john hawks weblog

Elizabeth Pennisi reports from the Biology of Genomes conference at Cold Spring Harbor, New York: "More Genomes From Denisova Cave Show Mixing of Early Human Groups". The article describes a talk by Svante Pääbo about new results from Neandertal DNA, as well as new analyses of the Denisovan genome. It has lots of details for those interested in these topics, but the article is paywalled, so I can only share a little of it here:

From the detailed genomes of both Neandertals and Denisovans, Pääbo and Montgomery Slatkin of the University of California, Berkeley, estimated that 17% of the Denisovan DNA was from the local Neandertals. And the comparison revealed another surprise: Four percent of the Denisovan genome comes from yet another, more ancient, human—"something unknown," Pääbo reported. "Getting better coverage and more genomes, you can start to see the networks of interactions in a world long ago," says David Kingsley, an evolutionary biologist at Stanford University in Palo Alto, California.

With all the interbreeding, "it's more a network than a tree," points out Carles Lalueza-Fox, a paleogeneticist from the Institute of Evolutionary Biology in Barcelona, Spain. Pääbo hesitates to call Denisovans a distinct species, and the picture is getting more complicated with each new genome.

We have been finding some of this in our comparisons of the genomes also. These were not isolated groups of ancient people, and some of them were more similar to living people than others. It is just wonderful to have more and more DNA coming out -- although that makes it hard to think we won't learn something new from high-coverage data that will require us to re-run various comparisons. That's the cost of discovery!

Meanwhile, the article sheds light on two interesting contradictions in the Denisova data. The analysis of the high-coverage data last fall [1] noted that the pinky bone genome is consistent with a very small long-term effective size, because of its limited genetic variation ("Denisova at high coverage". These results included a "drastic decline in size" around the time the Denisovans were estimated to have separated their population from the ancestors of living sub-Saharan Africans.

That result was curious in comparison with the mtDNA evidence. The Denisovan mtDNA is substantially more divergent from living human and Neandertal mtDNA, with an estimated time for the last common ancestor of mtDNA among these groups a bit more than a million years ago. In the initial analysis of the Denisova genome, Reich and colleagues [2] pointed out that even a deep divergence might be consistent with a neutral population history in a single population. But a population of radically reduced size, with a substantially more recent common ancestry shared with Neandertals and other ancestors of living people? Seems odd.

Now, we may be learning that the Denisovan genome itself represents different ancestral groups -- not only a more ancient "something unknown" population, but substantially the local Neandertals. That kind of mixture is not the population history described by papers on the Denisova genome so far. And a third Denisovan mtDNA from one of the third molars at the site is substantially different from the other two, pointing to greater mtDNA diversity within the Denisovan population than now known from either Neandertals or living people.

What does it mean? I don't think there's a contradiction here in the data. What this shows is that the methods applied to the data have been too simplistic. The methods will come to a result, but that result may not fit the data as well as a population model with more complexity. Looking only at one kind of comparison -- as the Li and Durbin model applied to the Denisova genome by Meyer and colleagues last year [1] -- will probably not give a result that describes the true population history. We need to keep our minds open to more complex population histories that may be more consistent with other sources of data, including archaeological and fossil information.

References

On Thursday, the Philosophy department of San José State University released an open letter to Michael Sandel, instructor of a Harvard edX MOOC. I reacted to the letter in my post, "Lessons in social justice from MOOCs". I combined a statement of approval for the SJSU department's aims with some pointed disagreement about the logic behind their arguments.

Since that post, I have gotten questions from several people asking me to expand upon my comments. One of the faculty members in the SJSU philosophy department, Janet Stemwedel, is a friend and blogger, who herself pointed to her department's open letter: "My department and a MOOC". My own role at UW-Madison is broader than my development of the MOOC course ("Announcing my MOOC, Human Evolution: Past and Future"), I have also been involved in faculty discussions about the role of online education more generally. With this dual role, I wanted to take some time to detail how I believe MOOCs may fit within higher education and how faculty governance should react to technological innovations and funding challenges.

I have framed my comments as an open letter in reply to that from the SJSU philosophers (at the Chronicle of Higher Education, "An Open Letter to Professor Michael Sandel From the Philosophy Department at San Jose State U.".

My open letter

Let me reiterate that I support your department's position, and hope that you are successful in pressuring your administration to support your teaching mission more effectively. I take an active interest not only as a MOOC instructor but also because I am chair of the curriculum committee of my college. Our major issue this year has been the role of online learning in our programs and departments. These interests have made me examine the open letter very closely. While I agree with much of it, I disagree strongly with its premise and central claim that MOOC developers like me are endangering education. Your department's letter is not the first to spread this mischaracterization, but as an open letter to a MOOC instructor, it targets me directly. Having been miscast in the role of department-dismantler, I feel I must speak out.

I have been watching developments in California, where the discussion of MOOCs has focused so strongly on both economic and pedagogical issues. Like San José State, UW-Madison also has many online degree programs and blended courses, and a large fraction of our classroom-based courses use online elements. This is not at all new, and we emphasize serving our student community better by providing flexibilities and access to information that we cannot easily provide in the classroom. At UW-Madison, we are very cognizant of other UW institutions with different missions and student populations, including some very popular online degree programs. These now include a state-level initiative to establish a new "flex degree" that would provide an avenue for people to receive a degree by applying real-world experience. As in California, Wisconsin institutions are working to find the best way to serve our students and advance our mission in this changing landscape.

The best parts of the open letter emphasize your department's teaching strengths, service to your diverse student community, and importance of online innovations in your own teaching. You don't need to offer Sandel's MOOC, JusticeX, because you are doing a better job in your mission than his course could do. I share your department's concern that curricular changes be approved and directed by faculty, not administrators.

"Knee-jerk guild thinking"

But I think some other parts of the letter misfire. Critically, the letter neglects entirely the major contribution of faculty oversight to the accreditation process. The parts of the letter that address public versus private universities have many omissions, and are ultimately counter-productive by raising the specter of elitism. In reality, public universities, including some small public universities, have been among the earliest innovators of massive online courses. Also, by framing the issue around this Harvard edX course, the letter neglects the participation of the University of California in edX. Here you miss an opportunity to clarify your position. Would your department be just as resistant to a MOOC created with the use of California tax dollars? I suspect it would, just as I sense that many of the "well-funded" versus "poorly-funded" arguments are oblique references to the very specific UC versus CSU divide. Illuminating those issues more concretely would have strengthened the letter more than the hand-waving arguments about employers wanting job training instead of liberal education. In surveys of employers who actually hire our students, we find quite the opposite: Employers want college graduates to have the thinking and writing abilities instilled by a liberal education.

I disagree most strongly with the letter's final call to action:

"It is in a spirit of respect and collegiality that we are urging you, and all professors involved with the sale and promotion of edX-style courses, not to take away from students in public universities the opportunity for an education beyond mere jobs training. Professors who care about public education should not produce products that will replace professors, dismantle departments, and provide a diminished education for students in public universities."

That final paragraph, like the letter, is addressed to Sandel. As a result, it targets me and anyone who is creating open educational resources. Your department's letter urges me to stop creating my MOOC. It claims that my course "will replace professors, dismantle departments, and provide a diminished education for students in public universities."

I disagree.

This is knee-jerk guild thinking. It says that I should serve the interests of tenured professors at other institutions before I serve my own students, my discipline, or the public.

With its open letter, your department is promoting among the public a misconception that I and other MOOC instructors are destroying the value of a traditional education. My interpretation is not a misreading, it is an inevitable consequence of the department's decision to write an open letter addressed to the instructor of a MOOC. That's me.

Learning with a MOOC

I have obligations to the public, who provide me a job, facilities, funding, and paid for my training. I have obligations to my own teachers, who generously shared their time and wisdom far beyond the strict requirements of any mere job. I have obligations to my department and to my university, to advance their missions and make the best use of their resources. I have an obligation to my students, to make the most effective use of my training and technology to involve them in the forefront of learning, including the research in my discipline. If I followed the call to action in the open letter, I would be cheating all these people.

My MOOC course will incorporate footage and interviews from the field, graduate student field journals, and some massive participatory science that involves students directly in research. This investment will yield many beneficial effects: My classroom courses will use some of the material in a blended format, some materials will plug into the new K-12 Next Generation Science Standards, we will publish and share research on the MOOC itself, and those insights will help improve existing courses and develop new courses for our UW-Madison students, including in my own department. This is a really good investment of our resources. It serves our own students and the public of Wisconsin, our research mission, and an international audience who may lack the resources to attend any institution of higher education.

Neither I nor anyone else is imagining that another institution will take my MOOC, clap on a teaching assistant, and charge students tuition to take it. I personally think such a plan would cheat students by charging them for learning they could do for free.

Still, I can imagine other scenarios that I would heartily encourage. For example, an instructor who is conducting field research for five weeks during the regular semester, might use five weeks of my MOOC as instructional materials during that time, supervised by a local TA. That would allow the instructor to bring more research experiences into the classroom, and probably would allow that instructor to provide deeper coverage of some topics where my resources are strong. The materials will be open, and I want other professors to use them to improve their students' experiences and their own opportunities. The flexibility of the open approach makes such uses possible, yet necessarily creates the risk that an institution will attempt to capitalize on the content by charging students for a credential in exchange for minimal additional instruction. If the alternative is that students at a small institution have no ability to integrate the subject of human evolution into their degree program, I wonder if this "risk" is a bug or a feature.

The problem of the pre-packaged course

Your department's open letter is focused on the use of "pre-packaged courses", because of the particular situation your department faces. Although I agree with your department's position, I note that this problem is neither new nor limited to MOOCs. The same problem has most notably been associated with textbooks. An instructor that adopts a commercial textbook may now be offered a package that include online lectures, quizzes, exercises, Powerpoint presentations, and study forums. These resources are neither open nor gratis. The costs are directly borne by students, through high textbook prices, which they pay over and above any tuition and fees. A department that adopts a mandatory textbook for its introductory course is essentially requiring its students to subsidize a "pre-packaged course", supervised by a local instructor, who may or may not be a professor with expertise in the subject. I do not have a general attitude about whether a MOOC should fit a similar role as textbooks for professors who are not content experts. But I do believe we are better off having more free and open high-quality learning resources, and that any learning resources should be used in for-credit courses only with faculty oversight.

At UW-Madison we have discussed this issue extensively as part of our discussions about online learning. Neither my college nor university advocate a one-size-fits-all approach to this question, as we leave the judgment about course materials to departments and faculty with oversight from cross-department faculty committees. Many commenters on the MOOC phenomenon fail to note the extensive history of using non-classroom experiences within college degree programs. We already accept transfer credit from a wide range of institutions, under long-standing higher education agreements, which include online and distance courses. We provide ways for students to receive academic credit for examinations (such as the AP tests), and we facilitate students carrying out academic projects in conjunction with service learning, internships, and field experiences. Whether or not we eventually accept MOOCs for credit, they will have to follow the same governance and oversight structures as these other long-established mechanisms.

Intrinsic to that oversight process is an unhindered ability of faculty to say, "no." Again, I applaud your department for making its pedagogical decision clear, based on the needs of SJSU students and the broader learning community. Your department is showing that the system works, a demonstration more important than the specifics of this single case. I hope that your administrators hear your message clearly.

Still, I hope the next department to say, "no", can find a way to do so without asking innovators to stop.