science – Page 5 – Jonathan Eisen's Lab

The latest genomics buzz

The latest buzz in genomics is about the honeybee genome. The people working on this genome have really done a good job of organizing themselves (a sort of model social genomics network in a way). They have a veritable slew of papers coming out this week on various things about the genome and about honeybees that were learned by making use of the genome.

There is an entire issue of Genome Research dedicated to studies of the honeybee (see the press release here) including papers on rates of evolution, circadian rhythms, chemical sensing, sex and death (of course), and even the royal jelly. If you don’t know what royal jelly is, do a google search for that. There is also an overview article in Nature and a genome report in Science. In total 170 researchers were involved in these papers.

Mind you, I am disappointed that these were not published in Open Access journals. And this is particularly sad given that the funding came from the NHGRI, the same group of sanctimonious individuals who kept talking about how the “public” human genome project was “open” in every way for the betterment of humanity. Unfortunately, what they mean by “open” even for the human genome project is a bit of a misnomer. They meant that people could look at the data immediately. But they restricted how people could use the data, despite their attempts to pretend otherwise. Consistent with this, the groups funded by the NHGRI generally do not publish their papers in Open Access journals. Shame shame shame.

OK, enough sniping. The honeybee is so fascinating biologically in so many ways that this genome sequence deserves a bit of extra attention. First, honeybees are social creatures. They have in fact been one of the key models in studying both the evolution of social behavior but also communication among organisms.

Another aspect of their biology that is very interesting is their genetic structure. Like other hymenoptera they have what is know as a haplodiploid life cycle with males being haploid (the result of unertilized eggs) and the females being diploid. This unusual genetics is another reason that honeybees and other hymenoptera have been studied extensively by biologists for many years. In fact, a great little bit of history about this is in a book on the history of studies of altruism from Princeton University press. One of Darwin’s biggest concerns in the origin of life related to the self sacrifical behavior, especially that in honeybee colonies. Apparently, honeybees were a topic of conversation among non scientists and the non reproductive worker castes were well known to the public. Darwin struggled quite a bit to come up with a good explanation that was consistent with natural selection for why some individuals would sacrifice their lives for others.

Dawrin actually cam up with a good logical explanation for this – that some individuals would sacrifice if they were related to others who would benefit. Bees and their relatives played a large part in studies that have revealed in much greater detail how altruism can evolve. They may not be as warm and fizzy as some other organisms being sequenced, but they certainly were a good pick for a genome sequencing project.

Science Lobbying – The role of science in politics and vice versa – Scientists and Engineers for America

I listened to a very interesting Science Friday Podcast today (I listen to them on my bike rides to/from work here in Davis, CA, the most bike friendly town in which I have ever lived). This particular podcast had as one of the guests Susan F. Wood. Some people may remember that she resigned from a top job at the FDA over what she felt was politics getting in the way of good science.

Well, rather than disappear as some higher ups in the executive branch do after quitting, she has jumped into a whole new realm. She has helped start a group called Scientists and Engineers for America. Their aim is to help elect to office people

who respect evidence and understand the importance of using scientific and engineering advice in making public policy

from the NY Times article about this.

They have even created a “bill of rights” for scientists. Among the rights they include:

Federal policy shall be made using the best available science and analysis both from within the government and from the rest of society.

The federal government shall never intentionally publish false or misleading scientific information nor post such material on federal websites.

Scientists conducting research or analysis with federal funding shall be free to discuss and publish the results of unclassified research after a reasonable period of review without fear of intimidation or adverse personnel action.

Federal employees reporting what they believe to be manipulation of federal research and analysis for political or ideological reasons should be free to bring this information to the attention of the public and shall be protected from intimidation, retribution or adverse personnel action by effective enforcement of Whistle Blower laws.

No scientists should fear reprisals or intimidation because of the results of their research.

Appointments to federal scientific advisory committees shall be based on the candidate’s scientific qualifications, not political affiliation or ideology.

The federal government shall not support any science education program that includes instruction in concepts that are derived from ideology and not science.

While scientists may elect to withhold methods or studies that might be misused there shall be no federal prohibition on publication of basic research results. Decisions made about blocking the release of information about specific applied research and technologies for reasons of national security shall be the result of a transparent process. Classification decisions shall be made by trained professionals using a clear set of published criteria and there shall be a clear process for challenging decisions and a process for remedying mistakes and abuses of the classification system.

I confess to being a little worried that they may become too partisan and to be effective I think they should try to be as non partisan as possible (although there is no doubt that the current administration has violated more of the items in their bill of rights than probably any previous administration). Neverthless, this sounds like a great idea and hopefully they can help increase the use of science in decision making.

To sign up go to http://www.sefora.org/

World’s Smallest Genome of a Cellular Organism?

A one page paper in Science reports on what I think is one of the most exciting findings in microbial genomics in years. The reports describes the sequencing and analysis of the genome of a bacterial endosymbiont of an aphid. This bacteria, known as Carsonella, has a TINY genome – only 160 kbp in length. This is ~ 3 fold smaller than the previously known smallest genome – that of Nanoarchaeum equitans which has a genome of 490 kbp.

I think almost certainly this symbiont should be considered an organelle. It is missing many cellular functions found even in the most reduced symbionts. Thus in essence it may not be the smallest genome of a cellular organism. But who cares how we define it. If it is a new organelle – that is amazing. If it is a tiny cellular genome – that is amazing too.

One thing that strikes me as strange is the fact that the paper is only one page long. It contains so little detail on what was done and what was found in the genome that the story is woefully incomplete. This I would guess is somehow related to a rush to publish but also likely due to it being published in Science, which has severe page restrictions.

This paper has been getting ENORMOUS press coverage for valid reasons. But I agree with Craig Venter (see the New Scientist article) that this genome is not of much relevance to efforts to create a “minimal” genome. This is because the ideal minimal genome is one that can support independent life. Carsonella, is far from independent and thus represents a really wild evolutionary story, but nothing of much relevance to minimal genome studies.

Some related links:

Commentary by Siv Andersson
NPR Story
Nancy Moran’s Home Page (one of the corresponding authors of the paper)
World Science article

Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H., Moran, N., & Hattori, M. (2006). The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella Science, 314 (5797), 267-267 DOI: 10.1126/science.1134196

Genomics Education highlighted at 14th Annual International Meeting on Microbial Genomics

Just got back from the 14th Annual International Meeting on Microbial Genomics, where I gave talk on microbial symbiont genomics. This was one of the best meetings I have been to in a while. It had the right combination of everything including:

Many excellent talks and posters (OK, in the interest of not upsetting people for not saying their talk or poster was great, I will not make a big list of all the ones I thought were good, but I will give a few highlights below).
Excellent location (UCLAs Lake Arrowhead Conference Center, which is in the mountains east of Los Angeles). This is a place that is very conducive to getting to know colleagues and it almost forces interaction among people. There is one central building where there is a dining hall, a nice deck if you want to eat outside, the conference room, rooms for posters, and a large living room for hanging out. The rooms for sleeping are mostly great (e.g., mine was a split level condo like structure with a living room and a bedroom/bath on floor one and a bedroom/bath on floor 2). And being in the mountains is very pleasant. Plus there is a pool, jacuzzi, and sports facilities that are very nice. The only annoying thing is that the Lake itself, which is 100 yards away, but it really almost private, with most of the shoreline occupied by houses and private docks.
Good food. The food is not spectacular or anything but better than the food at 90% of the conferences I have been at.

In terms of talks, there were quite of few that were both interesting topics and very well presented. For example, Jessica Green from U. C. Merced gave a great talk about spatial distributions of microorganisms, Julian Parkhill from the Sanger Center put together a really nice story about mechanisms by which microbial pathogens generate phenotypic diversity, and Julie Huber from MBL impressed many with her talk about the “Deep Rare Biosphere.”

But to me, the best two talks were ones on science education reform by two people from UCLA. Erin Sanders-Lorenz presented a summary of her course she has been teaching at UCLA that has students doing “phylogenomic” analysis which takes them from isolating and culturing organisms from environmental samples to building evolutionary trees of genes isolated from these cultured species.. This seemed like a very creative, hand on, novel way to teach students the excitement of science and some things about evolution. It sounded so well thought out that I asked for (and got) a copy of her lab manual.

Much as I liked this class, the one described by Cheryl Kerfeld knocked my socks off. She described a program they have developed at UCLA called the Undergraduate Genomics Research Initiative. This is an interdepartmental multi-course collaboration with the central theme involving the sequencing and analysis of the genome of a bacterium called Ammonifex degensii. The various courses are organized around a central course on genome sequencing. The linked courses include ones in many different departments at UCLA as well as various courses at other universities. They have clearly given enormous thought to how to do a truly project based course which likely will catch students attention and interest much more than standard lectures or standard labs.

There have been other successful hands on genome sequencing courses before – perhaps the first being one by Brad Goodner at Hiram College who had students participate in the sequencing and analysis of the genome of Agrobacterium tumefaciens (e.g., see a press release here). The Kerfeld UCLA UGRI program sounds like it has gone to the next level by integrating many courses across departments and by having creative ways to encourage participation of students in multiple aspects of the project. It really is worth giving a look at the UCLA UGRI program’s web site.

Other tidbits about the meeting:

Jeffrey H. Miller from UCLA organized it
This is the same Jeffrey Miller who identified most of the mutator genes in E. coli with a really creative genetic screen
There was another Jeffrey Miller from UCLA at the meeting (will leave this up to google for people to figure out who this other Miller is).

Fruit flies going into space

The plan is to send some fruit flies into space on the next shuttle mission and to compare them to some flies at home in terms of how their immune systems respond to the trip into space.
Not sure whether this is completely novel or not, but good to see that NASA is at least trying to still support scientific research. See the press release here.

There have been some serious controversies as of late at NASA about whether it truly is suportive of scientific research or whether it (like many other agencies) is succumbing to the anti-science rhetoric and attitude of some of the higher ups in the Bush administration.

For example, see the NYTime Article from February about how the NASA admiistrator had to make an announcment calling for scientific openness in the agency.