Francis Collins SteepingStepping Down from NHGRI

Just got forwarded this email from Francis Collins to multiple people. Collins is stepping down. I wonder what specifically triggered this ... my guess is he is being recruited by one of the presidential candidates to be some sort of advisor. Nothing like having a prominent scientist who also is born again being on your team ....

From: FSCollins (NIH/NHGRI)
Date: Wed, May 28, 2008 at 11:58 AM
Subject: News

Dear friends and colleagues in the many wonderful team projects that I have had the privilege of being part of,

I am writing to let you know of my plans to step down August 1, 2008 as Director of the National Human Genome Research Institute, a position that has been both a joy and privilege to hold for the past 15 years.

The key to success is having wonderful scientific opportunities and stellar colleagues with whom to work. Many challenges lie ahead as genomics increasingly becomes a leading force in medicine, and I leave my position supremely confident that NHGRI and NIH will continue to achieve notable success in meeting them.

Looking back, I'm tremendously proud of our collective work in leading the Human Genome Project (HGP) to its successful conclusion in 2003, and of our wide range of large-scale projects that built upon the foundation laid by the HGP. Collectively, these projects and the priceless data they generated have transformed biomedical research and empowered researchers all around the world. I'm also proud of these projects' commitments to protecting the privacy of genetic information and addressing the ethical, legal and social implications of genome research.

My decision to step down as NHGRI Director came only after much personal deliberation and was driven by a desire for an interval of time dedicated to writing, reflection and exploration of other professional opportunities in the public or private sectors. Rest assured that NHGRI's leadership will be in good hands. Alan E. Guttmacher, M.D., the current deputy director of NHGRI, will become acting director of NHGRI on August 1, and Mark Guyer, Ph.D., the long-time director of the Division of Extramural Research will continue his able leadership. A formal search process for a permanent NHGRI director will get underway shortly.

Finally, I'd like to let each of you know that while I may be leaving the NHGRI Director's office in search of other challenges, I will be cheering for the success of your dedicated and creative scientific achievements over the coming weeks, months, and years.

Keep up the good work!

Francis

Genomics By Press Release Award #2: Lieden Leiden University and the First "Female" Genome

Ooh. Ahh. That is what we should all be saying as it has been announced that the first "female" genome has been sequenced. The press has eaten this up a bit, because of course, the other human genomes that have been sequenced have been from males.

Sure, in terms of public perception, it will be good to have a woman's genome sequenced. And in terms of science, there could be some major uses (e.g., if phenotypes such as health status are made available along with the genome one could try to use the genome to dissect female specific health issues). But as far as I can tell, this whole story is about perception with no reality involved.

The problem is that thethere is no there there yet. The data is not released. There is no paper (e.g., MSNBC reports ""No other scientists have yet verified the Dutch data, but some experts said they were eager to see the sequence.") This is just some group wanting to stake out some territory in an area that certainly others are working on at the same time. Their press release, by the way, has some icky stuff in it. Most annoying is that they make a point to emphasize that the woman whose genome was sequences is a clinical geneticist. And then they say

“If anyone could properly consider the ramifications of knowing his or her sequence, it is a clinical geneticist,” says professor Gert-Jan B van Ommen, leader of the LUMC team and director of the ‘Center for Medical Systems Biology’ (CMSB), a center of the Netherlands Genomics Initiative.

I do not even know what to say to this. What exactly makes a clinical geneticist better able to think about these issues than say, a genetic counselor, or a ethicist or a priest, or a bioinformatician?

Anyway, they also say

Following in-depth analysis, the sequence will be made public, except incidental privacy-sensitive findings

And for this, Lieden University is becoming the recipient of my second "Genomics By Press Release Award." (see my first one here, where interestingly, the discussion of sequencing a woman's genome came up when I announced I was going to sequence a genome on my new Excercycler machine).

What to do when a billionaire loves your brother ...

Well, many people confuse me with my brother, Michael. I guess, if they do not know us, it is understandable. He is at Berkeley. I am at Davis. He works on genomics related things. So do I. We both are passionate about PLoS and Open Access publishing. We both went to Harvard. We both spent time at Stanford. I could go on (we used to look a bit alike ... see the lovely family portrait). Sure, sometimes I get sick of people asking me questions about microarray clustering software and Drosophila.

But most of the time, it only is good for me. Like today. If people want to confuse me with my brother today, fine by me. That is because today, HHMI announced the selection of their new "Investigators". Becoming an HHMI Investigator is the scientific equivalent of getting a sugar daddy. They give you money to do whatever research you want to do. They call it "People, not Projects." or something like that.

So - I saw some of the press on this and mostly it was very general - just talking about how HHMI is really important when NIH budgets are flat and all. But then this afternoon, I was listening to NPRs "Marketplace" when they do a story on the HHMI announcement. And I am thinking - wouldn't it be cool if they mention my brother? And so my ears perked up. And they discussed some background a bit and then Tom Cech, the head of HHMI, was explaining why they want to give money to people with no restrictions and he said

TOM CECH: Often in the course of research, you stumble upon leads to your question that were different from what you originally proposed and by funding the person, not the project, we are freeing people up to follow those leads.

For example, he says, one investigator started out studying retroviruses, but he switched gears and started building miniature arrays to look at the expression of genes in an organism -- don't worry, I have no idea what that means either.

CECH: But before long, he was looking at typing various sorts of leukemias and lymphomas and breast cancers. So he moved into the cancer area with tremendous results.

Certainly sounds like he was talking about my brother, who worked on flu viruses for part of his PhD (ok, they are not retroviruses, but they are RNA viruses), and did a post doc working on arrays (with Pat Brown and David Botstein) and also then used arrays to do cancer classification studies. Sure, he could also be talking about Pat Brown but hey, I am going to pretend he was talking about my brother since it is pretty close.

So, sure, I am a bit peeved they did not select me (thankfully, it seems on first glance that they people they did pick all pretty much rock in terms of science so it is not like I lost out to a bunch of dolts). But I am not jealous. Proud would be more accurate.

Search for life on Mars

Well the Phoenix lander has, well, landed on Mars. And it is, well, on a mission. To search for evidence of life (OK, that is not the only part of the mission, but it is the coolest part).

And it is time to place bets. Who out there thinks they will find some sort of evidence for life and how strong will that evidence be?

I for one think there will be life on Mars somewhere. And the Polar regions are not such a bad place to look for evidence of past or present life on the planet. Not sure what others out there think overall but here is some stuff from the web to consider:

Oliver Morton, my favorite Martian Blogger (interpret that however you want) says at MainlyMartian:

Having witnessed two Mars lander failures, Mars Polar Lander before this blog was even born and Beagle-2 back when it was young and active (Landing and prelanding in the December 2003 archive, and the whole sad story in the Beagle-2 archive), and having been absent for all the other attempts that have proved successful, it seemed to me only prudent not to cover the landing of Phoenix this weekend

Oliver also points to a "In the field" blog from Eric Hand.

Neil Saunders says:

If there ever was (or is?) microbial life there, Phoenix has a pretty good shot at finding the signs.

Others out there I am sure have more to say. What do you think?
(1) Is there life on Mars now?
(2) Was there ever life on Mars?
(3) Will Phoenix find and positive evidence?

ASM Meeting Preview: Give your input to the National Science Foundation's Microbiology Programs ...

If you are interested in the funding of microbiology research from the National Science Foundation, there is a good opportunity coming up to find out what NSF's plans are and to give your input. James Collins, the Assistant Directory of the Biological Sciences Division at NSF will give a presentation at the ASM Meeting in Boston.

His presentation will be June 4, 2008

At the ASM Meeting at the Boston Convention and Exhibition Center

Room 052A

12-1:30 PM

If you are in town and interested in microbiology research funding, it would be worth going to give your input.

And if you are going to be in the area for the meeting or otherwise, you might consider going to the Division R Symposium that is from 8-10:30 in Room 156A. The talks in that session are:

• Margrethe H. Serres -- Convener
• Jonathan A. Eisen -- Division R Lecture: Phylogenomics and the Diversification of Microbes
• Patricia Babbitt -- Functional Promiscuity and the Evolution of New Enzyme Functions: Implications for Annotation
• Kimmen Sjölander --The PhyloFacts Microbial Phylogenomic Encyclopedia: Investigating Protein Superfamily Evolution across the Tree of Life
• Margrethe H. Serres --Protein Families Provide Support for Functional Annotation and Reflect Metabolic Diversity of Organisms

Lederberg Workshop Rest of the Story

When I left off in my notes the first day of the workshop was basically ending. After the session ended, the speakers and the members of the Institute of Medicine Forum on Microbial Threats went out to dinner at a restaurant in Cleveland Park. A few of us walked over to the Metro together and talked along the way. Thankfully, I did not get lost, as (1) I grew up in the DC area (2) I worked around the corner from where the workshop was held for a summer 20 years ago and (3) Julian Parkhill from the Sanger Center was with us and I had sadly gotten very disoriented with him when I was at a NIH Human Microbiome meeting in Bethesda which is actually where I grew up.

The dinner was quite good and I had some good conversations with various folks about microbes and their lives as well as about science in general. Sometimes these types of events are a bit much for me but for whatever reason the whole dinner event was very pleasant. And this was despite the fact that I still had not even started working on my talk for the next day. Finally, as some people were getting coffee Stanley Cohen and a few others said they wanted to head back to the hotel so a gaggle of us left, and went back.

I then spent a few hours making an outline of my talk and finding some slides and worrying about what I was going to say. I was going to be the last talk of the meeting -- in essence wrapping things up. Normally I do not get stressed about such things but here I was at this workshop in honor of one of the greatest biologists of the 20th century. And many scientist's I really really respect were to be in the audience. To give those who know an idea of how big a deal I thought this workshop was - I wore a suit for both days of the meeting. Now, I have not worn a suit in probably two years. But it just seemed natural to do it here. Anyway, with all of these things together it was a big deal to me to give the closing talk of the workshop.

And so I slept very little piecing together a talk that I hoped would honor Lederberg and make people glad they stayed until the end. On a side note, I never met Lederberg. But I was trained in microbiology by one of his students - Ann Ganesan who worked as a Senior Scientist in Phil Hanawalt's lab where I did my PhD. Ann was amazing -- the grand guru of microbiology and I learned a great deal from her. And thus I felt a connection to Lederberg even if I did not know him.

And finally, after very little sleep, I headed out for day 2 of the workshop. And day 2 was as good or better than day 1. There was Stanley Cohen talking about Lederberg and plasmids, Julian Davies (one of my all time favorite speakers) discussing antibiotic resistance, Jo Handelsman talking about functional metagenomics and microbial commensals in insects, Steven S. Morse talking about emerging diseases, Peter Daszak from the Consortium for Conservation Medicine, Mark Woolhouse talking about the ecology of human pathogens, and then me. All of the talks before me were quite excellent. Thoughtful. Insightful. Entertaining. (I do not think I have ever been at a meeting like this - I normally cannot sit through more than a few talks in a day). Lederberg would have been proud.

And then me. I think I did a good job with the wrap up. A lot of the talks for the day had been about how we can use an understanding of the past to help predict the future. And I talked about the original of novelty and how understanding how new functions originate can certainly help us understand the present (e.g., analyzing genome sequences) and I tried to bring in examples from all the other talks at the meeting (ahh .. one of those times where having my laptop and modifying my slides during the day was a good thing).

And then there was a brief discussion session where some really good questions/suggestions came up and then it was over. But I did come back inspired. Lederberg was such an incredible scientist and person. His legacy hopefully lives on.

Lederberg Workshop LiveNotes

I am going to keep posting here notes from the various talks ...

• A good short introduction by Peggy Hamburg of David Hamburg. Peggy is a scientist but had a funny story about how Lederberg gave her her first job - making cookies. She then introduced David Hamburg and said about him “he had many accomplishments including being my father”
• Hamburg then gave a nice talk about Lederberg ... some highlights
• When he was sick earlier this year, he still took time to come over to Hamburg's to discuss Hamburg's book that he was working on ... to give him input
• Good story about Lederberg's building the department of genetics at Stanford
• Told story about how Lederberg helped create the "human biology" major at Stanford
• Emphasized that, despite the impression by many, Lederberg was not so aloof
• Emphasized that Lederberg was deeply committed to educating the public about science and society and went to Hamburg one day saying he wanted Hamburg to introduce him to people at the Washington Post so he could write a column. And together they convinced the Post to do the column and Lederberg wrote it for many years. Many thought this was below someone with his scientific gifts but he was really committed to it. Note you can see his columns here See his papers here. I hope we would have liked blogging ...
  
• Stephen Morse
• Lederberg very interested in evolution
• Coined phrase Exobiology
• Good line of Lederberg's about how infectious disease is "our wits versus their genes and their have been evolving much longer"
  
• Lederberg was an early adopter of email and bioinformatics and was a big fan of technology
• In his office at Rockefeller, Lederberg had all sorts of awards posted in the outside office and then in his inner office he had two things on the wall. A picture of David Hamburg and his ham radio certificate.
• Discussion
• Peggy Hamburg said Lederberg used to take her tidepooling at Pescadero Beach
• Lederberg seemed exceptionally fond of writing notes to people he knew to challenge them about some aspect of their work
• Stanley Cohen mentioned how Lederberg was very helpful when he started out in the Genetics department at Stanford and when some people were questioning his desire to focus on plasmids
• Julian Davies mentioned a story about giving his first "outside" talk - at Stanford - and being very nervous to go there with all the gurus of the field there. And Paul Berg warned him that Lederberg might appear to be sleeping during his talk but that he would ask some very challenging questions at the end. And Lederberg in fact did this - but that Julian had discussed the issue a bit during his talk. And with some trepidation, Julian said "Well, you may not have been listening ..." And though he was afraid of offending Lederberg, it did not.
• Afternoon #1 - A really good session on beneficial microbes and microbial communities
• Jill Banfield gave an exciting overview of her work on the Acid Mine Drainage ecosystem including examples of genome sequencing, proteomics, etc. But the most interesting part was a discussion of their work on microbe-virus interactions including looking at CRISPR elements. CRISPRs have been proposed (by Mojica et al, Makarova et al and some others) to be in essence a bacterial adaptive immune system to resist phage.
• Jean-Michel Ane discussed plant-root symbioses including some very interesting stuff on how different symbionts interact with the same or overlapping host pathways.
  
• Margaret McFall-Ngai discussed the Vibrio - Squid light organ symbiosis and among many things pointed out some detail about the signalling pathways and the develomental changes that occur in the squid
  
• David Relman gave an overview of human microbiome studies and did a good job of pointing out not only what we know, but what we do not know.
  

Lederberg Workshop Intro

Well, I am sitting in the Lederberg workshop right now with David Relman talking about Lederberg and the workshop. He is emphasizing how "microbes as threats" (which is similar to the name of the panel that convened this workshop) is a bit of a biased view point and that beneficial microbes are important too and that Lederberg recognized this. Relman is also mentioning the importance of Esther Lederberg (Josh Lederberg's first wife).

Now - some update on last night. I got to the hotel around 3 went walking around DC and then came back to the hotel. All the speakers were supposed to be staying there so I lingered in the lobby hoping to bump into people I knew and find someone to go to dinner with. And I sat down and started reading a book I just got - Microcosm by Carl Zimmer. Zimmer's book is about E. coli and the history of studies of this magnificent organisms. And I started by lookng up in the index the stuff on Lederberg and read that. The book really seems to be quite excellent --- it covers a wide range of topics in biology at the same time as highlighting the importance of this organism. And then the gurus of microbiology started coming by. And I snookered my way into dinner with Julian Davies, Bruce Levin and Stanley Cohen.  And it ewas a great time --- talking about Lederberg, microbes, plasmids, selection, etc.   A good start to the meeting for me.  More later.

Joshua Lederberg Papers on the Web (well, most of them)

As a follow up to my previous post about a symposium in honor of Josh Lederberg that is coming up in Washington on Tuesday. There is a nice collection of his "papers" on the web - Profiles in Science: The Joshua Lederberg Papers

By papers they mean everything - letters, notes, drafts, communications, etc.  It is quite comprehensive and quite interesting including many discussions with other leading researchers key moments in the history of 20th century biological sciences research.  It is worth checking out.  I note - despite the availability of this great collection, one part of this life as a scientists is not completely freely available - his publications.  Not all are at this site and many are hidden behind the walls of various journals.  What a shame.  Just about every one of his papers is worth reading.

Microbial Evolution and co-Adaptation: A Workshop in Honor of Joshua Lederberg - Institute of Medicine

Well, in a few days I am off to a cool workshop in honor of Josh Lederberg (for more detail see this link Microbial Evolution and co-Adaptation: A Workshop in Honor of Joshua Lederberg - Institute of Medicine). The goal of the workshop is to "to inform the Forum and the general public about the many scientific and policy contributions of Dr. Joshua Lederberg to the life sciences, medicine, and public policy."

The workshop is put on by the Institute of Medicine in Washington DC and it is open to the public. You have to register in advance and I am not sure how many more slots are available but it looks to be pretty good. The sessions topics are are: "The microbiome and co-evolution" "Microbial evolution and the emergence of virulence" "Mechanisms of resistance" "Anticipation of future emerging infectious diseases" and there are some heavy hitter speakers in there including David Relman, Jo Handelsman, Jill Banfield, Margaret Mcfall-Ngai, Stanley Falkow, Bruce Levin, Julian Parkhill, Stanley Cohen, Julian Davies, Steven Morse, Ian Lipkin, and well, me.

I will be blogging from there, but if you are in the DC area or can be, it could be a good workshop.

I am also going to be writing a bit more about Lederberg and his favorite bug (E. coli) in the next few days so stay tuned ...

Open Evolution - Open Taxonomy Mailing List

In my continuing series on Open Evolution I am posting an email I got regarding the creation of a new mailing list on "Open Taxonomy". For more on Open Taxonomy see "The Other 95%" which has some really good stuff on it.

Under the umbrella of the Open Biomedical Ontologies project (OBO; http://obofoundry.org/) we have created a new mailing list, called obo-taxonomy, for the discussion of ontological representation of taxonomies and phylogenies. The OBO Foundry supports the development of orthogonal, interoperable reference ontologies for biological science.

The Phenoscape project (http://phenoscape.org) develops methods and tools for using ontologies to integrate comparative morphological data with mutant phenotypes of genetic model organisms. As such we are very interested in participation from members of the evolutionary biology community to explore how best to integrate taxonomy into an ontological framework. Issues include proper semantics of the relationship between taxonomic groups, and between specimens and species.

Subscribe to the mailing list:
https://lists.sourceforge.net/lists/listinfo/obo-taxonomy

Additional info:
http://blog.phenoscape.org/2008/05/15/taxonomy-as-ontology-opening-the-debate/

Acknowledgments:
The Phenoscape project (http://phenoscape.org/) is funded by NSF-BDI and supported by the National Evolutionary Synthesis Center (NESCent; http://nescent.org).

Calling all microbiologists --- we need better PR to compete with the platypus and other cutesies

Well, much as I hate to admit it, I find myself agreeing with the notion that cuteness sells in genome sequencing. That is in essence the claim of Natalie Anger in an article in the New York Times about all the attention the platypus genome paper has been receiving over the last week (see
A Gene Map for the Cute Side of the Family - New York Times

Alas, microbiologists really do not have anything like this no? I mean, who feels that E. coli or yeast are, well, cute? (Well, even if you have one of those "giant microbes" stuffed animals, that just means you are a dork like me ... the public does not collect those). Sure, Carl Zimmer can get some attention for all the geeky tattoos out there and some of them did have something to do with microbes, but again, a platypus they are not.

So what are we forlorn microbiologists to do? We need better PR and imagery. We need cute microbes. We need more dark and evil microbes too (I mean, if anyone sequenced the T-rex genome - for real - it would get attention too).

So - I am calling all microbiologists and microbiology fans --- bring forth your imagery that will help microbes get the attention they deserve. And today I am suggesting just one simple thing we can all do to make a difference: get some new names.

That is, give your favorite microbe a good common name or nickname to bring out the cuddly or dark imagery we need. All microbes names should conjure up something to the public, like anthrax does (yes, I know, anthrax is the disease and not the microbe , but this adherence to rules is part of the problem we have).

Here are some proposed name changes for organisms I have worked on:

Wolbachia - "The Feminizer"
Tetrahymena - "The Hairy Beast"
Carboxydothermus hydrogenoformans - "Exploding Breath of Death"
Chlorobium tepidum - "Little Green Machine"

So - please - come up with nicknames for all your bugs and start to use them or at least post them here.

Explorit Videos on Youtube

A variety of videos are available from the Explorit Science Center on YouTube. They are worth browsing.

Icky Stuff at Long's

All I can say is I am glad I check my medicines before I take them.  I went to Long's in East Davis the other day to pick up some insulin and was given a box of my insulin pens.  When I got home I found that there was only one insulin pen in the box and that pen was used.  Not exactly confidence boosting in my pharmacy.  Only later did I figure out what happened which was even scarier.  This was insulin I had returned months before because of a defect that Long's was supposed to send back to the manufacturer (I had called the company who had handled this very well, and they told me a free box would be at Long's and that Long's would return the unused portion to them).  So I guess Long's put it in the fridge and did not return it and then saw my name on it and gave it back to me.  Yuck.  Even worse, they did it again, I think the next time I went in.  Double yuck.  

Note that I wrote this when it happened but decided not to post it (but saved it in my blogger account), since it seemed a bit too personal. But now (2009) I am having problems with Long's again and I figured I would make live some of my old postings about Long's.

Kudos to New Scientist's "24 myths and misconceptions" about evolution

New Scientist has a pretty good article on myths and misconceptions about evolution (see Evolution: 24 myths and misconceptions).

They really hit on many of my pet peeves on evolution. Among my favorites:

• Everything is an adaptation produced by natural selection
• Natural selection leads to ever-greater complexity
• The bacterial flagellum is irreducibly complex
• Darwin is the ultimate authority on evolution

Many of these fit in well with my Adaptationomics Award which I will start giving out again soon ....

Help save Davis' Schools ...

Normally I do not put too many things about Davis here as I post them on my Davis Blog here. But I am cross posting today since I know many people from Davis read this blog.

There is a financial crisis of sorts going on in Davis. Please consider donating to the Davis Schools Foundation by May 15 in order to prevent cancellation of programs and/or termination of teachers.

See the video below which was made to showcase Davis' children and what we stand to lose if we don't all act fast!

See also Jamie Madison's blog.

Save Davis' Schools

There is a financial crisis of sorts going on in Davis. Please consider donating to the Davis Schools Foundation by May 15 in order to prevent cancellation of programs and/or termination of teachers.

See the video below which was made to showcase Davis' children and what we stand to lose if we don't all act fast!

SPARC and Science Commons release guide to creating institutional open acces policies

A nice new release from SPARC and Science Commons is out. They put together a guide to creating institutional open access policies (see Press Release)

In the guide they have an overview of the new Harvard Open Access policy, suggestions for what one can do on one's own campus and a plan of action for bringing about policy change. I know I am going try some of their suggestions here at Davis as I am hoping Davis and the UC in general adopts a policy like Harvard's (they mention the UC consideration of such a policy in their site)

Science Commons » Blog Archive » Rockefeller U. Press Uses CC Licenses to Reduce Permission Barriers

Good Open Access news from Rockefeller Press. They have decided to change their publishing policies and are making them much more open. Emma Hill, who used to work at PLoS Biology and is now the Editor of J. Cell Biol. from Rockefeller has an editorial (with Mike Rossner) about the change including details of the new policy and some of the reasons for the change.

Among the changes they make and some of the reasons why

• Giving copyright to the authors.
  
• This is a good thing and about time for them to do it. They say: "Preying on authors' desire to publish, and thus their willingness to sign virtually any form placed in front of them, scientific publishers have traditionally required authors to sign over the copyright to their work before publication. "
• Adopting a Creative Commons license.
  
• They say "What does this Creative Commons License mean? It means that our published content will be open for reuse, distribution, data mining, etc., by anyone, as long as attribution is made to the original work. Share-alike means that any subsequent distribution must follow the rules set out in this license. Non-commercial means that published work can be reused without permission, as long as it is for noncommercial purposes."
• This to me is the most important part of their policy. CC licenses change everything - they make it easy for everyone to use the material.
  
• They retain an exclusive license for 6 months. After the 6 months, the material has the full CC license and can be distributed anywhere as long as it is attributed and not for commercial use.

Overall, I think this change is a good thing. It is still not the full Open Access I prefer, but it is a great step in the right direction. Also see a blog by Science Commons discussing the new policy - see Science Commons. They are overwhelmingly positive. See also Peter Suber here.

On extra nice thing about the policy is they are making it retroactive for all their publications in the past. So lots of Rockefeller press stuff from the past has now become much more open.

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