SALT: Craig Venter

Last Monday evening I was in San Francisco to hear J. Craig Venter talk on "Joining 3.5 Billion Years of Microbial Invention." (The talk was sponsored by The Long Now Foundation as part of their Seminars About Long Term Thinking, or SALT series). Here are my notes (with a minor amount of editing, including tracking down some links):

• Venter sees our knowledge of DNA as being both

1. Gathering (Reading)
2. Using (Writing)

• We humans differ from one other in our DNA by 1% - 3%, which is more than had been previous thought. (We differ from chimps by 4% - 5%.)
• The first human diploid (i.e., both chromosome pairs) genome sequence (called "HuRef") was published by researchers at the J. Craig Venter Institute (JCVI) in the open access journal PLoS Biology (Public Library of Science).
  
• Microbes make up about one-half(!) of the Earth's biomass.

• In 2003, the JCVI did "shotgun sequencing" of microbes in the Sargasso Sea (published in Science).
• According to Venter, biologists had told him they would find no life, since there are no nutrients available. However, it turns out that these microbes contain proteorhodopsin, which allows them to convert sunlight into energy! (Note: this is not photosynthesis.)
• Interestingly, these are essentially the same sort of photoreceptor cells found in the human retina, but performing a different function.
  
• Even more interesting, different microbes have adapted to their environments by evolving sensitivity to different wavelengths: blue, in the Sargasso Sea; green in coastal areas.
  

• In 2004, JCVI launched the Sorcerer II Global Ocean Sampling (GOS) Expedition.
• For every 200 miles, the team found that 85% of the organisms sampled are unique!

• Each of us humans is a "microbiome" teeming with bacteria and viruses.
  
• During a single hour indoors, each of us comes in contact with 10,000 bacteria, and 100K viruses!
  

• As to the writing of genetic information, two Qs:
1. Can the chemistry permit synthesizing?
   
2. Can we boot it up?

• In January, JVCI announced the creation of the first synthetic bacterial genome, Mycoplasma genitalium JVCI-1.0. (See my earlier post.) The genome has more than a half-million base pairs, and was created by assembling a series of overlapping segments of increasing length: starting at 50 base pairs (bp); then 5-7kbp; then 24kbp; then 72kbp; then 144kbp; and finally, the entire 582,970 base pair genome.

• The JCVI team has demonstrated that it is possible to take the genome from one species and (via use of restriction enzymes which cut apart the host DNA) have it take over and reproduce itself in another -- literally changing one species into another. "True identity theft," Venter remarked. "The software makes its own hardware."
  
• Then there's D. radiodurans, an organism that, after absorbing 1.75 million rads of radiation -- and having its DNA blown to pieces -- is able to reassemble its genome in about 24 hours and live on.
  

• Venter said that solutions to issues such as fuels and climate are more likely to come from disruptive technologies.
• We are heading toward a future of combinatorial genomics, with the ability to construct thousands, or millions of genomes a day.

Q-A Session

• About 200 kg of material are exchanged between Earth and Mars each year.
• The space station used to vent waste into space; now, it is packed in an (aluminum?) tube and launched back into orbit (to burn up in the atmosphere). "Good shit from space!"
• Venter said that there are two common long term views of human survival:

1. Move to a new planet
2. Alter our genome to exist in a higher CO2 environment
3. Venter would add: Genetically alter the environment

• In commenting on the resistance to GMOs, Venter pointed out that agriculture has always been about mixing genes -- albeit blindly. He recalled a conversation with the leader of the German Green party, where Venter said told him, "If you ask me if I'm for or against [GMOs] I'll always come down on the "for." But, if you want to have an intelligent discussion about it, then I'll say that there were many things that should have been done differently.
  

• Near the conclusion, Venter remarked, "Eventually, science trumps ignorance."
  

Sidebar

• Stewart Brand's notes on this seminar may be found in this post at the The Long Now Foundation blog.
• The Public Library of Science (PLoS) is "a nonprofit organization of scientists and physicians committed to making the world's scientific and medical literature a freely available public resource."
• Somewhere in the middle of all this, I remembered a classic Science Fiction short story (pub. 1941), The Microcosmic God, by Theodore Sturgeon.
• See the Ethical Considerations section of the JCVI's Synthetic Bacterial Genome press release for information on how the JCVI is dealing with societal issues surrounding the synthetic genome.