Salvation Through Genomics

November 16, 2008

Book Review
Philip J. Davis

A Life Decoded: My Genome: My Life. By J. Craig Venter, Viking Penguin, New York, 2007, 400 pages, $25.95.

A for adenine
C for cytosine
G for guanine
T for thymine.
The four combine
And intertwine
Are you a genomic case
On an assembly line?

A year ago my wife bought me a sweatshirt with the words "Travelling 33 RPM in an iPod world" printed on the front. If truth be told, 33 RPM is close to state of the art for me, as I grew up in the time of victrolas with hand cranks and large parabolic horns. This places me accurately along the time axis, and so if further truth be told, I am in a state of shock and awe when I consider the current turbulent world of reproductive technology (repro-tech) for both humans and the "lower" species. For a turbulent world it surely is, with technological advances announced all but daily, inducing or merging smoothly with radical changes in what was long considered standard societal behavior and operating practices. It is a world of contradictory ethical stances, with ecological, sociological, religious, and historically minded constituencies shouting "No, no, no, back off!" and their opponents crying "Yes, yes, yes, onward to the brave new worlds of genomics!" as perfected by J. Craig Venter and trumpeted in the book under review.

"Don't try to be more clever than nature" is the message of the former group. "But what is nature? People create the nature they seem to want and deserve," the latter group counters. In fact, we see quite clearly that we are all busy creating a nature whose features no one can really want. Ethics? Puh-leeze! If, say, a squeaky clean prostitution business were possible, free of crime and drugs (admittedly hard to arrange even in liberal Holland and Germany), what would be the moral or ethical distinction between a person who pays or gets money for sex services and people who pay or receive money for donor eggs and sperm?

Having registered my shock, I come to A Life Decoded. J. Craig Venter is a Phenomenon of Nature; there is no doubting it. Brilliant, controversial, a self-promoter who is both avid and jealous for the limelight, priorities, and patent rights. An American bioengineering colossus, he has earned a solid place in the biotechnical Valhalla. Akin to the stout and eagle-eyed Cortez, Venter admits to having been "the first chemical machine to gaze upon his own sequence." Responsible for the first instance of species transmutation, he generated headlines worldwide when he transplanted the genome of one bacterium into another. I have read that the transfer of genes across species has become a hot topic and a worry.

I conjecture that no computer program would find genes of the Shrinking Violet in Venter's sequence. He has swashbuckled across the techno-genetic arena since about 1991, "playing God" or acting at the very least as a Darwin/Edison combo. His book swashbuckles across time, theory, experiment, personalities, his 81-foot sloop, his creation of institutes and headlines, meetings, his divorce, publications; he winds up with a view of the future.

The great achievement of Venter was to implement the shotgun procedure, which is among the most advanced methods used today for large-scale DNA sequencing. This meant an enormous increase in the numbers of people working on, isolating, fragmenting, and cloning DNA from an organism and now from communities of organisms. Assembly of the genome from the sequenced fragments required an enormous amount of computation, and Venter accomplished it in spite of criticism from his peers in the scientific community.*

Many readers will know something of how mathematics fits into all this. SIAM has a biosciences activity group that held a successful conference this summer, the third in a series. Genomics and related fields come up all the time at SIAM conferences (for a recent example, see the first page in this issue).

For evidence that genetics is increasingly intertwined with applied mathematics, I had to look no further than my own university, which has a Center for Computational and Molecular Biology---and that is only one of numerous such genomic institutes. More specifically, the mathematical topics involved include combinatorics, probability, information theory, Markoff chain theory. One goal of genomics research is to make a model of the repeat strings within a sequence, to study their apparent power-law distribution, and to nose out the human significance of such repetitions; such work fits into the more general area of computational gene finding. Lots and lots of computer time is currently required for such work. The smart money is already telling physics to move over and give pride of place to biogenetics in all its aspects, from the highly abstract and theoretical to potentially lucrative commercial applications.

Venter's vision of the future embraces the detection, prevention, and cure of diseases, thus providing us with long life. It seems hard to object to that. Other targets are the synthesis of chromosomes, the design of new organisms and creatures that will soak up carbon dioxide and other forms of pollution, the engineering of bacteria to produce such fuels as butane, propane, or even octane, all from sugar or from cellulose---in short, creating instances of self-replicating artificial life for a variety of human-centered purposes suggested from outside the field.

By no means unaware of the conniptions of the average Joe and Molly regarding the ethical aspects of his vision, Venter writes:

"Before undertaking such a bold project, I commissioned an ethical review of the idea of making a genome from scratch. The exercise required more than eighteen months and the solicitation of opinions from most major religions."

I have a dim view of the efficacy of codes of ethics, whether promulgated by governments or by other institutions. Our daily papers are filled with stories of unethical actions. (Remember Isaac Asimov's code of ethics for robots?) Nonetheless, Venter says that he's backed off a bit and even refers to the existence of a government advisory board for biosecurity. Security frequently gets mixed up with ethics, as in privacy considerations.

Allow me to elaborate just a bit my view of Venter's vision of a genomocratic future. When I got married, my wife and I underwent mandatory Wasserman tests. It looks as though couples in the not-too-distant future may have to present---for compatibility and eugenic purposes---their genetic sequences (obtainable at the local drugstore for a song via a non-invasive process that will take only five minutes). So back to the future: In medieval days, it was fairly standard practice in the event of a potential royal marriage to have the couple's horoscopes examined for compatibility and future felicity (for reasons of politics and personal security, astrologers often faked the results).

I was interested to learn elsewhere that Freeman Dyson, prime futurologist of the Institute for Advanced Study, known for such optimistic studies as the feasibility of life at temperatures close to absolute zero, has jumped on-to the genomic bandwagon. Children of the future, Dyson conjectures, will play with genetic sets (even as my generation played with Erector Sets) and create all sort of delightful forms of life.

Praise, then, the genome, from whom all blessings and curses flow. What we have in Venter's book is a vision of salvation through genomics. But salvation from what and to what, inasmuch as salvation itself comes in many flavors? In my lifetime, I've seen salvation linked to good works, prayer, faith, money, ascetic practices, atonement, Marxism, black-strap molasses, open markets, democracy, and let us not forget the "new math."

Ladies and Gentlemen, please welcome the Age of the New Viktor Frankensteins who have been transfused with Faustian genes. (Muted applause.) Muted, for, as Venter rightly and modestly asks in his final sentence, is a life decoded a life understood?

Acknowledgments
I wish to thank my colleague Suzanne Sindi for guiding me through the genomic world.

*James Shreeve, The Genome Wars, Knopf, 2004.

"Make me a Hipporoo," New Scientist, February 11, 2006.

Philip J. Davis, professor emeritus of applied mathematics at Brown University, is an independent writer, scholar, and lecturer. He lives in Providence, Rhode Island, and can be reached at philip_davis@brown.edu.


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