Keynote: Craig Venter, JCVI - JGI User Meeting

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Keynote: Craig Venter, JCVI - http://www.jcvi.org/

Jonathan Eisen and Ricardo Vidal liked this

Craig is here, and the room is basically full. - Jason Stajich

Craig's talk entitled, "reading to writing the genetic code" - Jason Stajich

in honor of Craig I am posting a link to an interesting story about him and sequencing the ocean http://homepage.mac.com/jonatha... that I distributed on APRIL 1 (hint hint) two years ago - Jonathan Eisen

Jason beat me to the punch on the thread creation - Thomas Sharpton

Eddy says Craig's science is marked by "punctuated revolution" - Jonathan Eisen

April 1, 2009 is just around the corner..... - Thomas Sharpton

"new revolution on how to write the genetic code after reading it" - Jason Stajich

Craig gave a cool TED talk on this subject not too long ago for the less scientifically literate - Thomas Sharpton

Showing a picture of my old haunting grounds (the JCVI / ex TIGR campus in MD) - Jonathan Eisen

JCVI will be Designing and constructing the world's first zero-carbon facility - Jason Stajich

Big questions - can we be reductionists to pare down life to bare minimum. - Jason Stajich

Quote of the day "Plenty of people ask these types of big questions, usually after smoking something" - Thomas Sharpton

His big questions: what is life (which he says you ask after smoking something), can we digitize life, how extensive is it, can we pare it down to basic components, can we regenerate it - Jonathan Eisen

Talking about moving biology from analog to digital data - Thomas Sharpton

"digitizing life" being important. 50M EST sequnces in dbEST - that seems low... - Jason Stajich

1st genome was 14 years ago, 8 genomes per 454 run now (multiplexed) - Jason Stajich

Many completed genomes, JGI has done more than any other institution (by NUMBER) - Jason Stajich

tom - i dunno, "Sex with dead things is better than no sex at all" from peg riley is in competition - val

JGI has done more genomes than any other institutions, but together, JCVI and JGI have sequenced half of those available across the world - Thomas Sharpton

Says he JGI and JCVI have produced half the genomes in the world (left out TIGR there but he counts it as part of JCVI) - Jonathan Eisen

citing genome paper of a diploid individual (PLoS Biology paper) - Jason Stajich

see human genome paper in PLOS Bio http://biology.plosjournals.org/perlser... - Jonathan Eisen

Moving onto Sargasso Sea sequencing project, understanding genetic makeup of the environment - Thomas Sharpton

sorcerer II sampling around Europe. - Jason Stajich

showing slide entitled Fragment recruitment SAR11 - indicating regions where there are differences, like a viral genome insertion. - Jason Stajich

5 recuited taxa (37% of sequences sampled) are SAR11, SAR86, Prochlorococcus, alpha-Proteombacterium, Synechococcus - Jason Stajich

20 Million gene set being worked on. trouble is "computational tools and on these sets get harder at each stage" - Jason Stajich

With such a rapidly growing dataset, computational tools become taxed and present new challanges. - Thomas Sharpton

Rate of new gene finding in mammals has plateaued, but still moving at linear stage of discovery. - Jason Stajich

Shows this figure from Yooseph et al (http://biology.plosjournals.org/archive...) - Jonathan Eisen

Mentions that we've pretty much discovered all of the mammalian genes, but we're still in linear phase of gene discovery in microbes - Thomas Sharpton

not a fair comparison, though, given the phylogenetic distances that make up the groups he's considering with that argument - Thomas Sharpton

switching from diversity to what is the minimal set of genes, looking at Mycobacterium genitalium. ~400 genes, to figure out which ones are essential. hard to do sequential KO, so easier to synthesize the genome instead. - Jason Stajich

Raises question regarding which genes are essential and what's the small, or simplest, genome that can be synthesized - Thomas Sharpton

showing PNAS paper on bacterial phage synthesis. (phi-X174) - Jason Stajich

error rates are a fairly sizable problem in DNA synthesis when dealing with long fragments - Thomas Sharpton

Turning the digitization concept on it's head, now he's taking digital data and turning it into analogous biological sequence - Thomas Sharpton

Says that you can only synthesize something accurately if the database is accurate - Jonathan Eisen

bermuda standards are untolerable for synthetic biology... - Jason Stajich

"This software builds it's own hardware" - Thomas Sharpton

describing bootstrapping "software building hardware" Isn't this basically RNA world? - Jason Stajich

Bring back the RNA world - Jonathan Eisen

well, it's central dogma too - Thomas Sharpton

incorporated dna watermarks into their synthetic genome to ensure that what booted up in the cell was that which they synthesized - Thomas Sharpton

says you can write all sorts of things in a genome and he is trying to write more clever thigns in this genome - maybe he should write "SARAHPALIN" http://phylogenomics.blogspot.com/2008... - Jonathan Eisen

synthesizing genomes, troubles when get to 100kb. - Jason Stajich

Hierarchical DNA assembly of synthetic fragments - Thomas Sharpton

Referring to one of my favortie bugs - Deinococcus radiodurans - and using it to reassemble large DNA pieces b/c it can do this well - Jonathan Eisen

D. radiodurans is a great model for genome assembly as it can reconsititute it's genome sequence after RAD attack - Thomas Sharpton

Learning from Deinococcus radiodurans -- "Somehow it reassembles its genome" - Jason Stajich

Reinventing YACs...? - Jason Stajich

Bringing back YAC - Thomas Sharpton

Says it works better in yeast - Jonathan Eisen

Recombing YACs to make larger segments I guess. - Jason Stajich

TS - Great Minds.... - Jason Stajich

100% what they designed - Thomas Sharpton

He does a good job of referring to who did certain studies at JCVI --- even showing pictures of some of them --- - Jonathan Eisen

I've just learned to think like you ;) - Thomas Sharpton

583 kb synthesized genome. - Jason Stajich

Singleshot assembly of 25 pieces accomplished in yeast - Thomas Sharpton

Says the "genome transplantation paper" of his was one of the most profound that has come out of his group - Jonathan Eisen

Talking about how changing the DNA in the cell (and only the DNA) changed one species in the lab into another - Thomas Sharpton

Mentions recent paper to PNAS, but props that he also made it open access. http://dx.doi.org/10... - Jason Stajich

I think he's genuinely interested in others picking up this technique - he made a call to young students at Berkeley to think big about what can be done with this technology - Thomas Sharpton

Says he is still not certain what happened in the genome transplantation study - Jonathan Eisen

Is this what one refers to as an "Oops!" discovery - Thomas Sharpton

Genome transplants worked when going from bacteria to bacteria but not with the apparently the same DNA from yeast to bacteria - Jonathan Eisen

Transplanting the same synthetic sequence into yeast did no recapitulate the results - Thomas Sharpton

They think they now have a mechanism to take the DNA grown in yeas t and then in vitro convert it into somethign that can be taken up into a bacterium - Jonathan Eisen

Has figured out how to create bacteria from prokaryotic genomes engineered in Yeast. This means that all conventional yeast genetic tools can now be used in this system - Thomas Sharpton

Now is talking about "why do this" - Jonathan Eisen

Brilliant strategy by the way by the organizers to have Craig give the last talk - it is completely full in here which is almost unheard of for a half day at the end of a meeting - Jonathan Eisen

It seems like his vision for monetization of this is in the end products not the technology to get there? - Jason Stajich

Ok, enough of what's going on, now on to the why we need to do this. Citing increasing population growth and declining energy reserves, CO2 emissions climbing, etc. Wants these tools to be used to solve these problmes - Thomas Sharpton

genes as "design components" - Jason Stajich

Jason - agreed. I'm thinking industrial application of the technology to change how and what we manufacture - Thomas Sharpton

software to "design organisms". Lucy Shapiro getting mad props - like 4 mentions. - Jason Stajich

Introducing the Synthetic Genomics Organism Designer. I played with it pre 1.0, this looks quite a bit cleaner than it did a while ago - Thomas Sharpton

Says we need to know better how circuits work in organisms (and cross refs Lucy Shapiro's talk) - Jonathan Eisen

Combinatorial Genomics - rapidly screen genes via cassette based contstruction of 1000 - Ms of genomes/day - Thomas Sharpton

[me]what happens when we build organisms that become sentient? SchiNet [/me] - Jason Stajich

Sounds similar (but different) to Church's MAGE method of rapidly identifying optimal protein sequence - Thomas Sharpton

Many people are taking pictures of Craig and/or video --- I know I said George Church was a rockstar but I forgot Craig was coming to the meeting - Jonathan Eisen

designer fuels showing picture of what I thought was chlamy, says they have made algae that make fuels. - Jason Stajich

This really has been a meeting of the minds - great talks all around - Thomas Sharpton

referring to methanogens now --- b/c they are autotrophs that take CO2 to CH4 - Jonathan Eisen

I have the tendency to dream when I hear a talk like this - the future is very exciting - Thomas Sharpton

Says they have an anaerobic cell sorter to start to better characterize organisms that live off of coal - Jonathan Eisen

Coal to methane production - does this help reduce CO2 emissions though? Just cleaner than burning coal. - Jason Stajich

Wants to use these organims to convert deep earth coal into natural gas as they release methane - Thomas Sharpton

Says they should be able to convert large collections of coal into natural gas using enzymes from some of these bugs - Jonathan Eisen

Imagines people will be designing their own plant species in a few years ... - Jonathan Eisen

Says the day of creating unique plants isn't very far away - Thomas Sharpton

[me]Does it make sense to also look at the source of oil - is it purely chemical process from decomposed algae and pressure or is there a biochemical process facilitated by microorganisms? I thought we don't really know how oil is naturally made[/me] - Jason Stajich

Ends with a picture of a whale and says "thats my tail and Im sticking to it" - Jonathan Eisen

Part of the BP/EBI initiative is to look at this - they're going to sample oil wells and look for orgs that grow in them. - Thomas Sharpton

After a quesion Craig admits to having made a mistake with mycoplasma since it grows so slowly - Jonathan Eisen

I must say I don't like computer analogy to cells. - Jason Stajich

"There's no intention of putting these into the environment; that would be ethically wrong" - Thomas Sharpton

ethically wrong to put these (engineered) organisms into the environment. Nothing that can survive outside lab. 150 algae companies in last year? - Jason Stajich

I'm surprised he didn't talk a bit more about the ethics board he established to deal with a lot of the concerns that arise regarding this technology. - Thomas Sharpton

Craig says they are trying to work out laws, rules and regulations and that they are working to avoid this ... he even makes a comment about how some companies are planning to make and release genetically engineered algae --- nice criticism of the talk that he did not go to from two days ago that I had trouble with too - Jonathan Eisen

by the way - the question about ethics came from Dawei Lin from the UC Davis Genome Center - I did not see him but I know his voice - Jonathan Eisen

Even in answering questions Craig does a good job of referring to previous speakers (now he was referring to Jeff Miller) - Jonathan Eisen

Question - do you think you can make a bacterial chromsome boot up in yeast - answer - no we are trying to prevent DNA from booting up in yeast - Jonathan Eisen

We are not ready to release our software or our bugs because thesoftware has bugs - Jonathan Eisen

Great talk, user meeting has ended. - Thomas Sharpton

and we are done - Jonathan Eisen