Eisen Lab Blog

Trip to CALIT2 & CAMERA

Just got back from a one day trip to San Diego to visit the folks who run CAMERA, the metagenomics database being run out of CALIT2/JCVI. The main point of this meeting was to start to figure out how to take computational tools that we have developed in my lab or will develop in my new iSEEM project (with Katie Pollard and Jessica Green) and make them available in CAMERA.

But as usual, the most fun part of the trip was to see the CALIT2 toys. And boy do they have toys. Larry Smarr, the director of CALIT2 and the PI on the CAMERA project (funded by the Gordon and Betty Moore Foundation) gave us a quick tour around the building. My slide show is embedded below. Mostly we got to see the massive multimonitor “optiportal” display walls. We also got to see the big linux cluster that is the guts of CAMERA (and may favorite part, of course – the big PLoS Biology sign relating to the Global Ocean Survey papers in front of the computer).

CAMERA, which stands for Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (thus, why we say CAMERA), is a big and complex enterprise, hosting metagenomics sequence data, metadata associated with the sequence, and a variety of analysis tools for working with the data. You can find out more about it in a paper from PLoS Biology here.

Now, CAMERA is not the only metagenomics database out there. The other main one people seem to use is IMG/M from JGI. If you are interested in metagenomics analysis in any way, it is worth becoming familiar with both systems.

http://picasaweb.google.com/s/c/bin/slideshow.swf

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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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Picnic Day Pictures

http://picasaweb.google.com/s/c/bin/slideshow.swf

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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.

——–

Tree of Life Runners

More little ditties here

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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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Pictures of Covell Bike Tunnel Being Constructed

IMG_0903.JPG

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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.

——–

Open Access Week

I guess, in my effort to catch up on work after spending time working on an April fools joke, I missed that last week was the first “Open Access Week” at least, as promoted by some key OA bloggers (see here, here, here, and here). This was done in honor of the new NIH policy on Open Access to Publications that commenced last week.

Se McBlawg for more detail at: ‘Open Access Week’: Some Posts from the Blogosphere

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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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Tree of Life Runners Web Notes

Well, I needed a name for little mini tidbits to post on and “Runners” has won the competition. So here is my first “Runners” entry of things from the web that caught my eye this week

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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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Welcoming Pamela Ronald to the Blogosphere

Just a quick post here …. I recommend everyone check out the newbie Blogger on the Block, Pamela Ronald. In addition to having an office, at least temporarily, near mine, she is an author of a new book called Tomorrow’s Table discussing multiple marriages of organic agriculture and genetic engineering, an international known plant biologist (see her lab web site)., and a great person to bounce all sorts of ideas off of. As I have been going around the world (in reality and virtually) recruiting active scientists to do more blogging I am very happy to see her start a blog. So I encourage everyone who reads my blog to check out her blog.

——–
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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Confessions of an April Fool and the Dope on Brain Doping

Well, truth is imitating art in bizarre ways here. Nature today is running a news story by Brendan Maher (also see his forum here) and various related tidbits about a survey they conducted on brain doping. And the lead in to the news story? Well, it is the April 1 joke I coordinated where a group of co-conspirators (who I will name in a bit) and I posted stories about a new NIH crackdown on, yes, brain doping.

The US National Institutes of Health is to crack down on scientists ‘brain doping’ with performance-enhancing drugs such as Provigil and Ritalin, a press release declared last week. The release, brainchild of evolutionary biologist Jonathan Eisen of the University of California, Davis, turned out to be an April Fools’ prank. And the World Anti-Brain Doping Authority website that it linked to was likewise fake. But with a number of co-conspirators spreading rumours about receiving anti-doping affidavits with their first R01 research grants, the ruse no doubt gave pause to a few of the respondents to Nature ‘s survey on readers’ use of cognition-enhancing drugs.

So here I am going to tell the tale of the creation of this April 1 joke. In a way, it all started last April 1, when I created a fake New York Times story about how Craig Venter had been deceiving everyone with stories about sailing around the world studying microbes in the ocean, and in fact he has been studying the microbes living inside his body in order to scoop Francis Collins and others at the NIH on the “microbiome.” I made the fake story by taking an article by Nick Wade on Venter sequencing his own genome, downloading the html for the whole web page on the archive of the story, with all the NY Times background material, and editing the text, simply changing the story but keeping the main outline. For example, the title of the real Wade article was “Scientist Reveals Secret of Genome: It’s His” and I changed it to “Scientist Reveals Secret of the Ocean: It’s Him.”

I thought the html version of the story looked great. Here it is. And I tried to send it to people in email but they kept having problems viewing the thing. So in the end, I created a PDF file of the page and emailed that to a few key co-conspirators (who I knew knew a lot of people). And they sent it around. And around. And around. I did not originally post it on my blog, because, well I was worried that Venter would want to kill me. The funny part is, he liked it. And it was the real people who I had made up fake quotes from who wanted to kill me. ( I note, a friend of mine who works at Cold Spring Harbor Press and has the initials AG says he sent it to Nick Wade who also found it funny.)

Anyway, in the end, that April 1 joke worked OK but it has some limitations. First, since I did not post it on the web it did not really use the power of the blogging world to spread. Second, some people figured out it was fake when they went to YouTube or the New York Times web site to look for the things we claimed existed. So, I decided that for this year, if I could come up with a good April 1 joke, I would try and correct these issues.

So – somehow, I hit upon a funny story to do – a spoof in on the cycling and baseball controversies over performance enhancing drugs . But the target would be scientists. That was really the extent of my idea. And then I found the perfect venue to plan it. SciFoo camp (for more on it see here and here and here). Sponsored by Nature and the O’Reilly publishing group. At Google HQ. And with TONS of bloggers and other media types there. We ven considered having a session on humor in science. But that never happened. Fortunately, I cornered various people who seemed to think it would be fun to have a collaborative conspiracy to do an April 1 joke together. And they liked the performance enhancing drugs among scientists idea.

Alas, SciFoo camp was in August of 2007. April 1, 2008 was far away. And the plan slipped to the backburner. I created a private Blogspot blog for people to share information. And invited a few of the original co-conspirators. And we did not make much progress. And then I wrote to Bora (who, like Madonna, really does not need a last name). He was at SciFoo and I knew him through my new role in PLoS. And he knows EVERYONE. And I said:

Bora

Are you up for participating in a grand April 1 joke where I am
hoping to get lots of bloggers to write in different ways about the
same topic to make it really seem real?

J

And he agreed. And then he and I recruited some other bloggers. And then we saw a New York Times article on Brain Doping. We had not really completely formulated a plan to focus on brain doping per se yet (I still thought we could talk about EPO to have endurance at conferences, etc). And we got worried about being scooped by reality. But we soldiered on. At this point I thought maybe the best way to do the joke would be to have everyone separately write a story about some interaction with NIH that hinted at a crackdown on doping among scientists.

In the meantime, I came up with ANOTHER April 1 joke top do, but it seemed like this one had to be done before April 1 since for people to get it it needed to be done while the true news story was hot. So I posted a joke story spoofing the Eliot Spitzer resignation with my own fake resignation from my new position as Academic Editor in Chief of PLoS Biology over buying journal articles. I replaced his wife with my brother (and co-founder of PLoS) and placed a few friends in the story (Alex Gann at Cold Spring Harbor became my replacement, Emma Hill, who left PLoS Biology for a non fully OA journal became Kristen, and I made up a few quotes here and there). I had to post this before April 1 since I knew people would forget abouyt Spitzer quickly. And then I returned to the work on the brain doping joke.

And soon we saw that some people on the Nature Network were talking about trying to do a collaborative April 1 joke. And so I posted a message there and then recruited those who seemed interested. And we had a good core group of conspirators. And people were busy so not much happened. Although Chris Patil, who I used to work with at Stanford, made me freak out even more by posting a whole collection of stories about brain doping on our private blog.

And he and Anna Kushnir and others also said – we need a web site to link to and we need some story to jointly write about. So in a frenzy on March 31 I created a fake press release and a fake web site. To make the press release, I took a real NIH press release, and like with the New York Times story, I edited it a bit and then a bit more.

And fortunately, I had registered the domain name WABDA.ORG for the “World Anti-Brain Doping Authority) through Go Daddy and had paid a bit extra for their “WebSite Now” option, and using their not very easy to use system, I made a website and somehow got it live by about 12:10 AM on April 1.

And I sent the fake press release to the co conspirators, who did an amazing job or also writing fake blogs. And I send the story to lots of others too. And wrote my own fake blog post here. And then sat back and watched the story spread. Below are some of the formal or accidental co-conspirators blogs:

And then I got a call from Nature saying they were doing a REAL story on brain doping and wanted to interview me about the fake story we did. And I guess you can find out the rest at the Nature site.

Also see

——–
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.

——–

Mutualisms Rule – So Says Olivia Judson at the Wild Side

Nice blog today on mutualisms by Olivia Judson who writes the Wild Side blog/column for the New York Times (I seem to be writing a lot about writers for the NY Times these days … not sure what is going on with that). She even features one of my favorite organisms in the blog:

The clam Calyptogena magnifica, which lives on deep-sea vents, depends on a bacterium to supply it with nutrients; the bacterium is transmitted through the clam’s eggs

Last year we published a paper on the complete genome sequence of this symbiont (which I wrote about here when I was clearly in a whiny kind of mood). And Judson picks up on a part of the story on the clam that is rarely discussed – the symbionts are transmitted vertically from parent to offspring. Vertical transmission seems to be linked to multiple properties of the symbionts (see my discussion of this regarding the glassy winged sharpshooter symbionts here).

Judson’s post is really worth checking out for the symbiosis fans out there. She does a good job of highlighting diversity and evolution of mutualisms in a relatively short post.

See my video of a dissection of a baby Calyptogena:

——–
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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PLoS Biology – Darwinian Evolution on a Chip

For evolution afficionados, there is a cool new paper in PLoS Biology on using a microfluidic chip to conduct in vitro evolution experiments.

The paper, by Brian Paegel and Gerry Joyce from the Scripps Research Institute

relies on computer control and microfluidic chip technology to automate the directed evolution of functional molecules, subject to precisely defined parameters. We used a population of billions of RNA enzymes with RNA-joining activity, which were challenged to react in the presence of progressively lower concentrations of substrate. The enzymes that did react were amplified to produce progeny, which were challenged similarly. Whenever the population size reached a predetermined threshold, chip-based operations were executed to isolate a fraction of the population and mix it with fresh reagents. These steps were repeated automatically for 500 iterations of 10-fold exponential growth followed by 10-fold dilution.

They have a nice figure summarizing the system which I show below — and people should check out the article. Note – I can legally include this figure here because of the use of a broad Creative Commons License by PLoS Biology. Note – one of the stories I saw about this at Medgadget.Com also pointed out how they can use the article however they want because of where it was published. The power of true Open Access.

(A) The evolution chip is mounted on a temperature-controlled stage. Solutions containing polymerase enzymes (E) and mono- and oligonucleotide components (S) are delivered to the chip via capillary tubing and output to a pressure-controlled collection vial (O). A microscope objective is used to focus laser excitation (λex = 490 nm) on the microfluidic channel and to gather fluorescence (λem = 535 nm), which is detected with a confocal PMT. Valve actuation and fluid flow are controlled by six independent vacuum lines.

(B) The microfluidic device is shown with the active circuit filled with blue dye.

(C) The serial dilution circuit consists of a mixing loop with fluid flow channels (red), fluid access reservoirs (blue), and control valves (black). Fluid flow around the loop is controlled by three two-way valves (a, b, and c). Fluid access to the loop from the input reservoirs (RE and RS) and to the output reservoir (RO) is controlled by bus valves (in and out). The bus valves allow access when open, and prevent access while preserving fluidic continuity within the loop when closed.

(D) During operation of the circuit, the expanding RNA population is incubated while undergoing slow cyclic mixing until the fluorescence reaches a pre-determined threshold. Then an aliquot of the population is isolated between valves in and out as fresh solutions of E and Sin and out, and the aliquot is mixed with the fresh solutions by rapid serial actuation of valves a, b, and c. Open valves are indicated by filled circles; closed valves are indicated by a red X. are drawn into the loop and spent materials are delivered to the collection vial. Finally, the loop is sealed by closing valves

From: Darwinian Evolution on a Chip Paegel BM, Joyce GF PLoS Biology Vol. 6, No. 4, e85 doi:10.1371/journal.pbio.0060085

——–
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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