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.
  

Asteroid Tagging

The Planetary Society yesterday held a press conference and issued a press release announcing the winners of its $50,000 asteroid tagging competition. From the press release:

The Apophis Mission Design Competition invited participants to compete for $50,000 in prizes by designing a mission to rendezvous with and "tag" a potentially dangerous near-Earth asteroid. Tagging would allow scientists to track an asteroid accurately enough to determine whether it will impact Earth, thus helping governments decide whether to mount a deflection mission to alter its orbit.

NASA and the European Space Agency (ESA) co-sponsored The Planetary Society’s competition and will review the best mission designs offered. The winning designs will also be presented by The Planetary Society to other world space agencies.

The near-Earth asteroid, Apophis, was used as the target for the mission design because it will come closer to Earth in 2029 than the orbit of our geostationary satellites. (That’s close enough to be visible to the naked eye.) If it passes through a small “keyhole” as it travels by Earth, its trajectory could be diverted so that it will impact Earth in 2036. Current estimates do rate the probability of such an impact as very low.

The first place prize of $25,000 went to a U.S. team led by Spaceworks Engineering (Atlanta, GA) for their mission, named Foresight. European teams took the second and third place prizes ($10,000 and $5,000, respectively). Another $10,000 was distributed to the winners of the student competition.

The BBC News covered the announcement in this article.
[Thanks to georgef for the heads up on this one.]

The Biology that dare not speak its name

Evolution, the unifying principle of modern biology, can now be mentioned in Florida public schools! According to the AP story

TALLAHASSEE, Fla. (AP) -- Florida's public school science standards for the first time will use the word ''evolution,'' although the biological concept already was being taught under code words such as ''change over time.''

The new standards, part of a set of overall science changes adopted by the State Board of Education Tuesday on a 4-3 vote, require schools to spend more class time on evolution and teach it in more detail.
. . .
Opponents of evolution denied they had a religious motive, arguing that there are flaws in the scientific theory of evolution and that students should be allowed to explore them.

As a compromise, the standards refer to evolution as a scientific theory, explaining that a theory is a well-supported and accepted explanation of nature, not simply a claim.
. . .
John Sullivan, executive director of the Florida Baptist Convention, objected to calling evolution the only fundamental concept underlying biology. He wrote in an e-mail to Education Commissioner Eric Smith that Baptists firmly believe there's evidence of a ''Creator-initiated origin of life'' but did not object to teaching evolution. He argued, though, its scientific weaknesses should be taught as well as its strengths.

Among the standard tactics used by evolution opponents is to ensure evolution is labeled as (only a) "theory" -- which they recognize in common usage to mean, your guess is as good as mine. It's encouraging that the Florida standards "compromise" explains that evolution is a theory in the scientific sense -- which is to say, it is an explanation of nature that is well supported by known facts, and makes testable predictions. That this is a social, not a scientific, issue is quite apparent from the fact that evolution opponents spend no time lobbying against the germ theory of disease, quantum theory, or relativity theory to ensure that their scientific weaknesses be taught and that the competing claim that, simply, "God does it" be presented. After all, we know that the acceleration of gravity on earth is 9.8 m/s² (32.2 ft/s²), but beyond that, any explanation is "just a theory" and, if one allows supernatural explanations, it is just as plausible that God makes apples fall.

9/11 Conspiracy Theories

The 9/11 "Truthers" have apparently been harassing Michael Shermer on his book tour, due to Skeptic magazine's cover story (volume 12, number 4) investigating 9/11 conspiracy theories. (Here's a clip of Bill Maher's television show being disrupted by a "Truther.") James Meigs, editor-in-chief of Popular Mechanics, was interviewed on the Berkeley Groks radio show and the podcast is, I think, a good summary of the investigation by Popular Mechanics into claims that 9/11 was an inside job of the Bush administration. Even Noam Chomsky finds this too much to swallow! Skeptoid offers this more succinct analysis. I'm confident that the debate will continue long after I've shuffled off this mortal coil.

Those whom the gods would destroy, they first make mad (Bobby Fischer, Part 2)

[This is an addendum to an earlier post, Bobby Fischer.]

I just ran across this post, "Was It Only a Game?" on Dick Cavett's blog. I think Cavett's essay is just a beautiful piece of writing, and together with the clip of his first interview with Fischer (sumer of 1971, prior to the Spassky match) give a more nuanced and complex (and sympathetic) impression of an earlier, quite different intellect from the later raving paranoid Fischer became.
For those who choose not to read Cavett's post, I have to at least say that Cavett closes his essay by discussing those who did not have "a good death," and includes the closing lines from an E.E.Cummings poem, with no title but referred to by its first three words: “Buffalo Bill’s / defunct”:

Jesus
he was a handsome man
and what I want to know is
how do you like your blue-eyed boy
Mister Death

**********
Incidentally, the title of this post is, according to Wikiquote, an "Anonymous ancient proverb, wrongly attributed to Euripides."

Synthetic Bacterial Genome

I'm a little late with this, but here's the lead from the J. Craig Venter Institute press release:

ROCKVILLE, MD—January 24, 2008—A team of 17 researchers at the J. Craig Venter Institute (JCVI) has created the largest man-made DNA structure by synthesizing and assembling the 582,970 base pair genome of a bacterium, Mycoplasma genitalium JCVI-1.0. This work, published online today in the journal Science by Dan Gibson, Ph.D., et al, is the second of three key steps toward the team’s goal of creating a fully synthetic organism. In the next step, which is ongoing at the JCVI, the team will attempt to create a living bacterial cell based entirely on the synthetically made genome.

Here's the Science article.

* * * * *
Craig Venter was a participant in the 2007 Edge annual summer event: Life: What A concept. A transcript of the event has been published by Edge as a downloadable PDF. Here's the introduction to his discussion:

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.

[Here's a video of Craig Venter giving the Richard Dimbleby lecture, A DNA-driven world.]

"[T]he natural world around us does not care what we believe."

The intersection of two earlier posts (What have you changed your mind about? and Climate 'clearly out of balance' ) leaves us with these thoughts about climate change, from two very interesting minds:
In The Irrelevance of "Probability" Nicholas Nassim Taleb (author of The Black Swan) writes

As I said, consider that belief (i.e., epistemology) and action (i.e., decision-making), the way they are practiced, are largely not consistent with one another.

Let us apply the point to the current debate on carbon emissions and climate change. Correspondents keep asking me if it the climate worriers are basing their claims on shoddy science, and whether, owing to nonlinearities, their forecasts are marred with such a possible error that we should ignore them. Now, even if I agreed that it were shoddy science; even if I agreed with the statement that the climate folks were most probably wrong, I would still opt for the most ecologically conservative stance — leave planet earth the way we found it. Consider the consequences of the very remote possibility that they may be right, or, worse, the even more remote possibility that they may be extremely right.

In his essay The importance of doing something now about the environment Craig Venter (Human Genome Decoder; Director, The J. Craig Venter Institute) writes

Like many or perhaps most I wanted to believe that our oceans and atmosphere were basically unlimited sinks with an endless capacity to absorb the waste products of human existence. I wanted to believe that solving the carbon fuel problem was for future generations and that the big concern was the limited supply of oil not the rate of adding carbon to the atmosphere. The data is irrefutable--carbon dioxide concentrations have been steadily increasing in our atmosphere as a result of human activity since the earliest measurements began. We know that on the order of 4.1 billion tons of carbon are being added to and staying in our atmosphere each year. We know that burning fossil fuels and deforestation are the principal contributors to the increasing carbon dioxide concentrations in our atmosphere. Eleven of the last twelve years rank among the warmest years since 1850. While no one knows for certain the consequences of this continuing unchecked warming, some have argued it could result in catastrophic changes, such as the disruption of the Gulf Steam which keeps the UK out of the ice age or even the possibility of the Greenland ice sheet sliding into the Atlantic Ocean. Whether or not these devastating changes occur, we are conducting a dangerous experiment with our planet. One we need to stop.
. . .
Our planet is in crisis, and we need to mobilize all of our intellectual forces to save it. One solution could lie in building a scientifically literate society in order to survive. There are those who like to believe that the future of life on Earth will continue as it has in the past, but unfortunately for humanity, the natural world around us does not care what we believe. But believing that we can do something to change our situation using our knowledge can very much affect the environment in which we live.
[Emphasis mine]

What Have You Changed Your Mind About?

When thinking changes your mind, that's philosophy.
When God changes your mind, that's faith.
When facts change your mind, that's science.

The feature article in the current (2008-01-30) eSkeptic email newsletter is Michael Shermer's Response to the Annual Edge.org Question “What Have You Changed Your Mind About? Why?” Shermer's response concludes:

I have thus changed my mind about this theory of human nature in its extreme form. Human nature is more evolutionarily determined, more cognitively irrational, and more morally complex than I thought.

See the Edge Annual Question - 2008 to see read what 164 other contributers have changed their minds about, including:

• J. Craig Venter: The importance of doing something now about the environment.

• Nassim Nicholas Taleb: The Irrelevance of "Probablility"

• Ray Kurtzweil: SETI

• W. Daniel Hillis: Try the Experiment Yourself
  

The most recent Annual Questions have been: What are you optimistic about? (2007); What is your dangerous idea? (2006); What do you believe is true even though you cannot prove it? (2005). All of the annual questions and responses (back t0 1998) may be found at the Edge World Question Center.

"A Charge to Keep" or, "The Slipper Tongue"

A friend who heard the president's State of the Union address has drawn my attention to the 2d paragraph: "All of us were sent to Washington to carry out the people's business. That is the purpose of this body. It is the meaning of our oath. It remains our charge to keep." The emphasis is mine, and of course leads us back to this previous post about George W. Bush and his favorite painting -- which for the President depicts a Methodist circuit-rider with A Charge to Keep, but in the reality-based world apparently depicts a horse thief fleeing his captors who, "Had His Start Been Fifteen Minutes Longer He Would Not Have Been Caught."

[A discussion of the painting and its significance may be found on pp. 89-90 of The Bush Tragedy, by Jacob Weisberg (2008, Random House).]
* * * * *
Taxes, Terrorists, and Iraq
And speaking of the State of the Union address, The New York Times published a very interesting graphic showing frequency of the words that were used in this and each of President Bush's previous State of the Union addresses. This year's winning words were: Iraq/Iraqi(s); Terror/Terrorist(s); Tax(es), with the 2d tier finding Al Qaeda and Freedom(s). Popular words from previous addresses that were missing or out of favor this year include: Health Care; (Health) insurance; Medicare; Retirement(s); Social Security.
Other notables:

• Weapons of mass destruction/murder disappeared after 2006.
• Bin Laden, not mentioned until 2006, was mentioned once this year (the same as 2007).
• Surpluses was mentioned once this year, after being absent since being mentioned more than a half-dozen times in 2001.
  

Profits

Nothing really surprising here, but I was caught simply the juxtaposition of these two stories today:

Profit Declines 31% at Gannett
"Gannett, the country's largest newspaper publisher, said on Friday that its fourth-quarter profit dropped 31 percent because of a decline in broadcasting revenue and weak newspaper ad sales."

Exxon Sets Profit Record: $40.6 Billion Last Year
"By any measure, Exxon Mobil's performance last year was a blowout."

The company's sales, more than $404 billion, exceeded the gross domestic product of 120 countries.
Exxon Mobil earned more than $1,287 of profit for every second of 2007.
Like most oil companies, Exxon benefited from a near doubling of oil prices, as well as higher demand for gasoline last year. Crude oil prices rose from a low of around $50 a barrel in early 2007 to almost $100 by the end of the year -- the biggest jump in oil prices in any one year.