Tag: Misc.

Twisted Tree of Life Award #3: The Columbus Dispatch on Ancient Bacteria

Was browsing Twitter and I saw one post that caught my eye. @MicrobeWorld, which by the way, rocks, wrote

A microbe that is as old as dirt could one day help keep radioactive metals out of our drinking water http://bitly.com/15l9mR

This caught my eye because, well, I study radiation resistance some of the time and the “old as dirt” statement seemed weird.

The article being referred to was in the Columbus Dispatch (The Columbus Dispatch : Tricking toxins) and it was about some interesting work on Shewanella by Brian Lower and others from Ohio State. The work involves using one particular species of Shewanella for bioremediation of radiative waste. The problem however is in the lead in to the article. This is painful to me. It says

A microbe that is as old as dirt could one day help keep radioactive metals out of our drinking water.

Shewanella oneidensis bacteria have existed for billions of years, thriving even when the Earth’s atmosphere lacked oxygen.

This is just so so so wrong. Shewanella oneidensis is one species of a large group in the genus Shewanella which itself is part of one subgroup (the gamma group) of the Phylum Proteobacteria (I note I helped analyze the genome sequence of this species a few years ago – see paper here). While it is possible (though not certain) that the Phylum Proteobacteria was established billions of years ago, it is certain that Shewanella oneidensis did not exist at that time. Perhaps this species has been around for tens of millions of years but certainly not billions. This would be like saying “Humans have been around for hundreds of millions of years” simply because animals have been around for that long. In the context of humans the statement is clearly absurd. It is in fact equally absurd in the context of bacteria. And for this, the Columbus Dispatch is getting my third Twisted Tree of Life Award.

——–
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.

——–

A Postdoctoral research position in Antarctic Metagenomics and Microbial Ecology

Here is an ad for a post doc that is to work on a joint project between my lab and that of Craig Cary.

POST-DOC ANNOUNCEMENT

A Postdoctoral research position in Antarctic Metagenomics and Microbial Ecology

A Royal Society Marsden Funded project “Life at the extreme: resolving the genetic basis of microbial endemism in the super-heated soils of Mt. Erebus, Antarctica” is available at the University of Waikato, Hamilton, New Zealand.

Project description

Tramway Ridge geothermal site on Mt. Erebus, an active volcano in Antarctica, is the most geographically isolated geothermal site on earth providing an excellent system for studies of microbial speciation, biogeography, and evolution of thermal adaptation. A recent preliminary genetic survey of the Tramway Ridge microflora revealed an unprecedented diversity of extremely novel microbes only distantly related to any known bacteria [Soo et al., (2009). Environ. Microbiol. 11 (3), 715-728]. Most of these loose affiliations are with organisms identified from deep-subsurface systems suggesting the Tramway Ridge community may be archaic and of a sub-surface origin. A group dominates the community that to date has no known cultured or environmental representative. The successful candidate will employ cutting-edge high throughput DNA sequencing and bioinformatics to acquire and decipher the genetic capabilities and structure of entire microbial community at Tramway Ridge. A combination of these advanced genetic methods coupled with culture dependant approaches will be used to analyse the Tramway Ridge microflora and other Antarctic geothermal sites to address questions focused on endemism, biogeography, evolution, and adaptation.

The project is in collaboration with Dr. Jonathan Eisen, U.C. Davis Genome Center.

Required qualifications

We are looking for a highly motivated postdoctoral scientist with and interest in Antarctic microbiology and experience in metagenomics, microbial ecology, cultivation of microorganisms, and bioinformatics. The successful candidate will drive his/her own project within the context of the project and be actively involved with practical guidance of an MSc student. The University is especially interested in candidates who can contribute to the diversity and excellence of the academic community through research and service.

The position is full time with a salary of NZ$ $56,164 to $68,060 depending on experience. The initial appointment is for 1-year on this multiyear project; continuation beyond will be based on performance. Applicants should submit a CV, a statement of research interests, and the names of three referees to caryc@udel.edu or caryc@waikato.ac.nz. The position is available immediately and will remain open until filled.

——–
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.

——–

Congrats to Phil Bourne who beat out me and some others to win the Ben Franklin Award.

Congrats to Phil Bourne for winning the “Ben Franklin Award.” (Bio-IT World) I was honored to be one of the nominees, but if I had had a vote, I would have voted for him. He has been relentless as an Open Access advocate as well as as a bioinformatician.

——–
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.

——–

The Evolution Particle?

The New York Times is reporting that the Large Hadron Collider was not actually shut down over the winter but was actually apparently looking into the possibility that a new particle is particularly mutagenic.   It seems that when they fired up the accelerator, they found that some particles with unusual affinity for DNA were created.  So, no black hole but particles that could shape evolution.  Seems like the ID people will be all over this one — maybe this is the guiding hand they have been looking for?

——–
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.

——–

Sean Eddy in PLoS Biology on Open Revolution

Interesting article by Sean Eddy on “Open Education” in PLoS Biology on March 24. (see PLoS Biology – Open Revolution). The article is (mostly) a review of “Opening Up Education” a book from MIT Press.

For those not in the now, Sean is a big supporter and proponent of Open Science and is now at the HHMI’s Janelia Farm Campus. In addition to developing some smashing software and doing cool science, Sean was instrumental in my conversion to supporting Open Science so I pay attention to what he says. And there is some interesting material in this pub. The ending sums up a lot of what is in there:

More attention must be paid to the fact that someone still needs to spend time painstakingly developing artful ways to make difficult concepts understandable—to teach!—and that it will take even more time (thus money) to render these hard-won ideas using multimedia web technology compared with writing textbooks. Success hinges on the adoption of open licensing by the professionals who make digital educational resources, and on finding ways to finance their work.

Basically, Sean is saying the Open Education is great in concept but that many Open Education resources need work for them to be effective. And that work can take a lot of money. So we need to find ways to get more money into the development of Open Education materials.

——–
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.

——–

Lessons Learned at the JGI Users Meeting

Well, the Joint Genome Institute (JGI) Users Meeting is Over. For some rapid fire notes on the meeting see the FriendFeed room here. where Jason Stajich, Tom Sharpton and I (and occasionally a few others) took notes on the whole thing as it was happening.

So – what were the lessons learned? What were the main points? So – if you want to know what we were writing about – and don’t want to read the notes (they are quite fun actually) how about a word cloud? Well, here is one, which I made by taking the notes, editing out some of the names and other non notes text, and then pasting them into TagCrowd.Com and I got this to the left here:

Not actually a bad representation of many of the topics.  
But you know, this does not per se capture the big points, just the common points.  So I guess if you want the key points, you have to think a bit. First, you have to realize this is a JGI focused meeting (which of course is the whole point of the meeting – it is the JGI User Meeting after all) and most of the people work with JGI in some way so it is a bit hard to see the forrest of genomics for the JGI trees.    And here are my top lessons I got out of the meeting after trying to not get too biased by the JGI focus (note – I have an Adjunct Appt. at JGI and do lots of things through there so I am sure I cannot remove the JGI focus completely)
  1. NextGen sequencing continues to open up new windows into biology.
  2. Ecological and population genomics are truly the next big thing.
  3. Related to the above point, one of the next revolutions is going to be in high throughput phenotyping — after all, we cannot solve the genotype-phenotype problem when we only know the genotype.
  4. Model / reference organisms are still in, but every single organism on the planet is now in play.
  5. NextGen sequencing has completely outrun the ability of even good bioinformatics people to keep up with the data and to use it well.
  6. Related to the above point, the NextNextGen (e.g., Pacific Biosciences) seems to be barreling along and almost ready for prime time.  WTF are we going to do in terms of informatics then?
  7. Following up on the above point- we desperately need a MASSIVE effort in the development of tools for “normal” biologists to make better use of massive sequence databases.
  8. I am happy to report that just about everyone seems to be trying to use an evolutionary perspective as part of their work – especially in the selection of organisms for sequencing
  9. I am sorry to report that many of the evolutionary “perspectives” are a bit off kilter.
  10. Sequencing is definitely not over – it is just getting started.
  11. People pushing the technology (e.g., George Church, Craig Venter) into new arenas definitely inspire the crowds.
  12. If you study a plant or an animal and are not studying the microbes that live with them, you are missing something.
  13. If you study ANY organism and are ignoring epigenetics you are behind the curve
  14. Open Access journals like PLoS Biology and PLoS One and Open Science got some huge props at this meeting, for example, with Venter showing many PLoS related images, many others showing stuff from OA journals, George Church talking about Open Source sequencers and Open personal genomics, and many referring to Open genomics databases.  Still some areas in need of improvement (e.g., not enough publishing in open access journals still) but the move in the direction of openness is great.
  15. Genome Centers definitely each have their own flavors with JGI positioning itself well in the niches of Ecology, Evolution, and Energy.
  16. Genome Centers are definitely going to have to reinvent themselves as the sequencing capacity for individual labs goes up and up with Illumina/Roche/ABI Solid continuing to spread.  Bigger, better, faster, more is one way they can stay ahead of the curve.
  17. Education and training did not get as much play during the talks as I would have hoped.  I mentioned it a bit but I do not recall too many other mentions.  Too bad as the real potential for the democritization of sequencing comes from people getting trained in how to generate and handle the data and how to at least think about it even if they do not use it directly.
  18. Organismal biology is still desperately important in all of this work – if you know a lot about the organism as a whole then you already are a systems biologist.
  19. Genomic characterization of entire multi-organism systems is on the rise and this is not just microbiota stuff but also things like host-pathogen interactions and symbioses and so on.
  20. Reading DNA is being used in every which way imaginable.  Next up – writing DNA.  
——–
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.

——–

Extreme Ice Survey – Tonight 3-24-09 – Watch it

Check out the website Extreme Ice Survey and the NOVA tonight. It is guaranteed to be spectacular.

From their web site they say

“The Extreme Ice Survey is the most wide-ranging glacier study ever conducted using ground-based, real-time photography. EIS uses time-lapse photography, conventional photography, and video to document the rapid changes now occuring on the Earth’s glacial ice. The EIS team has installed 27 time-lapse cameras at 15 sites in Greenland, Iceland, Alaska, and the Rocky Mountains. EIS supplements this ongoing record with annual repeat photography in Iceland, the Alps, and Bolivia.”

——–
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.

——–

Sean Carroll at Davis

Went to a dinner last night that was in honor of Sean Carroll who is visiting Davis as part of the “Storer” lecture series.  It was the first time I have met Sean — but I have followed him and his writing extensively.  I already found him to be one of the best of the best in science and in explaining evolution.  I really liked “The Making of the Fittest” and now he has a new one — which I have not read but it sounds great.  It is called “Remarkable Creatures: Epic Adventures in the Search for Origin of Species“.  He was also quite entertaining at the dinner and handled being peppered with questions very well.  Alas I have to miss his talk today since I am at the Joint Genome Institute for a discussion about metagenomic sequencing of samples from Yellowstone National Park.  

Anyway – just wanted to write something because I found my brief interaction with him inspiring.  It makes me want to do more engagement of the public on evolution than I have been doing (I do some but he inspired me to do more). I also got to meet some of the Storer family who are the people who gave the money to set up the Storer lecture series.  It was also inspiring to talk to them – and good to see people giving money to spread knowledge in the life sciences.  It was overall a good day for me after being sick for a month and then spending two weeks writing grants …
——–
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.

——–

PLoS for Everyone

Just a little post here pointing out a new community blog at PLOS.  Looks pretty cool … but of course I am a bit biased.  

——–
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.

——–

2 week Metagenomics Course … Looks pretty good …

Microbial Metagenomics
MMG 490/MMG 890 Section 432
Drs. Thomas Schmidt and Jay Lennon, MSU
June 15th — June 27th
Kellogg Biological Station
MTuWThFSat 9am – 5pm

*Admission to this class is by application only; Scholarship support is available!*

This course offers students opportunities to use state-of-the-art genomic methods to address questions about the structure and function of microbial communities.
Our field site will be the Long Term Ecological Research Site at KBS. The nucleic acid based data generated during the course will be integrated with the expansive data set from the KBS LTER, which includes measurements of the flux of greenhouse gases. 
The ultimate goal of the course is to uncover relationships between changes in microbial communities and ecosystem functions.

Morning lectures will address pertinent ecological theories and principles underlying experiments that will be conducting during the afternoon. The afternoon laboratory sessions will be focused on molecular methods, including generation purification of DNA from soil, PCR amplification and construction of clone libraries, and quantitative PCR. This is an intensive 2-week course modeled after the longer and internationally acclaimed MBL Microbial Diversity Course that Dr. Schmidt directs. 3 Credits.

Admission to this class is by application only. 
——–
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.

——–