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Edge 318 — May 20, 2010 ON "CREATION OF A BACTERIAL CELL CONTROLLED BY A CHEMICALLY SYNTHESIZED GENOME" BY VENTER ET AL" Comments by Freeman Dyson, Kevin Kelly, George Dyson |
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ON "CREATION OF A BACTERIAL CELL CONTROLLED BY A CHEMICALLY SYNTHESIZED GENOME" BY VENTER ET AL" Freeman Dyson, Kevin Kelly, George Dyson Introduction On May 20th, J. Craig Venter and his team at J.C Venter Institute announced the creation of a cell controlled by a synthetic genome in a paper published in SCIENCE. As science historian George Dyson points out, "from the point of view of technology, a code generated within a digital computer is now self-replicating as the genome of a line of living cells. From the point of view of biology, a code generated by a living organism has been translated into a digital representation for replication, editing, and transmission to other cells." This new development is all about operating on a large scale. "Reading the genetic code of a wide range of species," the paper says, "has increased exponentially from these early studies. Our ability to rapidly digitize genomic information has increased by more than eight orders of magnitude over the past 25 years." This is a big scaling up in our technological abilities. Physicist Freeman Dyson, commenting on the paper, notes that "the sequencing and synthesizing of DNA give us all the tools we need to create new forms of life." But it remains to be seen how it will serve in practice. One question is whether or not a DNA sequence alone is enough to generate a living creature. One way of reading the paper suggests this doesn't seem to be the case because of the use of old microplasma cells into which the DNA was inserted — that this is not about "creating" life" since the new life requires an existing living recipient cell. If this is the case, what is the chance of producing something de novo? The paper might appear to be about a somewhat banal technological feat. The new techniques build on existing capabilities. What else is being added, what is qualitatively new? While it is correct to say that the individual cell was not created, a new line of cells (dare one say species?) was generated. This is new life that is self-propagating, i.e. "the cells with only the synthetic genome are self replicating and capable of logarithmic growth." The paper concludes with the following:
Will the new techniques described in the paper allow us to bring extinct species back to life? Here are three examples — three possible stages after the production of a bacterial cell: 1. generating a human, i.e. a Neanderthal; 2. generating a woolly mammoth; 3. generating a tasmanian wolf. Generating a Neanderthal, giving the recent mapping, seems to be feasible, but it will raise ethical hackles. Don't hold your breath waiting for someone to try it Generating a woolly mammoth will not be an ethical problem but it also seems feasible by using an elephant's placenta: inject mammoth DNA into a modern elephant egg from which elephant DNA has been removed, then import the elephant egg into an elephant. A real challenge will be to generate a truly extinct species such as a Tasmanian wolf for which no host cells exist. What does this mean? We don't know yet, and we may not know for years. For now, all we can do is speculate responsibly. As Freeman Dyson notes:
Life goes on ... but it won't be the same. To provide context, we have put together a retrospective of Edge events, transcripts, videos featuring the pioneers in this area who are among the key players in what we are calling "A New Age of Wonder" [click here] The Edge Reality Club discussion on the paper, "Creation Of A Bacterial Cell Controlled By A Chemically Synthesized Genome," is below. |
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FREEMAN
DYSON This paper reminds me of a saying that is well-known to pure mathematicians: "Every big discovery starts with a bad proof'". This is true in mathematics. The first proof in a new subject is bad, because the discoverer is a first-rate mathematician, struggling to overcome one obstacle after another and not caring about elegance. Afterwards, second-rate mathematicians tidy up the details and find good proofs. I think the same saying holds good in science if you replace "proof'" by "experiment". This experiment, putting together a living bacterium from synthetic components, is clumsy, tedious, unoriginal. From the point of view of aesthetic and intellectual elegance, it is a bad experiment. But it is nevertheless a big discovery. It opens the way to the new world of synthetic biology. It proves that sequencing and synthesizing DNA give us all the tools we need to create new forms of life. After this, the tools will be improved and simplified, and synthesis of new creatures will become quicker and cheaper. Nobody can predict the new discoveries and surprises that the new technology will bring. I feel sure of only one conclusion. The ability to design and create new forms of life marks a turning-point in the history of our species and our planet. |
KEVIN KELLY The major effect of this paper will be to force a redefinition of life, since we declare that nothing we manufacture can be life. |
GEORGE
DYSON There are two ways of looking at this experiment. From the point of view of technology, a code generated within a digital computer is now self-replicating as the genome of a line of living cells. From the point of view of biology, a code generated by a living organism has been translated into a digital representation for replication, editing, and transmission to other cells. In 1953, when the structure of DNA was determined, there were 53 kilobytes of high-speed electronic storage on planet earth. Two entirely separate forms of code were set on a collision course. Primitive as it may be, we now have one of the long-awaited results. |
In the summer of 2009, in a talk at the Bristol (UK) Festival of Ideas, physicist Freeman Dyson articulated a vision for the future. He referenced The Age Of Wonder, by Richard Holmes, in which the first Romantic Age described by Holmes was centered on chemistry and poetry, while Dyson pointed out that this new age is dominated by computational biology. Its leaders, he noted, include "biology wizards" Kary Mullis, Craig Venter, medical engineer Dean Kamen; and "computer wizards" Larry Page and Sergey Brin, and Charles Simonyi. He pointed out that the nexus for this intellectual activity — the Lunar Society for the 21st century — is centered around the activities of Edge. Dyson continued to articulate his vision for a new age of biology in a related article ("When Science & Poetry Were Friends") in New York Review of Books in which he wrote:
Indeed, he was one of the visionary scientists who was front and center in August 2007, at "Life: What a Concept", an Edge Special Event where he joined scientists Craig Venter, George Church, Robert Shapiro, Dimitar Sasselov, and Seth Lloyd. According to Sueddeutsche Zeitung, the event "was one of those memorable events that people in years to come will see as a crucial moment in history. After all, it's where the dawning of the age of biology was officially announced." As a follow up, the Edge Master Class 2009 featured a weekend course taught by the two leading genomic researchers in the world: George Church and Craig Venter. "A Short Course in Synthetic Genomics" for a small group of scientists, entrepreneurs, cultural impresarios and journalists that included architects of the some of the leading transformative companies of our time (Microsoft, Google, Facebook, PayPal). The proceedings of both events are available on Edge Video. Edge Is a Conversation The late Ernst Mayr, the distinguished biologist considered the "Darwin of the 20th Century" once remarked the "Edge is a conversation". One example of where this ongoing conversation takes place is the 2010 Edge Dinner celebrating "The New Age of Wonder". Among the guests were numberous individuals who are playing a significant role in the revolution envisioned by Freeman Dyson through their scientific research, enlightened philanthropy, and entrepreneurial initiative. They include Sergey Brin, George Church, Bill Gates, Dean Kamen, Kary Mullis, Larry Page, and Craig Venter. Edge is different from The Algonquin, The Apostles, The Bloomsbury Group, or The Club, but it offers the same quality of intellectual adventure. Closer resemblances are to The Invisible College and the Lunar Society of Birmingham. The early seventeenth-century Invisible College was a precursor to the Royal Society. Its members consisted of scientists such as Robert Boyle, John Wallis, and Robert Hooke. The Society's common theme was to acquire knowledge through experimental investigation. The nineteenth-century Lunar Society of Birmingham, an informal club of the leading cultural figures of the new industrial age — James Watt, Erasmus Darwin, Josiah Wedgewood, Joseph Priestly, and Benjamin Franklin. In a similar fashion, Edge gathers together those who are exploring the themes of the post-industrial age. Edge contributors are the pioneers in this "new age of wonder". We are pleaed to present some of the important conversations that have taken place in the last five years among the Edge contributors who can be considered the founders this "New Age of Wonder". This includes over 15 hours of video, complete transcripts, plus a 43,000-word downloadable PDF book, the complete transcription of the historic 2007 Life: What A Concept. Bookmark this page for updates to this ongoing conversation |
EAT ME BEFORE I EAT YOU! A NEW FOE FOR BAD BUGS
"Now we are starting to work with organisms that are more likely to appear in a hospital, like staph and influenza, and we have our sights on Clostridia difficile, Pneumococcus aeruginosa, Acetinobacter baumanii and an alarming number of other bacteria that are resistant to antibiotics. We are also working on influenza, which has a convenient little feature called M2e." ... |
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A
SHORT COURSE ON SYNTHETIC GENOMICS [7.30.09]
[George Dyson: From the Introduction] " On July 24, 2009, a small group of scientists, entrepreneurs, cultural impresarios and journalists that included architects of the some of the leading transformative companies of our time (Microsoft, Google, Facebook, PayPal), arrived at the Andaz Hotel on Sunset Boulevard in West Hollywood, to be offered a glimpse, guided by George Church and Craig Venter, of a future far stranger than Mr. Huxley had been able to imagine in 1948. "In this future — whose underpinnings, as Drs. Church and Venter demonstrated, are here already — life as we know it is transformed not by the error catastrophe of radiation damage to our genetic processes, but by the far greater upheaval caused by discovering how to read genetic sequences directly into computers, where the code can be replicated exactly, manipulated freely, and translated back into living organisms by writing the other way. "We can program these cells as if they were an extension of the computer," George Church announced, and proceeded to explain just how much progress has already been made. ..." The entire Master Class is available in high quality HD Edge Video (about 6 hours). The Edge Master Class 2009 advanced the themes and ideas presented in the historic Edge meeting "Life: What A Concept!". |
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. ..." |
ENGINEERING
BIOLOGY [2.12.08]
"The only thing that hasn't been engineered are the living things, ourselves. 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 ." ... |
LIFE:
A GENE-CENTRIC VIEW [1.23.08]
"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". — J. Craig Venter |
A DNA-DRIVEN WORLD: The 32nd Richard Dimbleby Lecture [12.6.07] "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. I contend that science has failed to excite more people for at least two reasons: it is frequently taught poorly, often as rote memorization of complex facts and data, and it is antithetical to our visceral-driven way we live and interact with our world." ... |
LIFE:
WHAT A CONCEPT! [9.4.07]
"The essential idea is that you separate metabolism from replication. We know modern life has both metabolism and replication, but they're carried out by separate groups of molecules. My version of the origin of life is that it started with metabolism only."
"I have come to think of life in much more a gene-centric view than even a genome-centric view, although it kind of oscillates. And when we talk about the transplant work, genome-centric becomes more important than gene-centric. From the first third of the Sorcerer II expedition we discovered roughly 6 million new genes that has doubled the number in the public databases when we put them in a few months ago, and in 2008 we are likely to double that entire number again. We're just at the tip of the iceberg of what the divergence is on this planet. We are in a linear phase of gene discovery maybe in a linear phase of unique biological entities if you call those species, discovery, and I think eventually we can have databases that represent the gene repertoire of our planet. "One question is, can we extrapolate back from this data set to describe the most recent common ancestor. I don't necessarily buy that there is a single ancestor. It’s counterintuitive to me. I think we may have thousands of recent common ancestors and they are not necessarily so common." ...
"Many of the people here worry about what life is, but maybe in a slightly more general way, not just ribosomes, but inorganic life. Would we know it if we saw it? It's important as we go and discover other worlds, as we start creating more complicated robots, and so forth, to know, where do we draw the line?"
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CONSTRUCTIVE
BIOLOGY [6.26.06] "As creative as we become, and as industrious and as good as we are at designing and manufacturing living things, which we've been doing since the stone age — no matter how good we get at that, it's like calling a candle a supernova. A candle is not a super nova; it's not even in the same league. And we, as intelligent designers, are not in the same league as the "Intelligent Designer" that designed the whole shebang. We're not designing sub-atomic particles from scratch; we're not designing the Big Bang. We're really not even designing life; we're just manipulating it." ... |
CHANGING
ONE SPECIES TO ANOTHER [6.30.07] 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." ... |
BIOCOMPUTATION [6.29.05]
"Trying to understand the basic components of a cell, we've tried knocking out genes, and trying to see what gene cells could live without, but we get different answers every time the experiment's done, depending on how it's done, whether it's a batch growth, or you require cloning out of the cells, different growth requirements. We decided some time ago the only way to approach this was to build an artificial chromosome and be able to do evolution in the laboratory the way it happens in the environment." ... |
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UN PROVERBIO HA TENUTO TUTTA L'UROPA A TERRA John Brockman is a "cultural entrepreneur, publisher, writer, and creator, among other things, the Edge Foundation, a laboratory of ideas and debates where, in my opinion, is being formed in the" Third Culture "which should become "the culture of the twenty-first century.
Many of the answers, very interesting. Summarize them all is impossible. To Haim Harari, a physicist and former president Ezer Weizman Institute in Tel Aviv, the current financial crisis and the crisis "dust" have much in common. Both are daughters of decisions taken by decision makers "do not understand math and science even at the elementary level" and "mathematicians and scientists who do not make no account of the consequences in real life, their calculations. So here is that "financial engineers" create complex financial instruments and navigated bankers and regulators implementing them, without admitting to not have the slightest idea of what these tools require. Similarly, manufacturers of mathematical models convince the authorities that "the cloud here or there, without the slightest worry of going for a far field." And no wonder, these "scientists" if the assumptions form the basis of their models are realistic or not. In both cases, anyone with a minimum of scientific, Harari added, immediately feel the smell test. And so here because without political scientific culture and scientists without managerial culture, are unable to adequately address both problems. Conclusion: "The World is That discovering an important profession is missing: Scientifically trained political decision makers. ... [continue Italian original ... Google translation] |
Having suffered from the closure of European airspace due to volcanic dust cloud, posted on the site www.edge.org some provocative questions. What psychologists are saying about the way decisions were made that have grounded million passengers, confined in makeshift camps for more than a week, in apparent total lack of evidence of real danger? What have economists learned behavior? And what they are saying engineers, physicists, meteorologists on? CRITICIZING THE CRITICS YOU ARE THE STRANGE SUMMIT
[BEYOND EDGE: For more on the work of Katinka Matson, Edge's artist-in-residence, click here] |
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HAKU MO'OLELO The testimony to Congress was on causes of political violence, the factors that lead young Muslims to join radical Islamist groups. But the observations appeared to apply to other sociopathic, violence-prone packs - criminal gangs and ideological militants. Scott Atran, a cognitive anthropologist and risk-modeling researcher, was testifying to the U.S. Senate Armed Services Subcommittee on Emerging Threats & Capabilities, invited to speak on his research on "pathways to and from violent extremism" (www.edge.org/3rd_culture/atran10/atran10_index.html/). Author of "In Gods We Trust: The Evolutionary Landscape of Religion," Atran has studied political violence among groups in the Middle East. His analysis of factors promoting jihadism mirrors the issues spawning criminal gangs. Atran says his research shows most young people successfully recruited by radical jihadists were from moderate secular backgrounds. They were recruited to radical religious militancy from outside, not within. ... |
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NATURALLY SELECTED Sarah Greene ...Every generation of scientists must keep the enlightenment flame alive, and much has been written about whether those weaned on the Internet will cause that flame to flicker and dim or to burn more brightly. Yet 150 years ago, certainly pre-Internet, Thoreau had premonitions: I fear that the character of my knowledge is from year to year becoming more distinct and scientific; that, in exchange for vistas wide as heaven’s scope, I am being narrowed down to the field of the microscope. I see details, not wholes nor the shadow of the whole. I count some parts, and say, “I know.” Back to the future, in a stimulating debate on Edge.org, based on Nicholas Carr’s Atlantic Monthly article “Is Google Making Us Stupid” (Jul/Aug 2008), W. Danny Hillis opined: Our problem is not so much that we are stupider, but rather that the world is demanding that we become smarter. Forced to be broad, we sacrifice depth. We skim, we summarize, we skip the fine print and, all too often, we miss the fine point. |
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BIG THINKERS ON WHAT THE ASH CLOUD MEANS
Caught up in Moscow because of the volcanic ash cloud last week, my biggest regret was missing the annual Edge dinner in London on 19 April. Well, just look at the sort of people that Edge Foundation president, literary agent and superconnector John Brockman manages to bring together. Guests at last year's London dinner ranged from Alfonso Cuarón and Terry Gilliam to Brian Eno and Richard Dawkins. So you can see why it was painful for me to be 3,000km away while all the big ideas were being nurtured over the entrees at Zilli Fish. But Brockman -- whose latest book This Will Change Everything (Harper Perennial) lies well thumbed on my desk -- is not a man to waste an intellectual opportunity. In town from New York for the "eerily deserted" London International Book Fair, Brockman became caught up in talk of stranded travelers and 20-hour road trips. "Something is going on here that requires serious thinking," he reflected. "We've had earthquakes before, and we've had plane stoppages, but nothing like the continuing effects of the ash cloud. Why?" So he invited the Edge community of smart and original thinkers -- from behavioural economists to psychologists, physicists to software engineers -- to think about the ash cloud and the reaction to it, and tell him (in 250 words) something "that I don't already know and that I'm not going to read in the newspapers". The thinkers came through. Edge received contributions from the likes of Haim Harari, Roger Schank, Charles Simonyi, Peter Schwartz, Stephen Schneider, Karl Sabbagh, Emanuel Derman, Mark Pagel, Joel Gold, George Dyson, Matthew Ritchie, Paul Romer, Eduardo Salcedo-Albarán, Greg Paul, Lawrence Krauss and Alexandra Zukerman. You can now read their conclusions -- an exercise that's worth your while. ... |
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THE EDGE ANNUAL QUESTION BOOK SERIES "An intellectual treasure trove"
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Contributors include: RICHARD DAWKINS on cross-species breeding; IAN McEWAN on the remote frontiers of solar energy; FREEMAN DYSON on radiotelepathy; STEVEN PINKER on the perils and potential of direct-to-consumer genomics; SAM HARRIS on mind-reading technology; NASSIM NICHOLAS TALEB on the end of precise knowledge; CHRIS ANDERSON on how the Internet will revolutionize education; IRENE PEPPERBERG on unlocking the secrets of the brain; LISA RANDALL on the power of instantaneous information; BRIAN ENO on the battle between hope and fear; J. CRAIG VENTER on rewriting DNA; FRANK WILCZEK on mastering matter through quantum physics. "11 books you must read — Curl up with these reads on days when you just don't want to do anything else: 5. John Brockman's This Will Change Everything: Ideas That Will Shape the Future" (Forbes India) "Full of ideas wild (neurocosmetics, "resizing ourselves," "intuit[ing] in six dimensions") and more close-to-home ("Basketball and Science Camps," solar technology"), this volume offers dozens of ingenious ways to think about progress" (Publishers Weekly — Starred Review) "A stellar cast of intellectuals ... a stunning array of responses...Perfect for: anyone who wants to know what the big thinkers will be chewing on in 2010. " (New Scientist) "Pouring over these pages is like attending a dinner party where every guest is brilliant and captivating and only wants to speak with you—overwhelming, but an experience to savor." (Seed) |
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