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

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

From their web site they say

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

Sean Carroll at Davis

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

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

PLoS for Everyone

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

Lie to Me, Darwin

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

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

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

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

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

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

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

Admission to this class is by application only. 

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

http://tinyurl.com/c73k62

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

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

PHYLOINFORMATICS SUMMER OF CODE 2009

http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009

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

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

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

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

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

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

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

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

Science and the Stimulus 1 NSF Announcement

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

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

National Science Foundation
Office of the Director
Arlington, VA 22230

March 18, 2009

Notice No. 131

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

Subject: American Recovery and Reinvestment Act of 2009

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

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

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

NSF Programs Receiving Recovery Act Funding

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

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

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

Funding Prioritization

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

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

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

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

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

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

Special Award Conditions

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

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

Working in Partnership

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

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

Arden L. Bement, Jr.
Director

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

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

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

[NSF Official Issuance]

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

Conyers, Eisen, the Huffington Post and Open Access

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

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

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

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

• Spit happens: Saliva's mysteries revealed
• Researchers Find a Unique Bacterial Ecosystem—In Your Mouth
• Study of spit offers insight into human health

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

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

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

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

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

And reference 4 is "Personal communication"

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

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

Clip of Harold Varmus on the Daily Show

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

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

Harold Varmus

Daily Show Full Episodes
Important Things With Demetri Martin

Political Humor
Joke of the Day

They copied my posting and I like it ...

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

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

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

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

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

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

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

Open Government Highlights: 1000 points of data

Kenneth Duberstein, who was the White House Chief of Staff from 1988-1989 had a very interesting Op-Ed piece in the New York Times Feb 23 (Op-Ed Contributor - 1,000 Points of Data - NYTimes.com). In it he calls for the US Government to allow for all citizens to assess the State of the Union themselves:

What we need now is a Web-based system for measuring our changing society with key national indicators — in a free, public, easy-to-use form. Ideally, it would be run by the nonpartisan National Academy of Sciences, which would ensure it has the best quality of information and is kept up to date. The system would enable us to offer in one place statistical information that we spend billions of dollars collecting but that is now underused and undervalued.

Noting that this idea is possibly going to be a reality, he writes:

Senators Edward M. Kennedy, Democrat of Massachusetts, and Michael Enzi, Republican of Wyoming, plan to soon introduce a bill that would allocate about $7.5 million a year for such a comprehensive database of key national indicators, and the idea already has wide bipartisan support.

Duberstein further states

Great steps forward in American history occur at moments when our deeply held values are reaffirmed in the face of changing realities. Such a moment is at hand. We need a shared frame of reference that will enable us to practice collective accountability.

I think this is a stellar idea. Access to information is critical for our future. Good to see this notion getting more and more support throughout the government.

Darwin in Davis

Since this is kind of a Davis thing too I am cross posting it from my work blog.

Well, this has been a good week for me in Davis in terms of things in which I am interested. First, the Tour of California started in Davis and then tonight we had a Darwin celebration (with cake and talks) in a movie theater in downtown. The three talks were by Rick Grosberg, who gave a good background on Darwin the person, Mau Stanton who talked about Evolution and Society and me, who talked about Uses of Evolution. The shindig was sponsored by the Center for Population Biology and funded by the Storer Endowment. And it was organized by Angus Chandler and Dena Grossenbacher and possibly some others. And the theater was packed to the gills. Food. Folks. And Fun. And I owe some thanks to folks who responded to my FriendFeed posting asking about other examples of Uses of Evolution.

Here are some pics ...




Also see

• The California Aggie Story
  
• The Bug Squad Blog

Darwin Celebration in Davis

Well, this has been a good week for me in Davis in terms of things in which I am interested. First, the Tour of California started in Davis and then tonight we had a Darwin celebration (with cake and talks) in a movie theater in downtown. The three talks were by Rick Grosberg, who gave a good background on Darwin the person, Mau Stanton who talked about Evolution and Society and me, who talked about Uses of Evolution. The shindig was sponsored by the Center for Population Biology and funded by the Storer Endowment. And it was organized by Angus Chandler and Dena Grossenbacher and possibly some others. And the theater was packed to the gills. Food. Folks. And Fun. And I owe some thanks to folks who responded to my FriendFeed posting asking about other examples of Uses of Evolution.

Here are some pics ...




Also see

• The California Aggie Story
  
• The Bug Squad Blog

Bad evolution puns award #1: Cod in the act of evolution

Sure - we are celebrating Darwin this month and through the year. But one negative of evolution in general is that it seems particularly ripe for puns, and bad ones at that. So I am starting a new award here - the Bad Evolution Puns Award. And the first winner is the Boston Globe for their new article "Cod in the act of evolution" by Murray Carpenter.

My favorite evolution stuff 1. 1900 Darwin Post Card

Just starting a new thread here --- my favorite evolution stuff.  And here is one.  It is a post card that I found inside a 1880s version of Origin of Species that I bought at a used book store.  The book was part of a collection from Ellison A. Smith which was being sold at a used book store in Georgetown many years ago.  I bought a bunch of old evolution books and inside many of them were post cards advertising portraits of some of the authors.  Here is one -- advertising a portrait of Darwin.  Wish I had the portrait ...

Is boycotting the right way to deal with anti-evolution sentiment?

Adam Nossiter in the New York Times is reporting that the Society for Integrative and Comparative Biology (SICB) has decided to in essence boycott New Orleans as a site for a future conference. They are doing this in response to a bill passed last year by Louisiana that is considered by many to be a hidden way to introduce religion into scientific teaching (the Times says the bill "allows teachers to “use supplemental textbooks” in the classroom to “help students critique and review scientific theories.”). The SICB wrote a letter to Governor Jindal saying

“It is the firm opinion of S.I.C.B.’s leadership that this law undermines the integrity of science and science education in Louisiana,” 

and

“The S.I.C.B. leadership could not support New Orleans as our meeting venue because of the official position of the state in weakening science education and specifically attacking evolution in science curricula,” “As scientists, it is our responsibility to oppose anti-science initiatives.”

I note that they are going to hold their meeting in Salt Lake City instead, which at least in regard to science evolution and science education and state policy, is a bit better (e.g.,the Utah State Board of Education has made it clear it supports teaching evolution (see here)).

Along with the letter, a group called the Loiuisiana Coalition for Science has issued a press release saying that the state is "reaping what is sowed" by passing the bill.

So the question I have been asking myself is - is a boycott the right thing to do here? I am not sure. On the one hand, I commend SICB for taking a public action that is more than just words. I think it is pretty clear that this bill was designed as a backdoor way to allow religion beliefs to shape what is taught in public school science classes, which is sad. In response to this, I think scientists should do something more than just say this is a bad idea so at least SICB did something.

On the other hand, a boycott is perhaps a bit extreme and comes with many complications. In many cases, engagement is probably a better strategy. It is ironic in a way for a science group to be taking a George Bush-esque approach to dealing with disagreement. I guess I lean away from the boycott step not because it seems completely wrong, but because it seems a bit premature. Perhaps AICB could have held the conference there and organized a series of public discussion about science teaching. And on top of that they could have made a small contribution to a community that has been really hit hard recently.

Boston University adopts Open Access policy

Just saw a nice story about BU adopting an Open Access policy.

See the BU Today article

Some detail with some nice quotes in support of OA:

Boston University took a giant step towards greater access to academic scholarship and research on February 11, when the University Council voted to support an open access system that would make scholarly work of the faculty and staff available online to anyone, for free, as long as the authors are credited and the scholarship is not used for profit.
...
“Open access will really highlight the tremendous productivity of our faculty,” says Millen. “Among the more important things needed to make it work is a collaboration between the libraries and our faculty to get their research onto the Web. It’s not an inconsequential task.”

....
“This vote sends a very strong message of support for open and free exchange of scholarly work,” says Hudson. “Open access means that the results of research and scholarship can be made open and freely accessible to anyone. It really has increased the potential to showcase the research and scholarship of the University in ways that have
not been evident to people.”

Hat tip to Tom Tullius ...

Some pics from the Tour in Davis

Well, it was really really really wet out there but tons of people were out in Davis nevertheless. I got some pics -- although my phone cam was not working great in the pouring rain. Anyway - here they are, including one of Floyd Landis ..

Tour of California before the start in Davis

Here comes the tour (of California) --- Davis is going big ---

Very excited that the Tour of California is starting in Davis this year (for Stage 1 on Sunday). It should be a good stage --- from Davis to Santa Rosa.

And there are many many big names in the tour this year - even more than last year. In particular of course is Lance Armstrong. I have been a big fan of Lance for many many years -- since I encountered him in Palo Alto when I was a grad. student. He had just won the World Championship and was in town to sing autographs and hang out at Wheelsmith, the best bike shop in the area. I was just getting into cycling and was going to Wheelsmith for some other reason and there was Lance. I got him to sign a few things and then thought, what would be coolest would be if he signed my favorite T-shirt (which I am wearing in the picture here). And he made my day by saying "Cool shirt" and asking where I got it.

Anyway --- it is going to be a big big day in Davis tomorrow with Lance Armstrong, and a whole gaggle of big time cyclists here in the best biking town in the country.

And here are some links related to the race ...

• Lance's Twitter RSS feed (pretty entertaining stuff)
• Livestrong
• City of Davis information about the tour
• Davis Bike Club
• Bicycle Friendly Community - Davis
  
• 
  

NSF looking OK in revised stimulus bill

Just downloaded what I think is the current bill that the House just passed for the stimulus.  And it looks like the National Science Foundation is coming out OK.  It says

NATIONAL SCIENCE FOUNDATION
NSF is directed to submit to the House and Senate Committees on
Appropriations a spending plan, signed by the Director, detailing its intended
allocation offunds provided in this Act within 60 days of enactment of this Act.
RESEARCH AND RELATED ACTIVITIES

For research and related activities, the conference agreement provides a total
of $2,500,000,000, to remain available until September 30,2010. Within this
amount, $300,000,000 shall be available solely for the major research
instrumentation program and $200,000,000 shall be available for activities
authorized by title II of Public Law 100-570 for academic facilities modernization.
In allocating the resources provided under this heading, the conferees direct that
NSF support all research divisions and support advancements in supercomputing
technology.

EDUCATION AND HUMAN RESOURCES
The conference agreement includes $100,000,000 for education and human
resources, to remain available until September 30, 2010. These funds shall be
allocated as follows:
Robert Noyce Scholarship Program .......................... .
Math and Science Partnerships ................................. .
Professional Science Master's Programs .................. .
$60,000,000
25,000,000
15,000,000
MAJOR RESEARCH EQUIPMENT AND FACILITIES CONSTRUCTION
The conference agreement includes $400,000,000 for major research
equipment and facilities construction, to remain available until September 30,
2010.
OFFICE OF INSPECTOR GENERAL
The conference agreement includes $2,000,000 for the Office of Inspector
General, to remain available until SeptemberJO, 2013.

"

Google LOVES Darwin

Love that image on Google in honor of Darwin's 200th.  You go google. 

Charles Darwin relic hidden in the chimp and human genomes

So - in honor of Charles Darwin and as a follow up to my analysis of Sarah Palin's name (which amazingly showed as a best hit a fungus called B. fuckeliana) I decided today to do some blast searches with old Charlie D.'s name. You see CHARLES DARWIN includes letters that all are abbreviations of amino acids that make up proteins, so you can compare his name, pretending it is a protein, to proteins from other organisms.

So I went to the NCBI blast page and did a BLASTP search. Blastp searches a peptide against a database of peptides and identifies in the database sequences if one or more have similar amino-acid sequences to the one used to search (which is known as the query) . To make this work, I had to adjust some of the default parameters to make it possible to better detect short matches (I raised the # of expected matches to 10000).

Alas, no good matches convincing matches to known or predicted proteins came up. So I was sad. Then I said, what if Darwin was hiden in the genome of some organism? So I did a "translational" blast search called tblastn which takes a peptide and searches it against a DNA database and translates the DNA into all possible peptides it could encode. When one does this, one can possibly find "hidden" proteins or relics of proteins in the DNA that may not have been labelled as proteins by whomever analzyed the DNA data.

And what did I find by this Tblastn search? A jackpot to make evolutionary biologists VERY happy. The best matches for CHARLESDARWIN the peptide? Pan troglodytes. AKA Chimps. And humans (the matches were equally strong).

So - hidden in the human and Chimp genomes is a relic of one Charles Darwin. Happy Birthday Charlie.

----------------------------------------------

See search results below:

Score E
Sequences producing significant alignments: (Bits) Value


gb|AC199643.3| Pan troglodytes BAC clone CH251-444E8 from chr... 25.8 1930
gb|AC093749.3| Homo sapiens BAC clone RP11-30B7 from 4, compl... 25.8 1930
gb|AF250324.1|AF250324 Homo sapiens chromosome 4q35 BAC clone... 25.8 1930
gb|AC217674.3| Pan troglodytes BAC clone CH251-398H5 from chr... 25.0 3549
gb|AC195095.2| Pan troglodytes BAC clone CH251-577A14 from ch... 25.0 3549
gb|AC188794.3| Pan troglodytes BAC clone CH251-69H24 from chr... 25.0 3549
gb|AC183104.3| Pan troglodytes BAC clone CH251-567E15 from ch... 25.0 3549
gb|AF105153.3| Homo sapiens alpha-satellite centromere border... 25.0 3549
emb|AL353763.14| Human DNA sequence from clone RP11-87H9 on c... 25.0 3549
gb|AC116618.4| Homo sapiens BAC clone RP11-98L17 from 4, comp... 25.0 3549
emb|CR786580.6| Human DNA sequence from clone RP11-764K9 on c... 25.0 3549
emb|AL591385.7| Human DNA sequence from clone RP11-391M20 on ... 25.0 3549
emb|AL445925.19| Human DNA sequence from clone RP11-403A15 on... 25.0 3549
emb|AL592183.10| Human DNA sequence from clone RP11-297D8 on ... 25.0 3549
ref|XM_787798.2| PREDICTED: Strongylocentrotus purpuratus sim... 24.3 6861
ref|XM_001201471.1| PREDICTED: Strongylocentrotus purpuratus ... 24.3 6861
gb|AC195625.1| Pan troglodytes BAC clone CH251-895L14 from ch... 23.9 7711
gb|AC175749.2| Pan troglodytes BAC clone CH251-1124N9 from ch... 23.9 7711



Pan troglodytes BAC clone CH251-444E8 from chromosome 7, complete sequence Length=155150
Score = 25.8 bits (55), Expect = 1930, Method: Composition-based stats. Identities = 8/13 (61%), Positives = 11/13 (84%), Gaps = 0/13 (0%) Frame = -2

Query 1 ____ CHARLESDARWIN 13
_____________CH RLE D+++IN
Sbjct 145762 CHVRLEQDSKYIN 145724


gb|AC093749.3| Homo sapiens BAC clone RP11-30B7 from 4, complete sequence Length=163102 Score = 25.8 bits (55), Expect = 1930, Method: Composition-based stats.
Identities = 8/13 (61%), Positives = 11/13 (84%), Gaps = 0/13 (0%) Frame = -3

Query 1 ___ CHARLESDARWIN 13
____________CH RLE D+++IN
Sbjct 31925 CHVRLEQDSKYIN 31887

10 simple ways to honor Charlie D (aka Darwin)

If you do not know, Thursday is a big day - Darwin Day 2009. A global celebration in honor of the 200th anniversary of Charles Darwin's birth. Today I am making a suggestion of 10 simple things you can do to honor Darwin:

1. Read one of his books OTHER than Origin of Species (see Darwin online for some there). My favorite is the Voyage of the Beagle but there are many others.
   
2. Stop using the terms Darwinism and Darwinian evolution (see Safina for more on this - I thought this article was a bit of overkill but still has some important points).
3. Vote against anyone who says Intelligent Design should be taught in science class or that you should "teach the controversy." Or at least endorse right thinking candidates.
   
4. Contribute to evolution education in some way - teaching, writing a book, releasing teaching materials, donate to a museum (e.g., California Academy) or other organization (e.g., NCSE) or even the cool HMS Beagle Project. Just help educate the world about the science of evolution.
   
5. Attend some Darwin Day celebration(s).
6. Get a cool evolution tattoo (see Zimmer for more) or display your support in some outward way.
   
7. Support the National Science Foundation (if you are in the US) as they are the strongest supporters of Evolution related research.
8. Name your kid or pet or boat or city after him.
9. Visit the Galapagos or at least check out the Darwin Station online.(see pics below ...)
   
10. Insert your own here .....
    

Open Evolution: Kudos to SMBE for creating a new Open Access publication - Genome Biology and Evolution

Another sign that Open Access is spreading.  SMBE, which publishes the journal MBE (Molecular Biology and Evolution) is announcing the creation of a new journal - Genome Biology and Evolution (GBE).  And happily it will be an Open Access journal being published by Oxford under the Oxford Open system (not quite a full creative commons license like PLoS journals, but pretty good).  I am VERY pleased to see this, especially since I quit the Editorial Board at MBE mostly because they were not moving fast enough to Open Access for me.  Kudos to SMBE, Bill Martin (the new Editor in Chief of GBE) and all the folks at Oxford for doing a good thing.

Please - bash my latest paper - for the benefit of humanity

My lab has a new paper that just came out on the sequencing and analysis of the genome of a pretty cool (or hot actually) bacterium, Thermomicrobium roseum, which was isolated from a Toadstool Spring, an alkaline siliceous hotspring in Yellowstone National Park. This paper is from a grant we had when I was at TIGR as part of the "Assembling the Tree of Life" program at NSF. Our grant was focused on generating genome sequences from phyla of bacteria for which no genomes were available.

At the time this species was a representative of a phylum that had no genomes. After we started sequencing, the phylum was dissolved, but never mind that for now. We report what I think are some very interesting things in the paper. Among them:

• We report the first example of a plasmid that encodes all the genes needed for chemotaxis including all the genes for making a flagellum. Given that they are on a plasmid this suggests that motility could be easily transfered between species.
• We report experimental work and genome analysis that helps understand the novel membrane and cell wall structure in this species.
• This is the first thermophile known to oxidize carbon monoxide
  

But I am not writing per se about the things I like about our paper. I am instead asking people out there to find things wrong with our paper. Why am I doing this? Because this paper is part of a broader experiment in publishing in that it is in PLoS One. And one of the main benefits of PLoS One is the features that allows commenting on publications. I personally believe such features are part of the future of scientific publication. But it is currently unclear just how effectively such commenting features are used (note Euan Addie is doing a survey about comments on PLoS One papers here).

So I am offering up my paper as a case study. If you comment and ask questions or make critiques, I will try to respond. And if you think something in our paper is wrong or weird, please say so. If you think something in our paper is supported by other work we do not cite, please say this too. If you have anything useful to say, please make comments.

How do you do this?

• Go to the paper at the PLoS One Web Site.
• In the upper right click on "Login" if you have an account or "Create account" if you do not.
  
• Return to the paper once you are logged in
• Find some part of the text you want to comment on
  
• Highlight that text and click over on the right "Add a note" or "Make a comment"
  
• Fire away.
  

Harold Varmus on Science Friday

There was a very interesting interview on Science Friday last week.  The discussion was with Harold Varmus (see Science Friday Archives: Harold Varmus).

In the interview, Varmus discussed his new book, his role as an advisor to Obama, and some issues relating to Open Access.  I found his comments to be very interesting and insightful and it is worth listening to.  

Pictures from Yolo Basin - Bitterns, Night Herons, Owl

Yolo Basin

An ever more famous science blogger

Just a little one here. Pam Ronald, a professor and blogger here at Davis is featured on the home page of CNN.COM in a story about "Fighting Hunger with Flood-Tolerant Rice." You can read about it at CNN or learn more about what Pam has been doing with rice from her blog or her book "Tomorrow's Table" that she wrote with her husband.

Nice little PLoS reference by Nicholas Kristof in the Times ...

Just a quick one here. In an article in today's Times, Nicholas Kristof writes about "Putting Torture Behind Us" and he has a little PLoS reference there ...

"Granted, returning the base to Cuba may not be politically realistic. So here’s a fallback alternative: turn the base into a research center for tropical diseases.

This was proposed in a medical journal, PLoS Neglected Tropical Diseases, a year ago, and it makes more sense now than ever

In Latin America and the Caribbean, there are still more than half-a-million cases annually of dengue fever (which causes excruciating pain and sometimes death), nearly 50,000 new cases of leprosy and more than 700,000 cases of elephantiasis (which causes grotesque deformities). In addition, 50 million Latin Americans have hookworms inside them, often causing anemia and making it more difficult for children to concentrate in school.

Peter Hotez, the president of the Sabin Vaccine Institute at George Washington University and the editor of PLoS Neglected Tropical Diseases, says that an international center on Guantánamo could become a symbol of United States cooperation in the region.

Imagine if people around the world came to think of Guantánamo as a place where America led a battle against hookworms and leprosy. That would help us fight terrorism far more effectively than the prison at Guantánamo ever did.."

Hat tip to Chris Schelleng for pointing this out. The original PLoS NTD article by Peter Hotez is here.

What's better than brain doping? Cello Scrotum is what.

OK I have a lot to learn. I was (and still am) pretty proud of the April 1 prank I pulled off this year with many other bloggers announcing a fake crackdown on brain doping. But my joke is not even close to this one. A letter in a recent issue of BMJ has announced that the malady known as Cello Scrotum was in fact made up. Why did they make this up? In response to a publication about guitar nipple (for more on this see CNN and the Times Online). And now they have confessed only 35 years later.

And I must say - God Bless Pubmed Central. Because here is the original very brief letter which I am posting below:

Benefits of Open Access: enabling musical interpretations of human genomics ...

Not this is one of the most creative uses of open access science publications I have seen in a while. The video is from a paper by Dan Falush and colleagues that was in PLoS Genetics. Listen/see how the music changes with the genetics/migration of humans.



So I guess given some of my recent posts, we must ask what should we call this? Musicomics (which has a following but most of the use of the term seems to refer to music and comics together, although I did find one site with a reference that is about genomics) or genomusic (most of which seems to refer to people named Geno making music). Maybe, maybe, we just should say it is "nameless" but nice.

Anyway --- a nice use of open access --- the material from the PLoS Genetics paper is under a broad Creative Commons license and thus this type of use is allowed (and the source is attributed in the YouTube notes). Not sure about the exact details of the origins of the music for the video, but Dan Falush has hinted to me that it was some spontaneous contribution by a band in LA.

Obama's Science Team Big on Evolution

Much has been written and will be written about how Obama is taking science seriously.  To me, one great sign of this is that not only is evolution OK to talk about now, but - gasp - many of his science team actually have worked on evolution.   For example:

• Eric Lander, part of Obama's council of advisors on science and technology, has written many papers either directly or indirectly about evolution. 
  
• Harold Varmus also on this Council, has written about evolution of viruses (e.g. here),
  
•  Jane Lubchenco is an ecologist who in much of her work has an evolutionary ecology angle

Even John Holdren, who is more of a physicist and as far as I can tell has not written explicitly about evolution recently certainly discussed it in some of his earlier publications with Paul Ehrlich.  

So - not only is science in general and life science in particular on the upswing.  But evolution is too.  Maybe this is why Darwin endorsed Obama so many months back. 

The Bush Administration IS NOT and WAS NOT anti-science

So much has been written about the supposed anti-science stance of the Bush administration (see for example Chris Mooney, AFP, many Nobel laureates, etc  and even me).  But I have been obsessing about this in my head for some time now.  And I think it misses the point.  Bush and his administration have not really been anti-science.  There I said it.  Ready to smack me over the head?

Before you do that.  Wait.  What I think Bush is is even more insidious.  He is anti-evidence.  Or, in other words, he does not believe science should be used to discover things but instead simply as a means to an end.  Sound familiar?  This was his approach to weapons, torture, Guantanamo, gathering intelligence about US citizens, and so on.   All these things were justified because evidence and objectively testing multiple possibilities was not really needed - we knew the answer and just had to back it up with something consistent with the theory.  In essence, everything he did titled against evidence in all sorts of areas.  

So - even though he was not anti-science per se.  The anti-evidence attitude hit scientists really hard.  Science is NOT about just trying to get to an end.  It is also about discovery.  And thus I look forward to a president who believes science is a way to discover things about the world that we do not already know.

You could call it symbiomics (but please do not)... but whatever name you use, this is $^@#&* so cool.

Once again, Nancy Moran's lab has knocked the scientific wind out of me with a cool paper. This seems to happen every 6 months or so (and I hope my paper with her lab a few years ago knocked the wind out of some others). And this new one, even though it is in a non OA journal which I usually avoid writing about here, is so cool, I just had to say something. So, if you are interested in a brilliant study of "The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria" see the recent Science paper by Moran, Heather McLaughlin and Rotem Sorek. Here are some key lines that summarize some of what they did:

We documented the dynamics of symbiont genome evolution by sequencing seven strains of Buchnera aphidicola from pea aphid hosts....

....A. pisum is native to Eurasia, but has been introduced worldwide. It was first detected in North America in the 1870s (11). We sequenced the genomes of seven Buchnera-Ap strains descended from two colonizers of North America (and hence diverging up to 135 years ago), including two strains diverging in the laboratory for 7.5 years. Solexa sequencing was combined with verification by Sanger sequencing (12), to determine genomic sequences of these seven strains (Table 1)....

...Our estimated mutation rate for base changes was unexpectedly high: more than 10 times the previous estimates of mutation rate calculated on the basis of silent site divergences in both Buchnera and free-living bacteria...

...Our model predicts that the initial step leading to genome reduction is a shift in nucleotide composition toward higher A+T content....

Alas, I am really busy right now finishing some grants and papers or I would try to write more, especially since some may not be able to get this paper.  Note for you conflict of interest aficionados -  much of the sequencing for this project was done at the Joint Genome Institute where I have an Adjunct appointment.

Microbiology blog video ...

Just got this from Jenna Morgan. I guess I did miss something in Toronto in 2007 ...

Worst New Omics Word Award: Museomics

OK.  So I coined my my omics word many years ago (phylogenomics).  Fine.  Sue me.  But the spread of omics words is getting really icky.  And a new one really seems lame.  The word is "museomics"which I saw for the first time in a press release today from Cold Spring Harbor Press about a paper in Genome Research. 

I mean, the study of the Tasmanian Tiger seems like it could be interesting (have not read the paper) and there is some really fun stuff happening these days using Roche/454 sequencing. 

But meseomics?  Not to disparage museums which are critical to all of biology in my opinion.  But to me the term in a way treats museums as simply a place we store organisms before we get DNA out of them.  For this, the team at Penn St. that led this project and apparently coined the term museomics (see here where they define the term) is getting my new "Worst New Omics Word Award." 

In addition I am proposing my favorite new Omics words using their model:

1. Roadkillomics (to go along with roadside field guides)
   
2. Backyardomics (e.g., could be some sort of native plant thing)
3. Hospitalomics (e.g., MRSA)
4. Backoftheenvelopomics (for the anthrax case)
5. Stuffinmypocketomics (hey, I have found some $&%$ stuff there)
6. Restaurantomics (e.g., O157H7)
7. Footballomics (there have been studies of MRSA transmission in games, why not omics)
8. Slowfoodomics (genomics of things you get within 50 miles of your neighborhood)
9. Ebayomics (genomics of things you get off Ebay)
10. Stuffthecatdraggedinomics (my cats would like this)
11. Wherethesundontshinomics (human microbiome?)

Any others suggestions?