Thursday, June 28, 2007

News Story titles you don't want to see - Va. May Increase Freshwater Fecal Bacteria Limit

Just a quick one here ... talk about story lines you really do not want to hear or see. What I really want is more fecal bacteria in my lakes and rivers.

Wednesday, June 27, 2007

Genome Transplantation - Coming to a Bacteria Bacterium Near You

Well, I was interviewed yesterday by the AP (see the AP article here) relating to an article in Science on Genome Transplantation by John Glass, Craig Venter, and crew and the Venter Institute. Their article is coming out in tomorrow's Science. Though this was not published in an Open Access journal, I think this one is definitely worth talking about and looking at.

Here is what they did, in a nutshell. Took one mycosplasma species (mycoplasma are bacteria that do not have cell walls and have very small genomes) and very carefully removed its chromosome. They then mixed this with a recipient mycoplasma that had some detectable genetic differences. And they then selected for cells that had a antibiotic resistance function found only in the "donor" genome. And they got some growth. And surprisingly, many of the cells that grew up appear to have COMPLETELY replaced the endogenous genome with the donor genome. Thus they use the term genome transplantation.

It seems like a pretty solid paper, although I still am not 100% convinced that these are not some relics of the original donor cells that simply made it through the genome extraction processes intact (this is very unlikely given their controls but still possible). Assuming that they really have genome transplantation, it is a pretty cool result.

Why? Well, it means that at least in some sense, they can use this as a tool in synthetic genomics. One of the big limitations of synthetic biology right now is how one would make a genome in vitro of a bacteria and then get this genome to "boot up" into a cell. For viruses, they can make genomes in the test tube and get the virus to be created because viruses are cellular parasites and all they have to do is get the DNA for the virus to be packaged in the right way into a cell or viral capsid. But for a bacteria, things are much different. The challenge has been how to get a recipient cell to boot up a new genome and delete its own or at least silence its own. And without going into all the gory details, this has proven challenging.

So - now genome transplantation. On the one hand, it can serve as a way to boot up a new genome. However, it probably has limited potential in many ways since to get the new genome to effectively replace the old one, it has to not only be replicated, but the machinery of the cell present in the recipient has to work well enough on all the key components of the donor genome to get the booting up to work. For example, all the promoters in the donor genome must be transcribed efficiently by the recipients machinery, at least for the RNA and protein synthesis machinery genes, so that the donor stuff can get made. And of course the replication origin and other replication features must all work as well. What this means is that I think genome transplantation will only work if the donor and recipient are very similar to each other for most of the housekeeping genes and functions. So this is not yet ready to work for all of synthetic biology. But it still seems pretty cool.

Monday, June 25, 2007

Evolution is ... WTF?

OK

I know I am a little dim (well, maybe a lot). And maybe something was lost in the translation of putting this on the web. But WTF? Can someone explain to me what the point of the NY Times "story" entitled "Evolution is" with a bunch of quotes?

And again, WTF? Why did they pick these quotes?

Like this one by Gould

"It touches all our lives; for how can we be indifferent to the great questions of genealogy: where did we come from and what does it all mean? and then, of course, there are all those organisms: more than a million described species, from bacterium to blue whale, with one hell of a lot of beetles in between - each with its own beauty, and each with a story to tell." - Stephen Jay Gould


and this one by Maynard Smith

"As an evolutionary biologist, I have learned over the years that most people do not want to see themselves as lumbering robots programmed to ensure the survival of their genes." - John Maynard Smith
Anyone out there have the inside scoop on this?

Thursday, June 21, 2007

Southwest Airlines Supports Evolution

Congrats to Southwest Airlines. On a recent flight coming back to Davis from San Diego I saw a nice 1 pager in their Spirit Magazine promoting the Darwin exhibit currently on display at the Field Museum in Chicago. Many places shy away from saying anything about evolution for fear of antagonizing ID supporters. In fact, I cannot recall ever seeing anything on evolution in anyother airline magazine. Kudos to Southwest. Another reason to fly them. For those airlines that shy away from topics like evolution in their magazines, do they also shy away from physics and math in their engineering departments?

Wednesday, June 20, 2007

Overselling genomics awards

Genomics is great. It really is. But is has also been absurdly oversold by many, starting with those who implied sequencing the human genome would cure all diseases. So I have decided to start a new line of this blog - the "Overselling genomics awards"

My first award goes to the Stuart Truelson for a Commentary for the California Farm Bureau Federation. The essay has some OK points about genomics but is a bit overzealous about the benefits that come from genomics. The essay ends with:

The genomics age is here, whether some like it or not. And, any effort to impede potential benefits that genomics offers humankind--from more and better food to breakthroughs in health and life-saving medicine--should raise moral and ethical questions that are even more serious than those surrounding the science itself.
Sounds a bit like those who say "Any discussion of the war makes you unpatriotic." And thus Mr. Truelson gets my first award, not just for overselling genomics, but for being so icky about it.

Monday, June 18, 2007

Scrap food to energy - here we come

Well, congrats to Martin Wu, who is a Project Scientist at Davis in my group for getting his pet project approved as a new Community Sequencing Proposal through the Joint Genome Institute. In this project (see the MIT technology review article here)Martin and Ruihong Zhang a Prof. at Davis are going to do some sequencing of microbes that like in Dr. Zhang's biogas reactors.

From the MIT article:
"Sequencing these organisms will give us a better idea of who the players are so we can better control the conditions or improve the design to further improve conversion of waste into biogas," says Ruihong Zhang, the UC Davis bioengineer who developed the system.
and
"We want to compare what kind of microbes are there at different conditions and try to figure out why one [set of conditions] works better than the other," says Martin Wu, a geneticist at UC Davis who will lead the genomics part of the project.
and
In nature, the microbes that carry out degradation of organic waste and generation of methane exist in a very complex anaerobic community, and individual isolates from the community are hard to grow," says Jim Bristow, head of the community sequencing program at the Department of Energy's Joint Genome Institute, in Walnut Creek, CA
Martin has been interested in this area for ages, since his family used to use a biogas reactor on their farm in China. I find this much more sensible than the plans to specifically grow plants to produce biofuels since these reactors simply make use of current solid waste.

Some other interesting stories and links about biogas:

Big biogas Africa project
Biogas project in India wins award
Google blog search on biogas
Google news search on biogas


Books on Biofuels

Friday, June 08, 2007

Good list of Science Blogs

Check out the list of science blogs at Blog Together. It has many I had never heard of or seen. It has a bit of a bent towards blogs from North Carolina but otherwise it is one of the more comprehensive lists I have seen.

Trip to the Creation Museum

Just a quick post suggesting people check out the slashdot story on a field trip to the creation musuem. Thanks to Doug Rusch for pointing this out.

First Ever Synthetic Organism Patent?

Wired is reporting that the Venter Institute has applied for a patent on the first fully synthetic organism (i.e., they synthesized the genome in the lab ... I am sure that the organism had to be "booted" up in some way using a living organism).

Wired reports:

Scientists at the J. Craig Venter Institute have applied for a U.S. patent on a minimal bacterial genome that they built themselves. According to the patent application, it's "a minimal set of protein-coding genes which provides the information required for replication of a free-living organism in a rich bacterial culture medium."

What do people think? I for one find the patent system completely incomprehensible. I think most biotech. related patents recently have been overly broad and/or represent something that should not be patented. But in this case, I do not know enough detail to really judge but it sounds like at least they did some real work here, which is more than the case for many genome sequence related patents from the past. Given that many places now have patents on mice and other organisms with single genetic knockouts, I do not see how the patent offices could reject a fully synthetic organism. This is not to say whether it is a good idea to synthesize an organism, but I think we are past that point anyway as clearly people will do it.

Another Good Kid's (and Adults) Activity in Davis - Take the Train to the Train Museum







I have been meaning to try this out for ages. I take the Capitol Corridor train West all the time from Davis to Berkeley and other parts of the Bay Area. But I had never taken it East to Sacramento. It looked from the schedule that it was just 15 minutes or so to Sac and that the Sac station was right near the train museum, which my daughter (2 yrs old) loves (she loves trains trains trains and trains).

So we did it. We went to the Davis station. And took the train to Sacramento. The train ride was great - only about 20 minutes long and my daughter got to see all sorts of cool things (she specially liked seeing the river and going over the Yolo Basin area). And then we were in Sac. And after not being sure where to go, we walked around a corner and right there was the train museum. Which we went into for an hour or so and then headed back to catch the train back to Davis. It was about a 2-2.5 hour outing (not sure exactly when we got back) and was definitely something different for my daughter to do.









Wednesday, June 06, 2007

Support Open Access - write your Congressional Reps

To all supporters of Open Access publications. Please consider writing / faxing your Congressional Reps as there is a lobbying effort going on by supporters of closed access. For more information see the Alliance for Taxpayer Access site.

The most important to write to are the members of the House Appropriations Committee

Nita M. Lowey (NY)
District: http://www.nationalatlas.gov/printable/images/pdf/congdist/NY18_109.pdf
Phone: (202) 225-6506

Rosa L. DeLauro (CT)
District: http://www.house.gov/delauro/our_community.html
Phone: 202-225-3661

Jesse L. Jackson, Jr. (IL)
District: http://www.house.gov/jackson/District.shtml
Phone: (202) 225-0773

Patrick J. Kennedy (RI)
District: http://nationalatlas.gov/printable/congress.html#ri
Phone: (202) 225-4911

Lucille Roybal-Allard (CA)
District: http://www.house.gov/roybal-allard/district.shtml
Phone: (202) 225-1766

Barbara Lee (CA)
District: http://lee.house.gov/index.cfm?SectionID=7&ParentID=0&SectionTypeID=2&SectionTree=7
Phone: (202) 225-2661

Tom Udall (NM)
District: http://tomudall.house.gov/display2.cfm?id=5266&type=KidsZone
Phone: 202-225-6190

Michael Honda (CA)
District: http://nationalatlas.gov/printable/images/preview/congdist/CA15_109.gif
Phone: (202) 225-2631

Betty McCollum (MN)
District: http://mccollum.house.gov/index.asp?Type=B_BASIC&SEC={7744FE23-1C14-4D6C-8864-2271EF5A7DBD}
Phone: (202) 225-6631

Tim Ryan (OH)
District: http://timryan.house.gov/index.php?option=com_content&task=view&id=122&Itemid=11
Phone: 202-225-5261


Monday, June 04, 2007

Agonizing massive loss for the world and for microbiology - Valley of the Geyseys in Kamchatka mostly destroyed


There has been an environmental disaster of epic proportions in Russia. The Valley of the Geyseys, one of the most spectacular places on the planet - an ecosystem of hotsprings and thermal sites much like that in Yellowstone National Park in the US, has apparently been destroyed by a massive mudslide.


See the news stories
This is a big tragedy for microbiology because Kamchatka has become a site of an enormous amount of really top notch microbiology research and a great place to compare results from those found in other thermal sites like Yellowstone.

TASS reports for example

most of the unique hot water springs in the Valley of Geysers have been damaged beyond repair.

This will affect many important research projects (including mine). For example see the web site of the Kamchatka Microbial Observatory (funded by NSF) on which I have a minor role.

If anyone out there has any additional information it would be appreciated.

PS Thanks to Jenna Morgan for pointing this out.

PPS - Nature has run a news story on this

Sunday, June 03, 2007

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

Saturday, June 02, 2007

Great kids activity in Davis - the U. C. Davis Raptor Center








We (me, my wife, my 2 yr old and our 4 month old) went for a visit a few weekends ago to the U. C. Davis raptor center. Our 2 yr old daughter went crazy, never wanting to leave and wanting to see all the birds over and over. The 4 month old loved the tranquil setting (he did not like the screeching hawks, but they have a nice little picnic bench area a bit away from the birds). The Center has a bunch of cages outside with all sorts of raptors, including eagles, hawks, harriers and owls. The also have a litte museum with displays. It is in a really nice setting along the flowing part of Putah Creek south of Davis and is definitely worth a visit.

Here are some pictures

Friday, June 01, 2007

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.