Peter Donnelly is an expert in probability theory who applies statistical methods to genetic data -- spurring advances in disease treatment and insight on our evolution. He's also an expert on DNA analysis, and an advocate for sensible statistical analysis in the courtroom.
Why you should listen to him:
Peter Donnelly applies statistical methods to real-world problems, ranging from DNA analysis (for criminal trials), to the treatment of genetic disorders. A mathematician who collaborates with biologists, he specializes in applying probability and statistics to the field of genetics, in hopes of shedding light on evolutionary history and the structure of the human genome.
The Australian-born, Oxford-based mathematician is best known for his work in molecular evolution (tracing the roots of human existence to their earliest origins using the mutation rates of mitochondrial DNA). He studies genetic distributions in living populations to trace human evolutionary history -- an approach that informs research in evolutionary biology, as well as medical treatment for genetic disorders. Donnelly is a key player in the International HapMap Project, an ongoing international effort to model human genetic variation and pinpoint the genes responsible for specific aspects of health and disease; its implications for disease prevention and treatment are vast.
He's also a leading expert on DNA analysis and the use of forensic science in criminal trials; he’s an outspoken advocate for bringing sensible statistical analysis into the courtroom. Donnelly leads Oxford University's Mathematical Genetics Group, which conducts research in genetic modeling, human evolutionary history, and forensic DNA profiling.
"Donnelly is at the forefront of looking at the variation of genes within the human species to try and find out what is really relevant to disease. He has developed a fundamental framework for analyzing genome data that is leading to conclusions about human evolution, and even early human history."Scientific Computing World
Blog Posts on TED
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Archive: Peter Donnelly on how stats can fool us – August 7, 2008
For the next two weeks, we're presenting some of our favorite TEDTalks from among the 270+ talks and performances we've posted since June 2006. Look for brand-new TEDTalks starting August 18. Until then, enjoy these gems -- and suggest your own by writing to contact@ted.com or joining the conversation on TED.com.
In the TED tradition of rethinking statistics, Oxford mathematician Peter Donnelly talks about the common mistakes we make in interpreting numbers -- and the devastating impact these errors can have on the outcome of criminal trials. Viewers who've seen this talk have discussed the coin-toss experiment in depth (read the comments to find a simulation); and then there's this comment: "OMGosh how sexy is this man's brain?" (Recorded July 2005 in Oxford, UK. Duration: 21:32)
Watch Peter Donnelly's 2005 talk on TED.com, where you can download it, rate it, comment on it and find other talks and performances.
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Reading the books of Craig and Jim – September 12, 2007
A few days ago TED2005 speaker Craig Venter (watch his talk) announced that his lab has finished sequencing a single human's genome -- his own. At his old company, Celera, Venter worked on sequencing his genome and four other genomes all mixed together, creating an anonymous composite. He told Newsweek:
What we got this time was a diploid genome—a genome that includes both sets of chromosomes from both my parents. We were surprised at how much variation between individuals there was.
You mean there's more genetic difference between one person and the next than we previously thought?
Absolutely. It's quite comforting to me as an individualist that we're not very close to being clones of one other. (...)
Why did you choose to decode your own genome?
It goes back to the government's notion that genetics has to be secret and anonymous. But there's really nothing anonymous with your genetic sequence—it's the ultimate identifier. I thought it was showing proper leadership—to show that I don't think there's any risk in it. I don't know if there's any scientist in this field that wouldn't want to have his own genome known.
(Read the full interview)Nobel laureate (for co-discovering the double-helix structure of DNA), and fellow TED2005 speaker (watch his talk), James Watson couldn't probably agree more: he also had his genome fully sequenced three months ago. "Project Jim", as it was called, took 67 days of sequencing time and cost around USD 1 million. (More in this Newsweek story from June.) The raw sequencing data of both Watson and Venter are publicly available in the US National Center for Biotechnology Information's Trace Archive.
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TED2008: What is life? – February 28, 2008
(Unedited running notes from the TED2008 conference in Monterey, California. Third session.)
Alisa Miller, head of Public Radio International, introduces the session with a 3-minutes talk on how America perceives the rest of the world and how the news shape the way the US sees the world. She pulls up a map of the number of minutes that American TV networks dedicated to news in January: there is basically only the US, Iraq, Saudi Arabia, Brazil and China. "The news networks have reduced the number of their foreign bureaus by half. Covering Britney Spears is cheaper. We can do better, and we cannot afford not to do so".
Inventor-collector Jay Walker presents some of the items displayed on stage from his private library: one of the remaining original seven Sputnik satellites; a Gutenberg Bible (picture right); a small flag that was carried to the Moon and back by the Apollo astronauts; etc. Needless to say, he's been asked by hundreds of TEDsters yesterday Craig Venter, the scientist who first sequenced the human genome in 2001, announced recently that with his team they have created the first synthetic bacterium -- "the largest man-made DNA structure" (photo below) -- along the way to create microorganisms that can produce alternative sources of enegy. Needless to say, his research is controversial.
"We've been digitizing biology, and now we're trying to go from that code to designing biology. We've tried various approaches, paring it down to basic components, digitizing it, now we're trying to ask: can we regenerate life or create new life out of this digital universe? The pace of digitizing life has been increasing exponentially. Our ability to write genetic code has been growing more slowly. Turns out synthesizing DNA is difficult. In a biological system the software builds its own hardware, but design is critical, and if you start with digital information, it has to be really accurate. How do we boot-up a synthetic chromosome? We can do a transplant of a chromosome from one cell to another and activate it. We may be about to create a new version of the Cambrian explosion, where there is massive new speciation (the formation of new and distinct species) based on this digital design. We have now a database with about 20 million genes, and we like to think of them as the design component of the life of the future. We now have techniques to do combinatorial genomics, to build a robot that can make a million chromosomes a day.
We're now focusing on fourth-generation designer fuels. Curent biofuels aren't the solution. The only way that biology can have an impact on fuel without incrising the price of food, it's to start with CO2 as the feed stock -- create new energy out of CO2, and we think we will have something within the next 18 months. Future uses of this technology: increase the basic understanding of life; replace the petro-chemical industry; become a major source of energy; enhance bioremediation. We're changing the evolutionary tree with new bacteria and species."
Follows a Q&A with Chris Anderson and with the audience:Question: With all the biodiversity out there, can't you use existing organisms rather than create new ones?
Craig Venter: We're indeed finding a lot of biodiversity. For example we found organisms in the environment that produce octane. But not on the scale that we need to cover our energy needs.
Q: Right now, is it possible on a computer to say what a
CV: We are using software to design pathways, metabolic mechanisms, so it's real biological design. We're trying to do it not only by trianl and error, but by direct design. Alot of people like to think in terms of Genesis and we're creating life from scratch. But we're really using the 3 million years of evolution, trying to take it over and take it to the next stage. We will see an increasing pace in the sophistication of the organisms.
Q: I could make the case that you and your company are the most dangerous humans on Earth. What do you do for security?
CV: It's a question that has been raised from the very beginning. Fortunately there aren't many people wanting to do harm with these tools. Very few biological agents that we work with could be weaponized.
Q: One of your slides says "suicide gene", what's that?
CV: It means that if it got out of the lab we could trigger the destruction of that organism.
Q: Can you talk about the intellectual property rights and how you fund your work?
CV: Institute has about 100 million dollars budget a year. About 70% from the government, the rest from private donation.
Q: How efficient can the photosynthesis of CO2 be?
CV: CO2 is a source of carbon. The photosynthesis we see with plants is not very efficient. Algaes are more efficient. We can engineer those to capture CO2 and instead of sequestrate it we think we can convert it back into energy.
Q: When you were asked if you were playing God, you said "we are not playing".
CV: I got very depressed being at Davos this year, it was clear that most of business executives there, buying into the CO2 issue is a pain for them, I had the impression that nothing's gonna change in the next 40 years because of entrenched interests. We're running a hell of an experiment on this planet, we need real solutions, I hope that some of these developments yield results in time, the urgency is not really there.Paul Rothemund presented some of his work at TED last year, showing nanometer-size artwork created using strands of DNA and folding them into desired shapes.
"People argue about the definition of life. Life involves computation. Take a computer program, boot it up in a cell and it will result in a person; with a small change it will result in another person, etc. There are lots of similarities between genetic programs and computer programs, including a sensitivity to small changes -- single mutations -- that result in "meaningful" large changes. Biology demonstrates the power of molecular programming. We use DNA and proteins. How small is the smallest organism that will function? How few molecules?"
Paul's approach, he calls it "DNA origami": folding DNA using long single strands of DNA and combining them with other helixes. He shows how he created smily patterns, the shape of China, all by folding DNA strands. Then he discusses an approach -- "tiles" -- to make something much bigger.Preventive medicine advocte Dean Ornish gives a short talk on recent research that shows how adopting healthy lifestyle and eating habits can affect a person at a genetic level.
"One way to change our genes is to make new ones, as Venter does The other is to change our lifestyle. When you live healthier, eat better, exercise, and love more, your brain cells actually increase. Your skin and heart and sexual organs get better blood flow. We're about to release new findings that healthier lifestyle can turn off disease-provoking genes and turn on the good ones. Our genes are not our fate. They are predispositions, but if we make these lifestyle changes we can actually change how genes are expressed."The work of British psychologist Susan Blackmore focuses on the nature of consciousness and on memes. She took Richard Dawkins intuition about memes (ideas that, like genes, that take a life of their own) and turned it into a fully-fledged theory.
"Cultural evolution is a dangerous child for every species to let loose on this planet. By the time you realize what's happening, it's too late to put it back into the box. We humans are the Earth's Pandoran species. Mimetics is founded on the principles of unversal Darwinism. His idea was so simple, and yet it explains all design in the universe. What Darwin said was something like this: if you have creatures that vary, and if there is a struggle for life such that nearly all of these species die, and if the very few that survive pass on to their offsprings whatever helped them survive, than these offsprings must be better adapted to these circumstances than their parents were. You just need those three principles: variation, selection and heredity. If you have those, you MUST get evolution, or "design out of chaos without the aid of mind". What's this to do with memes? Darwin didn't know about genes, but the principle of universal Darwinism is that everything that's copied with variation and selection will evolve. Information that's copied from person to person is information copied with variation and selection. That's a meme. A meme is not an idea, is "that which is imitated", information which is copied from person to person. If you copied an information from someone else, it's a meme. But why do they spread? They are copied if they can. Some because they're true, useful, beautiful. Some even if they're not. Here is a curious meme: you go to your hotel, check into your room, go to the bathroom, and what do you see? A folded end of the toilet paper. It's a meme that spread all over the world. What is that about? it's supposed to tell you that somebody cleaned the place. Think of it this way: imagine a world full of brains and memes using them (you and me) to propagate. Why is this important? it gives us a completely new wiew of what it means to be human. All these things that make us unique -- language etc -- are based on genes. But there are two replicators now on this planet: from the moment our ancestors began imitating, there was a new replicator, the meme, alongside the gene. And you get an arms race between the genes (which want a smaller, efficient brain) and the memes (which want a bigger brain). All other species on this planet are gene machines, we only are meme machines. We need a new word for technological memes, let's call them temes, because the processes are different. Our brains are becoming like temes, faster, etc. We are at this cusp now to have a third replicator in our planet. But it's dangerous: temes are selfish replicators, they use us to suck up more resources to produce more computers and more things. Don't think we created the Internet, that's how it seems to us. How to pull through? Two ways: one is that the temes turn us into teme-machines, with implants, merging of humans and machines, because we are self-replicators. The other: teme-machines will replicate by themselves. In that case, it woudl not matter if the planet would no longer be liveable for humans."Christopher de Charms brielfy shows some video of real-time brain imaging. He's the CEO of Omneuron, which has developed a machine that scans brain activity and allows to watch it in real time -- "I've seen inside my brain, you will be able to do it soon. When you will, what will you like to do and control? We are the first generation that's gonna be able to enter into the human mind and brain".
Documentary filmmaker David Hoffman's studio burned down 9 days ago. He lost his archive, 100+ films, most of his work is gone. "But you need to take bad and make some good out of it. I called my friends, come dig, dig it up I said, I want pieces", and turned that into his next project, a life in bits and pieces.
Historian Doris Kearns Goodwin is a US presidential biographer -- she has written books on all the great acronyms that have occupied the Oval office (JFK, LBJ, FDR) and on Abraham Lincoln. She's hence an authority on looking at history through the leses of a single person's life. Her speech focuses on Lincoln and Lindon Johnson and on some lessons that we can draw from their life.
"Lincoln life suggests that ambition is a good thing. Not ambition for power or office, but for making the world a better place. Lincoln was a curious boy. His mother died when he was still young, telling him "am going away and won't return", which convinced him that when we die our life is swept away; but later he realized that if you accomplish something worthy, that outlives you. During a period of depression, he said "I would die, right now, but I haven't not yet done anything that would make any human being remember me" -- he would go on to sign the emancipated proclamation. Kearns says that when he was about to put his signature on the document, his hand was trembling because he had shaken thousands of hands that morning. So he put down the pen, waiting for his hand to be steadier, because he thought that, had he signed a trembling signature, future generations would think that he had hesitated."
"LBJ: I met him when I was selected as a White House fellow, then worked in the WH. He was a great storyteller, but there was a problem with his stories: half of them weren't true. ... Because he was so sad and vulnerable, he opened up with me. From the surface LBJ should have had everything in the world to feel good: president, money, owned a spacious ranch, boats, and he had a family who loved him deeply. Yet years of concentration solely on work and individual success means that in his retirement LBJ could find no solace. It was as if the hole in his heart was so large that without work he could not fill it. He regretted not having spent more time with his children and grandchildren. He was alone when he died. Even the sphere of love requires some form of commitment. So deep was Lincoln love of Shakespeare for instance that even in the most difficult times I went to the theatre."
