Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

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.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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?

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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:

<!–details will soon be posted on www.nsf.gov/nsb/awards/nms/medal.htm.–>

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.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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.

Sincerely,
Ramunas Stepanauskas
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Rated my first paper in PLoS One

ResearchBlogging.org

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

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–