LIFE

MAPPING THE NEANDERTHAL GENOME

[7.4.09]

 

When I started out in '84/'85, intent on studying the genomes of ancient civilizations, I was, as is often the case in this kind of situation, driven by delusions of grandeur. I thought that I would be able to easily study the ancient genomes. I dreamt of addressing questions in Egyptology. For example, how do historico-political events that we read about impact the population? When Alexander the Great comes to Egypt, what is the influence on the population? Is it just a political change? The Arab Conquest: does that mean that a large part of the population is replaced? Or is it mainly a cultural change? There's no way we can answer this question from historical records. But my dream was to address questions like this. Then, after some initial success, I realized the real limitations on what I wanted to do.

SVANTE PÄÄBO, the founder of the field of ancient DNA, is Director, Department of Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig. In 2007 Time Magazine named him one of the 100 Most Influential People in the World.

Svante Pääbo's Edge Bio Page


HOW TO PREVENT A PANDEMIC

[4.30.09]

 

My organization and its collaborators have recently set up virus monitoring stations in China, Laos, Madagascar, Malaysia and the Democratic Republic of Congo. Yet this is just a beginning. To establish a worldwide safety net, we would need to monitor thousands of people exposed to animals in dozens of sites around the world — not only hunters but also people working on farms and in animal markets. It is important that the American government make pandemic prevention a priority and devote more resources to expanding disease surveillance in people and in wild and domestic animal populations throughout the world.

 

NATHAN WOLFE is the Lorry Lokey Visiting Professor of Human Biology at Stanford University and directs the Global Viral Forecasting Initiative (www.gvfi.org). His research combines methods from molecular virology, ecology, evolutionary biology, and anthropology to study the biology of viral emergence.

Nathan Wolfe's Edge Bio Page

WAITING FOR THE FINAL PLAGUE

[1.30.09]

 

We should be and we can be doing a much better job to predict and prevent pandemics. But the really bold idea is that we could reach a point—and this is a distant point in the future—where we become so good at this that we really reach a point where we have the "final plague," and where we are really capable of catching so many of these things that new pandemics become an oddity. I think that is something that we should certainly have as an ideal.


 

Introduction

Nathan Wolfe trained at Harvard under Marc Hauser (where he was Hauser's first doctoral student) and Richard Wrangham. "I started working with Richard and thinking about self-medicating behavior of chimpanzees," he says. "Richard encouraged me to understand what the chimps may be treating, and so I starting thinking about what are the viruses, what are the microorganisms of chimps that they may be consuming plants in order to treat. Then I never really came back from that."

Subsequently he lived in Malaysia for three years and then in Africa for close to seven years. He describes himself as "a nice Jewish boy from suburban Detroit", which opens up an interesting line of research for Edge scientists, given that our other pandemics expert, Larry Brilliant, Executive Director of Google.org. and the man credited with eliminating smallpox, is also "a nice Jewish boy from suburban Detroit"."I'm sure it was some kind of rebellion," Wolfe said, "but I'm not sure what it was. My grandmother, for years, even when I became an assistant professor at Hopkins, said, "Will this let you go back and get an MD now, Nathan?" Something like that. I do come from that sort of family background, but they just figure it is working out okay. They certainly wish I would make a lot more money. But I told them you were going to help me with that. "

-JB

NATHAN WOLFE is the Lorry Lokey Visiting Professor of Human Biology at Stanford University and directs the Global Viral Forecasting Initiative (www.gvfi.org). His research combines methods from molecular virology, ecology, evolutionary biology, and anthropology to study the biology of viral emergence.

Nathan Wolfe's Edge Bio Page.

CHANGING LIFESTYLE CHANGES GENE EXPRESSION

[12.3.08]

These findings may capture people's imagination—so often, people think there is not much they can do, what I call genetic nihilism. But even if your mother and your father and your sister and brother and aunts and uncles all died from heart disease, it doesn't mean that you need to. It just means that you are more likely to be genetically predisposed. If you are willing to make big enough changes, there is no reason you need ever develop heart disease, except in relatively rare cases.

DEAN ORNISH is a clinical professor of medicine at UCSF and the founder and president of the non-profit Preventive Medicine and Research Institute in Sausalito. His most recent book is The Spectrum.

Dean Ornish's Edge Bio Page


[12:05 minutes]

CHANGING LIFESTYLE CHANGES GENE EXPRESSION

Topic: 

  • LIFE
http://vimeo.com/80904248

"These findings may capture people's imagination—so often, people think there is not much they can do, what I call genetic nihilism. But even if your mother and your father and your sister and brother and aunts and uncles all died from heart disease, it doesn't mean that you need to. It just means that you are more likely to be genetically predisposed. If you are willing to make big enough changes, there is no reason you need ever develop heart disease, except in relatively rare cases."

ANTS HAVE ALGORITHMS

Topic: 

  • LIFE
http://vimeo.com/80903758

"Another example that we've been investigating arehuge swarms of Mormon crickets. If you look at these swarms, all of the individuals are marching in the same direction, and it looks like cooperative behavior. Perhaps they have come to a collective decision to move from one place to another. We investigated this collective decision, and what really makes this system work in the case of the Mormon cricket is cannibalism."

ANTS HAVE ALGORITHMS

[3.11.08]

...we've been investigating...huge swarms of Mormon crickets. If you look at these swarms, all of the individuals are marching in the same direction, and it looks like cooperative behavior. Perhaps they have come to a collective decision to move from one place to another. We investigated this collective decision, and what really makes this system work in the case of the Mormon cricket is cannibalism.

IAIN COUZIN is Assistant Professor in the Department of Ecology and Evolutionary Biology at Princeton University. His research focuses on understanding collective behavior; how large-scale biological patterns result from the actions and interactions of the individual components of a system. He studies self-organized pattern formation in a wide range of biological systems, including ants, fish schools, bird flocks, locust/cricket swarms and human crowds.

Iain Couzin's Edge Bio Page

ENGINEERING BIOLOGY

[2.17.08]

ED. NOTE: A theme appears to be evolving, beginning with the Edge event "Life: what A Concept!" in August, proceeding to Munich at DLD (Hubert Burda's Digital, Life, Design ) in January, where Craig Venter, and Richard Dawkins held an Edge conversation, "Life" A Gene-Centric View". Both events were important, and newsworthy. Next, the following conversation, Engineering Biology", with Drew Endy, a young researcher who is defining the cutting edge of synthetic biology.

-JB


The only thing that hasn't been engineered are the living things, ourselves. Again, what's the consequence of doing that at scale? Biotechnology is 30 years old; it's a young adult. Most of the work is still to come, but how do we actually do it? Let's not talk about it, let's actually go do it, and then let's deal with the consequences in terms of how this is going to change ourselves, how the biosecurity framework needs to recognize that it's not going to be nation-state driven work necessarily, how an ownership sharing and innovation framework needs to be developed that moves beyond patent-based intellectual property and recognizes that the information defining the genetic material's going to be more important than the stuff itself and so you might transition away from patents to copyright and so on and so forth. 

DREW ENDY, is Assistant Professor of Biological Engineering at MIT, where he is working to enable the design and construction of large scale integrated biological systems, and to develop and improve general methods for representing cellular behavior.

Drew Endy's Edge Bio Page


ENGINEERING BIOLOGY

Topic: 

  • LIFE
http://vimeo.com/80903691

"The only thing that hasn't been engineered are the living things, ourselves. Again, what's the consequence of doing that at scale? Biotechnology is 30 years old; it's a young adult. Most of the work is still to come, but how do we actually do it?

LIFE: A GENE-CENTRIC VIEW

Edge @ DLD
[1.23.08]

LIFE: A GENE-CENTRIC VIEW
Craig Venter & Richard Dawkins: A Conversation in Munich
(Moderator: John Brockman) 

Richard Dawkins & J.Craig Venter

It's not everyday you have Richard Dawkins and Craig Venter on a stage talking for an hour about "Life: A Gene-Centric View". That it occured in Germany, where the culture has been resistant to open discussion of genetics, and at DLD, the Digital, Life, Design conference organized by Hubert Burda Media in Munich, a high-level event for the digital elite — the movers and shakers of the Internet — was particularly interesting. This event was a continuation of the Edge "Life: What a Concept!" meeting in August, 2008.

Edgeis pleased to report on the event: the complete one hour video; the verbatim transcript; a sampling of the press from event articles in Sueddeutsche Zeitung, Spiegel Online, and Stern.

Introduction

Thirty-two years ago, Richard Dawkins publishedThe Selfish Gene, one of the landmark books of the 20th Century. In it, he set forth the "gene's-eye" view of life.

"Individuals are not stable things," he wrote, "they are fleeting. Chromosomes too are shuffled into oblivion, like hands of cards soon after they are dealt. But the cards themselves survive the shuffling. The cards are the genes. The genes are not destroyed by crossing over, they merely change partners and march on. Of course they march on. That is their business. They are the replicators and we are their survival machines. When we have served our purpose, we are cast aside. But genes are the denizens of geological time: genes are forever."

"Notions like Selfish Genes, memes, and extended phenotypes are powerful and exciting," notes computer scientist W. Daniel Hillis. "They make me think differently. Unfortunately, I spend a lot of time arguing against people who have over interpreted these ideas. They're too easily misunderstood as explaining more than they do. So you see, this Dawkins is a dangerous guy. Like Marx. Or Darwin."

Part of Dawkins' danger is his emphasis on models derived from cybernetics and information theory, and that such models, when applied to our ideas of life, and in particular, human life, strike some otherwise intelligent people numb and dumb with fear and terror. According to psychologist Steven Pinker, "Dawkins's emphasis on the ethereal commodity called "information" in an age of biology dominated by the concrete molecular mechanisms is another courageous stance. There is no contradiction, of course, between a system being understood in terms of its information content and it being understood in terms of its material substrate. But when it comes down to the deepest understanding of what life is, how it works, and what forms it is likely to take elsewhere in the universe, Dawkins implies that it is abstract conceptions of information, computation, and feedback, and not nucleic acids, sugars, lipids, and proteins, that will lie at the root of the explanation."

Dawkins, an evolutionary biologist, is Charles Simonyi Professor For the Understanding of Science, Oxford University. His most recent book is the international bestseller,The God Delusion. (See Richard Dawkins's Edge Bio page)

Craig Venter, who decoded the human genome, is on the brink of creating the first artificial life form on Earth. "I have spent", he says, "the last fifteen years of his career doing, digitizing biology. That's what DNA sequencing has been about. I view biology as an analog world that DNA sequencing has taking into the digital world."

According to Venter (in his recent BBC Dimbleby Lecture "A DNA-Driven World"), "the future of life depends not only in our ability to understand and use DNA, but also, perhaps in creating new synthetic life forms, that is, life which is forged not by Darwinian evolution but created by human intelligence

"To some this may be troubling, but part of the problem we face with scientific advancement, is the fear of the unknown — fear that often leads to rejection...Science is a topic which can cause people to turn off their brains".

At the end of June, Venter announced the results of his lab's work on genome transplantation methods that allows for the transformation of one type of bacteria into another, dictated by the transplanted chromosome. In other words, one species becomes another. In talking to Edge about the research, Venter noted the following:

Now we know we can boot up a chromosome system. It doesn't matter if the DNA is chemically made in a cell or made in a test tube. Until this development, if you made a synthetic chromosome you had the question of what do you do with it. Replacing the chromosome with existing cells, if it works, seems the most effective to way to replace one already in an existing cell systems. We didn't know if it would work or not. Now we do. This is a major advance in the field of synthetic genomics. We now know we can create a synthetic organism. It's not a question of 'if', or 'how', but 'when', and in this regard, think weeks and months, not years.

Venter is Director, The J. Craig Venter Institute, and the author of the recently published autobiography, A Life Decoded: My Genome: My Life.(See Craig Venter's Edge Bio Page).

~~~

DLD, Europe's conference for the 21st century, took place January 20-22, 2008 at HVB Forum in Munich, Germany. DLD covers digital innovation, science and culture and brings together thought leaders from Europe, the Middle-East, America and Asia. The three-day event was chaired by Edge contributors publisher Hubert Burda (See "Hubert Burda — Germany's Agent of Change" on Edge) and investor Yossi Vardi and hosted by Stephanie Czerny and Marcel Reichart.

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