Category: Misc.

Best genomics news article title …6 Billion Bits of Data About Me, Me, Me!

Gotta love the title of this article. It captures the essence of the new race to sequence ones own genome pretty well (with Jim Watson and Craig Venter leading the way). Clearly, this type of personal genomic medicine is coming whether we like it or not but, for those interested in getting ones own genome sequenced, here are some things to consider:

1. There will be many mistakes, at least with current methods. Get ready for lots of false positives and negatives relating to risk.

2. People will use it against you. Companies. Friends. Relatives. The government. This is not to discourage people from doing it (well, maybe a little bit). But given our current inability to keep anything important private in this country and our apparent inability to not snoop into people’s lives, this is going to be one overwhelming temptation for many people. Now is clearly the time to move forward with anti-discrimination laws.

3. Having your genome sequence will not automatically improve your health. It could even make it worse (e.g., see false positives above)

4. If you REALLY want to understand some of your biology from your genome, you are going to want to take a peak at the genomes of relatives. Good luck on all the family issues that will come up.

5. Just because Watson and Venter are releasing their genomes to the public does not mean you have to (for medicine it is VERY useful to have a genome associated with an individual … even many individuals, but there is no real need for names to be there)

6. The methods being used may not recover the haplotypes well (e.g., see Keith Robison’s blog).

ALSO check out some other articles on this topic

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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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Drug resistant TB and one really bizarre "coincidence"

This whole drug resistant TB travel story just keeps getting more and more outrageous and bizarrely interesting. Certainly it is helping call attention to antibiotic resistance as an issue. I guess that is good. But it is also generating a level of panic that fits in well with the previous panics over bird flu and other scares.

But one thing really strikes me as too bizarre to be a coincidence, although some news stories are presenting it as such. Extreme drug resistant TB is pretty rare in the US. Studying drug resistant TB is also pretty rare among scientists. Yet the father in law of the man flying around the world with this TB is Robert C. Cooksey, a CDC researcher studying, among other things, drug resistant TB (e.g., here is a link to one of his review papers).

The CDC put out a press release implying that he could not have been the source of the infection. Interesting, the release seems to have been removed from the CDC site but can be found at the google cache. Here is the text of the release:

Statement

May 31, 2007

Contact: CDC Media Relations
(404) 639-3286

Statement by Robert C. Cooksey

Research Microbiologist, Division of Tuberculosis Elimination, CDC

First and foremost, I am concerned about the health and well being of my son-in-law and family, as well as the passengers on the affected flights.

I am the father-in-law of Andrew Speaker, who was recently publicly identified as a person infected with extensively drug resistant tuberculosis. I do work at the Centers for Disease Control and Prevention. I have worked at the CDC for 32 years. I´m a research microbiologist in CDC´s Division of Tuberculosis (TB) Elimination, and my work does involve working with a wide range of organisms, including TB. As a research microbiologist, my laboratory work involves identifying the characteristics and features of bacteria.

As part of my job, I am regularly tested for TB. I do not have TB, nor have I ever had TB. My son-in-law´s TB did not originate from myself or the CDC´s labs, which operate under the highest levels of biosecurity.

I wasn´t involved in any decisions my son-in-law made regarding his travel, nor did I ever act as a CDC official or in an official CDC capacity with respect to any of the events of the past weeks.

As a parent, frequent traveler, and biologist, I well appreciate the potential harm that can be caused by diseases like TB. I would never knowingly put my daughter, friends or anyone else at risk from such a disease.

I would ask the media to respect my privacy and that of my family, and I will be respectfully declining all media requests. My thoughts and focus over the next few months will be with my family, and we are hopeful that Andrew will have a fast and successful recovery.

Robert C. Cooksey

I understand his request for privacy, but come on, his son in law apparently flew around the world with a horribly nasty, possibly contagious form of TB. And even if the authorities did not tell him he could not travel, there is no doubt this is something I want reporters looking into. It is entirely possible that it really is a coincidence (son in law having this TB and him working in a lab that probably studies this type of TB) but it is worth investigating this further.

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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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Metagenomics Meeting July 11-13, 2007 UCSD

Fro those interested in metagenomics, a meeting will be held July 11-13 at UCSD with many of the major players in the field participating in some way (I am on the planning committee, so no bias here).

This meeting is connected to the new CAMERA Metagenomics Database run out of UCSD (as a Joint Venture with the Venter Institute). I am about to head down to the Scientific Advisory Board meeting for CAMERA. So I am asking anyone out there who is interested in metagenomics to check out CAMERA and let me know what you think. Right now I am I guess kind of an insider/outsider in CAMERA. I am supposed to have a subcontract to Davis to help integrate some phylogenetic tools into the database but alas the Davis office has been a bit lax shall we say about getting my subcontract set up. So until that is set up I guess I am a CAMERA advisor.

Anyway, if anyone has any useful opinions out there about CAMERA I will be happy to share them with those at the SAB meeting.

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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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Sanger Center Google Ads a little off

OK – this is a bit pithy, but I could not resist …

Dear Sanger Center. You might want to tell google to stop printing your ad that says

“Sanger PhD Programme – http://www.sanger.ac.uk – Fully funded 4 year studentships in genomics. Deadline 10th Dec 2006″

It seems to be a bit out of date.

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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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Looming Open Access

People out there who know me know I like to talk. A blog is a perfect outlet for someone who has opinions about just about everything. But my favorite thing about blogging these days is finding other blogs out there that say what I might have wanted to say in a much better and more elegant manner. And this is the case today for Carl Zimmer’s blog on “An Open Mouse.“

Zimmer, for those who are not familiar, is a science writer who also now has a good blog (called The Loom) but is probably best known for his articles in the New York Times and his books. (I have not read all of his books, but his Evolution book is quite good and I have Parasite Rex but alas have not read it yet).

Anyway, Zimmer in his new blog writes about how Open Access science makes his blog easy because he can use a figure from a PLoS paper (on mouse genetic interactions) and rather than sue him, PLoS simply encourages him. I could blather on and on about this (and in fact have – see here for example). But better to just read his words:

And what do I now hear from PLOS? Do I hear the grinding of lawyerly knives? No. I hear the blissful silence of Open Access, a slowly-spreading trend in the journal world. PLOS makes it very clear on their web site that “everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish.” No muss, no fuss. If I want to blog about this paper right now, I can grab a relevant image right now from it. In fact, I just did.

I certainly appreciate the importance of copyrights (as the owner of many for my articles and books), but in these situations, keeping information behind a thick wall starts to seem a bit crazy, like the loss of precious bodily fluids. Far from committing some sort of violation to the PLOS paper, I have actually just spread the word about it. A few readers may even go back to read the original. And it was so easy and straightforward for me to do so that I will be very reluctant to bother with anything else.

You go Carl. Welcome to the wonderful world of OA.

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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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Another way to support open access – call in to radio shows

So – I was driving today from Davis to Walnut Creek to attend the Joint Genome Institutes Scientific Advisory Council meeting (more on this hopefully later as I got lots of good advice from the SAC group which includes George Weinstock, Bruce Birren, Joe Ecker, Mark Adams, and Eric Mathur (who is perhaps the most energetic person I ever met)).

Anyway – on the drive over, I was listening to KQED’s Forum Show and they were doing a story on Avandia, the type II diabetes drug. A recent report on this drug indicates that taking it leads to a significant increase in very negative “side effects” like death. Most interesting and upsetting to me, the lead author of the new study said something to the effect of “our new study was limited significantly because we could not get access to the full results of the clinical trials on Avandia.” This is really stunning. Here is a drug making GSK billions of dollars and yet the clinical trial data that underlies the approval of this drug is not readily available for other people to look at. What is wrong with this picture? I though science was about building on prior results. If you can’t get the data, how exactly do you confirm what someone else did and how do you build on their results? Apparently, medicine does not follow the same procedures.

So I seethed while in the car. And then, I got stuck in a traffic jam (normally I take the train, but was unable to today). And at the same time, they announced the call in number. So I called — the first time I have ever even tried to call one of these shows. And on the second try it rang. And a man answered and asked for my first name and my question/comment. And then, I was on the air … asking about whether there were any attempts to make clinical trial data more readily available (OK, I knew there were attempts, but I was not sure of the details and they needed to be asked on the air anyway).

And if you want to know what I said, and what they said, well listen to the show (I am on at minute ~ 34).

Wed, May 23, 2007 — 9:00 AM
Avandia and Diabetes

Listen Listen (RealMedia stream)
Listen Download (MP3)
(Windows: right-click and choose “Save Target As.” Mac: hold Ctrl, click link, and choose “Save As.”)

And to add to the bonus of being on the air, Jim Bristow, Deputy Director of JGI, was, like me, a bit late to the SAC meeting at JGI. And he came up to me and asked if that was indeed me on the air while I was supposed to be at the meeting. To learn more about clinical trial access, see PLoS Clinical Trials.

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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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Is Nature going Open Access?

Nature and EMBO are together publishing “Molecular Systems Biology” and all basic research in this journal is Open Access. I am wondering why this has not gotten more press as it seems Nature is experimetning with OA models here. Nature has done some experimentation previously by making certian types of papers available freely (e.g., many genomics papers). But this is definitely one step beyond and they deserve massive kudos for it.

So if you are looking for a new OA journal to submit some systems biology related papers, you should try here. And maybe with a little effort, we can convince Nature it is worth doing for more of their journals.

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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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Calling all microbiologists – please help save the world

I read with dismay today news reports of the discovery that much of the Southern Oceans are saturated with CO2. This has happened much sooner than anyone anticipated and bodes very poorly for limiting the damaging effects of global warming. So I am starting a new call in my blog here

To all you microbiologists out there. Are you bored with what you are doing? Looking for something important and challenging to do? Sick of working on yet another human pathogen? Switch to working on a topic relating to limiting global warming and climate change (note if you want to learn more about global climate change check out the recent New Scientists article here which I found out about from the Davis Egghead Blog). Among the topics you could work on:

Any other suggestions for topics welcome.

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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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Another education use of Open Access publications

I was reminded of another important use of Open Access publications last week when I gave a talk at Chico State University. Chico St. is one of the California State Universities (I guess it’s formal name is California State University, Chico). The people in the Biology Department there invited me to give a talk (I think this was because of the press coverage of my PLoS Biology paper on the symbionts of the glassy winged sharpshooter – a pest of great concern throughout California since it transmits Pierce’s Disease in grapes).

I had a great visit and a nice drive to and from Chico. I met with lots of faculty doing interesting stuff. And after my talk we went to a local pub with some faculty and students. I had opened up my talk discussing the benefits of Open Access publication and how it was just as important as databases like Genbank (In fact, I think it is a good idea to discuss the importance of OA in scientific presentations in general – spreading the word). And much of our conversation at the pub centered on Open Access.

The most interesting thing I found out was that for one of the journal club/discussion courses that they have there, they only use papers from OA journals like PLoS journals. There were two major reasons for this. (1) As a woefully underfunded university (note – read this Arnold), they do not have funds for their libraries to subscribe to a diversity of journals and (2) using OA publications means they can post all the publications or links to them on a web site for students and do not have to make them closed access / password protected to prevent illicit sharing of non Open publications.

So – another benefit of Open Access publishing. Easing access even o major universities in the US, and making it easier to use research papers as part of course readers and course web sites.

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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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California Metagenomics Meeting presentations available online

For those interested in metagenomics, the presentations from a metagenomics meetings that was held at the Moore Foundation HQ are now available online.

I wrote about the meeting previously in my blog.

The speakers were Eric Allen (UCSD-SIO), Doug Bartlett (UCSD-SIO), Weizhong Li (UCSD), Victor Markowitz (JGI), Jonathan Eisen (UCD), Victoria Orphan (Caltech), Adam Martiny (UCI), Jessica Green (UCM), Kimmen Sjolander (UCB), and Steven Brenner (UCB). All Powerpoint presentations are available in PDF format.

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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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