http://www.scivee.tv/flash/embedPlayer.swf
And here are Jason Stajich’s notes on FriendFeed
Nothing gets me more riled up in evolutionary writings than the use of the term primitive to describe organisms on a “deep” branch in an evolutionary tree. Thus for the following tree
many people would refer to Species 1 as a primitive organism solely on the basis of this tree. In fact, I just saw this in the Hoxful Monsters blog (see here) where it says:
In April 2008, Cassey dunn et el published their famous phylogenomics work in Nature, which placed Ctenophores at the base of the tree making them most primitive animal on Earth. Before that work Sponges were considered as first animals to branch off from rest of the animals and hence occupied a most basal position in the tree of animals for long time. However, some months later another phylogenomics study carried out by Bernd Schierwater et al ; changed things dramatically by placing Trichoplax as most primitive animal replacing Ctenophores. Now a new phylogenomic study published in online section of Current Biology is making headlines , where Sponges regain their position as most primitive animal on Earth.
This is simply wrong as the term primitive, which I avoid at all costs because it is so frequently misused, should only be used to refer to features of organisms not to the branching pattern in an evolutionary tree. Forget for a minute that “primitive” implies that something else is “advanced”, as if we could determine which is which. And lets pretend instead for a minute that “primitive” could be used in an equivalent manner as “ancestral.” Ancestral is a term used to refer to features of organisms present, as the term implies, in an ancestor. Thus is the organism(s) at the node in the tree labelled with the X had some feature (e.g., lets say, they were green) and Species 4 is green while Species 1 is orange and Species 2 and 3 are purple. In this case, in terms of color, Species 4 has ancestral feature and the other species have derived features. And thus, when I am feeling generous, I will grant that one could sort of use the term primitive to say “Species 4 is primitive in terms of color.” I don’t like this usage, because primitive implies something about quality that ancestral and derived do not. But it is not so horribly wrong that I cringe.
But I would like to make two more points in terms of the way primitive is misused.
This inaccurate use of phylogenetic trees to imply primitive features drives me batty. I was disappointed to see this phylogenetic gobbledygook being used in the HoxFul Monsters blog. And thus, Hoxful Monsters is the winner of my fourth “Twisted Tree of Life” award.
I am quite intrigued by the news stories based on a paper that just came out in Nature on the early history of oxygen producing bacteria (e.g., see the Canada.Com story Thank oxygen-producing bacteria for your existence
and the National Geographic Story Nickel “Famine” Led to Oxygen-Breathing Life?). In short, the paper suggests that about 2.5 billion years ago, the amount of nickel in oceans (and presumably elsewhere) began to decrease, possibly due to changes in volcanism. Furthermore they suggest the reduction in nickel harmed methanogenic microbes which require nickel for multiple processes. Thus the term “nickel famine.” As the methanogens declined, many changes occurred including an increase in the oxygen concentration in the atmosphere (with the oxygen coming from cyanobacteria). And presto, the world became just so much more hospitable for many of us and our relatives. Anyway, the term “nickel famine” really stuck with me, so I am making it my evolution phrase of the week.
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.
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.
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.
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?
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.
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 th
e names and other non notes text, and then pasting them into TagCrowd.Com and I got this to the left here:
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.”
