Metagenomics just keeps getting bigger ...

Yet another tip of the hat form the scientific community to the growing field of metagenomics. Today Ed Delong, one of the pioneers of using metagenomic methods to study microbes, was elected to the National Academy of Sciences. Congrats to Ed for this well deserved recognition (now I note, he has done many things in ocean microbiology that are not metagenomics ... but we will pretend here that this was all about his metagenomics work).

Other people elected of particular relevance to this blog -- David Hillis, a great evolutionary biologist, and Rosemary Grant, of Darwin's finches fame.

Francisco J. Ayala - Evolution - Scientists Who Believe in God - - New York Times

Good to see someone other than Francis Collins getting some press about bridging the gap between evolution and religion. Today it is Francisco Ayala, an evolutionary biologist at UC Irvine. There is an interesting story about him in the New York Times today (Francisco J. Ayala - Evolution - Scientists Who Believe in God ).

Now, I thought I knew a good deal about Ayala but I did learn a bit in the article about his life and background (e.g., he was a Dominican priest, which I did not know). I personally think the "religion" vs. "evolution" debate is pretty silly much of the time and succumbs to the modern obsession with controversy. Ayala's new book "Darwin's Gift to Science and Religion" apparently addresses this issue and I hope it does a better job than Collins' book, which I found to be wanting in many areas. Of course, I guess I am a bit biased since I have had a soft spot for Ayala for many years and since he just wrote a very positive review of my new Evolution textbook. Now, if Collins wrote a positive review, I do not think I would like his book any more, but who knows ...

Reminder About the NIH Public Access Policy

To all interested in Open Access publishing

Here is an email I just got from NIH

April 28, 2008

Dear Members of the NIH Research Community:

I am writing to remind you that the mandatory NIH Public Access Policy (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-033.html) applies to final peer-reviewed manuscripts accepted for publication on or after April 7, 2008. Making published research funded by NIH accessible to everyone, including health care providers, patients, educators and scientists, helps advance science and improve human health. We all have a role to play in achieving this goal, and I appreciate your efforts to make the NIH Public Access Policy successful.

The NIH Public Access Policy implements Division G, Title II, Section 218 of PL 110-161 (see http://publicaccess.nih.gov/policy.htm), which was signed into law late last year. Compliance with this Policy is a legal requirement and a term and condition for all active grants and contracts awarded as of April 7, 2008. Failure to comply may trigger one or more enforcement actions, depending on the severity and duration of the non-compliance.

Please see the Public Access Web site for the tools you need to comply with the Policy. The Web site houses Frequently Asked Questions (FAQs), training information, and other resources.

To ensure compliance with the Policy, please remember to:

Address Copyright - Make sure that any copyright transfer or other publication agreements allow your paper to be submitted to NIH in accordance with the Policy.

Submit Papers upon Acceptance for Publication

1. Some journals will submit the final published article on your behalf, without your involvement. See http://publicaccess.nih.gov/submit_process_journals.htm for a list of these journals.

2. For any journal other than those on this list, please:

a. When submitting a paper for publication, inform the journal that the final peer-reviewed manuscript is subject to the NIH Public Access Policy.

b. Make sure that any copyright transfer or other publication agreement allows the final peer-reviewed manuscript to be submitted to NIH in accordance with the Policy. For more information, see the FAQ Whose approval do I need to submit my article to PubMed Central? and consult with your Institution.

c. Submit the final peer-reviewed manuscript to NIH upon acceptance for publication at http://www.nihms.nih.gov/. See the Submission Process for more information.

Cite Papers

§ When citing your NIH-funded papers in NIH applications, proposals or progress reports, please include the PubMed Central reference number (PMCID) for each paper.

§ NIH will monitor compliance through citations. Effective May 25, 2008, when your NIH Program Officer reviews your progress report or application, he or she will be expecting a PMCID in the citation of every applicable paper that arose out of your NIH funding, or a manuscript submission system reference number (NIHMSID) if the PMCID has not been issued. See Section C of our FAQ for examples.

§ If you publish through a journal listed under http://publicaccess.nih.gov/submit_process_journals.htm, there might be a slight delay in assignment of a PMCID. That is okay. We have signed agreements with these journals that allow NIH to resolve submission with them without your involvement. To facilitate your Program Officer’s job, we ask that you indicate ‘PMC Journal- In Process’ until the PMCID is available.

The NIH Public Access Policy is a legal requirement and represents an important opportunity for science and medicine. We are very interested in your feedback on the Policy and are soliciting input through a request for information from March 31, 2008 to May 31, 2008. Please send any comments or suggestions to http://publicaccess.nih.gov/comments.htm.

Sincerely,

Norka Ruiz Bravo, PhD

NIH Deputy Director for Extramural Research

A good Earth Day for me

Well, Earth Day 2008 is almost over. And I guess I had a really good one. I was scheduled to give a talk at 1 PM at Lawrence Berkeley National Lab (LBNL) as part of their Genomics Division Seminar Series. Living in Davis, LBNL is about 1 hour away if there is no traffic and much longer if there is traffic. And so I said, why not try to honor the Earth and not drive and instead take the train. In part I was inspired by the Michael Pollan's article in this Sunday's New York Times about the little things we can do to help the Earth. In part I was inspired by Earth Day. In part I was inspired by going to the Department of "Energy". And in part I was just looking to get some exercise. But here is the story of my day ...

Part one of this adventure was pretty easy. It is about a fifteen minute ride on my mountain bike from my house to the Amtrak stop in Davis. So I headed out about 25 minutes before the train was supposed to leave. And I got my ticket and then hopped on the train with my bike.

And then we sat for 30 minutes or so at the Davis station waiting for a track inspection. Did I get frustrated? Nope. I had my iPhone and my laptop. And I worked on my talk while listening to Science Friday podcasts. And eventually we moved out of the station. And then we got stuck again near Martinez for 15 or so minutes. I was now getting a little worried about timing, but after a phone call with my brother in Berkeley, who I was going to meet, I calmed down (realizing that the people I was hoping to meet at Berkeley could wait for another day) and arranged to meet him at the train stop.

And we met a few blocks from the Berkeley Amtrak stop and began the ride up to LBNL. Past downtown Berkeley. Past UC Berkeley Campus. And up the hill past the Botanic Gardens. Now for real bikers and for me in my past, this would be nothing. But for a flatlander who only sees hills riding across the overpasses over roads, this was a big deal. And finally, we got there. And I changed into a PLoS shirt my brother brought and jeans I had brought and had lunch my brother made ( a PB & J sandwich using jam I had given him that I made from our apricots from my tree that I had frozen last summer). And I chatted with some people coming for my talk, including one of my co-conspirators for the my April 1 joke, Chris Patil, who writes the Ouroboros Blog. Also there were Eddy Rubin (my host and Director of JGI), Janet Jannson (an expert in the human microbiome, among many things), Paul Spellman, Todd Desantis (one of the top rRNA analysis folks around) Mina Bissel. And then I gave my talk (I think it went pretty well ... but I am not exactly objective).

Then after I talked to some people for 20 or so minutes. And then we rode down the hill. A lot quicker than up for sure. And I went to my brother's new lab on UCB's main campus for a party for one of his students who just passed his quals. After a little food and some discussions I headed out. And then I met my friend and co-author of my new Evolution textbook Nipam Patel for a 15 minute mini chat. And then I zipped down to the Amtrak station with 15 minutes to spare so I stopped at the Pasta Shop for a snack. And then I took the train back to Davis (it was on time) and looked out the window at the SF Bay and then the marshlands and then the farmlands. And finally, I rode back to my house by 5:30 PM to hang out with my family. What a nice day - no car. Some exercise. Some science. Some friends. Some fun. So - thanks for the inspiration, Earth, Michael Pollan and Michael Eisen.

Trip to CALIT2 & CAMERA

Just got back from a one day trip to San Diego to visit the folks who run CAMERA, the metagenomics database being run out of CALIT2/JCVI. The main point of this meeting was to start to figure out how to take computational tools that we have developed in my lab or will develop in my new iSEEM project (with Katie Pollard and Jessica Green) and make them available in CAMERA.

But as usual, the most fun part of the trip was to see the CALIT2 toys. And boy do they have toys. Larry Smarr, the director of CALIT2 and the PI on the CAMERA project (funded by the Gordon and Betty Moore Foundation) gave us a quick tour around the building. My slide show is embedded below. Mostly we got to see the massive multimonitor "optiportal" display walls. We also got to see the big linux cluster that is the guts of CAMERA (and may favorite part, of course - the big PLoS Biology sign relating to the Global Ocean Survey papers in front of the computer).


CAMERA, which stands for Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (thus, why we say CAMERA), is a big and complex enterprise, hosting metagenomics sequence data, metadata associated with the sequence, and a variety of analysis tools for working with the data. You can find out more about it in a paper from PLoS Biology here.

Now, CAMERA is not the only metagenomics database out there. The other main one people seem to use is IMG/M from JGI. If you are interested in metagenomics analysis in any way, it is worth becoming familiar with both systems.

Picnic Day Pictures

Tree of Life Runners

More little ditties here

• Harold Varmus was on Science Friday 1.5 weeks ago talking about Open Access. I think he did a fine job, no matter what Evolgen might imply. You can listen to the interview here. Glad Science Friday covered this.
• Just found the blog Evolution Minute. They seem to be trying to represent both sides of the ID vs. evolution debate. Not sure what to make of it yet, but it seems worth checking out.
• New publication available from the American Society of Microbiology. "Uncharted Microbial World: Microbes and Their Activities in the Environment". Thanks to Dan Drell at DOE for pointing this out.
• Obama shares beliefs about Islam and evolution. Note - in case you missed it. Darwin endorsed him here on my blog.
• Charles Darwin's theory of evolution drafts go online. Look behind the scenes at Darwin writing his big book.
• Scathing review of 'Expelled: No Intelligence Allowed' (Ben Stein monkeys with evolution) by Roger Moore.
  

Pictures of Covell Bike Tunnel Being Constructed

IMG_0903.JPG

Open Access Week

I guess, in my effort to catch up on work after spending time working on an April fools joke, I missed that last week was the first "Open Access Week" at least, as promoted by some key OA bloggers (see here, here, here, and here). This was done in honor of the new NIH policy on Open Access to Publications that commenced last week.

Se McBlawg for more detail at: 'Open Access Week': Some Posts from the Blogosphere

Tree of Life Runners Web Notes

Well, I needed a name for little mini tidbits to post on and "Runners" has won the competition. So here is my first "Runners" entry of things from the web that caught my eye this week

• Govt. acknowledges accidents at virus lab. Yes, shocking as it may be to some who believe the government does everything perfectly, they are finally acknowledging some mistakes at the Plum Island Bioweopons/Biodefense research facility.  I note, I think that, while a Bioterror attack is terrifying, I am possibly more worried about things leaking out of research labs than being introduced on purpose.
• Merging bacteria species reverse evolution - evolution. 
• I am not sure I buy this story completely.  It basically is about how two microbe populations that seemed like they were separating are now merging back together.  But some of the researchers involved are very very good so I think it is worth looking at. 
• The World's Smallest Whistle-Blowers, Microbes Warn of Ecological Damage. Forrest Rohwer in the news, again. See Rohwer Lab
• UC Davis News & Information :: Scholars: Open up publishing. Story about Open Access publishing issues associated with UC. Davis.  Oh and I am in it. Oh, and, thanks to Karen Higgins the photographer for making me look much better than reality.
• Bill would safeguard evolution doubters. Florida, being silly. 
• Begley: Blame the Bugs | Newsweek Voices - Sharon Begley.Microbes and xenophobia.
• Genomics and biology come together to fight HIV. Essay by David Goldstein on a new article in PLoS Biology on HIV.  Oh, and David is a co-author of my new Evolution textbook.
• Academy of Sciences names leader, sets fees. Appointment of David Mindell as head of the California Academy of Sciences. 
• Good bacteria and Eli Stone. The Eli Stone episode called "Heartbeat" that showed last week discussed the theory that the appendix is used to repopulate the gut with good bacteria.  This was discussed as an example of how we learn new things in medicine all the time.  Bizarre that this showed up on Eli Stone.  Especially as there seemed to be no evidence for the theory. 
  

Welcoming Pamela Ronald to the Blogosphere

Just a quick post here .... I recommend everyone check out the newbie Blogger on the Block, Pamela Ronald. In addition to having an office, at least temporarily, near mine, she is an author of a new book called Tomorrow's Table discussing multiple marriages of organic agriculture and genetic engineering, an international known plant biologist (see her lab web site)., and a great person to bounce all sorts of ideas off of. As I have been going around the world (in reality and virtually) recruiting active scientists to do more blogging I am very happy to see her start a blog. So I encourage everyone who reads my blog to check out her blog.

Confessions of an April Fool and the Dope on Brain Doping

Well, truth is imitating art in bizarre ways here. Nature today is running a news story by Brendan Maher (also see his forum here) and various related tidbits about a survey they conducted on brain doping. And the lead in to the news story? Well, it is the April 1 joke I coordinated where a group of co-conspirators (who I will name in a bit) and I posted stories about a new NIH crackdown on, yes, brain doping.

The US National Institutes of Health is to crack down on scientists 'brain doping' with performance-enhancing drugs such as Provigil and Ritalin, a press release declared last week. The release, brainchild of evolutionary biologist Jonathan Eisen of the University of California, Davis, turned out to be an April Fools' prank. And the World Anti-Brain Doping Authority website that it linked to was likewise fake. But with a number of co-conspirators spreading rumours about receiving anti-doping affidavits with their first R01 research grants, the ruse no doubt gave pause to a few of the respondents to Nature 's survey on readers' use of cognition-enhancing drugs.

So here I am going to tell the tale of the creation of this April 1 joke. In a way, it all started last April 1, when I created a fake New York Times story about how Craig Venter had been deceiving everyone with stories about sailing around the world studying microbes in the ocean, and in fact he has been studying the microbes living inside his body in order to scoop Francis Collins and others at the NIH on the "microbiome." I made the fake story by taking an article by Nick Wade on Venter sequencing his own genome, downloading the html for the whole web page on the archive of the story, with all the NY Times background material, and editing the text, simply changing the story but keeping the main outline. For example, the title of the real Wade article was "Scientist Reveals Secret of Genome: It's His" and I changed it to "Scientist Reveals Secret of the Ocean: It's Him."

I thought the html version of the story looked great. Here it is. And I tried to send it to people in email but they kept having problems viewing the thing. So in the end, I created a PDF file of the page and emailed that to a few key co-conspirators (who I knew knew a lot of people). And they sent it around. And around. And around. I did not originally post it on my blog, because, well I was worried that Venter would want to kill me. The funny part is, he liked it. And it was the real people who I had made up fake quotes from who wanted to kill me. ( I note, a friend of mine who works at Cold Spring Harbor Press and has the initials AG says he sent it to Nick Wade who also found it funny.)

Anyway, in the end, that April 1 joke worked OK but it has some limitations. First, since I did not post it on the web it did not really use the power of the blogging world to spread. Second, some people figured out it was fake when they went to YouTube or the New York Times web site to look for the things we claimed existed. So, I decided that for this year, if I could come up with a good April 1 joke, I would try and correct these issues.

So - somehow, I hit upon a funny story to do - a spoof in on the cycling and baseball controversies over performance enhancing drugs . But the target would be scientists. That was really the extent of my idea. And then I found the perfect venue to plan it. SciFoo camp (for more on it see here and here and here). Sponsored by Nature and the O'Reilly publishing group. At Google HQ. And with TONS of bloggers and other media types there. We ven considered having a session on humor in science. But that never happened. Fortunately, I cornered various people who seemed to think it would be fun to have a collaborative conspiracy to do an April 1 joke together. And they liked the performance enhancing drugs among scientists idea.

Alas, SciFoo camp was in August of 2007. April 1, 2008 was far away. And the plan slipped to the backburner. I created a private Blogspot blog for people to share information. And invited a few of the original co-conspirators. And we did not make much progress. And then I wrote to Bora (who, like Madonna, really does not need a last name). He was at SciFoo and I knew him through my new role in PLoS. And he knows EVERYONE. And I said:

Bora

Are you up for participating in a grand April 1 joke where I am
hoping to get lots of bloggers to write in different ways about the
same topic to make it really seem real?

J

And he agreed. And then he and I recruited some other bloggers. And then we saw a New York Times article on Brain Doping. We had not really completely formulated a plan to focus on brain doping per se yet (I still thought we could talk about EPO to have endurance at conferences, etc). And we got worried about being scooped by reality. But we soldiered on. At this point I thought maybe the best way to do the joke would be to have everyone separately write a story about some interaction with NIH that hinted at a crackdown on doping among scientists.

In the meantime, I came up with ANOTHER April 1 joke top do, but it seemed like this one had to be done before April 1 since for people to get it it needed to be done while the true news story was hot. So I posted a joke story spoofing the Eliot Spitzer resignation with my own fake resignation from my new position as Academic Editor in Chief of PLoS Biology over buying journal articles. I replaced his wife with my brother (and co-founder of PLoS) and placed a few friends in the story (Alex Gann at Cold Spring Harbor became my replacement, Emma Hill, who left PLoS Biology for a non fully OA journal became Kristen, and I made up a few quotes here and there). I had to post this before April 1 since I knew people would forget abouyt Spitzer quickly. And then I returned to the work on the brain doping joke.

And soon we saw that some people on the Nature Network were talking about trying to do a collaborative April 1 joke. And so I posted a message there and then recruited those who seemed interested. And we had a good core group of conspirators. And people were busy so not much happened. Although Chris Patil, who I used to work with at Stanford, made me freak out even more by posting a whole collection of stories about brain doping on our private blog.

And he and Anna Kushnir and others also said - we need a web site to link to and we need some story to jointly write about. So in a frenzy on March 31 I created a fake press release and a fake web site. To make the press release, I took a real NIH press release, and like with the New York Times story, I edited it a bit and then a bit more.

And fortunately, I had registered the domain name WABDA.ORG for the "World Anti-Brain Doping Authority) through Go Daddy and had paid a bit extra for their "WebSite Now" option, and using their not very easy to use system, I made a website and somehow got it live by about 12:10 AM on April 1.

And I sent the fake press release to the co conspirators, who did an amazing job or also writing fake blogs. And I send the story to lots of others too. And wrote my own fake blog post here. And then sat back and watched the story spread. Below are some of the formal or accidental co-conspirators blogs:

• Chris Patil
• Bora
• Anna Kushnir
• Genome Technology
• Sunclipse
• Egghead
• Eye on DNA
• Bob Ohara
• Martin Fenner
• Jennomics
• Castros Favorite Color
• Pedro Baltrao
• Rants and Raves

And then I got a call from Nature saying they were doing a REAL story on brain doping and wanted to interview me about the fake story we did. And I guess you can find out the rest at the Nature site.

Also see

• Ronald Bailey
• Andy Fell
• Matthew Herper
• Ars Technica
• AFP
• Wired
• Scientists: Brains On Dope
• Mienfolks
• Voodoo Knickers
• Genetic Maize
• PopFi
• Oca Sapiens
• Metastopheles
• Buzzle.Com
• Process Algebra
• Boing Boing
• Nerdist

UPDATE May 29, 2017 - going to try and rescue some of the links here by pointing to the internet archive.

Mutualisms Rule - So Says Olivia Judson at the Wild Side

Nice blog today on mutualisms by Olivia Judson who writes the Wild Side blog/column for the New York Times (I seem to be writing a lot about writers for the NY Times these days ... not sure what is going on with that). She even features one of my favorite organisms in the blog:

The clam Calyptogena magnifica, which lives on deep-sea vents, depends on a bacterium to supply it with nutrients; the bacterium is transmitted through the clam’s eggs

Last year we published a paper on the complete genome sequence of this symbiont (which I wrote about here when I was clearly in a whiny kind of mood). And Judson picks up on a part of the story on the clam that is rarely discussed - the symbionts are transmitted vertically from parent to offspring. Vertical transmission seems to be linked to multiple properties of the symbionts (see my discussion of this regarding the glassy winged sharpshooter symbionts here).

Judson's post is really worth checking out for the symbiosis fans out there. She does a good job of highlighting diversity and evolution of mutualisms in a relatively short post.


See my video of a dissection of a baby Calyptogena:

PLoS Biology - Darwinian Evolution on a Chip

For evolution afficionados, there is a cool new paper in PLoS Biology on using a microfluidic chip to conduct in vitro evolution experiments.

The paper, by Brian Paegel and Gerry Joyce from the Scripps Research Institute

relies on computer control and microfluidic chip technology to automate the directed evolution of functional molecules, subject to precisely defined parameters. We used a population of billions of RNA enzymes with RNA-joining activity, which were challenged to react in the presence of progressively lower concentrations of substrate. The enzymes that did react were amplified to produce progeny, which were challenged similarly. Whenever the population size reached a predetermined threshold, chip-based operations were executed to isolate a fraction of the population and mix it with fresh reagents. These steps were repeated automatically for 500 iterations of 10-fold exponential growth followed by 10-fold dilution.

They have a nice figure summarizing the system which I show below --- and people should check out the article. Note - I can legally include this figure here because of the use of a broad Creative Commons License by PLoS Biology. Note - one of the stories I saw about this at Medgadget.Com also pointed out how they can use the article however they want because of where it was published. The power of true Open Access.

(A) The evolution chip is mounted on a temperature-controlled stage. Solutions containing polymerase enzymes (E) and mono- and oligonucleotide components (S) are delivered to the chip via capillary tubing and output to a pressure-controlled collection vial (O). A microscope objective is used to focus laser excitation (λ_ex = 490 nm) on the microfluidic channel and to gather fluorescence (λ_em = 535 nm), which is detected with a confocal PMT. Valve actuation and fluid flow are controlled by six independent vacuum lines.

(B) The microfluidic device is shown with the active circuit filled with blue dye.

(C) The serial dilution circuit consists of a mixing loop with fluid flow channels (red), fluid access reservoirs (blue), and control valves (black). Fluid flow around the loop is controlled by three two-way valves (a, b, and c). Fluid access to the loop from the input reservoirs (R_E and R_S) and to the output reservoir (R_O) is controlled by bus valves (in and out). The bus valves allow access when open, and prevent access while preserving fluidic continuity within the loop when closed.

(D) During operation of the circuit, the expanding RNA population is incubated while undergoing slow cyclic mixing until the fluorescence reaches a pre-determined threshold. Then an aliquot of the population is isolated between valves in and out as fresh solutions of E and Sin and out, and the aliquot is mixed with the fresh solutions by rapid serial actuation of valves a, b, and c. Open valves are indicated by filled circles; closed valves are indicated by a red X. are drawn into the loop and spent materials are delivered to the collection vial. Finally, the loop is sealed by closing valves

From: Darwinian Evolution on a Chip Paegel BM, Joyce GF PLoS Biology Vol. 6, No. 4, e85 doi:10.1371/journal.pbio.0060085

NIH Mandate on Open Access - Good First Step, Thanks to PLoS et al, but still a long way to go

Well, today is the day. The day after the new NIH mandate on Open Access (also see here for more information) to publications has begun. I think this is a great great day for science. And for society and Congress should be commended for doing something that is good for the country and the world that may have upset some of their big donors (i.e., the publishing industry).

And I think we all owe a big round of thanks to those who worked towards this goal. Clearly, there were many involved in convincing Congress to do this, from concerned members of the public, to SPARC and other NGOs, to tireless individuals like Peter Suber, and of course the Public Library of Science. For those who do not know, or may have forgotten, the Public Library of Science got it's beginnings as an initiative to promote Open Access publishing (and it was not initially a publisher of journals). PLoS was founded by Harold Varmus, Pat Brown and Michael Eisen (my brother) in 2000. The first thing they did was circulate a petition to promote open access publishing. I signed the letter as did many many others. But alas, it was not enough. And so PLoS started its journals and many realized that it would be necessary for funding agencies to step in and require Open Access publishing for work they funded. And after a long struggle, we are now here with the new NIH mandate (as well as mandates from other agencies which got there before NIH). And I think that we all owe a big thanks to everyone behind this initiative. Also it is worth checking out Harold Varmus' essay today on the new NIH initiative in PLoS Biology.

I note, however, that the NIH policy is only a first step. It does not move us completely towards true Open Access to scientific publications. There are still issues that need to be addressed, including the timing of release of publications (I think everything should be released immediately, not after a 6 or 12 month delay), the issue of Copyright, the need to get old publications into the public domain, and how putting material in Pubmed Central does not completely open it up to the world (see Peter Murray-Rust's very interesting discussion of this on his blog). So there is still much work to be done. But nevertheless, I am happy to be living in this new world where NIH has made OA a key part of it's mandate.

Congrats to Amy Harmon: Pulitzer for DNA Age Stories.

Congrats to Amy Harmon, reporter for the New York Times, who writes a lot about DNA (see all the DNA Age stories), who won one of those Pulitzer things today. I guess, maybe leaving me out of one of your last stories was a good call. I have written about her stories before a few times and overall, I like her reporting. What we all really need to do is convince her to start a blog. Print media is so 21st century.

Also see some other stories:

• Editor and Publisher (thanks to the Gene Expression blog for pointing this out)

Passing of Jeremy Knowles

I write with sadness that Jeremy Knowles has passed away. Knowles was a Professor at Harvard, had been Dean of the Faculty of Arts and Sciences at Harvard, and an HHMI Trustee, among many things. I did not know him well, but I did have a recent scientific exchange with him regarding analysis we were doing of the Tetrahymena genome. Knowles has asked a question to Peter Bruns, who is a Tetrahymena guru (and also was at HHMI). The question related to intron splice junctions and whether that might support a paper he had written in 1992. The science here is not important.

I wrote back, basically saying we were sequencing the genome but alas our data might not be useful for his question since most of what we were doing at the time was predicting gene splice sites not actually determining them for real. And I said, in fact, much of the data in Genbank was also predictions not real cDNAs.

I expected him to be a bit disappointed. But instead, he wrote back to Peter:

Peter:
Thank you! Jonathan's response confirms that I was right to ask an expert. For if I had gone fishing in the gene bank pool, I should probably have drowned. I shall wait, calmly.
best,
Jeremy

What I was struck with was his sense of humor and warmth, which emanated from this and a few other simple email messages. Based on these communications, I was looking forward to interacting with him again as we are now writing up a paper including all of our new cDNA data (real sequences, not predictions). I am sorry to see him go.

Tree of Life Art

As someone who studies the "Tree of Life" in terms of evolution (the tree of life is an evolutionary tree relating all life forms) and who even named his blog after this, I am fascinated by different portrayals of the Tree of Life. We can see lots of things like the Tree of Life in the real word. Much of this is due to the use of the Tree of Life imagery by various religious groups. Some of it is more connected to evolution in some way. But whatever the inspiration, there are some pretty nice representations out there. And I am posting one of them today. At UC Davis the UC Davis Arboretum is a really spectacular place. I go walking there all the time and take my kids to play there and watch the ducks and other animals. One day, I was walking near some gardens that they have been renovating for a while, when I saw they had unveiled some new artwork.

Below are some pictures of this artwork.  I am going to start posting more "Tree of Life" art here in the future and would love to get examples from people out there too.

More on Tree of Life art in Arboretum

As someone who studied "The tree of Life" in terms of evolution I am fascinated by the Tree of Life art in the Arboretum.  Here are some more pictures

Can a spoof be scooped by reality?

Well, if you read this blog, or a few others, you may already know that what I reported on here on April 1 regarding NIH cracking down on brain doping, was, in fact an April Fool's joke. I will write more about this joke later and how we planned it, starting at something called scifoo camp at Google headquarters in the summer of last year. But I do want to write about one thing here -- we sort of got scooped by reality. I had been planning for some time to do an April 1 joke on performance enhancing drug use among scientists. And as I was recruiting others to be involved in this plot, reality got in the way when Nature and then the New York Times started to report on brain doping as a real issue. It kind of took the absurdity away from our joke and made it seem like we were making some real commentary on brain doping when in fact, we were at least originally just trying to come up with something ridiculous but possibly believable at first look.

And now it has happened again. The second spoof I considered doing was to write about doing DNA and drug testing on some water bottles I collected from the Tour of California - a bike race that came 1 block from my house. I went for a little ride on the route of the race a few minutes after the peloton came by and got about 10 bottles from different teams. (This was real). And then I was going to pretend that we took those bottles and (1) figured out whose they were by DNA testing and (2) did drug tests of them. And this would allow me to write about 23 and me and other DNA testing companies as well as to make some fun of performance enhancing drug scandals. And I thought this would be ridiculous in a way because it could not possibly be legal to test someone's DNA without any real just cause. And low and behold look at what comes along --- Amy Harmon has an article in the Times yesterday on people doing exactly this type of thing --- testing other people's DNA (good article, by the way).

So now twice my spoofs end up getting scooped by reality. To me, a good spoof/April 1 joke is completely absurd in hindsight even if it is believable initially. So every time one of these jokes/pranks I want to pull gets close to reality, it becomes much much less funny to me. Who knows, maybe Craig Venter will in fact sequence his own microbiome, as I joked about last April 1.

Maybe before my next joke, I should call up Amy Harmon and other reporters to make sure they are not working on related stories first?

Open Evolution: Google supports open source code for evolutionary studies - Deadline 4-08 for Summer of Code

See email I received via Iddo Friedberg from the National Evolutionary Synthesis Center which is seeking students and others to participate in the Phyloinformatics Summer of Code.

This is just a reminder that the student application period ends
definitively on April 7 (Monday), 5pm PDT/8pm EDT (0:00 UTC on April
8). (Google extended the period from the original end date of March
31.) There are still a few project ideas that have received little
attention from student applications so far. If you are interested,
please see below for URLs, and get in touch with us phylosoc {at}
nescent {dot} org to inquire for more information re: application
status of your favorite project(s).

Phyloinformatics Summer of Code 2008
http://phyloinformatics.net/Phyloinformatics_Summer_of_Code_2008

*** Please disseminate this announcement widely to appropriate students
at your institution ***

The National Evolutionary Synthesis Center (NESCent: http://
www.nescent.org/) is participating in 2008 for the second year as a
mentoring organization in the Google Summer of Code (http://
code.google.com/soc). Through this program, Google provides
undergraduate, masters, and PhD students with a unique opportunity to
obtain hands-on experience writing and extending open-source software
under the mentorship of experienced developers from around the world.

Our goal in participating is to train future researchers and
developers to not only have awareness and understanding of the value
of open-source and collaboratively developed software, but also to
gain the programming and remote collaboration skills needed to
successfully contribute to such projects. Students will receive a
stipend from Google, and may work from their home, or home
institution, for the duration of the 3 month program. Students will
each have one or more dedicated mentors with expertise in
phylogenetic methods and open-source software development.

NESCent is particularly targeting students interested in both
evolutionary biology and software development. Project ideas (see URL
below) range from visualizing phylogenetic data in R, to development
of a Mesquite module, web-services for phylogenetic data providers or
geophylogeny mashups, implementing phyloXML support, navigating
databases of networks, topology queries for PhyloCode registries, to
phylogenetic tree mining in a MapReduce framework, and more.

The project ideas are flexible and many can be adjusted in scope to
match the skills of the student. If the program sounds interesting to
you but you are unsure whether you have the necessary skills, please
email the mentors at the address below. We will work with you to
find a project that fits your interests and skills.

INQUIRIES:
Email any questions, including self-proposed project ideas, to
phylosoc {at} nescent {dot} org.

TO APPLY:
Apply on-line at the Google Summer of Code website
(http://code.google.com/soc/2008), where you will also find GSoC program
rules and eligibility requirements. The 1-week application period for
students opened on Monday March 24th and runs through Monday, March
31st, 2008.

Hilmar Lapp and Todd Vision
US National Evolutionary Synthesis Center

=====
URLs:
=====

2008 NESCent Phyloinformatics Summer of Code:
http://phyloinformatics.net/Phyloinformatics_Summer_of_Code_2008

Eligibility requirements:
http://code.google.com/opensource/gsoc/2008/faqs.html#0.1_eligibility

Stipends:
http://code.google.com/opensource/gsoc/2008/faqs.html#0.1_administrivia

Quote of the week "There are much yummier and easier things to eat in the human body"

An interesting new paper has appeared in one of the those non Open Access journals - Science. Normally I do not write about such closed access, closed minded things, but I want to make an exception here. The paper is by George Church and colleagues on bacteria that subsist on a diet of antibiotics.

The paper is perfectly reasonable, if not pretty cool. Although it is a bit over hyped. It is obvious that bacteria would be able to eat antibiotics. Not only has this been shown previously, (as Church is very careful to point out) but bacteria eat anything and everything. So of course they will eat energy rich antibiotic molecules. The real problem in this case is the fear mongering that will come with the reporting on this. In the first few articles we already see this. For example, Reuters says

Church said the finding underscores the extent to which bacteria have developed resistance to antibiotics, a process that started almost as soon as penicillin was introduced in the 1940s.

Ummm ... antibiotics have actually been around for billions of years. Microbes make them all the time. So resistance too has been around for a long time. Yes, we are selecting for strains resistant to all our classes of antibiotics. But resistance itself did not start with the introduction of penicillin. I note the AP story got this right:

Nor is it a surprise that soil bacteria can withstand some antibiotics; some had already been found. After all, a number of antibiotics are natural — think penicillin. Some antibiotics have been derived from soil.

The only sense in all the stories I saw came from Jo Handelsman who was quoted in many of them:

"Thank goodness we have those bacteria to eat at least some of the antibiotics," said bacteriologist Jo Handelsman of the University of Wisconsin-Madison, who wasn't involved in the study. "Nature's pretty effective." From AP article.

Even better, Handelsman tried to calm the fears about whether bacteria would eat antibiotics given to treat infections:

But bacteriologist Jo Handelsman of the University of Wisconsin, Madison thinks this is unlikely, as “there are much yummier and easier things to eat in the human body."

And for that, she gets the quote of the week.

Open Access metagenomics selections

A quick post --- here are some relatively new interesting papers in metagenomics that are fully Open Access

• A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. Schloss & Handelsman BMC Bioinformatics 2008, 9:34
  
• Picoeukaryotic sequences in the Sargasso Sea metagenome. Piganeau et al. Genome Biology 2008, 9:R5
• Microbial Ecology of Four Coral Atolls in the Northern Line Islands. PLoS ONE. 2008; 3(2): e1584
• The airborne metagenome in an indoor urban environment. PLoS ONE. 2008 3(4):e1862.

Yoga and Evolution - How are they related?

Trick question. They are related because I am posting YouTube videos on those topics here. Just a little YouTube humor to help everyone get through the week. Warning - the evolution one is truly over the top and might offend a few so click on it with caution.


EnlightenUp The Film




Dawkins Rap

Bill and Melinda (Gates that is) ask for your ideas ... lots of money on the line

Well, I signed up for emails from the Bill and Melinda Gates Foundation, hoping to apply for some of their trillions of dollars to do a little bit of research.

And I got an email today I would like to share, since, well, they said I should share it. And here it is ..

The Bill & Melinda Gates Foundation is now accepting grant proposals for Grand Challenges Explorations, a US$100 million initiative to help scientists pursue innovative ideas for solving major global health problems.

Grant proposals are being accepted online at www.gcgh.org/explorations until May 30, 2008, on the following topics:

-- Creating new ways to protect against infectious diseases
-- Creating drugs or delivery systems that limit the emergence of resistance
-- Creating new ways to prevent or cure HIV infection
-- Exploring the basis for latency in TB

Initial grants will be $100,000 each, and projects showing success will have the opportunity to receive additional funding of $1 million or more. Full descriptions of the topics and application instructions are available at www.gcgh.org/explorations.

We are looking forward to receiving innovative ideas from scientists around the world and from all scientific disciplines. If you don't submit a proposal yourself, we hope you will forward this message to someone else who might be interested.

Thank you for your commitment to solving the world's greatest health challenges.

###
Bill & Melinda Gates Foundation

Guided by the belief that every life has equal value, the Bill & Melinda Gates Foundation works to reduce inequities and improve lives around the world. In developing countries, it focuses on improving health, reducing extreme poverty, and increasing access to technology in public libraries. In the United States, the foundation seeks to ensure that all people have access to a great education and to technology in public libraries. In its local region, it focuses on improving the lives of low-income families. Based in Seattle, the foundation is led by CEO Patty Stonesifer and Co-chairs William H. Gates Sr., Bill Gates, and Melinda French Gates.

Davis Life Magazine

Just got an email announcing a new issue of Davis Life Magazine which I meant to post about here previously. It is a nice little web magazine about, well, life in Davis.

What is so bad about brain doping? Apparently, NIH thinks something is.

UPDATE - FAKE SCIENCE NEWS HERE.

Recently, there has been a lot of talk around the web about brain doping ... that is, using some sort of drug to enhance intelligence or intellectual performance in some way. For example see

• New York Times article
• Would you boost your brain power? from Nature News and Opinion ...
• Pumping up your brain with legal drugs
• Nootropic - Wikipedia
• Performance Enhancing Drugs in the Boardroom? — Micromotives
• LA Times Story

A key question is - is brain doping bad? I am not so sure. However, NIH apparently thinks otherwise. NIH has just announced the formation of the World Anti Brain Doping Authority in conjunction with the ever so annoying World Anti Doping Authority. For more information see http://wabda.org and I attach the announcement below. Apparently, they are working on making a list of banned drugs and punishment for misuse for anyone funded by NIH. I have also heard they will be doing drug testing to new grant awardees. Lovely.

What is funny is this so fits in with the new top down style at the NIH. Forget about the individual scientist and the need for independence and creativity. There are so many rules about everything now that I think I will just seek out funds from other agencies.

See also other bloggers writing about this:

• Chris Patil
• Bora
• Anna Kushnir
• Genome Technology
• Sunclipse
• Egghead
• Eye on DNA
• Bob Ohara
• Martin Fenner
• Jennomics
• Castros Favorite Color
• Pedro Baltrao
• Rants and Raves

Here is the announcement:

NIH Announces New Initiatives to Fight the Use of Brain Enhancing Drugs by Scientists

The National Institutes of Health (NIH) today announced three new initiatives to fight the use of brain enhancing drugs by scientists. The new initiatives are (1) the creation of the NIH Anti-Brain Doping Advisory Group (NABDAG), a new trans-NIH committee, (2) a collaboration with the World Anti-Doping Authority (WADA) and the European Commission to create the World Anti-Brain Doping Authority (WABDA) and (3) the adoption by the NIH of the World Anti-Brain Doping Code – a set of regulations on the use of brain enhancing drugs among scientists.

"These new initiatives are designed to level the playing field among scientist in terms of intellectual activities," said NIH Director Elias A. Zerhouni, M.D. "These three activities are designed to get NIH ahead of the curve in terms of performance enhancing drug use among scientists."

NABDAG will serve to coordinate activities across different NIH agencies in terms of regulating the use of brain enhancing drugs. The trans-NIH group will be directed by internationally renowned doping authority Jonathan Davis, Ph.D., current director of research at WADA.

"The priority of NABDAG will be to seek out input from the scientific community and from within NIH," Davis said. "The availability of tremendous expertise and the remarkable infrastructure at NIH will make our activities more robust and will allow us to tackle questions about brain doping that were not possible to address in the past. For example, new testing procedures will need to be developed and we will be able to bring the entire NIH infrastructure to this task."

While “doping” is now accepted as a problem among athletes, it is less widely known that so-celled “brain doping” has been affecting the competitive balance in scientific research as well. It is for this reason that NIH is collaborating with the World Anti-Doping Authority (WADA), which has led the fight against doping in athletics, to create the World Anti Brain Doping Authority (WABDA). “Because brain doping is not just an American problem,” said Richard Pound, the current Director of WADA and acting Director of WABDA until a permanent head can be found, “we are working with the European Union’s research funding agency, the European Commission Research, to make sure WABDA is effective.

NABDAG will be established within the NIH Office of Intramural Research and administered by the National Institute of Mental Health (NIMH). Additional support for the center will come from the NIH Office of the Director, the National Institute on Drug Abuse (NIDA) and the Center for Scientific Review (CSR). The research activities of NABDAG will take place on the NIH Bethesda campus. An additional focus of NABDAG will be to provide training opportunities for students and established scientists from developing countries and from minority groups in the United States.

Together with WABDA, NABDAG will work to develop the international rules for the use of performance enhancing drugs among scientists as well as testing and punishment procedures. Most importantly they will administer the World Anti Brain-Doping Code, a set of uniform anti-brain doping rules. The NIH and European Commission have formally adopted this Code for the conduct of all scientists which receive funding in any form (intramural or extramural) from these agencies. The Code includes regulations on which drugs are prohibited, what the recommended testing procedures should be, and what the punishments should be for positive tests. More information on the WABDA Code can be found at http://wabda.org/. We note that the implementation will include testing of all NIH funded scientists both at the time they receive funding as well as at random times during the course of working on an NIH funded project. Testing will also be implemented at all NIH-funded or NIH-hosted events such as conferences and workshops and at grant review panels.

NIMH, NIDA, and CSR are among the 27 institutes and centers at the NIH, an agency of the Department of Health and Human Services. The NIMH mission is to reduce the burden of mental and behavioral disorders through research on mind, brain, and behavior. More information is available at the NIMH website http://www.nimh.nih.gov. The National Institute on Drug Abuse is a component of the National Institutes of Health, U.S. Department of Health and Human Services. NIDA supports most of the world's research on the health aspects of drug abuse and addiction. The Institute carries out a large variety of programs to ensure the rapid dissemination of research information to inform policy and improve practice. Fact sheets on the health effects of drugs of abuse and further information on NIDA research can be found on the NIDA web site at http://www.drugabuse.gov. The Center for Scientific Review organizes the peer review groups that evaluate the majority of grant applications submitted to the National Institutes of Health. CSR recruits about 18,000 outside scientific experts each year for its review groups. CSR also receives all NIH and many Public Health Service grant applications — about 80,000 a year — and assigns them to the appropriate NIH Institutes and Centers and PHS agencies. CSR’s primary goal is to see that NIH applications receive fair, independent, expert, and timely reviews that are free from inappropriate influences so NIH can fund the most promising research. For more information, visit http://www.csr.nih.gov.

The National Institutes of Health (NIH) — The Nation's Medical Research Agency — includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. It is the primary federal agency for conducting and supporting basic, clinical and translational medical research, and it investigates the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit www.nih.gov.