Craig Venter

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    I’m heading off to the Foresight Conference and then a pilgrimage to the Venter Institute. (This photo by Ronnie Antik is from TED earlier this year.)

    Full disclosure: in all of my prior writing and blogging about Craig Venter (from TED, our life sciences conference and elsewhere), we had no economic ties to him, and working with him was just a dream. He now has a company called Synthetic Genomics, which I am very excited about, and we just became investors, and I joined the Board.

    For the curious or those as equally excitable as I, here is a summary of that earlier blogging:

    Craig Venter set sail around the world to shotgun sequence the millions of viruses and bacteria in every spoonful of sea water. From the first five ocean samples, this team grew the number of known genes on the planet by 10x and the number of genes involved in solar energy conversion by 100x. The ocean microorganisms have evolved over a longer period of time and have pathways that are more efficient than photosynthesis.

    Another discovery: every 200 miles across the open ocean, the microbial genes are up to 85% different. The oceans are not homogenous masses. They consist of myriad uncharted regions of ecological diversity… and the world’s largest digital database.

    From the collection of digital genomes, we are learning to decode and reprogram the information systems of biology. Like computer hackers, we can leverage a prior library of evolved code, assemblers and subsystems. Many of the radical applications lie outside of medicine.

    At the Venter Institute, Craig Venter and Hamilton Smith are leading the Minimal Genome Project. They take the Mycoplasma genitalium from the human urogenital tract, and strip out 200 unnecessary genes, thereby creating the simplest synthetic organism that can self-replicate (at about 300 genes). They plan to layer new functionality on to this artificial genome – to make a solar cell or to generate hydrogen from water using the sun’s energy for photonic hydrolysis – by splicing cassettes of novel genes discovered in the oceans for energy conversion from sunlight.

    Venter explains: “Creating a new life form is a means of understanding the genome and understanding the gene sets. We don’t have enough scientists on the planet, enough money, and enough time using traditional methods to understand the millions of genes we are uncovering. So we have to develop new approaches… to understand empirically what the different genes do in developing living systems.”

    The limiting factor is our understanding of these complex systems, but our pace of learning has been compounding exponentially. We will learn more about genetics and the origins of disease in the next 10 years than we have in all of human history. And for the minimal genome microbes, the possibility of understanding the entire proteome and metabolic pathways seems tantalizingly close to achievable. These simpler organisms have a simple “one gene : one protein” mapping, and lack many of the nested loops of feedback that make the human genome so rich (and humbling… When burned on a CD, the human genome is smaller than Microsoft Office).

    Much of our future context will be defined by the accelerating proliferation of information technology – as it innervates society and begins to subsume matter into code. It is a period of exponential growth in the learning/experimentation/feedback cycle where the power of biotech, infotech and nanotech compounds the advances in each formerly discrete domain.

    And it should be a wonderful time for explorers like Craig Venter – sailing through the frontiers of the unknown – and for the curious, in an era that will feel like an innovation Renaissance.

    oldcola_, davesag, Automatt, and 9 other people added this photo to their favorites.

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    1. Philosoap [deleted] 115 months ago | reply

      "If I take a blank computer disk and weight it on a scale, it will weigh about 0.7 oz. If I spend hundreds of dollars and load it with over a million bytes of software, it will still weigh 0.7 oz. Software has no mass. Although it may be resident in a physical system, it has no mass of its own. It can even be transmitted through the airwaves.

      It is significant that the real personality of a human — call it "soul," "spirit," or whatever — is "software," not "hardware." The "real" you and I are simply resident (written onto) a physical address which, hopefully, is destined for an upgrade!" — C. Missler

    2. jurvetson 115 months ago | reply

      substrate independence.... Viva!

      Kevin Maney from USA Today just blogged about this one.
      .

    3. Philosoap [deleted] 115 months ago | reply

      LOL. "Viva la substrate independence!" I love it.

    4. TheAlieness GiselaGiardino²³ 113 months ago | reply

      Hey, nothing to do with nothing, but... See this superb portrait of Craig, J (& all others here please):

      Taken by George Dyson... his pictures are fabulous. Have you ever seen a better portrait of Sergey than this? Me, no)

    5. benjiman 113 months ago | reply

      Let the data mining BEGIN!

      I love that their new system will be called "CAMERA" (Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis). How Flickr of them! ;)

    6. pellionisz 112 months ago | reply

      Generating hydrogen by a tweaked bacterium is both colossal (for global clean economy) as well it is the "dream of nanomania" (how can we get smaller in molecules?).

      But...

      I asked Craig 3 years ago what he thought about "junkDNA". (At that time he was not too hot on "junk"). Since a hefty 12% of the DNA of Mycoplasma Genitaliae is non-coding, the "trick" may be not so much reducing the number of genes, but (also) expanding the "non-coding" allotment. (Why? see FractoGene.com). I would like to discuss this with Craig Venter / Juan Enriquez, but they are not easy to reach...

      Any (viable) contact info?

    7. TheAlieness GiselaGiardino²³ 112 months ago | reply

      Juan Enriquez!!! When he is down Buenos Aires again, do let me know Steve! -so I can cry for I won´t be able to afford attending any of his conferences! ;-) -

      (you could accompany him, btw)

    8. malaparte 111 months ago | reply

      Steve, thanks for planting yet another though-inspiring seed.

    9. jurvetson 99 months ago | reply

      This just in, from Technology Review:

      The ocean hosts a stunningly--and surprisingly--diverse menagerie of microorganisms, according to a massive genetic study published today.

      "We have not understood much about our own planet and our own environment," Venter told Technology Review from his boat, the Sorcerer II, currently in the Sea of Cortez, in Mexico. "We've been missing as much as 99 percent of the life forms and biology out there."

      The first set of results, published this week in three papers in the journal PLoS Biology, revealed six million new proteins, doubling the number of known protein sequences. "Everywhere we sampled, we found new proteins," says Venter.

      In fact, every environment sampled showed high genetic diversity, both within and between samples. The findings are challenging the notion of species in microorganisms. "When you look at microbes, they don't appear to be individual species"

      "Microbial communities are almost like a superorganism, where each microbe is contributing to community as a whole," says Weinstock. "We really need to characterize the metagenome and analyze the genes and protein products as an aggregate."

      Venter and others eventually hope to find proteins that can be co-opted to create novel bacterial machines--proteins involved in hydrogen production or carbon fixation, for example, that could one day be engineered to boost the carbon-fixing capacity of the ocean or to create fuel-producing bacteria. "Genes are the design component of the future," says Venter.
      ------
      Also, PLoS has a special collection of open-access articles, including an interactive graphic display of the data and a slide-show presentation by Venter out in the Sea of Cortez.

    10. jurvetson 96 months ago | reply

      interesting stuff... Partnership with BP announced today...

    11. jurvetson 95 months ago | reply

      An important prelude to synthetic DNA transfer just came out in Science.... Here's the summary via Sci Am:
      Genome Swap Turns One Microbe into Another
      Scientists successfully transfer the entire genetic code of one germ to another, bringing them a step closer to synthesizing life

      As radical as this transformation is—transmuting one species into another by transferring just the genetic code—it represents only the first step toward man-made organisms. "Synthetic biology itself and the synthetic genome still remain to be proven but we are much closer to knowing that it is theoretically possible," biologist J. Craig Venter says. "Just the naked DNA, just the chromosome itself without any accessory proteins, is all that is necessary to boot up this cell system. It really simplifies the task."

      And www.edge.org/documents/archive/edge215.html#jcv has this tantalizing tidbit from Venter:
      Now we know we can boot up a chromosome system. It doesn't matter if the DNA is chemically made in a cell or made in a test tube. Until this development, if you made a synthetic chomosome you had the question of what do you do with it. Replacing the chomosome with existing cells, if it works, seems the most effective to way to replace one already in an existing cell systems. We didn't know if it would work or not. Now we do. This is a major advance in the field of synthetic genomics. We now know we can create a synthetic organism. It's not a question of 'if', or 'how', but 'when', and in this regard, think weeks and months, not years.

    12. PhOtOnQuAnTiQuE 91 months ago | reply

      And now you have your (very interesting) article with him, in the Financial Times ; )

      Financial Times : Leading the evolution out of the fossil fuel age (Article)


      PhotonQ- Craig Venter - Steve Jurvetson at Le Louvre =)

      Hope you ll like the little frenchy teleportation/ "clin d oeil" =)

    13. jurvetson 91 months ago | reply

      Yes! Very nice. (the author made some odd comments about assembling cars and attributed them to me. Oh well - consider it some obfuscation)

      I just started reading Venter's new book on the long flight to China. Very fun read so far...

    14. biotron 91 months ago | reply

      he's currently on BBC News 24 Hardtalk - link here

      enjoy China! :)

    15. PhOtOnQuAnTiQuE 91 months ago | reply

      "the author made some odd comments about assembling cars and attributed them to me"
      =) when i read this part my mind did a little ...."there s something wrong with this part... doesn t sound like Steve. But after i thought..it s F.T...not kurzweil.aiNews, so you needed to present some simple exemple....but now that you talked about it..i understand =)

      I had pre-order the book but didn t get it yet..so after reading your comment on "How fun it was" i went to buy one in Smith (english library in Paris) and stated it right away in the Jardin des Tuileries =)

      As you said...it s a lot of fun....he "mostly" looks so serious in his interviews..it s a "delice" to be reading him.

      "Y" confers many peculiarities, from.... and becoming rich, or having less hair on the top of the head..Loved it

      OH and..now i know what it means when somone tell you.... "I'd like you to meet the Good ol' Malcom =P

      @Biotron.. thanks for the link ; )

    16. nels1 91 months ago | reply

      what would be fantastic, and something that i would look forward to seeing, is when E.O Wilson's vision of the Encyclopedia of Life is fully functional and mapped with genomic data for each species as well - what an amazing experience it would be to be able to easily examine each species from its relationship to its environment and then being able to drill right down to its genetic code. the amount of information that humans have been able to gather in such a relatively short space of time is staggering, thanks to leaders such as Venter.

      like you said steve, it is an exciting time for us to be living in this "Innovation Renaissance"!

      ~Seen in Viva Evolution!

    17. jgury 42 months ago | reply

      This is highly relevant to some of the statements of JCV.

      If you could disturb the destiny of a fly, there would be no reason that could stop your making the destiny of all the other flies, of all the other animals, of all men, of all nature; you would find yourself in the end more powerful than God.

      Voltaire (2011-05-02). VOLTAIRE'S PHILOSOPHICAL DICTIONARY [DIGITALLY ENHANCED] (Kindle Locations 1263-1265). Classics-Unbound. Kindle Edition.

      Voltaire was doing a typically stoic assignment of destiny powers to God. The context is fascinating as it forces you to ask yourself what is the true destiny of a fly? You can't use genetic expression a basic irrefutable case. He was and was not thinking about genetic expression in this overall entry.
      "Either the world exists by its own nature, by its physical laws, or a supreme being has formed it according to his supreme laws: in both cases, these laws are immutable; in both cases everything is necessary; heavy bodies tend towards the centre of the earth, without being able to tend to pause in the air. Pear-trees can never bear pineapples. A spaniel's instinct cannot be an ostrich's instinct; everything is arranged, in gear, limited. Man can have only a certain number of teeth, hair and ideas; there comes a time when he necessarily loses his teeth, hair and ideas."
      Brilliant stuff. Makes you want to read the source language. Notable is the influence of Pascal's binary thinking. It seems God is less immutable due to the creation of man than we had thought. In fact mutability, randomness and paradox are more the operational rules;
      major parts of our human character we left out when we returned the favor of being created in God's image. We were more completely ruled by nature then and without science after all.
      Those laws seemed immutable even to (especially to?) an Issac Newton.
      Ok, so our ideas of what are God's powers keeps getting changed. God is getting less powerful? That is a moot point for a God of pure fiction but it is not if you just substitute in Nature for God. Nature is getting less powerful? Just because we control certain aspects of it does not really have that big an influence on something infinite by comparison. You have to think more in terms of fundamentals. Science did not create the world. Humanity did not create itself. So for fun just edit the quote with the substitution and change it to the interrogative: If you could disturb the destiny of a fly, there would be no reason that could stop your making the destiny of all the other flies, of all the other animals, of all men, of all nature; you would find yourself in the end more powerful than Nature? Not really. Many things could in fact stop you- reason, nature, force, madness, poverty, the IRS, the catholic church, the AMA,...

    18. jgury 42 months ago | reply

      "These simpler organisms have a simple “one gene : one protein” mapping,"
      But sure getting less simple due to genetic engineering. I spent some time hanging out in George Beadle's corn lab believe it or not.
      www.genetics.org/content/158/2/487.full
      en.wikipedia.org/wiki/One_gene-one_enzyme_hypothesis
      Beadle was one of the most brilliant and overall beloved guys in UofC history.
      “Hypotheses have to make sense, but facts don’t.”
      www.ias.ac.in/jbiosci/mar2007/197.pdf
      The celebrated point then was "one gene : one enzyme" (along with some good times at the committee on evolutionary biology) so what is really going on is the moving of the more complex proteins and enzymes synthesis paths and mechanisms down to the microbe level. What kind of stuff? Everything I think from growth hormones and pharma tech drugs to material science stuff to whatever. There are +s/-s of course. When this type of stuff crosses over into. GMO corn pollen (not due to this particular tech but relevant) with trace systemic pesticide in pollen fatal to honeybees for example. Bad stuff can get out for economic gains and human gains in other words. Don't kid yourself either. Think about bioweapon implications.

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