Tuesday, July 31, 2007

The human genome war from a fun perspective

So I was browsing around Amazon because I have a new Evolution Textbook that just came out. And when I searched for "genomics" and "evolution" up popped a "Listmania" list (which I had never heard of before) for Books about J. Craig Venter. And then I saw a new book by Craig - his autobiography "A life decoded: my genome: my life" coming out in October. And that's when I discovered that the people who bought his book (even though it has not come out yet) also bought
So people apparently link Craig to atheism and Einstein. So I said to myself - what about other books by the genome-war folks? What else did people buy when they bought them? This is where the fun began.

Francis Collins: The Language of God.
So apparently, Francis has the religious readers on his side but nobody seems to link him to science in much of any way.

John Sulston's a Common Thread
So it seems Sulston has gotten all the people interested in science history.

Michael Ashburner's Won for All
So I guess Ashburner gets the people interested in the science itself.

I am sure there is more fun to be had here with these. And as my brother pointed out - the Amazon function here of listing what other people bought does not say it is representative in any way (that is, they are trying to sell books so perhaps they list the most popular other books not the ones most commonly linked to the book in question). But it is kind of voyeuristic and fun to see the types of books people are buying in association with these books.

Monday, July 30, 2007

Metagenomics Based Discovery Highlight: Novel Photosynthetic Organism Discovered

Normally I avoid writing about discoveries in non Open Access journals. But I cannot help myself here. On Friday a wickedly cool paper was published in a journal that I will not name here. In this paper they describe a new bacterium: "Candidatus Chloracidobacterium thermophilum." It is REALLY rare for a new bacteria to be described in a journal like this one. How did they get it in this journal? Well this organism represents the first new photosynthetic lineage of organisms discovered in many many many years. The bacterium is in the phylum Acidobacteria and can carry out aerobic photosynthesis. Prior to this discovery, photosynthesis was only known in five evolutionary lineages - all of them bacteria: Cyanobacteria, Chlorobi, Chloroflexi, Proteobacteria and Firmicutes. Photosynthesis in plants, algae and other eukaryotes all came from symbioses with cyanobacteria to these five groups represented the only "primary" photosynthetic lineages. Thus it is a big deal to find a sixth lineage having photosynthesis.

And - here is the fun part. How did they find this? With the help of metagenomics.

Only five bacterial phyla with members capable of chlorophyll (Chl)–based phototrophy are presently known. Metagenomic data from the phototrophic microbial mats of alkaline siliceous hot springs in Yellowstone National Park revealed the existence of a distinctive bacteriochlorophyll (BChl)–synthesizing, phototrophic bacterium. A highly enriched culture of this bacterium grew photoheterotrophically, synthesized BChls a and c under oxic conditions, and had chlorosomes and type 1 reaction centers. "Candidatus Chloracidobacterium thermophilum" is a BChl-producing member of the poorly characterized phylum Acidobacteria.
That is, they saw the first hints of this through analysis of metagenomic data which was generated by isolating DNA from a Yellowstone hot spring and sequencing the snot out of it. Anyway - as some might have guessed - my only lament about this paper is that it is in a non Open Access journal (I tried to convince the lead author to submit elsewhere but was not convincing enough I guess). It really is too bad - it would be nice to post some of their figures here for others to look at and it this paper would make a great one to use for educating the public about metagenomics. But alas the public cannot get this from Science for at least 1 year and bloggers and other news sources cannot really run with the story because of the copyright limitations. So - great science and great example of the power of metagenomics but restricted public use.

Open Science like the start of Apple?

I know a lot has been written in support of Open Access publishing and Open Science but I must say this paragraph (from MungBeing magazine by Andrew Hessel) is one of my favorites is more over the top than I initially realized,

Garage Biology and Open Source Biology: Twenty five years ago, kids flocked to computers, pushing the limits of what they could do. Similarly, the next generation of genetic engineers won't need laboratories or even PhD: they'll have laptops, cheap mail order DNA synthesis, and, thanks to Google and Wikipedia and open journals like PLOS Biology, access to mountains of free biological data. They'll work in basements, garages, and cafes, and they'll trade ideas and collaborate on genetic designs the same way open source programmers now write computer code. Keep in mind that it was only 30 years ago that a little company called Apple started out of a California garage.

Thanks to Bill Hooker's blog response for calming me down a bit about how brilliant this quote is. The main issue I have is that there are risks associated with genome engineering that are different and more substantial than those associated with piecing together computers here and there.

Wednesday, July 25, 2007

The pope is committed to evolution

Well, in my last post I asked if people were committed to "Evolution" and I confess I got a bit worried that this might be misinterpreted by some as "We believe in evolution regardless of the facts." And in fact there was one flame-like comment posting that I deleted from the comments.

But now apparently the Pope has read my blog (or maybe someone told him about it) and he has come out in full support of evolution as a science and the facts of evolution as we evolutionary biologists know then (i.e., natural selection, macro and microevolution, etc).

As reported on MSNBC the Pope said
the debate raging in some countries —particularly the United States and his native Germany — between creationism and evolution was an “absurdity,” saying that evolution can coexist with faith.
In addition, he said
They are presented as alternatives that exclude each other,” the pope said. “This clash is an absurdity because on one hand there is much scientific proof in favor of evolution, which appears as a reality that we must see and which enriches our understanding of life and being as such.
Furthermore, and more importantly, the Pope has re-stated his belief that everyone must do something about global change and environmental destruction:
“We cannot simply do what we want with this Earth of ours, with what has been entrusted to us,” said the pope, who has been spending his time reading and walking in the scenic landscape bordering Austria.
I know I said recently that biology had a good day in the Bush administration. Unfortunately, that was mostly genetics and biochemistry. Evolution and environmental stewardship never seem to have good days there. Maybe just maybe, the Pope will have some impact around the world on both issues even as the U.S. sticks its head in the sand. NOTE - SEE COMMENTS - THE POPE IS PRETTY CLEARLY NOT DOING EVERYTHING HE COULD TO PROTECT THE ENVIRONMENT.

Monday, July 23, 2007

Are you committed to Evolution? Prove it!

Peggy Farnham at the U. C. Davis Genome Center sent me this picture. apparently of a real tattoo. After a google search I found at least an early source for it here.

This inspires me to ask everyone out there - are you committed to Evolution? What have you done to show your commitment?

What have I done? I think the biggest example of my commitment, though boring, is that I worked six years on a new evolution textbook which was just published a few weeks ago (which you can find out about here or order from Amazon here).

Less boring - I once stood on a street corner in New Orleans with Owen White and handed out altered forms of a pamphlet someone else was handing out in which we added some information about evolution.

So - rather that spout off about what I have done .. what has anyone else done? Are you committed?

Sunday, July 22, 2007

Good week for biology in the Bush Administration

It has been a really really good week for biology in the Bush Administration. First, the 2006 National Medals of Science were announced. I know this is administered by NSF but I am sure the Bush administration had some role in the selection but it still is happening during the Bush administration (see comment by Mayra Montrose from the National Medal of Science correcting my erroneous ways). Eight people were recognized (see the MSNBC CosmicLog of Alan Boyle for more information) and six of them do biology-related research:
  • Hyman Bass - University of Michigan. A mathematician.
  • Marvin H. Caruthers - University of Colorado, Boulder. A biochemist.
  • Rita R. Colwell - University of Maryland (College Park, MD). A microbiologist. One of my favorites.
  • Peter B. Dervan - California Institute of Technology. They list him as a chemist but he is really a biochemist with a biology focus, in my opinion.
  • Nina V. Fedoroff - Pennsylvania State University. A plant geneticist.
  • Daniel Kleppner - Massachusetts Institute of Technology. A physicist.
  • Robert S. Langer - Massachusetts Institute of Technology. Also listed as a chemist but does mostly biochemistry.
  • Lubert Stryer - Stanford University. A hard core biochemist.
There will be a presentation at the White House apparently broadcast live:

President Bush will present 2006 and 2005 Laureates with National Medals of Science and Technology during a White House awards ceremony on Friday, July 27, 2007. The ceremony will be broadcast via satellite feed for journalists.It will also be available as a live webcast at www.whitehouse.gov.

And then, even better, Condoleezza Rice announced her new science advisor is Nina Federoff, one of the National Medal Recipients and a plant geneticist (see above). So - the Bush administration has been justifiably criticized for much of the way it treats science, especially biology (can we say evolution anyone). But there are nevertheless pockets of good news. And hey - its better than nothing.

Thursday, July 19, 2007

Single Cell Genomics Workshop at Bigelow Laboratory

Just got this email from Ramunas Stepanauskas regarding a workshop on single cell genomics. I had mentioned in my blog last week about how this seems to be a critical technology for the future of environmental microbiology. And if you want to get in early into this new technology --- apply to this workshop.

I want to draw your attention to the workshop "Single Cell Alternatives to Metagenomics in Environmental Microbiology", which will take place in Boothbay Harbor, Maine, during September 9-11:

We want to gather the different groups developing microbial single cell genomics (SCG) methodology, exchange information, and thereby enable the field to make faster progress; to examine the dominant science questions that are best addressed by this powerful new tool. The use of SCG will likely have a major impact on the fields of microbial ecology, evolution, and bioprospecting, by enabling partial or complete genome assembly of the uncultured taxa from complex communities, thus providing a critical link between isolate genomics and metagenomics. We envision workshop participants as a mix of about 30 principal investigators, graduate students, and postdocs.

Please see the website (above) for more information and how to apply.

Ramunas Stepanauskas

Monday, July 16, 2007

Rated my first paper in PLoS One


Well, PLoS One has announced its rating system is open. See Chris Surridge's Blog for more detail here. This is basically the first good system for trying out ratings for scientific publications in much the way it is done at YouTube and other Web 2.0 type systems.

I personally am not sure if I think PLoS One is the perfect system for scientific publishing. But we desperately need to try out new systems and as an Open Access Web 2.0 scientific publishing system, the concept is worth trying. So - I decided to try it.

I rated my first paper. I picked a paper by Xiang Xia Min and Donal Hickey on DNA barcoding. Why did I pick this paper. Well a few reasons. First, when I searched PLoS One for "metagenomics" and "metagenomic" it was one of the papers that came up. As soon as I saw the Barcoding title line I knew I had to look at this paper. Why? Well a few years ago, I posted a "dissent" on Faculty of 1000 about a paper on Barcoding. I stand by my dissent in that article. Basically I said that Barcoding sounded a heck of a lot like what Pace and others have been doing with rRNA surveying of uncultured microbes for a long long time. And it seems to me that the barcoding researchers are rediscovering some of the same findings and challenges that Pace and others found. Of course, not all can see my Faculty of 1000 review. Why? Well it is not Open Access. Bummer. Especially since the response by Hebert was unconvincing too ... he basically said that rRNA was not used to delineate species. Apparently he had never heard of phylotypes or any of the extensive work using rRNA to do EXACTLY what they are suggesting mitochondrial genes could be used for in plants and animals.

Anyway - enough about Faculty of 1000. In the new paper, the authors discuss some aspects of barcoding and in particular they address whether one gene can represent all the genes in a mitochondrial genome. Basically, they say yes. But that is beside the point here. You want to know more. Read there paper here. And my comment here. That is yet another benefit of Open Access.

I call on everyone out there to find a paper in which you are interested and rate it and comment on it at PLoS One.

Min, X., & Hickey, D. (2007). DNA Barcodes Provide a Quick Preview of Mitochondrial Genome Composition PLoS ONE, 2 (3) DOI: 10.1371/journal.pone.0000325

Joining the DNA Network

So I got an email the other day from from Hsien-Hsien Lei who blogs at Eye on DNA asking if I would like to join "The DNA Network" a collection of blog feeds on Feedburner. So I did. There. And I feel better for it.

And here is the list of all the blogs on the DNA Network

  1. My Biotech Life
  2. Cancer Genetics
  3. Discovering Biology in a Digital World
  4. DNA Direct Talk
  5. Epidemix
  6. Epigenetics News
  7. evolgen
  8. Eye on DNA
  9. Genomicron
  10. henry >> genetics
  11. Mary Meets Dolly
  12. Microarray and bioinformatics
  13. Omics! Omics!
  14. Sciencebase Science Blog
  15. ScienceRoll
  16. The Daily Transcript
  17. The Gene Sherpa
  18. The Genetic Genealogist
  19. The Personal Genome
  20. The Tree of Life
  21. VentureBeat Life Sciences

Saturday, July 14, 2007

When is a worm a microbe? When it is in the New York Times (in 1996)

Well, it is dangerous I guess to follow the ways people get to my blog. One person used the search terms "dr. david relman and the new worm". And what did they get: this. The top hit is an article from 1996 in the New York Times by Lawrence Altman. The story reports on an article in the Lancet which itself reported the apparent connection of a new worm species to the death of an AIDS patient. The worm was identified by PCR surveys. Nevermind the details of the article. The most intriguing thing to me (especially since I did not then realize this was not a new article in the Times) ... the line:

"The sequences were distinct from human DNA and placed the microbe in the tapeworm class"

Yes that's right, the microbe was a worm. I know - it is a little late to be blogging about a 1996 article. But hey, I did not have a blog then and at the time I think I may have written a letter to the editor about the mistake, but I am not so sure anymore. So now I am correcting the record. Worms are in fact NOT microbes.

Friday, July 13, 2007

Metagenomics 2007 Update

Some brief notes on the Metagenomics 2007 meeting. For those who do not know - metagenomics is the simultaneous sequencing of the genomes of communities of microbes.

Day 1 : I missed the introductory talk by Larry Smarr (my flight was late). Then there was an opening poster session - a diverse collection of things. My favorite were those involving methods to sequence the genomes of single cells (e.g., one by Ramunas Stepanauskas). Such methods will be critical for getting reference genomes from organisms that are not abundant in a community but might nevertheless be important.

Then there was a dinner and a post dinner talk by Masahira Hattori. The talk was not overwhelmingly interesting ... sort of a good example of metagenomics as a fad. Hattori has extensive experience in genome sequencing - having been involved in sequencing the human genome as well as the genomes of other large charismatic furry organisms. As with many people who worked on the human genome, he moved into microbial genomic studies. He has done some interesting things in this arena, the most interesting to me being the sequencing of the genome of a symbiotic bacteria called Carsonella. He did talk about this and I learned something I missed in the paper - this genome was sequenced with the aid of genome amplification methods (see above).

Then Hattori talked about his recent work on human microbiome metagenomics. He has done a lot of work in this area including a big project in which 80,000+ sequence reads were generated for 13 healthy Japanese individuals (both adults and children). I confess much of his results/analyses were not convincing - they seemed to me to be something of the order of "I know I should be doing metagenomics - here is some." His talk did lead to one of the funnier moments of the meeting - someone asked a question that went something like this

"I know when I go to Japan my intestinal tract changes" leading to a groan from the audience and at least one "A little too much information" comment. The questioner was clearly going somewhere with then but before he got too far, Hattori interjected "It gets much better"

Day 2: Some notes.

Day 2 was a pleasant surprise. For many metagenomics related meetings you hear the same talks and the same data over and over and over again. That was not the case here.

The first talk was by Jed Furman. This was truly inspiring to me. He presented a tour de force of environmental microbiology where metagenomics was simply a component and he interwove the history of metagenomics too. Among his topics - use of ARISA in surveying microbes, studies of the functions present in marine archaea, species richness versus latitude, the scalar nature of sampling for microbes, changes in ocean communities over time, and functional redundancy. This to me is the ideal use of metagenomics - as a tool in other studies. In this sense I disagree with those who say metagenomics is a field. I view it more as a tool. A powerful tool, as Furman showed. But most powerful if used in the context of other studies. In particular he said "Remarkably few experiments other than sequencing have been done in environmental genomics and I hope that will change"

Other talks were by Dawn Field, David Relman, Jim Tiedje, Janet Jansson, Forest Rohwer, and Mitch Sogin. Just a few tidbits from these:
  • Janet Jannson who talked in part about a twin study of microbes associated with Crohn's disease lauded the idea of a Genomic Encyclopedia for Bacteria and Archaea (a project I am leading at the JGI ... if you want to know more stay tuned or ask). Also she referred to humans as "fermenters of microbes" a phrase I kind of like.
  • David Relman gave a good overview of his and others' work on the human microbiome. One thing he emphasized was the need to remember that rare organisms can be important and that most metagenomics projects do not sample the rare bugs well. And he too then talked about single-cell genomics. He also mentioned a paper I have been waiting for and did not know it had come out. This is a paper on microbial colonization of the human gut in infants by Chana Palmer et al. (with Pat Brown as senior author). In this paper they use a rRNA chip to track microbes colonization infants. This paper is spectacular. Really.
  • Forest Rohwer, who talked most about coral associated microbes and coral damage by people started off by saying "This is my humans suck talk"
There were also breakout sessions, one of which I chaired on "Computational Metagenomics." Our general conclusion from this - metagenomic informatics is really difficult, we need more interdisciplinary efforts to develop new approaches, and that more money is needed for computational efforts if we want to get the most out of metagenomic data (like we were going to say we need less money). All jokes aside, I do agree with this point - metagenomic sequence analysis is orders of magnitude more complex than analyzing any single-organisms genome. And we need a major ratheting up of computational efforts if we are to get the most out of these data sets that are being produced.

Thursday, July 12, 2007

Metagenomics 2007 - streaming live

If you are interested in Metagenomics - log on to the Webcast here.

More info on the meeting can be found here.

Saturday, July 07, 2007

I have been f*&$% tagged

I have been tagged by John Logsdon, a supposed friend and colleague of mine in his Sex, Genes and Evolution blog.

Here are the rules:
  1. We have to post these rules before we give you the facts.
  2. Players start with eight random facts/habits about themselves.
  3. People who are tagged need to write their own blog about their eight things and post these rules.
  4. At the end of your blog, you need to choose eight people to get tagged and list their names.
  5. Don't forget to leave them a comment telling them they're tagged, and to read your blog.

1. I once bumped into Michael Dukakis (ex governor of Massachusetts and presidential candidate) when he was shopping at a grocery store in Brookline, MA. I was living at my aunt and uncle's house in Brookline for the summer while working for Colleen Cavanaugh at Harvard on chemosynthetic symbionts. Dukakis had a bag of onions in one hand and a bag of garlic in the other. Sort of symbolized his political career at the time.

2. My grandfather, Benjamin Post was a physicist (specializing in powder diffraction and X-ray crystallography). When I went to graduate school with plans to work on butterfly population genetics with Ward Watt at Stanford, my grandfather was crushed, because he considered ecology and evolution to be the equivalent of sociology. Not hard science. I kept saying "But we use lots of math" But that did not sell him. It did not help my cause that my brother (who is now by the way an evolutionary biologist), at the time was in grad. school in X-ray crystallography. Then, I decided to not join the Watt lab, and joined the lab of Philip Hanawalt to pursue my dream of working on adaptive/Cairnsian mutation. Thankfully, Rich Lenski convinced me to work on something else. But I stayed in the Hanawalt lab because Hanawalt was the absolute perfect advisor. So when I went to Boston to visit my grandfather and told him I was working on DNA repair and mutation processes, this at least piqued his interest. DNA was after all something physicists worked on. And then I said, "And my advisor, Phil Hanawalt, is in the National Academy and was a biophysicist" my grandfather said "Hanawalt? Is he related to Don Hanawalt?" Turns out, my grandfather worked with Phil Hanawalt's father, J. Donald Hanawalt, who was an expert in powder diffraction. So my grandfather said, not completely in jest, "you may not be doing real science, but at least you are doing it with the child of a real scientist"

3. I worked with Condoleezza Rice. Not recently. When she was provost of Stanford. On redoing Stanford's Science, Math and Engineering requirements for non science majors. She was great in this role (no comment about her current role. I try to avoid politics here). I really liked working with her (OK, I worked mostly with her office, but I did interact with her a bit.

4. I am one of those people who had a horrible reaction to the SmallPox vaccine. I was 10. We were going to Kenya on a family trip to visit my uncle David Post who at the time was studying baboons in Amboseli as part of his PhD research with the Altman's. Never mind that he is now a law professor at Temple (and aspiring blues guitarist). Though getting the reaction sucked, it is a GREAT test of my doctor's knowledge and background. When they ask for allergies, I say "Small Pox Vaccine." Unfortunately, most of them are at a complete loss when they read this as they are beginning to talk to me in an appointment. Only the really good ones can discuss it coherently.

5. The best job I ever had was an internship at the Public Defender Service in Washington, DC. It helped me decide not to go to law school but was immensely interesting and fun. I got to go all over the city interviewing witnesses, taking pictures and generally snooping around. Plus the lawyers there were unreal - just *$&%# brilliant. This included people like Bernie Grimm who now is seen regularly on TV commenting on various lawyerly things. But the best by far was Michelle Roberts, who interns used to go to watch in court just because she was phenomenal.

6. I was originally an East Asian Studies major in college. I had studied Japanese in high school and thought for sure that this was the way to make money and get into the business world. Japan was on the rise and I was going to be prepared. Then in college my freshman year I took intensive Japanese classes and some East Asian Studies classes. At the same time I was taking Biology major classes since I was interested in that too. And when I took an Evolution class taught by Stephen Jay Gould (with Wayne Maddison and David Maddison as the TAs), my mind was torn. Do what my intellectual passion told me (Evolution). Or stay in E. Asian studies - which I was not really interested in anymore - but a friend kept telling me I should major in because Mira Sorvino was in some of my classes (this was before I met the even more smashing woman that became my wife). But Gould and team evolution won out. And I switched my registration to Biology as a major.

7. I can't read fiction anymore. I used to love it. And I even wanted to (and I guess still want to) write fiction (I am a co-author on a short story published in Nature -of course, it is not Open Access). But this all changed thanks to Roman Dial, who was a PhD student at Stanford in the Roughgarden lab when I was there. When Roman, who grew up in Alaska, found out we were going on a trip to Alaska, he gave us all sorts of crazy suggestions for things to do. It was only when someone told me Roman was a "crazy" adventurer and friend of John Krakauer's that I read some of his articles from Outside Magazine. First, this taught me that I did not want to do some of the things he suggested we do in Alaska (like getting dropped off on a glacier by some friends of his in Kennicott then hiking down to a river where some other friends would pick us up and go rafting. The hike he said was a few days. When I looked at the map I realized it might take us a month.) But the other thing that Roman did to me was get me reading non fiction outdoor stories. Then when Into thin Air came out, I was hooked (although Krakauer's book Into the Wild is even better). And I have barely been able to read any fiction since. I have however read just 100s of mountaineering, sailing, exploration, travel and other non fiction stories. But other than a wayward Pynchon novel here and there, no fiction reaches out to me.

8. I am a RedSox fan. A real one. Not one of these "Ooh, they finally won the Series and now I am going to wear an Ortiz shirt or a hat with a B on it." But one who still feels sick to my stomach when the '86 Series is discussed. And who wants to die when the Boone home run off Wakefield is shown on TV. I was born in Boston and though we moved when I was little, my mom helped make me and my brother into Sox fans. But this pain now comes with joy - finally. I told my friends and family when the Sox were down 3-0 to the Yankees in the ALCS in 2004 that this was the perfect set up for the biggest humiliation ever of the Yankees. And oh what a humiliation it was. I even keep the text messages my brother and I sent back and forth during games just as a reminder. And I had put up a RedSox shrine in my office at TIGR during the playoffs that year so now, being a true Sox fan and thus being superstitious about everything, the shrine is in my new office in Davis. That's me. Keeper of the flame.

And sorry to say, but I have accepted phase one of this tagging but am not keen on phase two (tagging eight people). So after consultation with my lawyer, I have decided that the rules are open to interpretation a bit.

And therefore I tag

1. John Logsdon
2. John Logsdon
3. John Logsdon
4. John Logsdon
5. John Logsdon
6. John Logsdon
7. John Logsdon
8. John Logsdon

Tuesday, July 03, 2007

Fishing for biofuels

Well, it sounds a bit crazy but amazingly it turns out to be true. I originally overheard this at a recent conference on biofuels where some venture capitalists hosted a lunch to discuss new possible sources of biofuel production. And a representative of a major international fishing company said they had been approached by a small Pacific Island nation promoting the following idea. The plan is to harvest ALL biomass in their territorial waters surrounding the island and to turn this biomass into fuel. The way they see it, fish, seaweed, algae, and other organisms contain vast reservoirs of material that if processes efficiently could become a significant new source for ethanol production. The questions they were asking related to how much it would cost to simply design giant nets that could collect everything in the water. Apparently, they were even interested in what it would take to collect algae and other microbes.

The way they see it, biofuel production may be more financially rewarding than selling fish and if they could make use of all the other stuff in the water, they might have enough biomass to produce vast amounts of fuel.

I personally love this idea. People are struggling to squeeze the last little bit out of the light that hits the surface of the land on the planet in terms of balancing food and fuel production. So why not simply collect biomass directly from the oceans and turn this into raw material for biofuels? The key question is - how much material could one get? It turns out, quite a bit. It is estimated that the microbial content of ocean surface water is enormous (in particular if one includes the viruses). All one would need is a way of filtering these organisms out of the water (or maybe precipitating them) to supplement the biomass found in the seaweed and larval invertebrates and other organisms. And much of this material will be much easier to process than plant biomass since one will not have the problem of converting lignin and cellulose into usable carbon compounds.

So I believe the time is ripe for an ocean biomass conversion program to be begun to supplement that biofuel production on land. Seems to me like BP and Chevron and the oil companies should be looking into this since they already know a great deal about harvesting material in a marine environment.

NOTE - this is the first posting in a new biofool initiative here at the Tree of Life. Though I support some aspects of the biofuel movement, other parts I think need some reworking. Stay tuned for more brilliant commentary on the issue.

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