Morgan Price - Pushing the Frontiers of Genomics

Well, this is one of those times when I feel completely blown away by some else's brilliance.  And, since I am a bit on the cocky side, this does not happen all that often. But last week it did.  We had a guest come and give a presentation for my lab meeting. His name is Morgan Price and he works in Adam Arkin's lab at Lawrence Berkeley Lab. He is truly pushing the bubble in terms of designing useful software for carrying out comparative and evolutionary genome analyses.  Among his software/tools are FastTree and FastHMM & FastBLAST and MicrobesOnline.org

all of which are of great value in the era of ever expanding genome data accumulation. FastTree is particularly nice, allowing one to build evolutionary trees for data sets including hundreds of thousands of sequences.  And on top of all of this he appears to be big on Open Access Publishing. Anyway - just a little posting here to get people to check out some of his cool computational toys.

Seeking information on undergraduate programs/majors in genomics and/or genome biology?

I am looking around to find examples of undergraduate programs/majors in genomics or genome biology.  I got a couple of potential examples from a post I made on friendfeed but am looking for more.  What I am looking for is not just courses in genomics but majors/programs in genomics ... do they exist and if so, where and what do they look like.  Any information would be helpful.  Here is what I have found so far:

From Google:

• MSU RO: Academic Programs: Genomics and Molecular Genetics
  
• PLoS Biology - The Undergraduate Genomics Research Initiative
  
• Meeting Report: Incorporating Genomics Research into Undergraduate ...
  
• MCB Undergraduate Program - Genetics, Genomics & Development
• Genomics/Bioinformatics :: New Option/Minor Proposal :: Curriculum ...
  
• Incorporating Genomics into Undergraduate Curricula at Wheaton College
  
• Phage Genomics Research Initiative - Division of Biological ...
  
• 123 Genomics - Bioinformatics and Genomics Courses
  

From friendfeed:

• Jason Stajich pointed to Duke's page from their IGSP program
  
• Iddo Friedberg suggested I look at George Mason  - still trying to figure out what is there ...

Anything else?

Francis Collins Launches Biologos - a strange re-working of theistic evolution

Biologos.  All I can say is, well, I am just really baffled by the whole thing. I am all for trying to have discussions about science and religion. But I do not think the two topics are really compatible in the sense of merging them together. Science (and medicine) should be about, well, science. And religion can be about whatever it wants to be. And when we can get religious and scientific leaders together to talk about the implications of each area on the other and on the world, fine too.  But merging the two together into one hybrid such as Christian Science and Creation Science?  Not for me.

Thus it is with some horror that I have been browsing the web site for Francis Collins' new The BioLogos Mission | The BioLogos Foundation (f0r some other discussions of it see e.g., Larry Moran's discussion here, and PZ Myers here and Time Magazine here and US News here). BioLogos appears to be Collins attempt to promote a slight variant of "theistic evolution" which he has been discussing for years and is also in his recent book.

And whatever you may think of theistic evolution, the Biologos version of it is just icky in many ways in my mind. For example, the site has many many links and pointers to books authored by the members of the Foundation (e.g., the front page says "Among other resources, this website posts responses to many of the questions received by Collins, Giberson, and Falk since the publication of their books, including: The Language of God; Saving Darwin; and Coming to Peace With Science.") There are also other links to this page with ads for their books. Not that there is anything wrong with selling ones books, but to have a foundation whose purpose seems in a large part to promote one's books really seems distasteful. 

And the details of Collins attempt to merge science and religion into a version of theistic evolution are really unclean.  Basically, he is trying to argue that on the one hand science and religion are completely separate activities (I support this) but at the same time argues that God can intervene in the setting up of natural laws and in providing some guidance here and there in order to, for example, produce human beings in his image.  

The web site repeats some things from Collins book that are equally illogical - such as saying that altruism can be explained by science (and even specifically saying that science is the way to explain the natural world) but then turning around and saying that science cannot explain extreme forms of altruism (and therefore implying that actually, the natural world cannot be explained by science).  Which is it?  Is science for the natural world or not?

What one wants to believe in terms of faith/religion is a highly personal issue.  But trying to both say that science and religion are completely separate but also that they are not is just completely illogical.  

UPDATE: See also:

• Collins answers the Big Questions on science and faith
  
• More From Francis Collins on God and Evolution
  
• Collins attempts to meld God and science
  
• The how and the why of creation
  
• Q & A: Francis Collins
  

Worst new omics word award: ethomics

Well, look at what I just saw on twitter:

tlemberger omics mania: 'ethomics' http://is.gd/wOcg - should be added to http://omics.org/ but perhaps also nominated for this http://is.gd/g2Bc

That is from Thomas Lemberger and so I followed the last link first, since I thought I might be to, well me. And indeed it was a link to my "Worst new omics word award" for museumomics.

And so then I went to the link on ethomics: High-throughput ethomics in large groups of : Drosophila : Abstract : Nature Methods.
And indeed they use "ethomics" - what is clearly a quite new omics word (only 62 google hits as of this PM). I confess, I stopped reading at the abstract because it was just too much:

---

Abstract

We present a camera-based method for automatically quantifying the individual and social behaviors of fruit flies, Drosophila melanogaster, interacting in a planar arena. Our system includes machine-vision algorithms that accurately track many individuals without swapping identities and classification algorithms that detect behaviors. The data may be represented as an ethogram that plots the time course of behaviors exhibited by each fly or as a vector that concisely captures the statistical properties of all behaviors displayed in a given period. We found that behavioral differences between individuals were consistent over time and were sufficient to accurately predict gender and genotype. In addition, we found that the relative positions of flies during social interactions vary according to gender, genotype and social environment. We expect that our software, which permits high-throughput screening, will complement existing molecular methods available in Drosophila, facilitating new investigations into the genetic and cellular basis of behavior.

For trying to extend omics to ethogram and beahvioral plots I am giving my second coveted "worst new omics word award" to Kristin Branson, Alice A Robie, John Bender, Pietro Perona & Michael H Dickinson. Here is a prediction - ethomics will not become widely used - not soon - not ever. Thanks for pointing this one out Thomas.

Worst new omics award: ethomics

Oops - posted this to the wrong blogspot blog.  Please go to my Tree of Life blog to see this post here.  

Oops. Seems like Davis, CA does not have the swine flu, yet.

See :
Probable swine flu cases in Yolo County found to be human flu - Daily Democrat Online
and News 10 and KCRA

Should evolutionary biologists "debate" creationists/ID advocates?

Last week I received an email also sent to a group of other local evolutionary biologists asking if one of us would be willing to participate in a "debate" with a creationist who was coming in to town to give some sort of talk.  The email said, among other things:

... we have a creationist (who holds to the 6-literal day creation and young earth 6,000 year position), (name deleted), coming on our campus challenging someone to debate him. 

And, well, I ignored the email as did the others apparently.  Then we all got a second email a few days later:

Dear Professors, 

The Creationist side is offering $300 for accepting the challenge! And another $250,000 to anyone presenting any empirical evidence for macro evolution! 

Why has this offer been out there for years? Where are the experts??? Where is the evidence?? How is  this possible?

If you are convinced that Darwin was right, if you accept it, if you teach it to students, as a career, then WHY DO YOU REFUSE TO DEBATE?!

You betray the students that look up to you!! Come on, Creationist don’t bite!

Sorry for this sarcastic tone, but it doesn't make sense. If you teach it in class you must be the first ones defending it.

We have a philosophy graduate wanting to debate, no science professors yet, especially Biology and Anthropology.

Please respond to this email asap!

Clearly, they people organizing this were trying to get someone to do the debate.  But this strategy just convinced me that debating creationists was an absurdly silly thing.  So I wrote back:

The issue is pretty simple to me.  There is nothing really to debate.  Creationism is not science.  It is a religion driven position that pretends (and does so poorly) to be about science.  I for one have perfectly pleasant interactions with many creationists and I understand their beliefs at least at some level.  But just as I would not encourage physicists to debate with those who deny gravity, and just as I would not encourage chemists to debate with those who claim the periodic table is invented, I think it is inappropriate to evolutionary biologists to "debate" with creationists in this type of setting.  Discussing creationism - fine.  Discussing criticism of evolutionary hypotheses - fine.  Having a reasonable panel discussion of science and religion - fine.  Meeting with creationists to discuss their ideas about evolution - ok too.  But engaging in a "debate" and thus even for a second implying that creationism stands on the same ground as evolution - completely ludicrous.  

Sincerely

Jonathan Eisen

Alas, the people doing the inviting were not particularly impressed with my answer:

You Sir, are a COWARD.
If it is so easy in your mind to refute Creationist's arguments, why don't you do it publically? FOR MONEY?! 
Your words do nothing to change the standing offer of $250,000 for evidence of Macro-Evolution. How about Actions, not Words only?

By denying there is a challenge, and at the same time refusing to accept the challenge you tell us that you're unable to defend your position.
We know why you are fine with a panel discussion: because there is no Looser or Winner, you are afraid to loose, that is the real reason behind your rhetoric.

your answer is a nonanswer

Try again.

I guess they did not get my point.  But anyway - I am asking readers out there - what do you think one should do?  Should one debate creationists/ID supporters?  

More on Swine Flu in Davis from the Davis Enterprise.

There is a mini update on the swine flu incidence(s) in Davis at the Davis Enterprise.

Basically it appears the city of Davis is backing off some of the extreme quarantine type measures that were reported yesterday.

GIS mapping of bike accidents in Davis

A PhD student in my lab has generated a nice GIS mapping of auto and bike accidents in Davis, CA.  Worth browsing ...

Swine Flu Hits Davis?

Seems like Swine Flu (aka H1N1) has hit Davis.  See here. 

Swine Flu Hits Davis?

Seems like Swine Flu (aka H1N1) has hit Davis.  See here. 

Open Access Pioneer Award: Rick Prelinger, Image Access

Just saw an interesting article in the UC Davis "Dateline" newsletter about Rick Prelinger who is the founder of the Prelinger Library in San Francisco (and see their blog here). He gave a talk at Davis and thus they wrote an article about him here.

Some good lines from the article include

Rick Prelinger’s biggest thrill is “mainstreaming" historical documents for public consumption.

But getting history into the hands of the average citizen is no easy task, the archivist says.

Overbearing copyright issues and rampant commercialism, he argues, threaten the free exchange of information on which a knowledge society — especially its libraries — depends.

...

Rather than concern themselves with rigid lending policies or copyright protections, library systems should focus on “more product, less process” to better serve patrons, Prelinger said.

...

“If the Google book deal is approved without any changes, we could soon lose 100 million books that society doesn’t know what to do with,” said Prelinger, referring to “orphan works,” or works under copyright, but whose owner is not known.

....

On the other hand, archives are empowering, Prelinger said. “Let’s open up the past. Interesting things happen when we do so.”

In general since Prelinger has been pushing for more openness in libraries and in images, I am giving him an "Open Access Pioneer Award".  Sorry I missed the talk but glad I read the article.  

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 ...

• PLoS Medicine - Modeling the Worldwide Spread of Pandemic ...
  
• PLoS Pathogens: Influenza Virus Transmission Is Dependent on ...
  
• PLoS Biology - Whole-Genome Analysis of Human Influenza A Virus ...
  
• PLoS Biology - Pandemic Influenza: The Inside Story
  
• PLoS Pathogens: H5N1 and 1918 Pandemic Influenza Virus Infection ...
  
• PLoS ONE: Replication and Transmission of H9N2 Influenza Viruses ...
  
• PLoS ONE: Estimation of Influenza Vaccine Effectiveness from ...
  
• PLoS Medicine - Reducing the Impact of the Next Influenza Pandemic ...
  
• PLoS Medicine - A Systematic Analytic Approach to Pandemic ...

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

• Cellular Proteins in Influenza Virus Particles
  
• Evolutionary Dynamics and Emergence of Panzootic H5N1 Influenza Viruses
  
• Influenza Virus Transmission Is Dependent on Relative Humidity and Temperature
  
• Changing Selective Pressure during Antigenic Changes in Human Influenza H3
  
• Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus
  
• Spatial, Temporal, and Species Variation in Prevalence of Influenza A Viruses in Wild Migratory Birds
  
• Multiple Reassortment Events in the Evolutionary History of H1N1 Influenza A Virus Since 1918
  
• Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia
  
• Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses
  
• Influenza in Migratory Birds and Evidence of Limited Intercontinental Virus Exchange
  
• The Evolutionary Genetics and Emergence of Avian Influenza Viruses in Wild Birds
  
• Phylogenetic Analysis Reveals the Global Migration of Seasonal Influenza A Viruses
  
• Growth of H5N1 Influenza A Viruses in the Upper Respiratory Tracts of Mice
  
• Estimation of Transmission Parameters of H5N1 Avian Influenza Virus in Chickens
  
• Molecular Epidemiology of A/H3N2 and A/H1N1 Influenza Virus during a Single Epidemic Season in the United States
  
• Evidence of Infection by H5N2 Highly Pathogenic Avian Influenza Viruses in Healthy Wild Waterfowl
  
• Superior Immunogenicity of Inactivated Whole Virus H5N1 Influenza Vaccine is Primarily Controlled by Toll-like Receptor Signalling
  
• Genetic Compatibility and Virulence of Reassortants Derived from Contemporary Avian H5N1 and Human H3N2 Influenza A Viruses
  
• Domestic Pigs Have Low Susceptibility to H5N1 Highly Pathogenic Avian Influenza Viruses

More from PLoS Medicine

• Influenza in Tropical Regions
  
• A Comparative Analysis of Influenza Vaccination Programs
  
• Influenza-Associated Hospitalization in a Subtropical City
  
• Delaying the International Spread of Pandemic Influenza
  
• Antiviral Resistance and the Control of Pandemic Influenza
  
• Influenza-Associated Hospitalization in a Subtropical City
  
• Health Benefits of Universal Influenza Vaccination Strategy
  
• Influenza Pandemic Vaccines: Spread Them Thin?
  
• Mapping Antibody Epitopes of the Avian H5N1 Influenza Virus
  
• Air Travel and the Spread of Influenza: Authors' Reply
  
• Test Your Knowledge: Ten Questions about Influenza
  
• A Step Closer to Meeting the Threat of Avian Influenza
  
• Sharing H5N1 Viruses to Stop a Global Influenza Pandemic
  
• Air Travel and the Spread of Influenza: Important Caveats
  
• Correction: Air Travel and the Spread of Influenza: Important Caveats
  
• A Systematic Analytic Approach to Pandemic Influenza Preparedness Planning
  
• Can Immunity Induced by the Human Influenza Virus N1 Neuraminidase Provide Some Protection from Avian Influenza H5N1 Viruses?
  
• Optimizing the Dose of Pre-Pandemic Influenza Vaccines to Reduce the Infection Attack Rate
  
• Pandemic Influenza: Risk of Multiple Introductions and the Need to Prepare for Them
  
• The Effect of Universal Influenza Immunization on Mortality and Health Care Use
  
• Modeling the Worldwide Spread of Pandemic Influenza: Baseline Case and Containment Interventions
  
• Priority Setting for Pandemic Influenza: An Analysis of National Preparedness Plans
  
• Prophylactic and Therapeutic Efficacy of Human Monoclonal Antibodies against H5N1 Influenza
  
• Monitoring the Impact of Influenza by Age: Emergency Department Fever and Respiratory Complaint Surveillance in New York City
  
• Antigenic Fingerprinting of H5N1 Avian Influenza Using Convalescent Sera and Monoclonal Antibodies Reveals Potential Vaccine and Diagnostic Targets
  
• Empirical Evidence for the Effect of Airline Travel on Inter-Regional Influenza Spread in the United States
  
• Neuraminidase Antibodies and H5N1: Geographic-Dependent Influenza Epidemiology Could Determine Cross-Protection against Emerging Strains
  
• Live, Attenuated Influenza A H5N1 Candidate Vaccines Provide Broad Cross-Protection in Mice and Ferrets
  
• The Effects of Influenza Vaccination of Health Care Workers in Nursing Homes: Insights from a Mathematical Model
  
• Reducing the Impact of the Next Influenza Pandemic Using Household-Based Public Health Interventions
  

More from PLoS Computational Biology

• Can Influenza Epidemics Be Prevented by Voluntary Vaccination?
  
• The Role of Environmental Transmission in Recurrent Avian Influenza Epidemics
• Neuraminidase Inhibitor Resistance in Influenza: Assessing the Danger of Its Generation and Spread
  
• Risk Maps for the Spread of Highly Pathogenic Avian Influenza in Poultry
  
• Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin
  
• Detecting Emerging Transmissibility of Avian Influenza Virus in Human Households
  
• On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A

More from PLoS One (see even more here)

• Transmissibility of the Influenza Virus in the 1918 Pandemic
  
• Synchrony of Clinical and Laboratory Surveillance for Influenza in Hong Kong
  
• Transdermal Influenza Immunization with Vaccine-Coated Microneedle Arrays
  
• The Impact of the Unstructured Contacts Component in Influenza Pandemic Modeling
  
• Influenza Virus in Human Exhaled Breath: An Observational Study
  
• Panorama Phylogenetic Diversity and Distribution of Type A Influenza Virus
  
• The Waiting Time for Inter-Country Spread of Pandemic Influenza
  
• Is Exercise Protective Against Influenza-Associated Mortality?
  
• Augmented Lung Inflammation Protects against Influenza A Pneumonia
  
• Predicting Pneumonia and Influenza Mortality from Morbidity Data
  
• Cross-Clade Protective Immune Responses to Influenza Viruses with H5N1 HA and NA Elicited by an Influenza Virus-Like Particle
  
• Baseline Levels of Influenza-Specific CD4 Memory T-Cells Affect T-Cell Responses to Influenza Vaccines
  
• A Biological Model for Influenza Transmission: Pandemic Planning Implications of Asymptomatic Infection and Immunity
  
• Estimation of Influenza Vaccine Effectiveness from Routine Surveillance Data
  
• Evolutionarily Conserved Protein Sequences of Influenza A Viruses, Avian and Human, as Vaccine Targets
  
• Activation of Interleukin-32 Pro-Inflammatory Pathway in Response to Influenza A Virus Infection
• Host Genetic Background Strongly Influences the Response to Influenza A Virus Infections
  
• Influenza A H5N1 Immigration Is Filtered Out at Some International Borders
  
• Environmental Factors Contributing to the Spread of H5N1 Avian Influenza in Mainland China
  
• Population-Wide Emergence of Antiviral Resistance during Pandemic Influenza
  

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"

Davis Picnic Day Parade 2009

Here are some pictures from the Picnic Day Parade today

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

Eisen.Geba.Jgi2009b

View more presentations from phylogenomics.

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.

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

• Davis lands Bicycling Hall of Fame - Sacramento Business Journal:
  
• Bicycle Hall of Fame will relocate to Davis
  
• US Bicycling Hall of Fame leaving Somerville for new home in ...
  
• Greensboro Won't Get Bicycling Hall of Fame
• All spokes are pointing to Davis

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.

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.  

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?

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.

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.

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 the 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)

1. NextGen sequencing continues to open up new windows into biology.
2. Ecological and population genomics are truly the next big thing.
3. 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.
4. Model / reference organisms are still in, but every single organism on the planet is now in play.
5. NextGen sequencing has completely outrun the ability of even good bioinformatics people to keep up with the data and to use it well.
6. 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?
7. 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.
8. 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
9. I am sorry to report that many of the evolutionary "perspectives" are a bit off kilter.
10. Sequencing is definitely not over - it is just getting started.
11. People pushing the technology (e.g., George Church, Craig Venter) into new arenas definitely inspire the crowds.
12. If you study a plant or an animal and are not studying the microbes that live with them, you are missing something.
13. If you study ANY organism and are ignoring epigenetics you are behind the curve
14. 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.
15. Genome Centers definitely each have their own flavors with JGI positioning itself well in the niches of Ecology, Evolution, and Energy.
16. 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.
17. 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.
18. 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.
19. 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.
20. Reading DNA is being used in every which way imaginable.  Next up - writing DNA.  

JGI Day2

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

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