Eisen Lab Blog

Fear and Loathing in Boston for the ASM Meeting


OK

Here is my confession.  I hate,  I mean hate, big meetings.  If a conference has more than 200 people I start to feel icky.  And now this AM I head off to Boston for the gigantic ASM “General Meeting“.  I am in part dreading the whole thing.  Anytime one needs to use an online planner to schedule which talks one might want to go to, it is not really my kind of meeting.
But, I was invited to give the “Division R” lecture.  Division R is the “Systematics and Evolutionary Microbiology” section of ASM and this year they are having a session on “Linking evolution of protein families to genome annotation efforts.”  This is right up my alley as it was for genome annotation that I first started working on phylogenomic methods (and for which I coined the phrase “phylogenomics”) (e.g., see my 1998 paper in Genome Research for more detail on this and see my 1995 paper on SNF2 proteins in NAR where I first discussed using evolutionary trees to predict gene function).
And since the meeting is in Boston (where I was born), I agreed to go.  Add I am sure I will see some great things there.  But travel and I do not agree well right now and I am I guess dreading the whole thing.  If you want to learn more about phylogenomics go to the division R session (Kimmen Sjolander, Patricvia Babbitt, and Margrethe Serres are also talking). And I will try to blog from the meeting but we shall see …
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Davis is indeed Friendly

I do not normally cross-post stories that I put on my blog about life in Davis, CA but I could not resist this one. Davis has been picked as one of the 5 friendliest cities in the US.

Here is the video from the Today Show. I suppose the people doing this did not take off too much for bloggers like me …

http://www.msnbc.msn.com/id/22425001/vp/24855776#24855776

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Davis Really Is Friendly

Two years ago, when we moved to Davis, my wife and I kept talking about how absurdly friendly everyone was here. We still can’t stop talking about it (yes, not everyone is friendly, but the average person is and I have never lived in a friendlier place).

Well, our feelings were confirmed by the recent Today show discussion of the five friendliest cities in the US and Davis was picked as one of them. Here is the video …

http://www.msnbc.msn.com/id/22425001/vp/24855776#24855776

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Simpsons Evolution Video

Just a little post showing this Simpsons Evolution Video from YouTube

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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UC Davis Beats Stanford Game 1 of NCAA Baseball Playoffs

Not much else to say here … Davis has beaten Stanford in the first game in the NCAA Baseball Playoffs. Good job Aggies.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Colbert is now obsessed with Microbes

Yes that is right, Colbert is now obsessed with Microbes. He has started a new report … “The Microbe Beat”. On this first one, Colbert discusses Martian Microbes, Penicillin and other microbial things. This is perhaps the greatest coup for getting microbes the recognition they deserve since, well, since ever. Please make this the most watched Colbert video ever.

Thanks to my PhD student/employee Jenna Morgan for pointing this out.

http://www.comedycentral.com/sitewide/video_player/view/default/swf.jhtml

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Top 10 Things Francis Collins Might Do After NHGRI

As I have said, I think Francis Collins, upon leaving the NHGRI, is well set up to become an advisor to some presidential candidate (not that I would pick him as my advisor if I were running, but alas I am not running this time around).
But if he does not become Obama’s science sidekick or McCain’s genomics guru, well, there are lots of things he might do.  Here are some possibilities:
  • 1. The 1000 genome songs project.  He is already further along in this than the 1000 genomes project …
  • 2. Get a job at Craig Venter’s Synthetic Genomics.  Hey, Collins says he wants to try something new.  And Craig has a history of hiring people who used to work at funding agencies.
  • 3. Sequence Jesus’ genome.  More on this later.
  • 4. Run the World Anti Brain Doping Agency (WABDA).  We need a crusader to run the organization.
  • 5. Start a blog.  Hey, there are worse things one could do with free time.  Not many.  But there are some.  
  • 6. Start a genomic information anti-discrimination lobbying firm.  Like others in government, he really should try to make money off of legislation he helped pass.
  • 7. Dancing with the stars.  He could even sing along too.
  • 8. Start giving talks about genetic inferiority of various races and genders.  Or did someone who once ran NHGRI already do that? 
  • 9. Try and apply for some of NHGRI’s money.  Oh wait, he does not run a huge sequencing center, so he may not qualify.
  • 10. Make jewelry out of disk shaped beads.  Also known as sequinsing.  
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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).

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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