The iPlant Collaborative - a new (and seemingly cool) collaborative informatics project

Just found out (from Steve Rounsley) about what seems to be a cool collaborative computational project on plants - the Iplant Collaborative. From their site:

The iPlant Collaborative (iPC) is a distributed, cyberinfrastructure-centered, international community of plant and computing researchers enabling new conceptual advances through computational thinking, and addressing an evolving array of the most compelling grand challenges in the plant sciences and associated, cutting-edge research challenges in the computing sciences.

For more info got to their web site. Also - they are having their 1st conference which apparently will be webcasted. So apparently anyone can watch.

iSEEM Wants You --- We are Recruiting Post Docs in Metagenomics Informatics

I am pleased to announce that a new project on "Integrating Statistical Evolutionary, and Ecological Approaches to Metagenomics (iSEEM)" is getting up and running. The iSEEM Project, funded by the Gordon and Betty Moore Foundation, takes an integrated, interdisciplinary approach to metagenomic analysis.

The project spans three labs (mine and those of Katherine Pollard (who is in the Davis Genome Center where I am) and Jessica Green (who is at U. Oregon)), each with different areas of focus. Overall, the plan is to develop and apply novel methods for analyzing metagenomic data with a focus on three main topics: phylogenetic characterization of organisms, ecological diversity, and population genomics. We will be posting more detail about the project at http://iseem.org.

We are seeking five post-doctoral scientists and a bioinformatics engineer to work on methodology for analysis of metagenomic data as part of this collaborative project. Each position will be associated with one of the PIs at their home institution. If you are interested in microbial diversity, metagenomics, or genome evolution, and are looking for a post doc and want to be part of a interdisciplinary collaborative project, please apply.

More detail on the jobs is below:

Qualifications

• We are looking for people with a demonstrated interest in working at the interface between the quantitative and biological sciences. We will offer a generous salary and benefits commensurate with experience.
  
• Postdocs: Applicants should have a PhD in a biological, computational, mathematical, or statistical field. Programming skills are highly desirable.
  
• Bioinformatics Engineer: Applicants should have substantial experience with database programming (e.g. SQL), scripting (e.g. Perl or Python), and bioinformatics tools.
  

Term: Appointments will last 2 years beginning in Summer 2008.

To Apply: Please apply using our online application system. You will be asked for:

1. a brief cover letter explaining your background, career interests, and preferred geographical location for work (if any),
2. CV (including publications),
3. names and contact information for three references.

Online Application System:

• Bioinformatics Engineer
• Postdoc

Punctuated equilibrium of my blog ... and a look at an old science rap

Well, with my new role in PLoS Biology as Academic Editor in Chief, I had planned to start blogging more about PLoS and PLoS Biology. And I will. However, I am going to have to do a half effort on this for at least a week or two as I have a lovely ailment called trigger finger which is making typing rather awkward. So in lieu of a detailed blog I simply have to make a brief comment on one of the articles in this months issue

The article in which I am interested is a nice primer on mutational meltdown in mammalian mitochondrial genomes by Dave Rand. This is in relation to a paper by Stewart et al. in this issue. But enough about science. For those who do not know, Dave Rand published what I believe was the first rap in a scientific article. In an article in Genetics he presented a rap about repeat induced point mutation (something known as RIPPING). This RAP about RIPPING I think was presented at the Evolution meeting in Berkeley (I think I was at the talk where he did the RAP but I am not sure --- I could have, like Andy Pettite, misremembered the whole thing).

And well, here it is:

Yo! you’ve got my DNA and you think it is a-RIPping,
Your dog is so excited her saliva is a-dripping,
She seems to think the polymerase is doing some a-skipping,
But then again, you never know, she might just be a-quipping.
Are you sure induction by repeats did make it happen?
If it’s just associated, why not call it RAPpin’?
What motifs are necessary to keep the strands a-snappin’?
I don’t know and I don’t care, but something did some zappin’.

A really good day at work

Overall, I like being a scientist. But some of the days can be quite dreary. As a grad. student you slog through days that resemble the reliving of events in Groundhog Day. Except that they are actually different days - they just seem the same. As a post doc you struggle to get work done to then get a job (OK, I skipped a post doc, but I heard about what it is like from others). And as a faculty member you spend an absurd amount of time wasted on useless administrative activities. And I sometimes seem to be stuck in these days a lot.

But today was a really good day. It was my first day after it was announced that I was the new Academic Editor in Chief of PLoS Biology. And I got lots of positive feedback from friends, colleagues and even strangers. And then we had "lab meeting" which I decided to turn into a picnic/hike. We went to a little spot only 2 miles from the UC Davis Genome Center, that was as close to wilderness as you can find in Davis. And I think everyone had fun, getting away from the grind AND I brought my 3 year old daughter too.

And this reminds me to say - in the past I have avoided talking about people in my lab in my blog because it seemed like it would be nice to give them some space from my blabbing. But today I was reminded of just how much I owe them. They of course do all the work that I end up getting credit for. So today I thank the current lab members specifically (Jenna Morgan, Amber Hartman, Marcel Huntemann, Dongying Wu, Martin Wu, and Sourav Chatterji) and with their permission you will probably be hearing more about them later.

PLoS Biology 2.0

Well, I guess it is official now so I should post about it here. As for this afternoon, I am now the new Academic Editor in Chief of PLoS Biology. To read more about this new role of mine go to the source. I will probably cross post the editorial here at some later point.

• My editorial on becoming AEIC.
• An editorial by the PLoS staff

Also see other blogs/notes about this

• Egghead - UC Davis Research Blog
• PLoS Blog
• Coturnix's Blog Around the Clock
• Deepak Singh at BBGM
• Pedro Baltrao at Public Rambling
• EVOLGEN
• Genome Technology Blog
• nsaunders at What you're doing is rather desperate
• Pimm blog
• Highlight Health "More steps for Open Access"
  

For more on what I think about Open Access publishing see some of my other blogs on the issue.

See Evolgen for a field guide to seminar audiences

EVOLGEN has a great post on the people at your department seminar. It is worth checking out and bringing with you next time you go to a seminar. Even better than looking around --- choose which one fits you the best. Up until a few years ago, I was definitely the pre-schooler

The pre-schooler: This dude uses the departmental seminar as his nap-time. He sits in the back, and when the lights go out, he's nodding off faster than River Phoenix in My Own Private Idaho. Someone get this guy a good-night's sleep.

I simply could not stay awake in any seminar so I would have to sit at the back. Now that I have kids, I am used to sleep deprivation and only rarely nod off in a seminar. I am no longer sure which one I am ...

Calling Michael Ashburner - please start a blog

I just got done with reading Won for All by Michael Ashburner which came out a few years ago. This book discussed the sequencing of the Drosophila genome by Celera and is a fascinating read. The best part is the snarky, obsessive, and funny commentary by Ashburner on the players and the games they played in the course of this project. I know the book came out a while ago, but if there ever was a science author perfectly built for blogging it has to be Ashburner. So I am calling all science blog fans to try and find a way to get him to start a blog. Also - he is a big supporter of open access publishing ... as can be seen in the videos below:






See also some other Reviews of the book:

• John Sulston in PLoS Biology
• Matt Ridley in Nature
• Craig Venter in Science
  

How human rights work and microbial ecology are similar

The New York Times has a brief one page article in the Sunday Magazine on "The Forensic Humanitarian" In the article, Jim Giles describes the work of Patrick Ball, a statistician working on searching for evidence for war crimes. The work is clearly important. But what caught my attention was his method. Basically, he uses a form of mark-release-recapture statistics taken from ecology studies. In the article, Giles writes

To understand Ball’s accomplishments, you might start with the problem of counting rattlesnakes.

And then he goes on to describe how one can estimate how many rattlesnakes are in a population by marking ones that you find and then counting how many times you refind one you have marked previously. This is a method generally known as mark-release-recapture (e.g., see the Wikipedia entry here, which seems OK but I have not read too carefully).

Apparently, Ball uses a similar type of statistic to estimate the number of murders and/or deaths in particular areas, by looking for overlap among different reports of deaths.

What you say does this have to do with microbial ecology? Well, everything. Because one of the most common methods for estimating the number of microbial species in a sample is to use a gene survey method where one isolates DNA from environmental samples and then one looks in the DNA for multiple versions of a gene found in all species (the gene most commonly used is known as small subunit rRNA). The gene survey method is needed because appearance is not a robust method of identifying microbial species.

From the gene sampling data, one then compares each version of the gene to the others and counts how many times one sees the same form of the gene (suggesting that one has found two different cells of the same species). If one keeps seeing the same forms of the gene even with only a few samples, one would estimate there are few species in the sample. If one keeps seeing different forms of the gene, one would estimate there are many species in the sample.

Things that seem to be hidden - be the murders or populations of rattlesnakes or microbes - can still be studied with what the Times perfectly refers to as

"A statistical sleight of hand"

Forget McCain - the Real Problem in the New York Times - Adaptationism

Unlike McCain and his followers, generally, I really like the New York Times, especially the Science articles. But they do continuously irk me in one area - they repeatedly include lame adaptationistic evolutionary arguments. Now I am not the only person in the bloggersphere railing against people who say something MUST be adaptive simply because it is there (Larry Moran is the most persistent and interesting critic of adaptationism out there).

This week the Times has a doozy in the article on "Play" from the Sunday Magazine. In the article, Robin Henig writes

"If play is an extravagance, why has it persisted? It must have some adaptive function, or at least a benefit that outweighs its cost, or it would have been winnowed out by the forces of natural selection."

This is nearly a PERFECT adaptationistic line. And more importantly, it is simply not true. Some things persist in biological systems even when they have a cost that outweighs the benefit. And other things persist when they are neutral. Now I am not saying one way or another whether play has a benefit (the article is interesting and reasonably sound in many ways). But such statements as the one quoted above show a common misunderstanding of evolution. Evolution is NOT only about beneficial things persisting and detrimental ones going away. It is much more complex and interesting in fact. If you want to learn more about the perils of adaptationism, go to Larry Moran's blog. He really has some good stuff on it. Or go to the great gurus themselves - Gould and Lewontin.

Some pics of the new treefall

Harvard's Moving To Open Access - Let's Use this to Push for OA at other places

Well, Harvard is frequently criticized for being a bit conservtive in responding to new ideas and initiatives. But it seems that recently Harvard is more like a oceangoing yacht than an oil tanker. And yesterday, the New York Times reported on a proposed new initiative that could make Harvard a leader in the movement towards "Open Access" publishing.

The Times reports

"Faculty members are scheduled to vote on a measure that would permit Harvard to distribute their scholarship online, instead of signing exclusive agreements with scholarly journals that often have tiny readerships and high subscription costs."

and

"Under the proposal Harvard would deposit finished papers in an open-access repository run by the library that would instantly make them available on the Internet. Authors would still retain their copyright and could publish anywhere they pleased — including at a high-priced journal, if the journal would have them."

In my opinion, there is no doubt this is a smart move. Sure, there are some potential downsides to open access. Some journals do good things and they may have to reinvent themselves to continue to bring in revenue. But welcome to the 21st century. It is not like other industries - like music and TV and movies and electronics and so on - have not had to reinvent themselves.

And the result are in --- Harvard approved the initiative (see here for example). Now - I think we should use this as an example to get other institutions to do the same thing. As reported in the Boston Globe, Harry Lewis a CS Professor at Harvard said:

"Harvard is in a unique position to do the right thing in the academic world," he said. "In this case, I think others will be emboldened by Harvard to follow its lead, and the course of collective action will be greater than the course any individual school will take."

I will do my best to get UC Davis to do the same thing, but given the animosity towards open access exhibited by our acting provost Barbara Horwitz, it may be a tough ride here. Fortunately, they are interviewing candidates for provost now and hopefully whomever they pick will be more supportive.

So - here is a call to others out there. Push for the same type of thing at your institution. I will be posting more on this in the coming days/weeks. Maybe collectively we can follow Harvard's lead on this and make Universities more about what they are supposed to be about - spreading knowledge.

Creating Mitochondria and a sign that we need open peer review

Well, since everyone else is posting about this I figured I should too (see for example Steven Salzberg's Blog, The Harvard Crimson, Pharyngula). If you have not heard yet, there is an article in the journal Proteomics that discussed how mitochondria must have been created by an intelligent designer.

For example on p8 the authors say:

"Alternatively, instead of sinking in a swamp of endless
debates about the evolution of mitochondria, it is better to
come up with a unified assumption that all living cells
undergo a certain degree of convergence or divergence to or
from each other to meet their survival in specific habitats.
Proteomics data greatly assist this realistic assumption that
connects all kinds of life. More logically, the points that show
proteomics overlapping between different forms of life are
more likely to be interpreted as a reflection of a single common
fingerprint initiated by a mighty creator than relying on
a single cell that is, in a doubtful way, surprisingly originating
all other kinds of life."

Say what you want about the journal Proteomics but boy did they screw this one up. I think they probably should have caught this without much effort but who knows exactly what happened. In all fairness to them, it is possible for weird thin gs to slip through at any journal. Reviewers are busy. Editors are busy. Everyone is busy. How can we prevent this from happening again. There is a simple change we could make that would help. It is called Open Peer review. That is, if reviewers names were publicly attached to papers they reviewed, and their reviews were published, we would be less likely to see things like this happen. Then, if someone agrees to do paper review, they would be careful about it. Sure, we would probably have a harder time getting reviewers, but that would be better than publishing crap.

What are the risks with Open Peer review? Well, some people might feel afraid to criticize others especially people with power. Well, I find this sad. Scientists criticize our collaborators and friends ALL the time in private. Why not be public about it? Aren;t we supposed to be searching for the truth? If we are, shouldn't we be willing to give our opinions in public forums?

Marco Island - Saving Some of the Best for Last

Well, the Marco Island AGBT meeting just wrapped up and I they definitely saved some of the best for the end. I do not have a ton of time but here are my favorites:

Stephan Schuster gave a funny, entertaining and interesting talk on mammoth mitochondrial genomics. He riddled the talk with funny stories and one liners about his efforts to sequence old DNA and to publish the results. He did a good job of showing why Roche-454 sequencing is quite ideally suited for studies of old DNA.

John Leamon from Raindance Technologies summarize some of their work on droplet based microfluidics. He showed videos of droplets moving through their system and showed how it sould be used for various digital PCR-like activities.

But it was the last talk of the whole meeting that really did blow my mind. It was from Steve Turner from Pacific Biosciences. He presented an overview of their sequencing technology as well as a tiny bit of data. Now, normally I am uninterested in marketing talks where little data is presented. But this talk was different. First, their technology clearly has enormous potential for revolutionizing the sequencing field. Basically, what they are doing is reading the activity of a DNA polymerase as it replicates a single DNA molecule and they do it in real time. He referred to this as using the DNA polymerase as a sequencing engine and then he took the crowd through the details of the technology and some of the modifications they have made to make it work better. I will try to post later with more detail on their methods.

No - they are not quite ready for prime time yet. But the potential is pretty absurd. I see two key major advantages of their method if it can be fine tuned to work well -- (1) it is screamingly fast - because they let the polymerase do all the work in essence (2) it can potentially get long reads -- right now he claimed they could do up to 1500 base pairs and theoretically it could go much higher. If they can get this to work with reads of 10,000 bases for example, this will completely reconfigure the field. No longer will one have to worry about the complexities of mapping short reads as with many of the current "new" methods. And the long reads, coupled with many molecules per run, plus the high speed, this technology is the first I have seen that has shown some results and that could really lead to the $1000 human genome. Again, not clear when/if they will be ready for release to the world so don't hold off buying one of the other systems that currently work (i.e., Illumina, Roche, ABI Solid) if you want to do "next gen" sequencing. But this company is one to keep an eye on.


NOTE - SEE ALSO

• Bio IT world report on PacBio
• Eye on DNA
• GenomeWeb
• New York Times article #2
• New York Times #1

Marco Island sequencing frenzy - are we getting lost in all the data?

So - the Marco Island meeting could be summed up as a sequencing frenzy. Everyone and their mother presented something about how the next generation sequencers are revolutionizing their work. People are using these systems (well, people are using mostly Illumina and Roche sequencers and some are using ABI Solid) to do all sorts of new things - RNAi, gene expression, methylation, mutations, population genetics, comparative genomics, metagenomics, infectious disease, etc etc etc.

Certainly, much of this new work is truly revolutionary. Sequencing has gotten so cheap, and so easy, relative to even 3-4 years ago, that it can be used in all sorts of new ways. And new developments in sequencing seem poised to happen too, to make sequencing even cheaper and even better. Sequencing will get even better for a few reasons.

First, the current players in the market (Roche, Illumina, and possibly soon ABI Solid) are improving both their systems and their informatics such that they are getting more and more robust and easy to use and producing more data (Roche for example presented details on how they can extend their sequence reads to ~350 base pairs mostly by software and reagent changes). Lots of companies can say "We have some sequencing system about ready to be introduced" And lots of them are doing this at this meeting. But there is nothing like having sequencers in the hands of scientists to really test how well they work and to really help push the development of the technology.

Second, it does seem like some competitors for Illumina and Roche are coming. ABI presented multiple results from ABI Solid technology that makes it seem like these systems are ready for prime time. Whether other systems are ready for prime time is unclear. Helicos presented what could be seen as data. It was disappointingly minimal on detail but though I am rooting for them, it was far from convincing. But the discussions in the hallway seemed to suggest that Helicos is getting close. And there are 5+ other players itching to get into the market (some of which are apparently presenting later today). Some will fail. Some will succeed. And as long as their are a couple of good systems, the competition will push further development and reductions in costs. Thus everyone at the meeting I talked to said basically the same thing --- this is an exciting time in sequencing.

So - sequencing is getting better and cheaper. That certainly will be good in many ways. But there are some negative aspects to this frenzy. I see two in particular. The first, which was discussed extensively at the meeting, is that nobody is really prepared to deal with the sheer volume of data coming out of these new systems. Data storage, transfer and analysis will unquestionably be the rate limiting steps in turining the new sequence data into knowledge.

And this is the other negative aspect of the new frenzy. Right now there seems to be a mad rush to apply the new sequencing methods to everything under the sun. And the data piles up. And piles up. And the biology seems to have taken a back seat in some cases. Perhaps the bext example of this is exemplified by something Neil Hall pointed out yesterday to me. There has been almost no mention at this whole meeting of things related to function of genes. For example, I have not heard "gene ontology" once. I do not think I have even heard "annotation" once. Function and process have been replaced by terms like "systems biology" and "SNPs" and "networks" and "massively parallel." We have in a way regressed in terms of treating organisms (or communities) as a black box. Fine scale detail has been lost in a sea of data. In a way, we have all become born again geneticists. And I do not mean to disparage genetics. But I mean the part of genetics that treats organisms as a bit of a black box and focuses just on transmission of traits. We need to find a way to not get lost in all the data. I am not sure how to do that, but when we do, then the full potential of the new sequencing methods will be realized.

Coolest Thing at Marco Island - The Polonator

Without a doubt, the coolest thing at AGBT/Marco Island is the Polonator. This is a new sequencing system build by Denaher Motion based on the polony method from George Church's lab. Now I have no idea if this machine even works. And even if it works, I have no idea how useful it will be. But the idea is brilliant and appealing. They are trying to be an "Open Development" Massively High Throughput Sequencing system. By Open they mean, they will use open source software (and would love developers to help) and will use non proprietary reagents and supposedly try to make everything as cheap as possible. They will still make the main piece of equipment and I assume this is what they hope to make money off of.

I went to a showing in a room nearby the seminar room. There were many skeptics there. Most were concerned about the read lenght coming from the machine. But it should get better. And if the price is a lot less for reagents and the machine than anyone else's system --- this could be an important player in the market.





See also

• GenomeBoy

More notes from Marco Island/ AGBT

Some notes on talks here:

My favorite talk yesterday morning was David Cox from Perlegen. He had as usual some good one liners including "Everybody and their mother is doing this so doing this is not so novel. What is novel about it is that it worked." I should add that David Cox helped shape my career indirectly in many many ways. When I was a PhD student at Stanford, I got into genomics in part by teaching a course with David Botstein, Rick Myers and David Cox. When Craig Venter offered me a job at TIGR in 1998, I was not sure if moving to a non university was a good idea or not. So I asked many people for their opinions. Some said "You must do an academic post doc or you will never get a faculty job" I pretty much knew to ignore those folks. Cox gave the best advice. He said as long as I published things while at TIGR, it would not hurt me in any way. It probably would help. And so I took the job. And no doubt that was a great career move.

Other talks that were good were one by Joe Ecker, who discussed methylation in Arabidopsis and one by Andy Clark.

I skipped out on some of the lunch time to finish my talk for the PM session and also worked on my talk in the back of the room during the other PM talks. The PM session was on metagenomics and the most pleasing thing was that David Relman did not show up and he was replaced by Peter Turnbaugh from Jeffrey Gordon's lab. Now - I wam not saying it was good that Relman was not there --- he usually gives smashingly good talks. But Turnbaugh, a PhD student, stepped in as pinch hitter and gave a great talk on gut microbiome studies, really setting the stage for the whole session. I do not know if he was nervous stepping into a session like this but it did not show if he was. He certainly seemed relaxed when he said "Thanks to Dr. Relman for getting stuck in Chicago"

Forest Rowher gave a good talk on metagenomics and pointing out that viruses still get ignored in this field relative to their likely importance in communities. I have written about Forest before so I am going to discuss the other talks more ... but if you have not heard him talk before try to find a way. He has a VERY different perspective on genomics and metagenomics than most of the people doing it. And he is dead right about the need to do more work on viruses.

Garth Ehrlich gave a talk on "bacterial plurality" and why he thinks gene content variation within communities of microbes in biofilms is important. His data certainly seemed solid and he showed some results that call into question the claims that some aspects of the "pangenome" hypothesis (he showed that the total number of genes in the Steptococcus strain collection does seem to level off after sequencing ~ 30 genomes and thus that the number of genes is not infinite as some people have suggested). So I liked some aspects of his talk. But he did make some evolution statements I found disagreeable (for those who care about the nitty gritty - he showed a cluster diagram of strain similarity and then used the position of strains within the cluster diagram to reflect relative branching order and historical patterns. A cluster diagram is a bad thing to use and one should use a phylogenetic tree for this. In addition he implied that one could make a genome-phylogeny from gene presence/absence information that would be more robust than a standard alignment phylogeny. This is not a reasonable thing
in my opinion --- gene presence/absence patterns tend to end up grouping together unrelated lineages that have separately undergone gene loss. I just do not understand why people so badly want to not use alignments to build trees). Anyway - overall many of the things he said were interesting but I find certain non-evolution evolutionary analyses really grating.

Anyway - I was going to ask him a question after his talk about this, but then decided that, since I was talking next, getting into an argument with him just before my talk might seem lame. So I passed on the question. And then I gave my talk on the need to fill in the tree of life in terms of genome sequencing projects. I discussed a project we are just wrapping up that was part of the NSF "Tree of Life" program in which we sequenced genomes of eight bacteria that are from phyla that at the time had no genomes available. And then I talked about a new project I am coordinating at the Joint Genome Institute in which we are sequencing 100 genomes to really fill in some of the bacterial and archaeal tree. Next week I will post more about this project but I note - this is not done to study the tree of life per se. It is being done because if we have reference genomes from across the tree, all of our genome analyses of other systems and of metagenomes get better.

After dinner and some shell cllecting on the beach, there were evening talks and I went to the informatics session. Some of the talks there were good but the best thign I saw there was someone (I think Ben Blackburne) saying his slides were going to be on something called slideshare.net. I had never heard of this and checked it out and it seems pretty cool. I may use it in the future ... but gotta go off to other things.

Marco Island Evening One - The Strange and the Good

Well, I made it through my talk at Marco Island without too many scars. It seemed to go pretty well - I talked about a new project in which I am involved at the Joint Genome Institute on creating a Genomic Encyclopedia for Bacteria and Archaea. I will write about that more here at another time.

But what I want to do now is discuss some of the marketing ploys from last night. One of the strangest was from the Pacific Biosciences group which sponsored a beach party with fireworks. It was completely surreal. People lingering at the beach with drinks and loud music and then all of a sudden - fireworks were launched into the sky. Not the "greenest" of activities I must say. But never mind that. What was the reason for fireworks in the middle of February? I guess the company is trying to make a big splash but the whole thing was just strange to me.

Much better was the party sponsored by Genome Technology magazine. It was a few hundred yards down the road at a bar. Everyone had to walk there which was good since many people end up never leaving the halls around the conference area. And the place was packed to the gills with people drinking and eating and seemingly having a good time. No fireworks (thankfully) and a good respite from the hotel.

Needless to say, these types of festivities do not happen at any evolution or ecology conference I have been to. The genomics world is still heavy on the marketing and self promotion. Sometimes that makes it fun (Genome Technology) and sometimes it just makes me want to run away (Pacific Biosciences).

AGBT Marco Usland Update - Long Live Sequencing

Well, I am sitting in the back of the room at the AGBT meeting and just heard Eric Green give the introduction and Joe Ecker is talking right now. And the theme of the meeting is pretty clear:
LONG LIVE SEQUENCING

Basically, the meaning of this is that, though many said sequencing was dead a few years ago, sequencing is alive, thriving, and going a bit crazy. With the new massively parallel high throughput sequencing machines sequencing is being used for everything and anything. For example, Ecker is using sequencing to study methylation of the genome of Arabidopsis. And others are usign sequencing for expression studies. And of course there is population genetics. And genetic mapping. And my favorite - metagenomics. And so on. So, despite the push to move into a "post genomics" world, sequencing is growing in use not shrinking.

Advances in Genome Biology and Technology Meeting - First Post

Well, I have just finally gotten online at the "Advances in Genome Biology and Technology Meeting" also known as the Marco Island Genome Meeting (because it is held in Marco Island in Florida), or, as we used to call it at TIGR when I worked there, the "I don't want to go to Venter's Genome Meeting Meeting".

My flight in had some issues so alas I missed the workshop today on new technologies, and cannot report on that here, but I think I will get enough on the new technologies at the rest of the meeting to report later.

I got in to Ft Myers Airport at about 5 PM and took a shuttle bus ride from the airport to the Marriott on Marco Island. As usual, I blabbed away on the bus ride. Somehow, I always end up talking about my time at TIGR and my interactions with Craig Venter and Claire Fraser and my witnessing the fights between the Venter camp and the TIGR camp (if you do not know what I am talking about, feel blessed).

I checked in, dumped my bags and then went to the meeting registration where I got a free backpack full of meeting marketing material. Then I bumped into some colleagues and friends including Neil Hall, who was on the faculty at TIGR when I was there and has now moved back to the UK to Liverpool. I also saw Elaine Mardis, who was just at Davis giving a talk about new sequencing technologies (I missed her talk but took her out to lunch in Davis).

After ditching the backpack full of dead trees, I went to the reception/party by the pool. The food was not so bad, the drinks were free, and I bumped into many other colleagues, some of whom I have not seen in many years, and some who I should see more often (e.g., Chuck Langley, who is a colleague at Davis was there as was Len Pennacchio who is at the Joint Genome Institute where I have an Adjunct Appointment and where I try to spend some time, but alas, usually do not).

Anyway - I will post notes and pictures from the meeting as the days go by ... I will try to do it in some regular manner but we will see how that goes.

Charles Darwin Endorses Obama as the "Natural Selection"

LONDON (AP).

Charles Darwin, famous for his work on the evolution of species, has announced that he is endorsing Sen. Barack Obama for President of the United States. Darwin through his family website said

"I have been watching the election in the States closely from my resting place. And though I like both Clinton and McCain in some ways, Obama is the clear choice from an evolutionary perspective."

Darwin has not endorsed a political candidate since Churchill and has never weighed in on elections in the US. He went on to say

"With all the trouble in the US over evolution, they need a strong candidate that embodies what evolution is all about. In this respect he is the natural selection. He stands for change and for survival. Plus he is the strongest advocate for science among the bunch"

Representatives from the Clinton camp would not discuss the endorsement on the record but one who asked to not be named since they were not authorized to discuss the issue said

"You know, we tried to reason with Charlie about this. We even got Bill to send some messages his way. But in the end, there is no changing the minds of some people, especially the dead."

Obama was thrilled. He said

"Since I was a little boy, I have been fascinated by dinosaurs. And I have carried that with me to today, where I am a strong supporter of having science education be independent of religion. I cannot think of a better person to get behind my candidacy."

Other deceased scientists are also considering endorsing candidates but none had made an announcement as of press time.

Top Roles of Microbes in the Superbowl

Well, it is the time of year for everyone to hunker down and watch some good ads on TV in between football plays (I am a football fan, but most years, the ads are better than the game).

And in the spirit of microbiology education I have created a my list of some of the fun roles microbes will play in the superbowl.

• Can anyone say HGH? Sure you can get it from grinding up cadavers, but it is a bit easier to get it from engineered bacteria.
• Cleanliness is next to Godliness.With all the blood, grass, sweat, and other stuff from the Championship games, cleaning those uniforms is going to be tough. Better use some detergents with extra enzymes like these.
• Victory celebration. To the victor goes the bubbly. And boy, that bubbly would really rot without microbes.
• Making a good football. Without some serious processing, a cowhide or pigskin is not something you would want to throw around. Enzymes are a key part of most leather processing. And hey - who makes most of the best enzymes on the planet. That's right, microbes.
• Obesity epidemic. Sure, pumping iron and taking steroids will get you big. But maybe those linemen just have a health dose of some of Ruth Ley's gut bacteria.
• Avoid double dipping. MSNBC (and everyone else) is reporting this story. MSNBC says "Keep an eye on the salsa this Super Bowl Sunday: A researcher inspired by a famous “Seinfeld” episode has concluded that double dipping is just plain gross." Not just gross. "They found that three to six double dips transferred about 10,000 bacteria from an eater’s mouth to the remaining dip sample."
• Football transmits bacteria much like STDs. Yes that is right. Tara Parker-Pope in a blog via the New York Times is reporting about a Salon.Com discussion of MRSA (methicillin resistant Staphylococcus aureus). Salon was weighing in on a recent study that focused on transmission of MRSA among gay men. Salon dug out an New England Journal of Medicine article about MRSA transmission among football players. And Salon says "When it comes to spreading the bacteria, it is not homosexuals we have to worry about….The medical researchers were not studying gays, they were studying the St. Louis Rams. That is correct: football players; in particular, linebackers."