better job of telling us what happened to our African ancestors, I'll have more confidence about the story of how a minority of them left Africa.

Goodall plagiarism case

Fri, 2013-03-29 16:39 -- John Hawks

I'm back home now from a week on family vacation, catching up on news from the last few days. I have been dismayed to read about Jane Goodall's book debacle. She has been accused of plagiarism, fabricating meetings and interviews that did not happen, and spreading misinformation about the safety of genetically modified organisms. Michael Moynihan, who played a key role uncovering the plagiarism and fabrications of science writer Jonah Lehrer last year, has written the most in-depth account of Goodall's alleged transgressions: "Jane Goodall’s Troubling, Error-Filled New Book, ‘Seeds of Hope’"

There is a sense in many of the reported accounts that Goodall’s co-author, Gail Hudson, is to blame. This is, of course, possible (Hudson did not respond to an email request for comment), but if Goodall had read her own manuscript—the one with her name on it—would she not have noticed the quotes from interviews with people she hadn’t spoken to? Wouldn’t a noted scientist double-check her source material? She is, after all, the person who accepted the publisher’s check and Seeds of Hope is written in the first person.

Pat Shipman's reactions largely mirror my own: "Betrayal and Disappointment".

Naturally the plagiarism is disturbing. But the shameful part is that poorly-researched and specious anti-GMO arguments in the book probably would not have been scrutinized without these charges of plagiarism. I see this lack of scrutiny as akin to the continuing science illiteracy of mainstream media, which I noted earlier this year: "Recantation of a former genetic know-nothing".

Mitochondria from another mother

Wed, 2013-03-20 11:32 -- John Hawks

This seems a newsworthy story by Ian Sample at the Guardian: "Britain ponders 'three-person embryos' to combat genetic diseases".

If ministers and MPs give the procedures the green light, Britain would become the first country to offer treatments that lead to children being born with DNA from three people: their parents and a woman donor. The amount of DNA from the donor is tiny compared with the parents.

About one in 6,000 people is born with a disease caused by genetic glitches in their mitochondria, the biological batteries that power the cells in our bodies. Mitochondria are inherited only from mothers and contain just 37 genes, held separately to the 23,000 genes that shape our appearance and define much of who we are.

Nuclear transfer is in principle one of the easiest methods of genetic engineering. In this case, they are talking about taking a donor egg and then transferring the nuclear genetic material from the parents' fertilized egg into that donor egg. It's taking the cytoplasm from one woman (including all the mitochondria in that cell) and grafting on a whole diploid genome from a cell with two other parents. It is a cloning technique, although interestingly the Guardian article does not use the word "clone" anywhere.

This technique would really only be useful to parents where the mother has a heritable mitochondrial disorder, so that's a small population. But it's possibly a growing population as genetic tests become more widespread, as some disease-linked mitochondrial variants go without noticeable effects in younger adults.

A new high-coverage Neandertal genome

Wed, 2013-03-20 00:32 -- John Hawks

Today, Svante Pääbo's group at the Max Planck Institute for Evolutionary Anthropology released high-coverage sequence data from a toe bone from Denisova Cave. The new genome comes a year after the same group released the high-coverage genome of the Denisova finger bone, several months before they published the first high-coverage analysis of this ancient genome [1]. Today's announcement is here: "A high-quality Neandertal genome sequence". It adds a second high-coverage genome from Denisova Cave, this one from a toe bone. Unlike the first finger bone genome, this toe has produced a genome very much like Neandertal specimens from much further west, including the Vindija Neandertals.

Something interesting in these data: the presence of a Y chromosome.

There's not so terribly much we can say about a toe. This particular bone was first reported in 2011 by Mednikova [2], who described the specimen's anatomy. She found the toe similar in some respects to equivalent Neandertal toe bones, but also like recent humans in a couple of details. Still, the anatomy wouldn't be enough to conclude that the bone is a Neandertal, because we don't know much about the toes of other ancient human populations.

The genetics are fairly clear about the level of similarity of this new genome to other Neandertals. From the announcement:

Similarity of Neandertals and Denisova genomes

The figure shows a tree relating this genome to the genomes of Neandertals from Croatia, from Germany and from the Caucasus as well as the Denisovan genome recovered from a finger bone excavated at Denisova Cave. It shows that this individual is closely related to these other Neandertals. Thus, both Neandertals and Denisovans have inhabited this cave in southern Siberia, presumably at different times.

This is a cluster diagram based on genome-wide similarity, which doesn't tell us about possible mixture among the populations. But it does show the high degree of similarity among the known Neandertals. This new specimen from Denisova (labeled "Altai") is a bit further from them than they are to each other, but not much. It will be interesting to assess this degree of similarity in comparison with the within-population similarity of more living human populations.

I'm reluctant to accept a dichotomy of "Denisovan" versus "Neandertal". Distinguishing the samples in that way invites a typological assumption about the ancient people, giving an impression of distinctness that I'm not yet convinced about. It remains to seriously investigate the hypothesis that one or both of these putative samples represents some amount of gene flow from each other, or from yet more ancient populations. But I suppose we're stuck with the "Neandertal from Denisova" and the "Denisovan from Denisova".

Unless we go for "manual genome" versus "pedal genome", which is admittedly unappealing.

There's not much meat in this announcement, that will wait for the full published analysis that we can expect later this year. The most important aspect of this, like the Denisova data availability from last year, is that we can now start working with the high-quality data. As someone who works with sequences, I cannot overstate the importance of having the best high-coverage data available for our work.

I have a paper in preparation where I make a relevant analogy, in this case noting last year's high-coverage Denisovan genome in comparison to the history of ancient DNA sequencing:

To put this into context: the original 360bp sequence from Feldhofer 1 has been memorialized on a cross-shaped plaque at the site outside Mettmann, Germany. This plaque is approximately 1 square meter in size. A similar monument to contain the Denisova high-coverage data would need to be more than 14 kilometers across. Compared to the first sequencing effort in 1997, today’s state of the art involves the generation of more than 200 million times more data.

It's a pretty awesome time for those of us exploring human evolution!


References

The problem of Lance retraction

Mon, 2013-03-18 14:46 -- John Hawks

Retraction Watch comments on a provocative case: Should a scientific paper that measured Lance Armstrong's exercise physiology during his Tour de France days now be retracted in light of revelations about his use of performance-enhancing substances? "Lance Armstrong in the scientific literature: A 'reconsideration'". The comment is prompted by an editorial in the Journal of Applied Physiology, which published the initial research [1].

Should Coyle’s paper therefore be retracted? We do not think so; the data are the data, free of author-related ethical concerns. His editorial seems to be the best solution, especially because there can be no definitive answer. How much of the subject’s performance was attributable to his genetics and training, compared to how much was contributed by possible doping, may never be known, but that does not constitute grounds for retraction.

Interesting just how often the paper has been cited in the years since its 2005 publication, although I'm not familiar enough with the physiology literature to judge.


References

Cynthia Kenyon profile

Sun, 2013-03-17 15:37 -- John Hawks

The Guardian has a profile interview with aging researcher Cynthia Kenyon: "Cynthia Kenyon: 'The idea that ageing was subject to control was completely unexpected'".

This finding built on her earlier research, but to the rest of the scientific community, "the idea that ageing was subject to control was completely unexpected," Kenyon says, before struggling to find the words to describe how she felt when she realised the magnitude of the discovery. "It was very profound because you look at these worms, and the normal worms are dying, and the worms in this other culture dish are young. And you think: 'Oh my God, they should be dead.' It was like finding something that shouldn't be. It makes your hair stand up." Then came a second realisation: "You just think, 'Wow. Maybe I could be that long-lived worm.'"

Kenyon's story is a great one, because it illustrates how a productive research path can depend on one serendipitous observation.

How mad scientists are made

Sat, 2013-03-16 19:32 -- John Hawks

Talking to my clones today during their St. Patrick's Day preparations:

Me: (skeptical) So you've filled your leprechaun trap with lots of food?

Lucy: Yeah, there's lots to eat in there.

Sadie: We don't want him to escape, but we can't really hold him in there, so we want him to decide to stay all night.

Lucy: Yes, he won't want to leave.

Me: So won't he need a potty?

Both: OOOOOH! WHAT A GREAT IDEA!

Sadie: I'm going to make an outhouse so he will go outside and then come back in to eat more!

Lucy: Mine is going to be an INSIDE toilet.

Sadie: Hey, we could collect his DNA!

Both: *laughing*

Sadie: Thanks, Daddy, you have the greatest ideas!

Lucy: Yes, you're brilliant, Daddy!

Sadie: (walks away with evil laugh) We're going to get leprechaun DNA!

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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.