Open Flu: Up to date Open analysis of Human/Swine A/H1N1 Influenza

Just got a pointer to a fantastic site with detailed up to date analyses of flu (e.g., swine flu) data. The site is http://tree.bio.ed.ac.uk/groups/influenza/. The site says
These pages are to allow the rapid dissemination of results and analysis of genetic data from the ongoing Influenza A/H1N1 outbreak attributed to swine flu.
And there is some great stuff there posted by among others, Andrew Rambaut, Oliver Pybus, Nicholas Grassly, Mike Worobey and Gavin Smith. Definitely worth checking out. Hat tip to Eddy Holmes for pointing this out.

Marketplace piece on open access

Marketplace on NPR had a mini story on Open Access publishing. See Marketplace: Publicly funded research for a price. Hat tip to Aaron Gussman and Keith Bradnam for pointing this out. I did not listen to the piece but the text is online here. Here are some bits (does not seem to be a particularly well researched piece but it is still something)
KAI RYSSDAL: A lot of the scientific research that goes on in this country is really expensive. And, as it happens, a lot of it is publicly funded. But when taxpayers want to read a particular study that has been paid for with their money, they have to pay again to read about it in, say, The New England Journal of Medicine.
...

JANET BABIN: People who grew up with the Internet expect information to be free. That's what 21-year-old Josh Sommer thought. In 2006 he was a typical college freshman. Studying environmental engineering, hanging out, making new friends. Suddenly, he started to get severe headaches. He had a series of routine tests.

JOSH SOMMER: End up having an MRI and being told that I have a mass right in the very center of my head, entwined with critical arteries, in one of the most difficult locations to operate on. The cancer Josh has is called Chordoma. It's a rare disease with a low survival rate. Even doctors don't know much about it. So Josh threw himself into Chordoma research. He Googled the disease to find out all he could about it, but kept hitting roadblocks.

SOMMER: I'd find an abstract, and I'd click on it. And oh, you have to pay $60 to read this article. Oh, you have to pay $40 to read this article. I mean, I have this disease, I want to know about it. Journal subscriptions -- like the Journal of the American Medical Association -- can cost thousands of dollars each year. With universities and libraries trimming budgets, they can't afford all of them either. What Josh needed was free access to the research online. Last year, the National Institutes of Health unlocked the gates on a lot of research. Through its Web portal called PubMed Central, you can now search research papers for any disease scientists are studying with public funds. It's an estimated 80,000 articles a year. Duke University law professor James Boyle says open access is only fair.

JAMES BOYLE: Why would you possibly say that when the taxpayers funded something, then the public can't get to read it afterwards without paying again?
...
Then they quote Martin Frank from the American Physiological Society. saying something defending restricted access. They also quote rebuttal from Professor Boyle, at Duke:
BOYLE: The Web works great for porn or for shoes, or for flirting on social networks. But it doesn't work really well for science. We haven't done for science what we did on the rest of the Web, which is basically to have this open Web with everything linked together.

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

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")
More from PLoS Medicine
More from PLoS Computational Biology
More from PLoS One (see even more here)

A blog posting of my email signature to reduce clutter.

-----------------------------------------------------------
Jonathan A. Eisen, Ph.D
With appointments in:      UC Davis Genome Center
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"

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 

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.

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.

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



And here are Jason Stajich's notes on FriendFeed

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.

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.

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.

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.

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?