The Tree of Life

Monday, April 27, 2009

Assembling the Marine Metagenome, One Cell at a Time

As I have already divulged on twitter and friendfeed, a paper on which I am an author just came out in PLoS One. The paper is Assembling the Marine Metagenome, One Cell at a Time

It represents a collaboration between a bunch of different institutes including the Joint Genome Institute, UC Davis, and the Bigelow Lab in Maine. The main thing in the paper is the use of whole genome amplification to aid in the sequencing of the genome from a single cell.

The first author on the paper Tonja Woyke at the Joint Genome Institute has been adopting and developing methods for this type of single cell work (extending for example the MDA "multiple displacement amplification" protocol. Woyke is one of those rare types who can do both complex lab work and genome analysis and a variety of other things and is also great to be around.

The other main player in the project was Ramunas Stepanauskas from the Bigelow Lab in Maine who is the "biologists" with an interest in the specific samples which were being worked on. These samples were flavobacteria (a type of bacteria) that live in surface ocean waters but have never been grown in isolation in the laboratory. And in such cases, single cell genomics is very useful and powerful. In the paper we show that having this genome is quite useful for interpreting metagenomic data (not surprising, but good to show).

Anyway - check out the paper if you are interested in microbial ecology and/or metagenomics. Or look at the press release here.

Figure 2. Biogeography of microorganisms closely related to MS024-2A and MS024-3C.
A. Geographic distribution of the Global Ocean Sampling (GOS) metagenome fragments with >95% identity to MS024-2A and MS024-3C DNA. Numerals on the map indicate GOS station numbers. B. Sea surface temperature in December 2003, which demonstrates hydrological separation of GOS aquatic samples collected north and south of Cape Hatteras (near GOS station 13). Provided is a composite Aqua-MODIS image for December 2003 (http://oceancolor.gsfc.nasa.gov). The GOS stations were numbered in the order of their sampling, and stations 12, 13 and 14 were sampled on December 18, 19 and 20, 2003.
doi:10.1371/journal.pone.0005299.g002

Saturday, April 25, 2009

Open Access Flu - Updated

In regard to the swine flu infections going on, here are some Open Access PLoS papers articles about flu. In total they provide some useful background reading on flu that anyone can get access to. I have updated the list after prodding from @bpb on Twitter ...

More from PLoS Pathogens (click here for a link to a title search for "influenza")

Wednesday, April 22, 2009

A blog posting of my email signature to reduce clutter.

-----------------------------------------------------------
Jonathan A. Eisen, Ph.D

Professor, University of California, Davis

With appointments in: UC Davis Genome Center

UC Davis Center for Population Biology Dept. of Evolution & Ecology, College of Biological Sciences
Dept. of Medical Microbiology & Immunology, School of Medicine

Adjunct Scientist, DOE Joint Genome Institute

Academic Editor in Chief, PLoS Biology

Mailing address:
UC Davis Genome Center
451 East Health Sciences Drive
Davis, CA 95616-8816

Blog: http://phylogenomics.blogspot.com/
Twitter: http://twitter.com/phylogenomics/
FriendFeed: http://friendfeed.com/treeoflife/
LinkedIn: http://www.linkedin.com/in/jonathaneisen
--------------------------------------------------------------
Support open access to scientific literature:http://www.publiclibraryofscience.org

--------------------------------------------------------------
In order to reduce the length of my signature in my email, I am posting my signature here and then am tinyurling the link in order to make it as short as possible and not clutter up my email (so now my signature reads http://tinyurl.com/jonathaneisen). I do not know if anyone else does this or if there is a better way to do it I would love to know. I have deleted the phone # and email address portions of this but it does have most else.

The dope on brain doping take 2

The New Yorker has a long article on Brain Doping (or as others like to call it, cognitive enhancement) by Margaret Talbot. I was interviewed for it a while ago because of my mischevious April 1, 2008 blog/web joke I coordinated announcing that NIH was cracking down on brain doping.

And although they do not mention my April 1 joke in the New Yorker article, they do quote me

Still, even if you acknowledge that cosmetic neurology is here to stay, there is something dispiriting about the way the drugs are used—the kind of aspirations they open up, or don’t. Jonathan Eisen, an evolutionary biologist at U.C. Davis, is skeptical of what he mockingly calls “brain doping.” During a recent conversation, he spoke about colleagues who take neuroenhancers in order to grind out grant proposals. “It’s weird to me that people are taking these drugs to write grants,” he said. “I mean, if you came up with some really interesting paper that was spurred by taking some really interesting drug—magic mushrooms or something—that would make more sense to me. In the end, you’re only as good as the ideas you’ve come up with.”

I am sure the quote is reasonably accurate. However, it does not include the whole discussion behind the quote. What I said was that staying up all night while on ritalin to write a grant proposal seems silly (and after my Arpil 1 joke was outed, multiple people told me they actually do this). What you need to get a grant funded is good ideas and these do not seem to come from just popping some drug to keep you mind clear when you should be sleeping. So I said something like taking a drug to help give you new ideas - that could make sense (and thus my reference to shrooms which I have by the way never done). Because if that helped you devise some cool new things to do - that it what people look for in grant proposals. Elegant text about something boring - who cares. Not that the writing part of a grant is unimportant but I still do not see how most of these brain doping drugs would help with doing something interesting in science. Ideas without good text - unlikely to get a grant but possible. Good text without a good idea - I would hope no grant would be awarded.

But the quote does make me sound like I am encouraging hallucionagens, which was not the point ... oh well. In this case, no criticism of the New Yorker - just wish they had included a bit more about why I said what I apparently said ... I guess next time I should just say "Ideas are the key. Not churning out bad text at the last minute"

Saturday, April 18, 2009

Davis Picnic Day Parade 2009

Here are some pictures from the Picnic Day Parade today

Friday, April 17, 2009

Genome sequences are not enough

For those interested in either ciliates like Tetrahymena species or how to make sure that a genome sequence is broadly useful to a community of researchers, this email I just got might be of interest. Basically, in a nutshell, a consortium (of which I led in the past - see our main genome paper in PLoS Biology here and a follow up paper in BMC Genomics here) has been sequencing the genome of Tetrahymena thermophila a really cool ciliate (one clade of eukaryotes) that has been a model organism for much molecular and cellular work. As part of the NIH portion of funding for sequencing the genome we subcontracted Mike Cherry at Stanford to create the Tetrahymena Genome Database (TGD) based upon his highly successful Saccharomyces Genome Database (SGD). Now that the grant is over, there is no support for TGD anymore and it is going to at some point become obsolete. Fortunately, there is support (see email) for a Tetrahymena Stock Center to provide resources to the community like strains and now it looks like this stock center will also take on the task of helping maintain the TGD (with Nick Stover, who used to work at TGD). Great news and might give some people something to think about in terms of building and maintaining resources for other genome sequencing projects.

Dear Tetrahymena Community members,

We are delighted to announce that the Tetrahymena Stock Center has been awarded funding by NIH and the National Center for Research Resources (NCRR).

We are very grateful to NIH for continued funding, and to all the members of the Tetrahymena community who have supported our efforts to establish a functional stock center at Cornell University. We are excited that this new funding will allow us to expand the purview of the Stock Center and pursue several goals that will benefit the Tetrahymena community as a whole.

First, we will continue to maintain a large variety of genetic stocks in our secure facilities at Cornell University and make them available to the scientific and educational community. We are constantly seeking to expand the diversity of the strains in the Stock Center as a resource for the community at-large. We are currently are working to complete the acquisition and documentation of several large strain collections, including the critical collections developed by Dr. Eduardo Orias, Dr. Martin Gorovsky, and Dr. Joseph Frankel. In addition, we are now accepting strains from other laboratories to provide a secure site for strains they wish to share with the community. We are also actively providing strains to researchers and educators around the world. We encourage everyone to visit our updated website at http://tetrahymena.vet.cornell.edu/ . We have new expediated online ordering and have streamlined the process for depositing cells. We welcome any comments, suggestions, ideas for other things that you would like to see on this site.

Second, as part of our continuing efforts to make the Tetrahymena Stock Center as useful as possible to the entire Tetrahymena community, we have expanded the purview of the Stock Center to include support for the Tetrahymena Genome Database (TGD). TGD is no longer actively maintained at Stanford and is fast becoming outdated. We believe that making TGD operational under the auspices of the Stock Center and linking support efforts to community annotation strongly complements the overall mission of the Stock Center to facilitate the use of Tetrahymena as a research and teaching organism. We look forward to working with Dr. Nick Stover at Bradley University, who will supervise the development of a genome Wiki and further annotation of the database. Revising the TGD format will be an exciting and challenging task that we hope will involve many members of the Tetrahymena community. We will send out a more detailed explanation of the new TGD format soon. For now, we thank Dr. Mike Cherry for his continued support and help in working with Dr. Stover to make the transition to the Wiki format as easy as possible.

Finally, please continue to use the Stock Center for all of your strain needs, and don't forget to include the costs for strain ordering in your respective grant applications. Contact us with any questions, suggestions, ideas at tetrahymenastockcenter-mailbox@cornell.edu . We look forward to working with the community to enhance the scope and function of the Tetrahymena Stock Center over the next 5 years.

Sincerely,

Ted Clark
Donna Cassidy-Hanley

Thursday, April 16, 2009

Kids Science Book Recommendation #1: Pat Schrödinger's Kitty

OMG. I just got my copy of "Pat Schrödinger's Kitty" by Tiffany Ard. I only found out about this kid's science book because the author (at least, I think it was the author) linked to a posting of mine from her "electric boogaloo" blog (in a post about April Fools). And from there I read about how she was invited to Scifoo this year (Damn her -- why can't I get invited again) and how it was a really good day because someone wrote a post about her kids science book. So, since I am a total geek and love reading sciency things to my kids I took a look. And it looked pretty good so I ordered one for me and one to give to my geeky brother.

And I just got it today. And I must say, it is f*$# brilliant. It is a spoof on Pat The Bunny (which I had to read over and over to kid #1 and #2) wherein the same general things that happen in Pat the Bunny are replaced by Schrödinger kind of things (e.g., "Paul can interact with billions of neutrinos"). This means a lot to me since as a small child my grandfather, a physicist, used to tell me about relativity and Einstein thought experiments. So I encourage all to get this book, even if you do not have little kids. It is worth a serious giggle for anyone. Still haven't read it to the kids - had to post about it 20 minutes after opening the mail.

Tuesday, April 14, 2009

Michael Eisen gives the bird to the Redsox and A's

Yup, that is my brother, Michael Eisen, on his birthday yesterday, giving the bird to the As and Redsox. RIP Mark Fidrych.

Probiotics Trying to Appeal to Kids with "Cool" Bacteria

Was at the Davis Coop on the way home today and saw something new to me. Looks like companies are trying to make bacteria seem "cool" to kids so that kids will start asking for their probiotics much like they might ask for Captain Crunch. See below:

Not sure I like the trend but I do like the attempt to spread the word about how bacteria are not all bad.

Monday, April 13, 2009

A genomic encyclopedia of bacteria and archaea (video of my talk from the JGI user meeting)

My talk at the JGI meeting on "A genomic encyclopedia of bacteria and archaea" is now up at SciVee. See below:

And the slides are up at Slideshare

Eisen.Geba.Jgi2009b

View more presentations from phylogenomics.

And here are Jason Stajich's notes on FriendFeed

Sunday, April 12, 2009

Twisted Tree of Life Award #4: Hoxful Monsters Blog on "Primitive" Animals

Nothing gets me more riled up in evolutionary writings than the use of the term primitive to describe organisms on a "deep" branch in an evolutionary tree. Thus for the following tree

many people would refer to Species 1 as a primitive organism solely on the basis of this tree. In fact, I just saw this in the Hoxful Monsters blog (see here) where it says:

In April 2008, Cassey dunn et el published their famous phylogenomics work in Nature, which placed Ctenophores at the base of the tree making them most primitive animal on Earth. Before that work Sponges were considered as first animals to branch off from rest of the animals and hence occupied a most basal position in the tree of animals for long time. However, some months later another phylogenomics study carried out by Bernd Schierwater et al ; changed things dramatically by placing Trichoplax as most primitive animal replacing Ctenophores. Now a new phylogenomic study published in online section of Current Biology is making headlines , where Sponges regain their position as most primitive animal on Earth.

This is simply wrong as the term primitive, which I avoid at all costs because it is so frequently misused, should only be used to refer to features of organisms not to the branching pattern in an evolutionary tree. Forget for a minute that "primitive" implies that something else is "advanced", as if we could determine which is which. And lets pretend instead for a minute that "primitive" could be used in an equivalent manner as "ancestral." Ancestral is a term used to refer to features of organisms present, as the term implies, in an ancestor. Thus is the organism(s) at the node in the tree labelled with the X had some feature (e.g., lets say, they were green) and Species 4 is green while Species 1 is orange and Species 2 and 3 are purple. In this case, in terms of color, Species 4 has ancestral feature and the other species have derived features. And thus, when I am feeling generous, I will grant that one could sort of use the term primitive to say "Species 4 is primitive in terms of color." I don't like this usage, because primitive implies something about quality that ancestral and derived do not. But it is not so horribly wrong that I cringe.

But I would like to make two more points in terms of the way primitive is misused.

First, even if one species had a large number of ancestral features (and thus for those features resembled an ancestral organism), that species certainly will have some derived features as well. Thus ancestral, derived, and primitive (ick) should only be used to refer to features, not organisms.
Second, the particular position a species occupies in a tree does not tell use whether it has ancestral or derived features. Thus is my color example above, Species 1 does not have the ancestral phenotype -- it has a derived one. Thus calling organisms that branch deeply in a tree "primitive" is wrong not only because it is referring to an organism not a feature but also because deep branching does not imply ancestral features.

In other words, the fact that if you look only at species in the tree, that Species 1 is the deepest branching individual species, does not in any way tell whether Species 1 has primitive (i.e., ancestral) features. Features present in the common ancestor of the entire group (i.e., the organisms at node X) are the ancestral features. These features could change on any of the branches leading to Species 1,2,3, and 4. If they change, then the descendants will have derived features. If they stay the same they will have ancestral features. The branching order of the species does not explicitly tell us which one retains ancestral features.

This inaccurate use of phylogenetic trees to imply primitive features drives me batty. I was disappointed to see this phylogenetic gobbledygook being used in the HoxFul Monsters blog. And thus, Hoxful Monsters is the winner of my fourth "Twisted Tree of Life" award.

Saturday, April 11, 2009

Davis is new home of Bicycling Hall of Fame

Good news for Davis. It was announced today that Davis is the new home of the Bicycling Hall of Fame. Yay. See stories here

Wednesday, April 08, 2009

Evolution phrase of the week: "nickel-famine"

I am quite intrigued by the news stories based on a paper that just came out in Nature on the early history of oxygen producing bacteria (e.g., see the Canada.Com story Thank oxygen-producing bacteria for your existence
and the National Geographic Story Nickel "Famine" Led to Oxygen-Breathing Life?). In short, the paper suggests that about 2.5 billion years ago, the amount of nickel in oceans (and presumably elsewhere) began to decrease, possibly due to changes in volcanism. Furthermore they suggest the reduction in nickel harmed methanogenic microbes which require nickel for multiple processes. Thus the term "nickel famine." As the methanogens declined, many changes occurred including an increase in the oxygen concentration in the atmosphere (with the oxygen coming from cyanobacteria). And presto, the world became just so much more hospitable for many of us and our relatives. Anyway, the term "nickel famine" really stuck with me, so I am making it my evolution phrase of the week.

Tuesday, April 07, 2009

Twisted Tree of Life Award #3: The Columbus Dispatch on Ancient Bacteria

Was browsing Twitter and I saw one post that caught my eye. @MicrobeWorld, which by the way, rocks, wrote

A microbe that is as old as dirt could one day help keep radioactive metals out of our drinking water http://bitly.com/15l9mR

This caught my eye because, well, I study radiation resistance some of the time and the "old as dirt" statement seemed weird.

The article being referred to was in the Columbus Dispatch (The Columbus Dispatch : Tricking toxins) and it was about some interesting work on Shewanella by Brian Lower and others from Ohio State. The work involves using one particular species of Shewanella for bioremediation of radiative waste. The problem however is in the lead in to the article. This is painful to me. It says

A microbe that is as old as dirt could one day help keep radioactive metals out of our drinking water.

Shewanella oneidensis bacteria have existed for billions of years, thriving even when the Earth's atmosphere lacked oxygen.

This is just so so so wrong. Shewanella oneidensis is one species of a large group in the genus Shewanella which itself is part of one subgroup (the gamma group) of the Phylum Proteobacteria (I note I helped analyze the genome sequence of this species a few years ago - see paper here). While it is possible (though not certain) that the Phylum Proteobacteria was established billions of years ago, it is certain that Shewanella oneidensis did not exist at that time. Perhaps this species has been around for tens of millions of years but certainly not billions. This would be like saying "Humans have been around for hundreds of millions of years" simply because animals have been around for that long. In the context of humans the statement is clearly absurd. It is in fact equally absurd in the context of bacteria. And for this, the Columbus Dispatch is getting my third Twisted Tree of Life Award.

More Science Stimulus Spam

Updated ---

Getting even more Science Stimulus Spam from a company called Metabolon. I have gone back and forth about whether to post text of such messages. Originally I posted the full text here.. After the comment from Cariaso I have decided to remove some of the text but to leave some to giver the gist of the spam.

"Research using metabolomics, the global profiling of biochemicals, was a common topic in the recent NIH Challenge Grant request. Metabolon, the leading provider of metabolomics services, is supporting many of these grant submissions by providing free quotes and a description of services and deliverables."

"Please visit" XXXX (deleting their link) "to submit a brief overview of your study and Metabolon will provide a free quote for services which can be included in your proposal."

Metabolon self promotional text here.

More self promotional text here.

"Please visit" XXX "to submit your study now."

"We look forward to working with you.

The Metabolon Team"

A Postdoctoral research position in Antarctic Metagenomics and Microbial Ecology

Here is an ad for a post doc that is to work on a joint project between my lab and that of Craig Cary.

POST-DOC ANNOUNCEMENT

A Postdoctoral research position in Antarctic Metagenomics and Microbial Ecology

A Royal Society Marsden Funded project “Life at the extreme: resolving the genetic basis of microbial endemism in the super-heated soils of Mt. Erebus, Antarctica” is available at the University of Waikato, Hamilton, New Zealand.

Project description

Tramway Ridge geothermal site on Mt. Erebus, an active volcano in Antarctica, is the most geographically isolated geothermal site on earth providing an excellent system for studies of microbial speciation, biogeography, and evolution of thermal adaptation. A recent preliminary genetic survey of the Tramway Ridge microflora revealed an unprecedented diversity of extremely novel microbes only distantly related to any known bacteria [Soo et al., (2009). Environ. Microbiol. 11 (3), 715-728]. Most of these loose affiliations are with organisms identified from deep-subsurface systems suggesting the Tramway Ridge community may be archaic and of a sub-surface origin. A group dominates the community that to date has no known cultured or environmental representative. The successful candidate will employ cutting-edge high throughput DNA sequencing and bioinformatics to acquire and decipher the genetic capabilities and structure of entire microbial community at Tramway Ridge. A combination of these advanced genetic methods coupled with culture dependant approaches will be used to analyse the Tramway Ridge microflora and other Antarctic geothermal sites to address questions focused on endemism, biogeography, evolution, and adaptation.

The project is in collaboration with Dr. Jonathan Eisen, U.C. Davis Genome Center.

Required qualifications

We are looking for a highly motivated postdoctoral scientist with and interest in Antarctic microbiology and experience in metagenomics, microbial ecology, cultivation of microorganisms, and bioinformatics. The successful candidate will drive his/her own project within the context of the project and be actively involved with practical guidance of an MSc student. The University is especially interested in candidates who can contribute to the diversity and excellence of the academic community through research and service.

The position is full time with a salary of NZ$ $56,164 to $68,060 depending on experience. The initial appointment is for 1-year on this multiyear project; continuation beyond will be based on performance. Applicants should submit a CV, a statement of research interests, and the names of three referees to caryc@udel.edu or caryc@waikato.ac.nz. The position is available immediately and will remain open until filled.

Monday, April 06, 2009

Science Stimulus Spam II - Double Yuck

And another science stimulus spam, this one from Perkin Elmer

PerkinElmer self promotional statement deleted to not help them distribute it.

"As you know, the American Recovery & Reinvestment Act of 2009 (ARRA) is providing large opportunities for grant funding through the NIH.

NIH Challenge Grants in Health and Science Research (RC1)
Recovery Act Limited Competition: High-End Instrumentation Grant Program (S10)
Recovery Act Limited Competition: Biomedical Research Core Centers to Enhance Research Resources (P30)
View More NIH Grant Funding Opportunities
PerkinElmer is here to assist you. "

More self promotional text deleted.

More yuck.

Science Stimulus Spam - Yuck

Just got this email from Sequenom

"NIH Challenge Grants

As part of the American Recovery and Reinvestment Act of 2009, the NIH invites Challenge Grant (RC1) applications from domestic institutions/organizations proposing research on Challenge Topics that address specific scientific and health research challenges in biomedical and behaviorial research that will benefit from significant two-year jumpstart funds.

Challenge Areas, defined by the NIH, focus on specific knowlege gaps, scientific opportunities, new technologies, data generation, or research methods that would benefit from an influx of funds to quickly advance the area in significant ways. The research in these areas should have a high impact in biomedical, behavioral science and/or public health.

We are here for you!"

Sequenom self promotional text here deleted to not aid them in distribution.

I mean, Sequenom might do some cool things but yuck. SSS. Science stimulus spam.

Congrats to Phil Bourne who beat out me and some others to win the Ben Franklin Award.

Congrats to Phil Bourne for winning the "Ben Franklin Award." (Bio-IT World) I was honored to be one of the nominees, but if I had had a vote, I would have voted for him. He has been relentless as an Open Access advocate as well as as a bioinformatician.

Saturday, April 04, 2009

Yet Another Reason Davis Should Be Selected for the Bicycling Hall of Fame

Davis is just an incredible bike town. There is good reason it is one of two finalists for being the host city of the Bicycling Hall of Fame. And here is one example of why it should win --- the bike paths and bike lanes around town make this city great for commuting on ones bike. Here are some pictures I took yesterday of my favorite bike ride to work. It is a little bit out of the way but it is worth it. About 7 or so miles total each way and it only has ~ 4 road crossings and one short stretch of a few hundred yards on a bike lane - and the rest is on off road bike paths.

Wednesday, April 01, 2009

The Evolution Particle?

The New York Times is reporting that the Large Hadron Collider was not actually shut down over the winter but was actually apparently looking into the possibility that a new particle is particularly mutagenic. It seems that when they fired up the accelerator, they found that some particles with unusual affinity for DNA were created. So, no black hole but particles that could shape evolution. Seems like the ID people will be all over this one --- maybe this is the guiding hand they have been looking for?

Tuesday, March 31, 2009

HHMI early career scientists

HHMI has announced a new list of anointed ones (HHMI News: HHMI Gives 50 Early Career Scientists a Jump on Their Next Big Idea).

A few comments.

First, it is really really surprising that they are so low on females here (41 men, 9 women by my count). Given that this is for early career scientists and that women have on average sometime more challenges in the early career than men, it would have been nice to see this the other way around.

That being said, they did pick some good people in this list (shocking, I know). Here are a few I want to highlight as they are related to things I tend to write about here:

Rob Knight, at U. Colorado at Boulder who has been developing computational methods to study microbial diversity and has developed lots of cool methods.
Harmit Malik, FHCRC, who does some great stuff on genome evolution.
Michael Laub , MIT who works on Caulobacter development.
Martin Cohn, U. Florida who has done some very cool work on evolution of development in vertebrates.
Neil Hunter UC Davis. UCD's first HHMI awardee. And a good one to pick. He does some cool work on recombination.
Molly Przeworski, U. Chicago, who works on population genetics on a genome-wide scale.
Aviv Regev, Broad Institute, who has done some interesting work on regulatory networks.

I love the idea of finding people not projects. Too bad there is not more of this type of thing from Federal Agencies. We would probably save money in the long run --- review people once every few years and give them some money to do work. Not that competitive grant programs should be eliminated, but funding people more would reduce the # of grant proposals and panels and would probably save $$ in the long run by allowing people to focus on doing work.

Monday, March 30, 2009

Sean Eddy in PLoS Biology on Open Revolution

Interesting article by Sean Eddy on "Open Education" in PLoS Biology on March 24. (see PLoS Biology - Open Revolution). The article is (mostly) a review of "Opening Up Education" a book from MIT Press.

For those not in the now, Sean is a big supporter and proponent of Open Science and is now at the HHMI's Janelia Farm Campus. In addition to developing some smashing software and doing cool science, Sean was instrumental in my conversion to supporting Open Science so I pay attention to what he says. And there is some interesting material in this pub. The ending sums up a lot of what is in there:

More attention must be paid to the fact that someone still needs to spend time painstakingly developing artful ways to make difficult concepts understandable—to teach!—and that it will take even more time (thus money) to render these hard-won ideas using multimedia web technology compared with writing textbooks. Success hinges on the adoption of open licensing by the professionals who make digital educational resources, and on finding ways to finance their work.

Basically, Sean is saying the Open Education is great in concept but that many Open Education resources need work for them to be effective. And that work can take a lot of money. So we need to find ways to get more money into the development of Open Education materials.

Saturday, March 28, 2009

Lessons Learned at the JGI Users Meeting

Well, the Joint Genome Institute (JGI) Users Meeting is Over. For some rapid fire notes on the meeting see the FriendFeed room here. where Jason Stajich, Tom Sharpton and I (and occasionally a few others) took notes on the whole thing as it was happening.

So - what were the lessons learned? What were the main points? So - if you want to know what we were writing about - and don't want to read the notes (they are quite fun actually) how about a word cloud? Well, here is one, which I made by taking the notes, editing out some of th

e names and other non notes text, and then pasting them into TagCrowd.Com and I got this to the left here:

Not actually a bad representation of many of the topics.

But you know, this does not per se capture the big points, just the common points. So I guess if you want the key points, you have to think a bit. First, you have to realize this is a JGI focused meeting (which of course is the whole point of the meeting - it is the JGI User Meeting after all) and most of the people work with JGI in some way so it is a bit hard to see the forrest of genomics for the JGI trees. And here are my top lessons I got out of the meeting after trying to not get too biased by the JGI focus (note - I have an Adjunct Appt. at JGI and do lots of things through there so I am sure I cannot remove the JGI focus completely)

NextGen sequencing continues to open up new windows into biology.
Ecological and population genomics are truly the next big thing.
Related to the above point, one of the next revolutions is going to be in high throughput phenotyping --- after all, we cannot solve the genotype-phenotype problem when we only know the genotype.
Model / reference organisms are still in, but every single organism on the planet is now in play.
NextGen sequencing has completely outrun the ability of even good bioinformatics people to keep up with the data and to use it well.
Related to the above point, the NextNextGen (e.g., Pacific Biosciences) seems to be barreling along and almost ready for prime time. WTF are we going to do in terms of informatics then?
Following up on the above point- we desperately need a MASSIVE effort in the development of tools for "normal" biologists to make better use of massive sequence databases.
I am happy to report that just about everyone seems to be trying to use an evolutionary perspective as part of their work - especially in the selection of organisms for sequencing
I am sorry to report that many of the evolutionary "perspectives" are a bit off kilter.
Sequencing is definitely not over - it is just getting started.
People pushing the technology (e.g., George Church, Craig Venter) into new arenas definitely inspire the crowds.
If you study a plant or an animal and are not studying the microbes that live with them, you are missing something.
If you study ANY organism and are ignoring epigenetics you are behind the curve
Open Access journals like PLoS Biology and PLoS One and Open Science got some huge props at this meeting, for example, with Venter showing many PLoS related images, many others showing stuff from OA journals, George Church talking about Open Source sequencers and Open personal genomics, and many referring to Open genomics databases. Still some areas in need of improvement (e.g., not enough publishing in open access journals still) but the move in the direction of openness is great.
Genome Centers definitely each have their own flavors with JGI positioning itself well in the niches of Ecology, Evolution, and Energy.
Genome Centers are definitely going to have to reinvent themselves as the sequencing capacity for individual labs goes up and up with Illumina/Roche/ABI Solid continuing to spread. Bigger, better, faster, more is one way they can stay ahead of the curve.
Education and training did not get as much play during the talks as I would have hoped. I mentioned it a bit but I do not recall too many other mentions. Too bad as the real potential for the democritization of sequencing comes from people getting trained in how to generate and handle the data and how to at least think about it even if they do not use it directly.
Organismal biology is still desperately important in all of this work - if you know a lot about the organism as a whole then you already are a systems biologist.
Genomic characterization of entire multi-organism systems is on the rise and this is not just microbiota stuff but also things like host-pathogen interactions and symbioses and so on.
Reading DNA is being used in every which way imaginable. Next up - writing DNA.

Thursday, March 26, 2009

JGI Day2

Jason Stajich set up a friendfeed room for today. See below where I am using the FriendFeed embed function ...

Wednesday, March 25, 2009

Live Blogging the JGI Users Meeting

Well, I am at the JGI (Joint Genome Institute) User Meeting - and I am going to try and do some live blogging right here. I am going to do it differently than I have previously and do things in the comments not in the main page here. If it works, great. If not I might switch to FriendFeed. So check out the comments for new updates ....

So - see the comments for this posting but also see FriendFeed where Jason Stajich and I posted many comments. Here are some links:

My FriendFeed
Jason Stajich on one talk
Jason on another talk
Jason on another talk
Jason friend feed

Tuesday, March 24, 2009

Extreme Ice Survey - Tonight 3-24-09 - Watch it

Check out the website Extreme Ice Survey and the NOVA tonight. It is guaranteed to be spectacular.

From their web site they say

"The Extreme Ice Survey is the most wide-ranging glacier study ever conducted using ground-based, real-time photography. EIS uses time-lapse photography, conventional photography, and video to document the rapid changes now occuring on the Earth's glacial ice. The EIS team has installed 27 time-lapse cameras at 15 sites in Greenland, Iceland, Alaska, and the Rocky Mountains. EIS supplements this ongoing record with annual repeat photography in Iceland, the Alps, and Bolivia."

Sean Carroll at Davis

Went to a dinner last night that was in honor of Sean Carroll who is visiting Davis as part of the "Storer" lecture series. It was the first time I have met Sean -- but I have followed him and his writing extensively. I already found him to be one of the best of the best in science and in explaining evolution. I really liked "The Making of the Fittest" and now he has a new one --- which I have not read but it sounds great. It is called "Remarkable Creatures: Epic Adventures in the Search for Origin of Species". He was also quite entertaining at the dinner and handled being peppered with questions very well. Alas I have to miss his talk today since I am at the Joint Genome Institute for a discussion about metagenomic sequencing of samples from Yellowstone National Park.

Anyway - just wanted to write something because I found my brief interaction with him inspiring. It makes me want to do more engagement of the public on evolution than I have been doing (I do some but he inspired me to do more). I also got to meet some of the Storer family who are the people who gave the money to set up the Storer lecture series. It was also inspiring to talk to them - and good to see people giving money to spread knowledge in the life sciences. It was overall a good day for me after being sick for a month and then spending two weeks writing grants ...

PLoS for Everyone

Just a little post here pointing out a new community blog at PLOS. Looks pretty cool ... but of course I am a bit biased.

Sunday, March 22, 2009

Lie to Me, Darwin

Hey - that looks like good old Charlie D. in the room of the lead character in Fox's Lie to Me. Seems likely that it is, given that the show is advised by Paul Ekman from UCSF who is into Darwin. And of course, it really looks like some of the classic pics of Charlie. Good to see Fox TV is not too sold by the lame anti-evolution rhetoric sometimes spouted on Fox News.

Friday, March 20, 2009

2 week Metagenomics Course ... Looks pretty good ...

Microbial Metagenomics
MMG 490/MMG 890 Section 432
Drs. Thomas Schmidt and Jay Lennon, MSU
June 15th -- June 27th
Kellogg Biological Station
MTuWThFSat 9am - 5pm

*Admission to this class is by application only; Scholarship support is available!*

This course offers students opportunities to use state-of-the-art genomic methods to address questions about the structure and function of microbial communities.
Our field site will be the Long Term Ecological Research Site at KBS. The nucleic acid based data generated during the course will be integrated with the expansive data set from the KBS LTER, which includes measurements of the flux of greenhouse gases.

The ultimate goal of the course is to uncover relationships between changes in microbial communities and ecosystem functions.

Morning lectures will address pertinent ecological theories and principles underlying experiments that will be conducting during the afternoon. The afternoon laboratory sessions will be focused on molecular methods, including generation purification of DNA from soil, PCR amplification and construction of clone libraries, and quantitative PCR. This is an intensive 2-week course modeled after the longer and internationally acclaimed MBL Microbial Diversity Course that Dr. Schmidt directs. 3 Credits.

Admission to this class is by application only.

http://www.kbs.msu.edu/summercourses/documents/Microbial-applic.doc or

http://tinyurl.com/c73k62

Thursday, March 19, 2009

Phyloinformatics gets some love from Google (get your students to apply ...)

Just got this from the good folks at Nescent ...

PHYLOINFORMATICS SUMMER OF CODE 2009

http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009

The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of
the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/).

Students in the program will receive a stipend from Google (and possibly more importantly, a T-shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project.

NESCent is particularly targeting students interested in both evolutionary biology and software development. Initial project ideas are listed on the website. These range from hardware accerelation for phylogenetic inference, to tree visualization within a wiki, to
alignment of next-gen sequencing data, to development of a reusable ontology term markup module for biocuration. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests.

TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students opens on Monday March 23rd and runs through Friday, April 3rd, 2009.

INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible.

2009 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009

Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs

Cyberinfrastructure Traineeships (managed separately from GSoC; postdocs also eligible): http://hackathon.nescent.org/
Cyberinfrastructure_Summer_Traineeships_2009

Wednesday, March 18, 2009

Science and the Stimulus 1 NSF Announcement

Posting some notices here I have been getting from various federal agencies ...

Important Notice 131, American Recovery and Reinvestment Act of 2009
Available Formats: PDF
Type: Announcements and Notices Subtype: Important Notices
Organization/Group: Office of Budget, Finance, and Award Management

National Science Foundation
Office of the Director
Arlington, VA 22230

March 18, 2009

Notice No. 131

IMPORTANT NOTICE TO
PRESIDENTS OF UNIVERSITIES AND COLLEGES
AND HEADS OF OTHER NATIONAL SCIENCE FOUNDATION
AWARDEE ORGANIZATIONS

Subject: American Recovery and Reinvestment Act of 2009

On February 17, 2009, President Obama signed the American Recovery and Reinvestment Act of 2009 (Recovery Act) into law. One of the principal purposes of the law is to “provide investments needed to increase economic efficiency by spurring technological advances in science and health”.[1] During the signing ceremony President Obama stated,

"Even beyond energy, from the National Institutes of Health to the National Science Foundation, this recovery act represents the biggest increase in basic research funding in the long history of America’s noble endeavor to better understand our world. Just as President Kennedy sparked an explosion of innovation when he set America’s sights on the moon, I hope this investment will ignite our imagination once more, spurring new discoveries and breakthroughs that will make our economy stronger, our nation more secure, and our planet safer for our children."[2]

In response to this landmark legislation, NSF has developed policies, procedures, and Frequently Asked Questions for use by the awardee community. These documents provide up-to-date information regarding NSF’s implementation of the Recovery Act, and are available at www.nsf.gov/recovery. The key elements of NSF’s implementation of the Recovery Act are highlighted below.

NSF Programs Receiving Recovery Act Funding

The Recovery Act supplements NSF fiscal year 2009 funding by $3.0 billion. NSF currently has many highly rated proposals that it has not been able to fund. For this reason, NSF is planning to use the majority of the $2 billion available in Research and Related Activities for proposals that are already in house and will be reviewed and/or awarded prior to September 30, 2009.

The Foundation also expects to expeditiously award funds as specified in the Recovery Act for: the Math and Science Partnership program (funded at $25 million); the Robert Noyce Teacher Scholarship Program (funded at $60 million); the Major Research Equipment and Facilities Construction Account (funded at $400 million); the Academic Research Infrastructure (ARI) program (funded at $200 million); and the Science Masters program, (funded at $15 million). Solicitations for these latter two programs will be posted this spring.

NSF will post a solicitation this spring for the Major Research Instrumentation Program (MRI) in order to make a sufficient number of awards to utilize the $300 million provided in the legislation. The Foundation currently anticipates that no other solicitations will be posted that are solely in response to the Recovery Act.

Funding Prioritization

NSF will ensure that Recovery Act funds are awarded in a timely manner while maintaining its commitment to its established merit review processes.

In keeping with this, NSF’s overall framework for Recovery Act investments emphasizes the following:

All grants issued with Recovery Act funds will be standard grants with durations of up to 5 years. This approach will allow NSF to structure a sustainable portfolio.

Funding of new Principal Investigators and high-risk, high-return research will be top priorities.

With the exception of the MRI, ARI and Science Masters programs, the majority of proposals eligible for Recovery Act funding include those that are already in house and will be reviewed and/or awarded prior to September 30, 2009.

NSF also will consider proposals declined on or after October 1, 2008. The reversal of the decision to decline must be based on both the high quality of the reviews received on the initial submission and the lack of available funding at the time the original decision was made. The cognizant program officer will contact the institution when a reversal is being considered by NSF. Specific procedural information regarding this new process is available on the NSF Recovery website.

Special Award Conditions

The Recovery Act mandates a significant level of transparency and accountability. The law and implementing guidance identify specific award conditions for awards made with Recovery Act funding. Therefore, award notices will include special award conditions identifying the funding as coming from the Recovery Act, and indicate the specific awardee reporting responsibilities mandated by Section 1512 of the Recovery Act.

Given the goals of the Recovery Act, awardees will be informed that they are expected to expend funds in a timely manner on allowable award costs and that NSF will be monitoring awards for expenditures. If, after 12 months, no allowable expenditures have taken place, NSF may consider reducing or terminating the award and reallocating the funds.

Working in Partnership

NSF is honored by the recognition of the Foundation's role in stimulating the American economy with its inclusion in the Recovery Act. The law and implementing guidance issued by the Office of Management and Budget (OMB) set clear expectations for accountability and transparency from both Federal agencies and from recipients of Recovery Act funding.

The high expectations embodied in the Recovery Act acknowledge the contributions that NSF and its partners in the research and education community have made to the economy and welfare of the nation over the past six decades. This partnership is one of the nation’s greatest strengths, and we look forward to working with you as we continue to pursue the promise of science and engineering and meet the goals of the Recovery Act for securing the nation’s future.

Arden L. Bement, Jr.
Director

[1] P.L. 111-5, Section 3 (a) (3). The full text of the American Recovery and Reinvestment Act of 2009 is available electronically at: http://frwebgate.access.gpo.gov/cgi-bin/getdoc.cgi?dbname=111_cong_bills&docid=f:h1enr.pdf
[2] The full text of President Obama’s remarks at the signing ceremony is available at: http://www.whitehouse.gov/the_press_office/Remarks-by-the-President-and-Vice-President-at-Signing-of-the-American-Recovery-and-Reinvestment-Act/

All NSF official issuances can be found on Inside NSF at http://infoshare.nsf.gov.

If you need a paper copy of this issuance, contact the Supply Unit on P-1 at ext. 8134.

[NSF Official Issuance]

=======================================
InfoShare
http://infoshare.nsf.gov/
Please send questions and comments to feedback-int@nsf.gov

Friday, March 06, 2009

Conyers, Eisen, the Huffington Post and Open Access

In case you are not aware, my brother (Michael Eisen) and Larry Lessig have been engaging in a public "debate" with John Conyers over Conyers' sponsorship of a bill to revoke the NIH policy on Open Access to publications. First the elder Eisen and Lessig wrote a posting:Is John Conyers Shilling for Special Interests? which they then followed up with John Conyers, It's Time to Speak Up. Now Conyers has written a reply: A Reply to Larry Lessig (which I note should have been titled A Reply to Eisen and Lessig, but that is for another day). Anyway it is worth reading them all and if I had not been sick for the last like 3-4 weeks I would write more but I have a million things to catch up on now that I have mostly gotten rid of nasty microbe #3.

Tuesday, March 03, 2009

The human microbiome - term being used in many ways - but at least it is getting some press

Well, the human microbiome is all over the news recently thanks to a new paper on the diversity and biogeography of microbes in human saliva. The paper "Global diversity in the human salivary microbiome Global diversity in the human salivary microbiome" was by Mark Stoneking's lab and is in press in Genome Research (I am following my brother's trend and not putting a link here since the paper in non Open Access). In the paper Nasidze et al report on the use of PCR and sequencing of the rRNA genes from bacteria in human saliva from 120 people. They compare and contrast the samples (14000 sequences in total) and make some conclusions about the connection between bacterial diversity and genetic biogeography of the people from which the samples came.

And this has been covered in the press a bit here and there including

Get ready for much more in the next few years about microbes in and on us (see my discussion of this previously).

My only complaint is that I and Stoneking and many others have unfortunately made a mess of the terminology. The "microbiome" was originally used to refer to the collection of the genomes of the microbes in a particular ecosystem. And the terms "microbiota" was used to refer to the actual organisms. Since Stoneking et al did not survey the genomes, they surveyed rRNA (which really at best tells you about what types of organisms are present) then they should have used microbiota riight? (And if they had I would not have been searching for the genomics component of their work).

Not so fast, even the person who coined the term microbiome (Josh Lederberg) who originally seemed to use it to refer to all the genomes of the microbes also used the term ambiguously (e.g., in one paper he sad "the microbiome flora" meaning I guess the microbiota.

I note, everyone seems to cite A paper by Lederberg called "Infectious History" in Science (Science 14 April 2000:) as the place he used microbiome but I cannot find the term there. I did however find the term in a paper in 2001 by Lora Hooper and Jeff Gordon (Commensal Host-Bacterial Relationships in the Gut Science 11 May 2001: Vol. 292. no. 5519, pp. 1115 - 1118).

The Nobel laureate Joshua Lederberg has suggested using the term"microbiome" to describe the collective genome of our indigenousmicrobes (microflora), the idea being that a comprehensive geneticview of Homo sapiens as a life-form should include the genes inour microbiome (4).

And reference 4 is "Personal communication"

Anyway, others have taken the term microbiome and run with it because it does conjure up to many "microbial biome" which could be used to refer to all the microbes in a system. I prefer the original definitions with microbiota being the organisms and microbiome being the collective genomes of all the organisms.

I have been as guilty as others in mixing up the terms but in the future I plan to push for "microbiome" to be an omics word and not a biome word and for microbiota to be the biome word. That way if you skim a paper or title you might be able to better guess what it is about.

Monday, March 02, 2009

Clip of Harold Varmus on the Daily Show

There really is no better advocate for Science these days than Harold Varmus. He balances politics and science incredibly well and also simultaneously advocates for applied and basic science as well as access to scientific information. Here is the clip of his latest interview on The Daily Show.

The Daily Show With Jon StewartM - Th 11p / 10c

Harold Varmus

Daily Show Full Episodes
Important Things With Demetri Martin

Political Humor
Joke of the Day

They copied my posting and I like it ...

To me, science is about the spread of ideas and knowledge. And as long as I get credit for my ideas and my writing, I am more than happy for people to run with them. I feel the same way about my blog. Thus I was happy when a blog called The Reef Tank said they wanted to include more science about marine biology there and wanted to cross post some of my marine focused postings. And they have done the first one here. All the power to them for wanting to include more science there and happy they are giving my postings another life ...

Finally, PDFs of my papers from my home page starting to show up in Google Scholar.

Well, it has finally happened. And not sure how. But PDFs of all my papers, which I have posted on my MAC.COM (or now known as ME.COM) homepage are finally showing up on Google Scholar. If you go to Google Scholar and type Eisen JA into the window and then look for PDFs for each of the papers some of the files on my .MAC site show up.

When I originally discovered a few months ago that none of my PDFs from this site where showing up on Google Scholar I dug around and discovered in Google's Faqs that it helps to have links to the PDFs of papers. This seemed strange since I had links from my blog and that is run by Google now so it was weird that those did not help. But I added some more links here and there and presto, now the links to the PDFs are showing up inside Google Scholar results.

Mind you, not all of the PDFs have shown up yet and I have no clue why some did and some did not, but this is part of my continuing effort to free up my past publications. Good start. Not done yet, but getting there.

Open Access Notes: Harold Varmus on the Daily Show tonight (3/2/09)

Just a quick note here. For anyone interested in Open Access and science policy in general, Harold Varmus, Nobel Laureate and CoFounder of PLoS, will be on the Daily Show tonight to promote his new book The Art and Politics of Science. Now when are they going to have my brother on the show? He was a CoFounder of PLoS. So what if he does not have a Nobel and never ran NIH. He has won some cool awards here and there, is an HHMI Investigator, and more importantly, he has a blog and Varmus does not. Doesn't that count for something?