Life at the Speed of Light

by J. Craig Venter, 2013

Craig Venter goes his own way. This can appear like a big ego - or like a person who is aware of his capabilities and maximizes their effect. Demonstrated competence attracts more competent people, and annoys the hell out of folks who prefer a more leisurely pace or have less ambitious life goals. I do not know what Venter would like to achieve during his life, but I'm guessing he's working on a biotechnology "moonshot": practical life extension and enhancement technologies that extend far beyond current capabilities, while solving the global problems that make an extended life worth living. Even Venter's grueling pace may be inadequate for a man born in 1946. Craig Venter is impatient.

His first book - "My Genome, My Life" - appears at first to be a celebration of ego. But the deeper message is that a beach bum can develop into a driven innovator and accomplish mighty deeds. It isn't a cookbook for success - instead, it shows how a particular accomplishment, the sequencing of the human genome, was accomplished far more quickly and cheaply than the forecasts of institutional scientists. There are hundreds of important problems like this, and Venter-style no-holds-barred assault could solve many of them.

"Life at the Speed of Light" is a richer book, and gives more insight into this complex man and the way he builds competent teams to solve big problems. Literary agent John Brockman has shepherded many science best sellers through publication, and his contributions show in this one. The book aknowledges but does not explicitly credit as co-author Venter's third wife, publicist Heather Kowalski, but more than one expert communicator helped guide the creation of this book, and I'm grateful to Ms. Kowalski if the extra helping hand was hers.

The main contributors are a stellar team of lab biologists, working long hours for years, and dozens are acknowledged in the dedication and throughout the book. They made Venter's goals their own, and he made their productivity and success his most important goal. Venter may not live long enough to see the most important results of his work, but his younger collaborators will, and are building a richer world for all of us. They are deferring gratification; even if that does not lead to individual wealth and fame for every member of the team, the very long term effects of their work will be much larger than any historical fortune or dynasty. Few people achieve so much.

"Life at the Speed of Light" is a story about scientists and what they do. Unlike Rutherford's Creation and similar books about genomic discovery, this does not start with the appearance of life on earth, but the development of the idea of "life as mechanism". The same people who disparage mechanism and mechanics dislike viewing life as mechanical, and appeal to ineffable dieties and life forces to exempt biology from chemistry and physics. The biological world is indeed grand and incredibly complex, but as Venter and many others are demonstrating, it can be comprehended. Feynman's aphorism "What I cannot create, I do not understand" tell us that we will not really understand biology until we can copy it in the lab. If we ignorantly destroy too much of nature, we may need that creative capability to arduously restore it.

Large macromolecules are far too complicated to derive directly from quantum mechanics with present-day models and computation capabilities. But it was quantum physicist Erwin Schroedinger who set the agenda for molecular biology in 1943, and inspired scientists to think quantitatively and mechanically about the behavior of molecules, decades before we possessed the tools to observe those molecules with precision. It was computer scientists such as Turing and von Neumann who taught us to see these molecules as information driven machines.

Again, this is not to denigrate life, but to celebrate it by seeing it as clearly as is humanly possible. Only lazy misanthropes consider ignorance of mechanism and mechanics as a virtue. For the rest of us, collaboration and the shared understanding that results is the true measure of intelligence. In 2014, this collaboration is between scientists, engineers, and machines; by the end of this century, it may include all humans and all life on earth. If life is mechanism and computation, than all of life can process a vast amount of information.

Venter writes of Digital Biology and digitizing life. This is not "reducing" life to a sequence of bits, but bridging between domains and using each for what it is best suited. Biology requires continuity; every living thing must continously manifest the behaviors of life, with unpredictable external support and much external interference. A lifeform in a computer can be discontinuous, starting and stopping and moving backwards, making large "saltational" leaps that nature cannot duplicate. The biosphere is vast, but they aren't making any more if it, while computation increases 200x per decade. If we can continue to increase computation without burdening the biosphere, we can use the digital bridge to bring nature back to full health.

The center of Venter's book is the 10 year effort to create the 1 million base pair synthetic bacterium M. mycoides JCV1-syn1.0. Much of the detail was over my head, but the resemblance to a large integrated circuit design project is uncanny. The most important lesson is that the best way to solve some problems is to make them larger. The original target was M. genitalium, a bacteria with half as many base pairs, but M. genitalium reproduces in 12 hours, while M. mycoides reproduces in 1 hour. Since amplifying a colony of bacteria to measurability requires dozens of reproductive doublings, the time-to-completion of the project was actually reduced by halting the nearly-complete synthesis of genitalium and restarting with mycoides, reusing the successful techniques developed the first time.

This is like developing an integrated circuit with on-chip testability; this increases the time to tapeout, but it provides a "parallax view" of design that eliminates errors and increases the probability of first-silicon success. Testability shortens the total time to product shipment, and helps with robust, high-volume automated production, both for the chip and for the system that uses it. Visionary management looks at the whole process, end-to-end, and does not favor the initial tasks at the expense of the final result. If there are not enough resources to competently address all the initial tasks, either more resources should be gathered, or they should be returned to the investors for more concentrated effect on other projects.

Whenever I run into a problem I can’t solve, I always make it bigger.  I can never solve it by trying to make it smaller, but if I make it big enough I can begin to see the outlines of a solution.” – Dwight D. Eisenhower

Venter's book concludes with a forecast for what I label telegenomics. If the genome is a sequence of digital information, it can be sent through time and through space, with errors corrected through redundancy, just as the overlaps from shotgun sequencing of small snippets of DNA help us reassemble a vast genome in a computer, or through selection in colonies of bacteria. If we ever discover life on Mars (which may be archaea hundreds of meters down in the relative geological warmth), we can sequence them on Mars and send the sequence by microwave beam to earth, rather than the enormously expensive and ecologically risky process of returning the actual atoms. In time, we can save the genomes of threatened species, including the ones we intentionally drive towards extinction, like smallpox and influenza.

The most exciting short term prospect in the book (out of many) is Venter's sequencing the genomes of known influenza viruses since 2005. Influenza viruses recombine in their hosts, sometimes mixing human and bat, avian and swine, to produce new strains and sometimes global pandemics, such as the one competently portrayed in the film Contagion (2011). In that film, the sequence is determined rapidly, but the process of discovering and mass producing a vaccine takes months. Novartis and SGI have developed a bank of seed viruses which can shave vaccine production time by up to two months, potentially saving hundreds of millions of lives in the worst case. With rapid digital-to-virus synthesis, quality vaccines can be produced in days. Investment in detection and production infrastructure may take years, but when this system is in place, pandemics that can potentially spread globally in weeks can be detected and stopped long before they do major harm.

The standard science fiction paradigm of sending humans to the stars involves vast, slow "colony ships" carrying megatons cargos of living human beings (and the machines and biomass that supports them) over light years. But microscopic life, in a digitally managed environment, weighs nanograms, and potentially that environment can weigh grams also. We can send gram-weight von Neumann replicators to the stars, and amplify nanomachine environments and biomaterials into macroscopic lifeforms, habitats, and environments rich enough to support human-like intelligence. Once established, and after the construction of deep-space receiving dishes large enough to receive high-bandwidth laser data from Earth, we can send the blueprints for complete biospheres, as well as the digitized minds of colonists. Grams move much faster than megatons, and bits move much faster than both. Spacemen with blast guns may be entertaining fantasies for the masses, but the future will be digital - at the speed of light.

VenterSpeed (last edited 2014-02-06 21:19:29 by KeithLofstrom)