Tuesday, December 30, 2008

What to do when your sick? Sickblogging (and a little bit about Adm. Dennis Blair)

Well, I have had some unpleasant winter bug that on top of everything my kids seems to have or at least have something similar.  It has been fun at night here to say the least.  I was hoping to get some work done over winter break especially since I was overwhelmed with teaching in the fall quarter.  That is not happening.  But in the few moments of peace here, I have looked for something to do --- and hey there is one thing I could do with only a little time.  Blogging.  And of course I am not alone in this.  So here are some links to others on sickblogging:
And what have I to say today?  Not much but here is a preview of things to come.  I have a feeling that Obama is stalking me scientifically.  Why?  Well, I am one or two steps removed from a huge number of his appointees and I plan to write about them in the next few weeks once I get better.  One things the science bloggers might not have heard about is the passion Adm. Dennis Blair has for science.  Dennis Blair is Obama's pick for DNI (Director of National Intelligence) and I know him through a program called the Defense Science Studies Group (DSSG).  I will write more about this later, but what I can say here is I think Blair is a brilliant pick by Obama.  Not only does he have a strong military and intelligence background, but more importantly to me, he believes in evidence, and is a strong supporter of science.  And below is a little pic of me getting my certificate from Adm. Blair.  

Tuesday, December 16, 2008

Open Evolution Highlights - the Population Genetics of dN/dS

An interesting new paper in PLoS Genetics (PLoS Genetics: The Population Genetics of dN/dS) by Sergey Kryazhimskiy and Josh Plotkin that discusses the use of the widely used parameter dN/dS (in essence a measure of the ratio of non synonymous to synonymous substitutions in protein coding genes). This parameter is commonly used to estimate the type of selection that has occurred in a protein coding gene.

Here is their summary of their article:
Since the time of Darwin, biologists have worked to identify instances of evolutionary adaptation. At the molecular scale, it is understood that adaptation should induce more genetic changes at amino acid altering sites in the genome, compared to amino acid–preserving sites. The ratio of substitution rates at such sites, denoted dN/dS, is therefore commonly used to detect proteins undergoing adaptation. This test was originally developed for application to distantly diverged genetic sequences, the differences among which represent substitutions along independent evolutionary lineages. Nonetheless, the dN/dS statistics are also frequently applied to genetic sequences sampled from a single population, the differences among which represent transient polymorphisms, not substitutions. Here, we show that the behavior of the dN/dS statistic is very different in these two cases. In particular, when applied to sequences from a single population, the dN/dS ratio is relatively insensitive to the strength of natural selection, and the anticipated signature of adaptive evolution, dN/dS>1, is violated. These results have implications for the interpretation of genetic variation sampled from a population. In particular, these results suggest that microbes may experience substantially stronger selective forces than previously thought.
The key to me is that it seems that many may have been using dN/dS ratios inappropriately when comparing samples within a species. For more, well, see the paper.

Monday, December 15, 2008

Obama indicates his clear support for science with Chu as Secretary of Energy

Well, say what you will about Steve Chu, but the fact that Obama has nominated him to be the Secretary of Energy is only a good sign for science and society as far as I am concerned.

It is a good sign for science because it shows explicitly Obama's respect and support for science. Most recent Secretaries of Energy have been non scientists (the #s depends on whether you count an engineer as a scientist - I do - but some don't) and Bush (who I want to say is out previous president but we still have him for another month) does not believe in evidence in any way, let alone science.

It is a good sign for society because it is important for the president to understand and respect science. So - some may criticize Chu for some issues - but none of the criticisms I have seen really hit home with me. Sure, I would like a Biologist in their in the Cabinet, but Chu seems to actually understand that the biological diversity of the planet is under threat from global change and he wants to do something about it. I cannot really ask for much more from a Physicist/Administrator. For full disclosure - I have an Adjunct position at LAwrence Berkeley Lab where Chu just happens to be the Director. So maybe I am not completely objective, but anyway, I think this is a good day all around.

Saturday, December 13, 2008

Creative Commons- New Video and Fundraising Campaign



Everyone interested in Open Access and the open spread of information should check out the new video from the Creative Commons folks. This is being released as part of a fundraising campaign for Creative Commons  and I recommend that people consider donating to this great organization.  As a side note, the video was directed by Jesse Dylan, the director of the Emmy- award winning "Yes We Can" Barack Obama campaign video and features musical artist will.i.am from the Black Eyed Peas. 

Friday, December 12, 2008

Outdoor Art at Robbins Hall

There is some relatively outdoor art at Robbins Hall at UC Davis. The art features plants, evolution and DNA -- things I dig. Here are some pics.

Robbins Hall Outdoor Art


The only issue I have is that they did not highlight the bacteria that should be present on the bean roots (legumes fix nitrogen via nitrogen fixing bacteria that hang out in nodules in the roots). But if we take an artistic interpretation of the bean roots, some of the little black triangles there can be considered root nodules.

Anyway, just thought I would share the pics. The art is worth checking out if you are in the area.

Tuesday, December 09, 2008

New Dope on "Cognitive Enhancement"

Well, the world works in mysterious ways. April 1 this year, I coordinated a blogosphere hoax regarding the NIH cracking down on brain doping. See Confessions of an April Fool and the Dope on Brain Doping for more detail. And then Nature and many other publications wrote about brain doping when Nature published the results of a survey suggesting many academics take cognitive enhancing drugs. And now, perhpas most interestingly, a group has written a letter to Nature has published a commentary arguing for more research into " responsible use of cognitive-enhancing drugs by the healthy"

From their conclusion:
Like all new technologies, cognitive enhancement can be used well or poorly. We should welcome new methods of improving our brain function. In a world in which human workspans and lifespans are increasing, cognitive enhancement tools — including the pharmacological — will be increasingly useful for improved quality of life and extended work productivity, as well as to stave off normal and pathological age-related cognitive declines. Safe and effective cognitive enhancers will benefit both the individual and society.

But it would also be foolish to ignore problems that such use of drugs could create or exacerbate. With this, as with other technologies, we need to think and work hard to maximize its benefits and minimize its harms

On the one hand I agree that more work in this area is good. On the other hand, people compete all the time based upon cognitive performance. The article discusses thesae and other issues and is worth looking at. As I am on Campus right now I am not sure if the letter is Open Access or not, but I hope it is.

See also
Hat tip to Bora for pointing this out.

Monday, December 08, 2008

Aphid-bacterial symbiosis in more detail, and in the New York Times

Nice little bit in the New York Times tomorrow about aphids and their symbionts. Henry Fountain writes (Observatory - How Tiny Insects, With a Little Help, Survive on Plant Sap - NYTimes.com) about a new article by Angela Douglas, one of the true pioneers of endosymbiont research. In her study she dissects in fine scale detail which essential amino acids are missing from the aphid sap only diet and which ones are made by the symbionts. Interestingly, the research apparently shows that the aphids may have figured out how to make methionine by themselves. I say apparently since I have been unable to track down the paper which I assume is coming out soon.

I should note, in one of the symbioses like this that I have studied with Nancy Moran we found that there were two symbionts contributing to the nutrition of the host. We found that one of the symbionts was likely making amino acids for the host (an insect called the glassy winged sharpshooter which eats only xylem sap) and the other symbiont was likley making vitamins. Nancy showed later with John McCutcheon that the symbiont that was making vitamins also was predicted to be making methionine for the host. So it seems possible there might be a missing symbiont in the aphid study? Although it would be cool if the aphid has figured out how to make an amino acid most animals are not able to make.

Hat tip to Max Lambert for pointing this out.

Tree of Life Gift Recommendation - Climate Kits

Just a quick recommendations for a gift for this holiday seasons that seems cool (metaphorically and literally). It is the climate kit. It comes from a friend of mine from college, Kathy Washienko and this is some of their text:
Kits are convenient collections of tools and tips that will help your family and friends reduce your environmental impact. By grouping what you need in one handy package, a kit makes it easy and fun to take energy-saving steps. Each kit is ultimately a gift to our environment, but will also save you money in reduced energy costs.* And every kit comes with our innovative "rebate." Check them out!
Sounds good to me. And given that I am trying here to promote trees (albeit phylogenetic ones, not real ones) I like that they are planting a tree and trying to be green.

Congrats to Pamela Ronald et al. for Award for Flood Resistant Rice

Congrats to Pam Ronald, colleague, Davis faculty member, and fellow science blogger for receiving a USDA Discovery Award for helping develop a flood resistant rice variety. For more on this see

Thursday, December 04, 2008

"Free" large scale sequencing for Department of Energy related projects ...

Interested in Department of Energy-related missions such as global carbon cycling, alternative energy production, and biogeochemistry? And want some genomes, metagenomes, or other things sequenced that are relevant to these topic areas? All you have to do is write a proposal to the Joint Genome Institute (JGI) Community Sequencing Program, get it selected by the review committee, and then the JGI will do the sequencing and some analysis for you.

Go to this web site to learn more ....JGI - CSP Overview.

Monday, December 01, 2008

UC Davis giving further props to blogs (mine that is)


Hey - thanks UC Davis.  Thanks for promoting blogs on your front page (under the Blogs, iTunes and Facebook section) and thanks for promoting my "Things Scientists should be thankful for"posting.  

Thursday, November 27, 2008

What scientists should be thankful for ...

Well, it is Thanksgiving. I am up late as usual catching up on email. On this day, there is something I have been meaning to post for a few years. I think scientists should take a breath today and give thanks to those who have helped them along the way. I have some specific postings about this in terms of who I want to thanks, but I wanted to make a list here of the types of things scientists should be thankful for. So here goes.

10 things scientists should be thankful for
  1. Teachers. Scientists had to learn science at some point. And most of us have had some stellar science teachers, or teachers of science-related things like math, along the way. We should give thanks to these people.
  2. Inspirers. Similar to #1 except in many cases we have been inspired to become scientists by someone who may not have been a teacher of ours. Perhaps it was a famous scientist, or even a fictional one. Or even someone we knew. It is that inspiration that frequently gets one through the tough times.
  3. Benefactors In general, scientists have a pretty nice life. We get paid (sometimes well, sometimes poorly) and are given research funds, to unlock the secrets of the universe. How cool is that? We should therefore be very thankful for the immediate source of our funds - such as the institutes where we work and the agencies that provide us funds.
  4. Taxpayers. Unless one is funded by private foundations, taxpayers are the ultimate source of those funds mentioned in #3. This source of funds is frequently overlooked but should never be forgotten. Don't forget - we take money people from people that in theory they could have gotten to keep if their taxes were lower. We should thank these taxpayers..
  5. Research personnel (including student researchers, post docs, technicians, etc). Most of the time, scientists get credit for some work that was in a large part actually done by people in our labs. They deserve our eternal gratitude.
  6. Students we teach. Overall, for those scientists who teach, though it may be a required part of our jobs, it is also a great way to learn and to become a better scientist.
  7. Staff at publishers. An important part of communicating science is of course publishing. And though I am a big fan of new ways to disseminate information, let us not forget that there are many many people who aid and abet this dissemination by working for publishers. These folks deserve our thanks.
  8. Study subjects or objects. Whether one studies organisms, rocks, molecules, planets, forces, or whatever, we should all be thankful that there is interesting stuff out there to study. And for those who study living things, if one disturbs them along the way, we should
  9. Librarians and library staff. Access to information is critical for both learning to become a scientist and being a scientist. And libraries play a key role in providing this access.
  10. Family and friends. Late nights at the lab? Working on a grant over the weekend? Writing papers all the time? In school for years and years? All of this takes a toll on friends and family. And we owe them some props.
I am sure there are more categories. But these are some that came to me on this Thanksgiving. Any categories I missed?

Wednesday, November 26, 2008

Tackling a Hairy Beast II


For all out there who love ciliates and their relatives, you might want to check out the second paper to come out of my Tetrahymena thermophila Genome Sequencing Project for which the preprint is available in BMC Genomics.

In this project we have been sequencing, annotating and finishing the macronuclear genome of this lovely organism. Like other ciliates Tetrahymena has two nuclei and two nuclear genomes - the macronucleus (MAC) and the micronucleus (MIC). The MIC is analogous to germ cells in animals -- it is sort of a genomic repository for sexual reproduction. After sexual reproduction, the MIC genome is processed to generate the MAC genome which is then used in an analogous way to soma cells in animals (the MAC is the site for most/all gene expression in Tetrahymena). I have been the PI on this project which was supported by grants from NSF and NIH and was a collaboration involving TIGR (where I used to work), Stanford, UCSB, JCVI (which subsumed TIGR a few years ago) and the Tetrahymena research community.

Our first paper on this project was published in PLoS Biology two years ago. I have written about it previously here.

The new paper describes further work on the MAC genome including finishing many of the chromosomes (which was done spectacularly by Luke Tallon and Kristie Jones), sequencing and analyzing a larger number of ESTs, refining the annotation (coordinated by Mathangi Thiagarajan), and some other analyses. The new paper was led by Bob Coyne, who, with Barb Methé took over coordinating the work at TIGR/JCVI after I moved to UC Davis a few years back. I think they did a stellar job (ni biases here).

Note - I took the title of the posting 'Tackling a Hairy Best" from an NIH press release that was put out when we got the grants for this project.

Attack of the Robo Lizards from Davis

OK - the robo lizards are not attacking. But they are used for some cool behavioral science research here at Davis. Terry Ord and Judy Stamps from UC Davis have a new paper in PNAS coming out this week where they used robo lizards to study the behavior of Anole Lizards. Check out the UCD news site here which has some videos (UC Davis News & Information :: Robo-lizards Help Prove Long-Standing Signaling Theory)

Tuesday, November 25, 2008

Open Metagenomics Highlight - Metagenome Annotation using massively parallel undergrads.


Another fun metagenomics related paper in PLoS Biology. In it Pascal Hingamp et al discuss an Open Source, Open Science system for metagenome annotation (see PLoS Biology - Metagenome Annotation Using a Distributed Grid of Undergraduate Students).

They do this as part of a course on metagenome annotation. And the software for running this is all Open Source and available. They say
"Teachers wishing to use the Annotathon for their courses are invited to create new teams on the public server at http://annotathon.univ-mrs.fr/ (course logistics and team management are detailed in the instructor manual:http://annotathon.univ-mrs.fr/Metagenes/index.php/Instructor_Manual). The underlying open-source software (PHP and MySQL scripts, under a General Public License) is also available for local installation (https://launchpad.net/annotathon/). In addition, a special “Open Access” team is available for freelance students (volunteer instructors are most welcome to help oversee the Open Access team)."
IN a way this is a metagenomics version of the Undergraduate Genomics Research Initiative (UGRI) which was described in a PLoS Biology paper previously.

Well, this is really the end all be all for me combining so many things I like - genomics, metagenomics, annotation, OA publishing, open source software, etc. Nice job Pascal et al ...

Monday, November 24, 2008

Open Microbial Diversity: PLoS papers on using 454-Roche pyrosequencing for rRNA studies

ResearchBlogging.org

Two new papers that just came out in PLoS Journals are definitely worth checking out. They are
Of course I am a bit biased I suppose as I am heavily involved in PLoS and also served as Academic Editor for these papers. But with that being said, I encourage people to check them out. In the PLoS Genetics paper from the labs of Mitch Sogin and David Relman labs discusses continued development of the use of 454-Roche pyrosequencing technology to carry out deep rRNA sampling. Anybody interested in characterizing a microbial community deeply in terms of what organisms are there should consider this approach.

And in the second paper, the same two labs present an in depth study using the 454-Roche rRNA sequencing to characterize the response of microbes in the human gut to antibiotic treatment. Though there have been a few other such studies this is the one that has the deepest characterization of the microbes present.

Note - one thing I find kind of humorous is that one of the authors is listed as Susan M. Huse in one of the papers (she is the first author on the PLoS Genetics paper) and Sue Huse in the other.

Huse, S., Dethlefsen, L., Huber, J., Welch, D., Relman, D., & Sogin, M. (2008). Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing PLoS Genetics, 4 (11) DOI: 10.1371/journal.pgen.1000255

Dethlefsen, L., Huse, S., Sogin, M., & Relman, D. (2008). The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing PLoS Biology, 6 (11) DOI: 10.1371/journal.pbio.0060280

Friday, November 21, 2008

Open Genomics: Genome Evolution Simulator

Quick post here.   Cool new paper (and the software could be cool too but have not tried it yet) on simulating genome evolution.  The paper is from Ian Holmes and others at Berkeley (see his lab page on BioWiki here) and the paper can be found here in Genome Biology. Here is the abstract:
Controlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three new open-source programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic structured features) and SIMGENOME (for syntenic genome blocks). Each offers algorithms for parameter measurement and reconstruction of ancestral sequence. All three tools out-perform the leading neutral DNA simulator (DAWG) in benchmarks. The programs are available at http://biowiki.org/SimulationTools.

Tuesday, November 18, 2008

Genomicron on Science by press release.

Just a quick one here. Ryan Gregory is going on against science by press release - one of my biggest pet peeves. Check it out at:

Genomicron: Science by press release.

I see PLoS in everything IV: PLoS at Metagenomics 2008 meeting

I may see PLoS even when it is not there, but in this picture, which was the group photo for the Metagenomics 2008 meeting at CalIT2, I weaseled my way to the front hoping to get my PLoS bag and PLoS shirt into the picture. And looky there - it worked.

Woodland Native Dustin Pedroia Wins AL MVP Award

As a Boston native, one of the worries I had moving out to Davis a few years ago related to being too far from the RedSox, Sure they come to Oakland and sure my brother has season tickets to the A's mostly to get RedSox tickets, but California is really far from Fenway Park. Well, at least there are lots of RedSox fans around here, especially if I go up to Woodland. Woodland, if you do not know, is the home town of the newest RedSox superstar, Dustin Pedroia, who nearly carried the Sox into the World Series and today was awarded the American League MVP Award. Way to go Dustin and thanks Woodland for helping out my team.

Sunday, November 16, 2008

Visit to the Raptor Center and Putah Creek

Just thought I would share some pics from a nice outing we had yesterday. We went to the UC Davis Raptor Center for their open house and then went for a walk along Putah Creek.

Microbiology in the news: How bleach kills germs

I am starting a new thread here - microbiology in the news. And my first posting is about bleach. Everyone probably has used it at one time or another to clean something. And some people use it to kill "germs" (aka microbes) too. Well, MSNBC is reporting (Mystery solved: How bleach kills germs - Science- msnbc.com) on a Cell article that presents evidence regarding how the active ingredient in bleach (hypochlorous acid) kills bacteria. Apparently, it works in a similar way to heat in destabilizing protein structures. Anyway, the researchers claim that this is relevant to killing of microbes inside of people because
"Hypochlorous acid is an important part of host defense," Jakob said. "It's not just something we use on our countertops."
Whether this is true or not, I do not know. But what I do know is that microbes are in the news. And that is good.

For more on the bleach story see

Friday, November 14, 2008

ERIC, E. coli, and you

Just a little posting here. I have been playing around with a website called ERIC and thought I would post about it since it seems pretty useful. ERIC - Enteropathogen Resource Integration Center is
one of eight Bioinformatics Resource Centers (BRC) for Biodefense and Emerging/Re-Emerging Infectious Diseases. Funded by the National Institute of Allergy and Infectious Diseases (NIAID), ERIC serves as an information resource for five members of the bacterial family Enterobacteriaceae.
So if you want to learn more about E. coli and its relatives and their genomes, this is a good place to start

Thursday, November 13, 2008

Suggestions for Obama's CTO

Want to suggest priorities for Obama's CTO? Go to http://www.obamacto.org.

Plug of the week - Extreme 2008: A Deep-Sea Adventure: University of Delaware

Just a little plug here to suggest people might want to check out the web site for a Deep Sea Research Cruise going on right now (Extreme 2008: A Deep-Sea Adventure: University of Delaware). The focus of the cruise is summarized as follows:
The scientists will focus on marine viruses and other tiny life called protists and their roles in the food chain. These organisms prey on bacteria, a primary food that sustains the vent ecosystem.
Some friends/colleagues of mine are involved in this adventure and it sounds like some cool stuff could come out of it. Also you might want to check out the blog of Lisa Z (ExtremeVirus), who is posting about the cruise.

This press release deserves some sort of award ...

Just got pointed by Ruchira Datta to a new press release from Princeton (Princeton University - Evolution's new wrinkle: Proteins with cruise control provide new perspective) that makes some interesting claims about evolution. Ruchira asked if the press release made sense to me. And alas, it does not. It has all sorts of bizarre evolution claims in it including the following
A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.
...

"Our new theory extends Darwin's model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness."

"What we have found is that certain kinds of biological structures exist that are able to steer the process of evolution toward improved fitness,"
....
Unlike Darwin, Wallace conjectured that species themselves may develop the capacity to respond optimally to evolutionary stresses. Until this work, evidence for the conjecture was lacking.
....
"In this paper, we present what is ostensibly the first quantitative experimental evidence, since Wallace's original proposal, that nature employs evolutionary control strategies to maximize the fitness of biological networks,"
It sounds like complete nonsense to me. But I am not sure. Anyone else out there know more?

Wednesday, November 12, 2008

Underselling Genomics Award #1: David Whitworth for "Genomes and Knowledge: A questionable relationship"

I do not normally write too much here about non Open Access publications but this one is so good I had to. Everyone with access to Trends in Microbiology should check out Julian Parkhill's rebuttal to an article written by David Whitworth in the same issue. Whitworth's article is "Genomes and knowledge – a questionable relationship? " and it is in my opinion, filled with some unsuppoerted and over the top statements. In essence, he is arguing that we should stop genome sequencing because there are a bunch of genomes out there already and after all, all that matters is work on model organisms so if you have enough genomes related to your model organism you should move on. Alas I do not have time to detail them here. But fortunately, Parkhill does a great job of responding in his article Time to remove the model organism blinkers. The end of his article reflects how I feel too:
In the end, when faced with the astonishing diversity of microorganisms, if all we manage to do is to describe a few random organisms in painstaking detail, then we will have failed to understand microbiology. To suggest we curtail the remit of microbial genomics is bad enough; to suggest it now, when we are on the brink of finally being able to truly study genomic diversity, is absurd.
So sure, sometimes we in genomics oversell the benefits of genome sequence data (and in fact, I give out a little award here for those people). But Whitworth is at the other end of the spectrum, wearing, as Parkhill states "blinkers" to the benefits of genome sequence data. As a reflection of how much I disagree with most of Whitworth's implications, I am giving him my first "Underselling Genomics Award".

Saturday, November 08, 2008

Outdoor art at the Farmer's Market







Love the outdoor art in the renovated Gardens in Central Park in Davis ...




DNA Dynasty "Company" - Stealing and Lying

Well, just adding my two cents to the pissed off blogosphere regarding a company in Singapore called DNA Dynasty.  Not only are they purveying complete crap in terms of genetics/genomics (e.g., they say they have a genetic test to determine the innate abilities of your children) but they have apparently stolen the logo of the DNA Network of which I am a member.  Lovely.  I figure, if we make enough blogging noise, then when people search for them with google they will at least also see some of our postings.  So here is mine.  See also

Wednesday, November 05, 2008

Metagenomics 2008 Meeting Notes

I am going to post notes here for the Metagenomics 2008 meeting.

#1 - most everyone here seems really happy about the election

#2 - mooched a ride this morning to the conference site from some of the folks who run "The Seed" and related annotation and analysis servers.  I have written about them before but people really should check them out if you are interested in microbial genome analysis. 

#3 - Alex Worden is talking now about picoeukaryotes.  Alex does some of the coolest environmental microbiology out there and just happens to focus on groups of organisms that are frequently ignored.  She just said a key quote "Physiology is not a bulk or an average property" basically saying what I say which is that an environment is not simply a bag of genes.  That is we need to remember that there are real compartments in communities.  Alex just showed an interesting figure on rRNA sampling of uncultured eukaryotes from the Sargasso See (Not et al. EM 2007).   Another key point she has made is that microbial eukaryotes are barely sampled in terms of genomics

#4 - a ridiculously short break (the organizers of this meeting really really need to change the scheduling to have more time to talk to people in breaks).  

#5 - Oded Beja is talking now.  He is really one of the key people behind the entire metagenomics revolution as he was the lead on many of the papers from the Delong Lab onthe discovery of proteorhodopsin

#6 - Shannon Williamson is showing an incredibly cool contraption that she uses to take water samples and size fractionate them in the bottom of the ocean.  It is basically a series of filter systems that works on a platform that is run by a deep sea submersible ... this allows them to sample large volumes of water in the deep sea (larger volumes than they could bring back up to the surface)

#7 - a little note --- already many talks referring to using IMG, IMG/M and MG-RAST tools to help with annotation and analysis of genomes and metagenomes.  Clearly there is enormous demand for getting ones data analyzed by some public or semi-public tools ...

#8 - Yuri Gorby --- gave a talk about nanowires which are basically little mini cables that cells use to connect to other cells and shuttle electrons around.  This stuff is beyond cool --- it is completely fascinating.

Tuesday, November 04, 2008

Metagenomics Meeting --- Competing with the Election

Well, I apologize but I am not going to post anything today about the metagenomics meeting in San Diego since I came late today as I wanted to be at home for the beginning of the election. But I made my way down to San Diego and made it to dinner. The dinner "entertainment" was a talk by one of the grand gurus of ocean microbiology - Steven Giovannoni. Alas, even he realized that he was competing with people wanting to know about the election and I confess I spent most of his talk hitting reload on my phone and surfing between sites. But So I have no notes to post about his talk. But I can say that I am happy about the election. And tomorrow I will try to post some notes about talks. But I may be still too happy to take notes ...

((Note added later --- in retrospect, I (and others I talked to) felt Steve G's talk had way way too much detail for an after dinner talk so I spent the next day taking out much of the detail from my talk to lighten it up. What did this get me? After my talk and later after drinks Steve G. made it clear he thought it stunk because it was too light on details of something he thought should have been in it. Oh well, I guess this goes to show you cannot make everyone happy.)).

More about How I feel - from my iPhone

How I feel - drawn on my iPhone

Monday, November 03, 2008

Charles Darwin Reiterates Endorsement of Obama

Charles Darwin has again spoken from the grave. In February I reported how Darwin endorsed Obama in the primary against Hilary Clinton (The Tree of Life: Charles Darwin Endorses Obama as the "Natural Selection") (note - his candidacy took off immediately after the 2/5 endorsement). And Darwin is getting in his own November surprise for the election tomorrow. Darwin spoke through a variety of media (I am using this term in reference to the plural of medium - people who speak to the dead .. but I am not sure whether media or mediums is the plural) and said
"This one is such a complete no brainer. Obama is so far and away the fitter candidate. Plus if Palin and McCain do not believe in my greatest work, well they can ..." (we cannot print the rest)
So there it is. Of course, most living well known scientists who have made public statements also endorse Obama, but getting Darwin's support is an extra feather in his cap.

Friday, October 31, 2008

Conflict between religion and evolution? Not according to the Papal Conference on Evolution ...

Not to beat a dead horse here, but some people out there still think there is a absolute conflict between religious beliefs and believing that evolution occurs.  And if you still think that, you might want to check out the schedule for the Vatican Conference on Evolution (and related topics) that is going on right now (see here for the PDF and here for an outline).  

Held at the Vatican from Oct 31 - Nov 4 and sponsored by the Pontifical Academy of Sciences is a conference on "Scientific Insights into the Evolution of the Universe and of Life."  Among the speakers: Takashi Gojobori, Werner Arber, H.Em. Cardinal Christoph Schönborn, Martin Rees, Stephen Hawking, David Baltimore, Luca Cavalli-Sforza, Christian de Duve, Francis Collins (who is the only one of the speakers with God in the title of his talk) and Maxine Singer.  Sounds like a pretty good conference and I really wish I had been invited.  But suffice it to say that (1) the Pope has strong religious beliefs and (2) that the Pope and the Vatican are enthusiastic about evolution as a science.  

Too bad one of our VP candidates seems still stuck on the notion that we need to teach "the controversy" about evolution.  Just what controversy is that?

Genome Technology Runs the Table on Open Access ...

Wow.  Again, wow.  Genome Technology Magazine has dedicated in essence an entire issue to Open Access and they have a whole series on interesting things to say about it.  In addition they are making the issue available under a Creative Commons License so everyone can check it out.  Among the articles are:

Wednesday, October 29, 2008

Nature Endorses Obama for President

Nature has an editorial (America's choice : Article : Nature) on the US Presidential Election that is worth looking at. For those interested in the Cliff Notes Version they end the piece with
"This journal does not have a vote, and does not claim any particular standing from which to instruct those who do. But if it did, it would cast its vote for Barack Obama."
For more detail, I think the key point is here:
On a range of topics, science included, Obama has surrounded himself with a wider and more able cadre of advisers than McCain. This is not a panacea. Some of the policies Obama supports — continued subsidies for corn ethanol, for example — seem misguided. The advice of experts is all the more valuable when it is diverse: 'groupthink' is a problem in any job. Obama seems to understands this. He tends to seek a range of opinions and analyses to ensure that his own opinion, when reached, has been well considered and exposed to alternatives. He also exhibits pragmatism — for example in his proposals for health-care reform — that suggests a keen sense for the tests reality can bring to bear on policy.
They basically reiterate my concern for the McCain-Palin platform regarding science but they do not really go far enough. McCain and Palin have expressed decidedly anti-science positions recently (well, Palin has expressed them previously too). And thus it is not simply what advisors they surround themselves with but whether they would listen to any of them. Sadly the hints are that McCain and Palin will not listen to scientific advisors on many issues. Obama has made it clear that he will. Not that he puts science above all else (nor should he) But at least he will listen and make rational decisions that include science as a component. McCain and Palin seem dead set against "evidence" of any kind much of the time (note - McCain still exhibits occasional glimpses of the reasonable person he used to be on some issues like Global Warming - but these are few and far between).

Hat tip to Oliver M. for sending this around ...

Tuesday, October 28, 2008

PLoS Biology at 5: The Future Is Open Access

Just a quick one here. All those interested in Open Access should look at this editorial on PLoS Biology from the PLoS Biology staff PLoS Biology - PLoS Biology at 5: The Future Is Open Access

Tomorrow's Table on Today's Table x 2

So - I was having breakfast with my daughter this morning and she was in a funky mood.  She wanted some stories so to make life easy and not get up, I opened up the only thing near the table to read - a copy of Nature Biotechnology that I received for free in the mail (not sure why) - and was going to show her some pictures of things.  And there was a review of my friend and colleague Pam Ronald's book "Tomorrow' Table."  And so I told my daughter that this was a story about a book by my friend Pam and reminded her about how we had gone over to Pam's house and how she worked in the office next to mine.  And then I asked my daughter if she wanted to see Pam's book, which I had in the office and she said yes.  And so I got the book and then we told stories about Pam.  So - here in living color is a picture of my daughter and Tomorrow's Table the book and the review of Tomorrow's Table on my table, today. 

Monday, October 27, 2008

Links on Outdoor Art in Davis from DavisLife Magazine

Just got some links to a collection on outdoor art in Davis from people at DavisLife magazine.

Palin announces opposition to research on Homo sapiens

Sarah Palin today has followed up her attack on fruit fly research by condemning much of the NIH Budget and a variety of other scientific earmarks.  At a town hall meeting yesterday while campaigning in Guam, Palin said
"We asked federal agencies to give us a summary of key words relating to research projects and we found an enormous number of them focused on homosapiens. I kid you not."
When asked by a teenage audience member to explain what was wrong with this research Palin said
"You probably are a homosapiens no? Or have many friends that are?  What we need to do is spend money on helping people change and not on studying these homosapiens"
The teen tried to respond but was escorted forcefully out of the hall by security while Palin continued on in her meeting.  At the end of the meeting Palin returned to the topic of science research and said "If elected, the McCain-Palin ticket will reallocate federal funds to eliminate waste on topics like homosapiens and fruit flies.  Enough is enough."

Sunday, October 26, 2008

Proposition 8 - My Vote

I generally shy away from non sciency topics here but occasionally a few slip in. And as I was filling out my absentee ballot I just felt I had to post something about California's horrendous Anti-Gay-Marriage Proposition 8.  Originally, I was going to post a picture of my no vote on my absentee ballot but then  I read this New York Times article about how many states have laws that say something like

"No person shall photograph, videotape, or otherwise record the image of a voted official ballot for any purpose not otherwise permitted under law."
So instead of a picture I am going to simply put words here.  And since a picture is worth 1000 words, here are mine.

No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. 

Evidence Based Healthcare and Baseball

Love the Op Ed piece in the Friday New York Times entitled "How to take American Healthcare from Worst to First."  First, one reason I love this article is it is discussing how we need to move to more "Evidence Based" medicine.  You may be amazed to know that much of medicine is not evidence based but that is the sad truth.  When I first heard about how not all medicine was evidence based medicine (in a talk by David Cox when I was a grad. student) I was blown away.  Anyway, the article is worth a read from this point of view.  

More amazingly is the author list -- Billy Beane (general manager of the Oakland A's), Newt Gingrich, and John Kerry.  What a combination.  They make the argument that medicine needs a wholesale change in the way it is done just like baseball is shifting to more evidence based decisions.  It is a nice analogy.  Too bad the current administration believes that simply thinking about something is the equivalent to evidence.  And also too bad that McCain-Palin seem to be following in the trend of Bush to not hold "evidence" in high regard.  I wonder what Newt (who is a big science and technology advocate) thinks of the recent anti-science push of the Republicans in power.

Saturday, October 25, 2008

McCain Palin going after fruit flies

As if scientists did not have enough reasons to vote against McCain-Palin who seem to have decided that Bush was overly supportive of science. Now Palin is attacking of all things "fruit-fly research." Lovely. Proof that they are both clueless (not knowing what a fruit fly is probably) and anti-science at the same time. For more on this see:



Tuesday, October 21, 2008

Brain Doping April 1 Joke still getting some press

Well, my April 1 collaborative joke on brain doping is still getting some press. See El Pais which reports
Como muestra, algo que empezó como una broma. "Los centros del NIH (los Institutos de Salud de Estados Unidos) pedirán a todos los científicos que quieran optar a sus ayudas y subvenciones a que pasen pruebas antidopaje para comprobar que no han tomado estimulantes cognitivos para aumentar su rendimiento intelectual". Una supuesta World Anti-Brain Doping Authority (WABDA) se encargaría de los análisis. Es el mensaje de una nota de prensa falsa. Una fake lanzada en Internet el pasado 1 de abril, el día de los inocentes en Estados Unidos, por Jonathan Eisen, biólogo evolucionista de la Universidad de California. Comenzó como una travesura, pero el rumor acabó por extenderse por la red.

La broma apunta, sin embargo, a un debate abierto entre la comunidad científica. Si se controla el dopaje en deportes como el ciclismo, ¿por qué no controlarlo en la comunidad científica, donde también compite el intelecto por conseguir becas, ayudas e incluso premios en reconocimiento de su inteligencia? Esa era la reflexión original que, según explica Eisen, le llevó a colgar su broma de Internet. Sin embargo, también afirma que nunca aceptaría que se realizasen ese tipo de controles.

Monday, October 20, 2008

Roan Press Web Site Live

Well, I wrote about Roan Press ("Sacramento's Small Literary Publisher") a while ago (see here) since a friend of mine from grad. school Brad Buchanan had published a new poetry book through them and was on the air on KDVS.  And now the Roan Press web site is live.  You can order Brad's book Swimming the Mirror there (and see a review here).  Brad will be doing a reading at the Avid Reader in Sacramento (1600 Broadway) at 1 PM on October 26. 

Friday, October 17, 2008

Blocked Access Bummer #1

I have decided to start posting when I want to read an article at home but cannot due to lack of access (even though I might have it at work).  Today's bummer is I wanted to read an article by Joel Sachs on "Resolving the first steps to multicellularity" but I could not get it because I do not have access to Trends in Ecology and Evolution at home.  Bummer.  Looks like it could be good. 

Thursday, October 16, 2008

Larry Moran on Phylogenomics, my new paper, and species

Just a quick note to encourage people to check out Larry Moran at The Sandwalk blogging about my new phylogenomics paper (with Martin Wu) and talking about whether one can use species as a term for bacteria.

At Davis Today - Chris Somerville on Cellulosic Biofuels

Quick Post Today --- For THose Interested in Biofuels --- you might be interested in this

Distinguished Lecturer
Dr. Chris Somerville
Director, Energy Biosciences Institute (EBI)
Presents On:
“Cellulosic Biofuels”
UC Davis ARC Ballroom October 16, 2008, 3:00-4:00 PM

Tuesday, October 14, 2008

Happy Open Access Day: Back to Genome Biology for Me

Well, good timing on this one. A new paper from Martin Wu in my lab has recently been accepted to Genome Biology and the provisional PDF was posted online 10/13. The paper ( A simple, fast, and accurate method of phylogenomic inference ) describes a new program Martin wrote called AMPHORA and shows how it can be used to build phylogenetic trees based on concatenated alignments of housekeeping proteins and also for metagenomic phylotyping using a diversity of protein markers. As today is Open Access Day I thought I would just put in a plug for this OA paper and thank Martin for his great work and commitment to Open Access.

I should note - I really really like Genome Biology as a journal - even though they have been rejecting many of my papers lately (or maybe in part because of this). I am really glad this one got in there. I published my first fully OA paper in Genome Biology in 2000 (on symmetric genome inversions in bacteria and archaea -- a paper co-authored with Steven Salzberg, Owen White and John Heidelberg - see Evidence for symmetric chromosomal inversions around the replication origin in bacteria). It is one of my favorite papers from my entire career, as in it we report on a pattern that turns out to appear to be one of the few rules of bacterial and archaeal genome evolution. Anyway - glad to be back in Genome Biology.

Open Access Day: Video of a Talk I Gave About OA

Well, I was going to write all this blather about OA. But I realized it would be easier to share a video of a talk I gave at U. Washington on Open Access as part of their Biomedical Research Integrity Series (U. Washington Program). I cannot figure out how to download/embed the video so instead I am just posting the links. If someone has software for downloading it and wants to help me embed it and/or upload to YouTube and SciVee that would be great ((NOTE - VIDEO IS NOW EMBEDDED BELOW THANKS TO FRANCOIS MICHONNEAU) . Here are the links:

Lecture #2, Responsible Authorship:

Thursday, August 7, 2008; Speaker: Jonathan Eisen, Ph.D., "Responsible Authorship and the Ownership of Scientific Knowledge: Thoughts on Open Access Publishing"
To view the lecture, click here: Flash Player version, Windows Media Player version, or QuickTime Player version (for QuickTime players you may have to open the player and paste the url: rtsp://media.depts.washington.edu/uwbri/BRI_Eisen_2008.mov)



Open Access Day: Thanks to OA Journals Staff

Well, today is a big day for Open Access, as it is, well, Open Access Day. And one thing I really wanted to put out there is that I think we all should say a big thanks to all of those who have worked tirelessly at various OA journals to help move OA into the mainstream and to produce a vast collection of fully open biomedical and scientific literature.

As I am involved in PLoS journals in many ways, I want to thank all of the staff who work behind (and sometimes in front) of the scenes there. There is a relatively full list of these people here. And I am publishing that list here too, with, along with a heartfelt thank you. Thank you. You all rock. And we should also thank all the staff at other OA Publishers (e.g., BMC). You rock too.

PLoS Staff

Finance/Administration Team

Strategic Alliances/Development

IT/Web Team

Publishing Teams

Marketing Team

Production Team

PLoS Biology Team

PLoS Medicine Team

PLoS Community Journals Team

PLoS ONE Team

Irresponsible reporting on "poop doping" from the Washington Post

UPDATE 1 - see below - the author updated her article including some of my critiques. UPDATE 2 - also see Embryette Hyde's post about u...