“A Short Course On Synthetic Genomics”

LAWRENCE KRAUSS
Physicist, Director, Origins Initiative, ASU; Author, Hiding In The Mirror

What struck me was the incredible power that is developing in bioinformatics and genomics, which so resembles the evolution in computer software and hardware over the past 30 years.

George Church’s discussion of the acceleration of the Moore’s law doubling time for genetic sequencing rates,, for example, was extraordinary, from 1.5 efoldings to close to 10 efoldings per year. When both George and Craig independently described their versions of the structure of the minimal genome appropriate for biological functioning and reproduction, I came away with the certainty that artificial lifeforms will be created within the next few years, and that they offered great hope for biologically induced solutions to physical problems, like potentially buildup of greenhouse gases.

At the same time, I came away feeling that the biological threats that come with this emerging knowledge and power are far greater than I had previously imagined, and this issue should be seriously addressed, to the extent it is possible. But ultimately I also came away with a more sober realization of the incredible complexity of the systems being manipulated, and how far we are from actually developing any sort of comprehensive understanding of the fundamental molecular basis of complex life. The simple animation demonstrated at the molecular level for Gene expression and replication demonstrated that the knowledge necessary to fully understand and reproduce biochemical activity in cells is daunting.

Two other comments: (1) was intrigued by the fact that the human genome has not been fully sequenced, in spite of the hype, and (2) was amazed at the available phase space for new discovery, especially in forms of microbial life on this planet, as demonstrated by Craig in his voyage around the world, skimming the surface, literally, of the ocean, and of course elsewhere in the universe, as alluded to by George.

Finally, I also began to think that structures on larger than molecular levels may be the key ones to understand for such things as memory, which make the possibilities for copying biological systems seem less like science fiction to me. George Church and I had an interesting discussion about this which piqued my interest, and I intend to follow this up.






THE NEW YORK TIMES — TIERNEY LAB
August 3, 2009, 8:00 AM

Synthetic Life
By JOHN MARKOFF

There is a growing consensus (at least in Silicon Valley) that the information age is about to give way to the era of synthetic genetics. That was underscored recently when Harvard geneticist George Church and J. Craig Venter — of the race to decode the human genome fame — gave lectures before a small group of scientists, technologists, entrepreneurs, and writers in West Hollywood.

The event, billed as “A Short Course on Synthetic Genetics”, was organized by John Brockman, the literary impresario (and book agent for several New York Times reporters, including this one) who publishes the cybersalon-style website www.edge.org, a forum dedicated to scientists (many of whom are his clients) and their ideas.

In roughly six hours of lectures both scientists tried to convey how the world will be changed by the ability to routinely read genetic sequences into computing systems and then store, replicate, alter and insert them back into living cells.

The rate at which this technology is now improving puts silicon to shame. Dr. Church noted that between 1970 and 2005 gene sequencing had taken place on a Moore’s Law pace, improving at about 1.5 times per year. Since then it has improved at the rate of an order of magnitude, or ten times annually.

In the process the cost of sequencing the human genome has plunged from $3 billion to $5 thousand and continues to fall. Dr. Church identified 17 companies and one “open source” project all pursuing different technologies to further push down cost and speed up the pace of sequencing.

As a consequence, the structure of the emerging synthetic genetics industry is beginning to mirror that of the semiconductor and computer industries, which are based on modular components and design tools.

The key to the vast growth of the computer industry took place during the 1970s when physicist Carver Mead helped give the industry a standard design approach based on modular components. Now that appears to be happening in the synthetic biology world as well.

For someone who has spent the past three decades writing about computing, Dr. Venter’s talk was eye-opening.

“I view DNA as an analog information system,” he said. ” and I hope to convince you in fact that it is absolutely the software of life.”

http://luckybogey.wordpress.com/2009/08/08/life-evolution-genomics-and-clouds-from-outer-space/