Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Good sources for Air Quality Information for Davis

Just in case anyone needs it here are a couple of good sources for air quality information for Davis and the area

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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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Do you get permission to engineer your microbe?

Well, lots of researchers manipulate microbes in various ways in the lab. They delete genes. They make mutants They insert genes. Sometimes, they insert antibiotic resistance genes to help with the genetic manipulations they are doing.

Do researchers always think about the potential risks of what they are doing? Well, probably not. Most of the time that is OK as the risks are negligible. But some of the time, there are real risks to consider. One example of a real risk is the introduction into some pathogen of genes encoding a form of antibiotic resistance not seen normally in that pathogen. If that strain escapes from the lab, it could, in theory, spread into the real world and make treating infections by that pathogen more difficult.

All Things Considered had a very interesting story on “Making Drug-Resistant Germs In The Lab” about exactly this issue a few days ago where they discussed how one researcher submitted to an NIH oversight panel a request to carry out this type of experiment. It seems as though very few researchers actually submit requests to carry out these experiments, even though many are doing it. NPR also discussed how the CDC reviews requests to manipulate certain really nasty pathogens and that most of the requests have been granted. Unfortunately, I cannot find a transcript for this story to quote, but it is really worth listening to.

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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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Wanted -Microbial Genomics Lead at JGI

The Joint Genome Institute, where I work part of the time, is seeking a lead scientist for their Microbial Genomics work.

Sr. Research and Management Opportunity

The DOE Joint Genome Institute (JGI) in Walnut Creek, CA has an exciting Staff Scientist opportunity available. Will be responsible for leading the JGI’s Microbial Genome Program including the development of an independent research program in microbial genomics. Will manage all aspects of the program from application review through sequencing and genome analysis. Will be expected to collaborate with external scientific communities, present scientific data and publish results independently and with collaborators. Will also participate as a member of the JGI senior management team. This position reports to the Deputy Director of Scientific Programs.

For more information see here. If you want to play a leadership role in microbial genomics, this job is for you.
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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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How will I survive? iPhone Upgrade crashed …


Well, not my normal posting here. But I have been trying to use my iPhone more and more for blogging and was excited about some of the new software upgrades that were made available today. And so I started the upgrade. And the iTunes server has apparently crashed and now my phone is stuck in “Emergency calls only” mode. So much for mobile blogging for today at least.

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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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Phylojeanomics and The Jeans of Life

Well after the PLoS Nature dust up, I thought we needed a little humor in our lives.  So here is an old Levis add with a distinct evolution theme.  Maybe Jindal should propose a Levis boycott?

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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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Starting pumping

Well after 24 years of Type I diabetes I am now switching from multiple daily injections to using a pump. Not sure if this will be a permanent shift but it is worth a try.

I note, I have been in excellent control with the injections and do not really find them that annoying. But lately I have had some issues with control (both on the high and low end) and I thought it would be worth trying the pump.

So I went to my doctor, who happens to also have Type I diabetes. And he recommended I go on the Medtronic Paradigm 722 pump. And so, without much fanfare I did it.

It took a month or so for the paperwork from my insurance to work through the system and I was approved for the pump. And then they sent me a big box with all sorts of stuff in it. And I scheduled an appointment with a Medtronic tutor who would show me how to use it.

And that is what I did today. I went in to my doctor’s office and me the tutor. And we went through the basics (I had spent about two hours playing around with the pump the day before). And then we got some insulin from the doctor and she showed me how to connect the tubing. And then I connected myself (using one of the Medtronic Quick-Set systems).

It was not too painful, but I got some sort of stress response – pale and sweaty – much like the last time I gave blood. But I got through that and felt a bit better. And then I was sent home. Just like that I was a cyborg on the pump.

I confess – despite being a biologist (Professor) and having lots of knowledge about how these things work, I spent the rest of the day kind of freaking out with a tube connected to my belly fat. Nothing rational in the freak out session – just felt weird being connected to this pump when normally I would just give a shot and then be “free.” Oh well, we will see how it goes. I even went from the doctor’s office to a meeting I had on my campus about teaching a new course and managed to not completely flip out and run out of the meeting.

And then I went home and kind of sulked around the house while I tried to figure this thing out. So – not too bad but not sure I like this thing. When using injections between shots I could at least pretend to be somewhat normal. Now with a tube sticking into my side that is not going to happen.

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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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Forget Lincoln-Douglas – How about a Lincoln-Darwin debate?

In case you did not see it – it is worth seeing the discussion of Lincoln vs. Darwin in Newsweek (How Darwin and Lincoln Shaped Us).  They set up the discussion by pointing out that they had the same birthday.  They say Lincoln was more important.  Not going to argue but not sure they are right.  My favorite section on this article:

This questioning spirit is one of the most appealing facets of Darwin’s character, particularly where it finds its way into his published work. Reading “The Origin of Species,” you feel as though he is addressing you as an equal. He is never autocratic, never bullying. Instead, he is always willing to admit what he does not know or understand, and when he poses a question, he is never rhetorical. He seems genuinely to want to know the answer. He’s also a good salesman. He knows that what he has to say will not only be troubling for a general reader to take but difficult to understand—so he works very hard not to lose his customer. The book opens not with theory but in the humblest place imaginable: the barnyard, as Darwin introduces us to the idea of species variation in a way we, or certainly his 19th-century audience, will easily grasp—the breeding of domestic animals. The quality of Darwin’s mind is in evidence everywhere in this book, but so is his character—generous, open-minded and always respectful of those who he knew would disagree with him, as you might expect of a man who was, after all, married to a creationist.

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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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Evolution education, Jindal and the election

There is an interesting piece on the “Science Education Act” in Louisiana in the New Scientist (see New legal threat to school science in the US ). by Amanda Gefter. This act seems to be designed to “lip ID in “through the back door” and is promoting itself as a bill for “Academic Freedom” Personally, I am all for academic freedom, including the ability to study and discuss all sorts of controversial things. However, it is clear this is not what the bill is really about. It is about teaching religion as science. The New Scientist reports

“Supporters of the new law clearly hope that teachers and administrators who wish to raise alternatives to evolution in science classes will feel protected if they do so. The law expressly permits the use of “supplemental” classroom materials in addition to state-approved textbooks. The LFF is now promoting the use of online “add-ons” that put a creationist spin on the contents of various science texts in use across the state, and the Discovery Institute has recently produced Explore Evolution, a glossy text that offers the standard ID critiques of evolution (see “The evolution of creationist literature”). Unlike its predecessor Of Pandas and People, which fared badly during the Dover trial, it does not use the term “intelligent design”.”

All I can say is that if McCain picks Bobby Jindal (the governor of LA and supporter of this bill) as his running mate it will be the ultimate proof that McCain is no longer the independent thinker he used to be and is instead a complete tool of others.

It is worth reading this article if you care about science education.

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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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Overselling genomics Award #5: Duckweed will save the world

OK. I really wanted to leave this one alone because it involves the Joint Genome Institute (JGI) where I work part of the time. And I really like JGI and what it is doing in many aspects of genomics. But this one is just so over the top that I could not leave it alone. There is a press release from Rutgers that came out regarding a new project to sequence the duckweed genome (see News: Duckweed genome sequencing has global implications) and the Eureka release here

And this one is just so over the top in terms of overselling I do not know where to begin. First, they had me at the title

Duckweed genome sequencing has global implications

But the subtitle is even better

Pond scum can undo pollution, fight global warming and alleviate world hunger

There is really little else to say. I commend the JGI and DOE for supporting this work as it sounds reasonable and work on this organism may have many uses. But, umm, this was the most obvious “Overselling genomics award” I have ever given.

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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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Only Nature could turn the success of PLoS One into a model of failure

Now, mind, you I like Nature as a publishing unit. They publish some very fine journals. Now, most of them are not Open Access, so I choose not to publish there if I can avoid it. But I still like them. And many of the editors and reporters there are excellent – smart, creative, insightful and such. But Nature the publisher can also be completely inane when it comes to writing about Open Access and PLoS. In a new article by Declan Butler, Nature takes another crack at the PLoS “publishing model”

The problem with PLoS now is … wait for this … the success of PLoS One. PLoS One it turns out is publishing a lot of papers (including one by me, today). And bringing in a decent amount of money to PLoS apparently (note for full disclosure – I am involved in PLoS Biology as “Academic Editor in Chief” and PLoS Computational Biology as an Academic Editor … although I should note I am not involved in financial discussions at PLoS in any way).
So why is the success of PLoS One a problem? Well, because it allows Nature to do the old good cop bad cop routine and to write, again, about the “failings” of the PLoS publication model. Now, mind you, the article does not quote a single source for what the PLoS publication model is. But they do say it has failed. From what I can tell here is the logic of the failure argument:
  1. Nature believes PLoS’ model for success revolved solely around PLoS Biology and PLoS Medicine and some of the other other PLoS journals being self sustaining after a few years.
  2. Analysis of some financial information suggests that PLoS Biology and Medicine currently are not breaking even
  3. PLoS One is apparently wildly successful and thus is brining in some money to PLoS.
  4. PLoS One publishes a lot of papers (they discuss this a bit and imply that this is a bad thing because some of the papers must be bad. Note – they do not back this up with any evidence. Silly for me to ask a science journal to use evidence)
  5. Therefore, the entire PLoS Publication model is a failure.
The problems with this logic are, well, large. Here are some:
  1. Does Nature really think that there ever was a single “model” for how PLoS should be evaluated?
  2. If so, where is the documentation of what this model actually was?
  3. Even if there was a PLoS model and even if it turns out to be not exactly what PLoS is doing now, what is the big deal? If you were a stockholder of any company and they told you “we are never going to change our business model no matter what happens in the world around us” I would recommend you not buy their stock. It is simply farcical to expect any entity to stick to a single simple model forever.
  4. Does not Nature supplement some of their bigger journals with their higher volume other journals?
  5. Most companies these days use high profile entities such as PLoS Biology and PLoS Medicine to attract attention to other portions of their company in order to help bring in money. Is this somehow not allowed by PLoS? Doesn’t Nature do the same thing?
  6. If you look at the figure Nature shows of PLoS $$$, it shows income rising in 2007 and expenses going down. How did that get turned into a bad thing?
So – I still do like Nature publishing because much of the time it has high quality stuff. It even has high quality stuff commenting/criticizing the Open Access movement and pointing out some of the challenges with it. But this article by Butler is not an impressive piece of work. I really wanted to give him an award but could not think of what to give.
See also (thanks to Bora for pointing out a bunch of these links)
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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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