Science / Engineering / Mathematics

Education Uncubed

Mon, 11/02/2015 to Wed, 11/04/2015


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Journal article speculates that Crick and Watson would have difficulty today publishing findings on DNA

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Article speculates that their landmark work on DNA, if evaluated by today's standards, might not have found a journal.

Microbiologists show it's possible to achieve gender equity in scholarly presentations

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American Society for Microbiology shows that a scientific group with relatively few female speakers can change things dramatically in just a few years.

Review of Beth Shapiro, "How to Clone a Mammoth: The Science of De-Extinction"

So it turns out that -- title notwithstanding -- Beth Shapiro’s How to Clone a Mammoth: The Science of De-Extinction (Princeton University Press) is not a do-it-yourself manual. What’s more, cloned mammoths are, in the author’s considered opinion, impossible. Likewise, alas, with regard to the dodo.

But How Not to Clone a Dodo would never cut it in the marketplace. Besides, the de-extinction of either creature seems possible (and in case of the mammoth, reasonably probable) in the not-too-distant future. The process involved won’t be cloning, per se, but rather one of a variety of forms of bioengineering that Shapiro -- an associate professor of ecology and evolutionary biology at the University of California at Santa Cruz -- explains in moderate detail, and in an amiable manner.

Her approach is to present a step-by-step guide to how an extinct creature could be restored to life given the current state of scientific knowledge and the available (or plausibly foreseeable) advances in technology. There are obstacles. Removing some of them is, by Shapiro’s account, a matter of time and of funding. Whether or not the power to de-exterminate a species is worth pursuing is a question with many parts: ethical and economic, of course, but also ecological. And it grows a little less hypothetical all the time. De-extinction is on the way. (The author allows that the whole topic is hard on the English language, but “resurrection” would probably cause more trouble than it’s worth.)

The subject tickles the public’s curiosity and stirs up powerful emotions. Shapiro says she has received her share of fan and hate mail over the years, including someone’s expressed wish that she be devoured by a flesh-eating mammal of her own making. Perhaps the calmest way into the discussion is by considering why reviving the mammoth or the dodo is possible, but would not be the same thing as cloning one. (And dinosaur cloning is also right out, just to make that part clear without further delay.)

To clone something, in short, requires genetic material from a living cell with an intact genome. “No such cell has ever been recovered from remains of extinct species recovered from the frozen tundra,” writes Shapiro, whose research has involved the search for mammoth remains in Siberia. Flash freezing can preserve the gross anatomy of a mammoth for thousands of years, but nucleases -- the enzymes that fight off pathogens when a cell is alive -- begin breaking down DNA as soon as the cell dies.

What can be recovered, then, is paleogenetic material at some level of dismantling. The challenge is to reconstruct an approximation of the extinct creature’s original genome -- or rather, to integrate the fragments into larger fragments, since rebuilding the whole genetic structure through cut-and-paste efforts is too complex and uncertain a task. The reconstituted strings of genetic data can then be “inserted” at suitable places in the genome of a related creature from our own era. In the case of the woolly mammoth, that would mean genetic material from the Asian elephant; they parted ways on the evolutionary tree a mere 2.5 million years ago. In principle, at least, something similar could be done using DNA from the taxidermy-preserved dodo birds in various collections around the world, punched into the pigeon genome.

“Key to the success of genome editing,” writes Shapiro, “has been the discovery and development of different types of programmable molecular scissors. Programmability allows specificity, which means we can make the cuts we want to make where we want to make them, and we can avoid making cuts that kill the cell.”

Cells containing the retrofitted genome could then be used to spawn a “new” creature that reproduces aspects of the extinct one -- pending the solution of various technical obstacles. For that matter, scraping together enough raw material from millennia past presents its own problems: “In order to recover DNA from specimens that have very little preserved DNA in them, one needs a very sensitive and powerful method for recovering the DNA. But the more sensitive and powerful method is, the more likely it is to produce spurious results.”

Also a factor is the problem of contamination, whether found in the sample (DNA from long-dead mold and bacteria) or brought into the lab in spite of all precautions. Shapiro leaves the reader aware of both the huge barriers to be overcome before some species is brought back from extinction and the strides being made in that direction. She predicts the successful laboratory creation of mammoth cells, if not of viable embryos, within the next few years.

It will be hailed as the cloning of an extinct animal -- headlines that Shapiro (whose experiences with the media do not sound especially happy) regards as wrong but inevitable. The reader comes to suspect one motive for writing the book was to encourage reporters to ask her informed questions when that news breaks, as opposed to trying to get her to speculate about the dangers of Tyrannosaurus rex 2.0.

Besides its explanations of the genetics and technology involved, How to Clone a Mammoth insists on the need to think about what de-extinction would mean for the environment. Returning the closest bioengineerable approximation of a long-lost species to the landscape it once inhabited will not necessarily mean a happy reunion. The niche that animal occupied in the ecosystem might no longer exist. Indeed, the ecosystem could have developed in ways that doom the creature to re-extinction.

Shapiro is dismissive of the idea that being able to revive a species would make us careless about biodiversity (or more careless, perhaps), and she comes close to suggesting that de-extinction techniques will be necessary for preserving existing species. But those things are by no means incompatible. The author herself admits that some species are more charismatic than others: we're more likely to see the passenger pigeon revived than, say, desert rats, even though the latter play an ecological role. The argument may prove harder to take for the humbler species once members of Congress decide to freeze-dry them for eventual relaunching, should that prove necessary.

By now we should know better than to underestimate the human potential for creating a technology that goes from great promise to self-inflicted disaster in under one generation. My guess is that it will take about that long for the horrible consequences of the neo-dodo pet ownership craze of the late 2020s to makes themselves fully felt.

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Essay argues that public universities, not privates, are key to engineering education

A colleague at the University of Illinois at Urbana-Champaign (where I am dean of the College of Engineering) recently emailed me Bloomberg’s interview with Harry Lewis, interim dean of Harvard University's Paulson School of Engineering and Applied Science. Lewis talked about the school’s plans for the $400 million gift it received in early June. My colleague highlighted Lewis’ description of an ascendant engineering program at Harvard and a cultural shift at the school in which “making things, doing useful things is no longer … considered the sort of thing that gentlemen and gentlewomen don’t do.”

My colleague added, “Welcome, Harvard, to the work that public research universities with great engineering schools have been doing for 150 years.” Sarcasm, apparently, isn’t the exclusive province of the Ivies. We heard it all over the place after the announcement of the Paulson gift. But, in my opinion, it’s misguided.

I’ll paraphrase venture capitalist (and University of Illinois alum) Marc Andreessen’s tweet on the topic. This gift and Harvard’s vision for what it wants to accomplish are “moral virtues, full stop.”

Harvard has set the standard for the liberal arts and sciences. Public institutions like the Universities of Illinois, California at Berkeley, and Michigan have done the same for world-class engineering education for the masses. That combination is extremely powerful, and it has made America the most innovative and prosperous country in the world.

Lewis made it clear that Harvard intends to redefine what a well-rounded education means in the 21st century. And John Paulson's investment allows the university to develop an engineering and applied science program to match Harvard’s reputation.

Harvard and similar private research universities lack one major virtue, however: excellence at scale.

Private institutions simply cannot satisfy the demands of 21st-century engineering alone. And turning away top talent is in no one’s interest.

It limits our nation’s economic growth, our ability to make the engineering profession more diverse, and our ability to help students find their true calling regardless of their socioeconomic background. However, growth in student numbers and innovations in how we educate them require more resources.

Given this fact, and the fact that state funding for public universities has declined precipitously in the last two decades, philanthropic support has become just as important to Illinois as it is to the Harvards of the world. Without new levels of philanthropy and new investment models, the American public research university, the world's golden goose, will not be able to deliver on its goal to ensure there are enough top-flight problem solvers available to advance our civilization and to look after our future.

Consider some of the very best engineering universities in the world, public and private. According to U.S. News and World Report, the schools with the most top-five-ranked undergraduate engineering specialties are the University of California at Berkeley, Massachusetts Institute of Technology, Stanford University, the University of Illinois, Georgia Tech and the University of Michigan. Meanwhile, Illinois, Berkeley and the University of Texas at Austin rank right alongside Stanford and MIT in the top five of the Academic Ranking of World Universities in Engineering/Technology and Computer Science from Shanghai Jiao Tong University.

But here’s the difference: Illinois and Georgia Tech each produce more world-class undergraduate engineers than Stanford, MIT and Caltech combined. And Berkeley, Michigan and Texas are each twice the size of Stanford.

Undergraduate Engineering Degrees Awarded, 2014

University Undergraduate Engineering Degrees
Georgia Tech 1,977
U of Illinois 1,782
U of Michigan 1,492
U of California at Berkeley 1,195
U of Texas at Austin 1,140
MIT 675
Stanford 545
California Institute of Technology 104

That isn’t to say that elite and exclusionary is still a universal condition at Harvard and other small, private institutions. As Lewis points out, Harvard’s demographics are changing with more rural and first-generation students. Students from these backgrounds tend to gravitate to engineering because it leads to a secure career. An engineering degree is rarely an opportunity to go into the family business. Instead, it’s a way for those from low-income backgrounds -- bright, marginalized and ambitious -- to invent the family business.

Thus, the art of engineering appeals to an ever-broader swath of students, from those interested in entrepreneurship to those creating solutions for the engineering challenges that underpin the modern world. For example, more than 3,100 students applied for about 200 slots in the Illinois computer science program this year. Carnegie Mellon receives twice that many applications for about 30 percent fewer seats.

With demand like that, we are all in an unparalleled position to serve a broad spectrum of students in ways we haven’t before. That’s not only a moral virtue for Harvard. It’s a moral virtue for all of us.

Students are driven by a desire to solve problems with real and lasting societal impact. Today, “making and doing” extend far beyond the disciplinary confines of engineering and the fine arts. With the Paulson gift, Harvard is in a unique position to bring down disciplinary boundaries, to inspire new curricula and experiential learning, and to transform the very concept of a university education.

I have no doubt that Harvard’s engineering and applied sciences program will catalyze such a transformational change. But will all that effort and all those resources transform Harvard’s educational model or the world’s?

Harvard has to take full advantage of this incredible opportunity, and so do the engineering powerhouses. Globally, more and more students recognize the sheer impact they can have by studying engineering. How do we support and serve them?

Even more students seek an education founded on disciplinary depth and enriched through cross-disciplinary experiences. How do we embrace their interests and turn them into the idea creators, the problem solvers and the makers of the new and the better?

How do we inspire them and empower them as they put ever more pervasive digital technology and ever more important engineering principles to work? What does that well-rounded and well-educated student of the 21st century look like?

These are questions for us to answer together, taking full advantage of our variety and our diverse strengths.

So welcome, Harvard, to the conversation.

Andreas Cangellaris is dean of the University of Illinois at Urbana-Champaign’s College of Engineering and the M. E. Van Valkenburg Professor of Electrical and Computer Engineering.

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2016 2nd International Conference on Knowledge Engineering

Mon, 01/04/2016 to Wed, 01/06/2016


Los Angeles
United States

Essay on how new Ph.D.s can ace informal interviews


There may not be an opening, but there is opportunity, and you always need a strategy, writes Stephanie K. Eberle.

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New data show countries gaining and losing in European research competition

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Scientists based in Britain win more grants than those of other countries. But Belgium, Germany, Israel and Switzerland have some boasting rights as well.


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