Jonathan Eisen

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

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:

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 (λ_ex = 490 nm) on the microfluidic channel and to gather fluorescence (λ_em = 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 (R_E and R_S) and to the output reservoir (R_O) 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

NIH Mandate on Open Access – Good First Step, Thanks to PLoS et al, but still a long way to go

Well, today is the day. The day after the new NIH mandate on Open Access (also see here for more information) to publications has begun. I think this is a great great day for science. And for society and Congress should be commended for doing something that is good for the country and the world that may have upset some of their big donors (i.e., the publishing industry).

And I think we all owe a big round of thanks to those who worked towards this goal. Clearly, there were many involved in convincing Congress to do this, from concerned members of the public, to SPARC and other NGOs, to tireless individuals like Peter Suber, and of course the Public Library of Science. For those who do not know, or may have forgotten, the Public Library of Science got it’s beginnings as an initiative to promote Open Access publishing (and it was not initially a publisher of journals). PLoS was founded by Harold Varmus, Pat Brown and Michael Eisen (my brother) in 2000. The first thing they did was circulate a petition to promote open access publishing. I signed the letter as did many many others. But alas, it was not enough. And so PLoS started its journals and many realized that it would be necessary for funding agencies to step in and require Open Access publishing for work they funded. And after a long struggle, we are now here with the new NIH mandate (as well as mandates from other agencies which got there before NIH). And I think that we all owe a big thanks to everyone behind this initiative. Also it is worth checking out Harold Varmus’ essay today on the new NIH initiative in PLoS Biology.

I note, however, that the NIH policy is only a first step. It does not move us completely towards true Open Access to scientific publications. There are still issues that need to be addressed, including the timing of release of publications (I think everything should be released immediately, not after a 6 or 12 month delay), the issue of Copyright, the need to get old publications into the public domain, and how putting material in Pubmed Central does not completely open it up to the world (see Peter Murray-Rust’s very interesting discussion of this on his blog). So there is still much work to be done. But nevertheless, I am happy to be living in this new world where NIH has made OA a key part of it’s mandate.

Congrats to Amy Harmon: Pulitzer for DNA Age Stories.

Congrats to Amy Harmon, reporter for the New York Times, who writes a lot about DNA (see all the DNA Age stories), who won one of those Pulitzer things today. I guess, maybe leaving me out of one of your last stories was a good call. I have written about her stories before a few times and overall, I like her reporting. What we all really need to do is convince her to start a blog. Print media is so 21st century.

Also see some other stories:

Editor and Publisher (thanks to the Gene Expression blog for pointing this out)

Passing of Jeremy Knowles

I write with sadness that Jeremy Knowles has passed away. Knowles was a Professor at Harvard, had been Dean of the Faculty of Arts and Sciences at Harvard, and an HHMI Trustee, among many things. I did not know him well, but I did have a recent scientific exchange with him regarding analysis we were doing of the Tetrahymena genome. Knowles has asked a question to Peter Bruns, who is a Tetrahymena guru (and also was at HHMI). The question related to intron splice junctions and whether that might support a paper he had written in 1992. The science here is not important.

I wrote back, basically saying we were sequencing the genome but alas our data might not be useful for his question since most of what we were doing at the time was predicting gene splice sites not actually determining them for real. And I said, in fact, much of the data in Genbank was also predictions not real cDNAs.

I expected him to be a bit disappointed. But instead, he wrote back to Peter:

Peter:
Thank you! Jonathan’s response confirms that I was right to ask an expert. For if I had gone fishing in the gene bank pool, I should probably have drowned. I shall wait, calmly.
best,
Jeremy

What I was struck with was his sense of humor and warmth, which emanated from this and a few other simple email messages. Based on these communications, I was looking forward to interacting with him again as we are now writing up a paper including all of our new cDNA data (real sequences, not predictions). I am sorry to see him go.

Tree of Life Art

As someone who studies the “Tree of Life” in terms of evolution (the tree of life is an evolutionary tree relating all life forms) and who even named his blog after this, I am fascinated by different portrayals of the Tree of Life. We can see lots of things like the Tree of Life in the real word. Much of this is due to the use of the Tree of Life imagery by various religious groups. Some of it is more connected to evolution in some way. But whatever the inspiration, there are some pretty nice representations out there. And I am posting one of them today. At UC Davis the UC Davis Arboretum is a really spectacular place. I go walking there all the time and take my kids to play there and watch the ducks and other animals. One day, I was walking near some gardens that they have been renovating for a while, when I saw they had unveiled some new artwork.

Below are some pictures of this artwork. I am going to start posting more “Tree of Life” art here in the future and would love to get examples from people out there too.

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

More on Tree of Life art in Arboretum

As someone who studied “The tree of Life” in terms of evolution I am fascinated by the Tree of Life art in the Arboretum. Here are some more pictures

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

Can a spoof be scooped by reality?

Well, if you read this blog, or a few others, you may already know that what I reported on here on April 1 regarding NIH cracking down on brain doping, was, in fact an April Fool’s joke. I will write more about this joke later and how we planned it, starting at something called scifoo camp at Google headquarters in the summer of last year. But I do want to write about one thing here — we sort of got scooped by reality. I had been planning for some time to do an April 1 joke on performance enhancing drug use among scientists. And as I was recruiting others to be involved in this plot, reality got in the way when Nature and then the New York Times started to report on brain doping as a real issue. It kind of took the absurdity away from our joke and made it seem like we were making some real commentary on brain doping when in fact, we were at least originally just trying to come up with something ridiculous but possibly believable at first look.

And now it has happened again. The second spoof I considered doing was to write about doing DNA and drug testing on some water bottles I collected from the Tour of California – a bike race that came 1 block from my house. I went for a little ride on the route of the race a few minutes after the peloton came by and got about 10 bottles from different teams. (This was real). And then I was going to pretend that we took those bottles and (1) figured out whose they were by DNA testing and (2) did drug tests of them. And this would allow me to write about 23 and me and other DNA testing companies as well as to make some fun of performance enhancing drug scandals. And I thought this would be ridiculous in a way because it could not possibly be legal to test someone’s DNA without any real just cause. And low and behold look at what comes along — Amy Harmon has an article in the Times yesterday on people doing exactly this type of thing — testing other people’s DNA (good article, by the way).

So now twice my spoofs end up getting scooped by reality. To me, a good spoof/April 1 joke is completely absurd in hindsight even if it is believable initially. So every time one of these jokes/pranks I want to pull gets close to reality, it becomes much much less funny to me. Who knows, maybe Craig Venter will in fact sequence his own microbiome, as I joked about last April 1.

Maybe before my next joke, I should call up Amy Harmon and other reporters to make sure they are not working on related stories first?

Open Evolution: Google supports open source code for evolutionary studies – Deadline 4-08 for Summer of Code

See email I received via Iddo Friedberg from the National Evolutionary Synthesis Center which is seeking students and others to participate in the Phyloinformatics Summer of Code.

This is just a reminder that the student application period ends
definitively on April 7 (Monday), 5pm PDT/8pm EDT (0:00 UTC on April
8). (Google extended the period from the original end date of March
31.) There are still a few project ideas that have received little
attention from student applications so far. If you are interested,
please see below for URLs, and get in touch with us phylosoc {at}
nescent {dot} org to inquire for more information re: application
status of your favorite project(s).

Phyloinformatics Summer of Code 2008
http://phyloinformatics.net/Phyloinformatics_Summer_of_Code_2008

*** Please disseminate this announcement widely to appropriate students
at your institution ***

The National Evolutionary Synthesis Center (NESCent: http://
www.nescent.org/) is participating in 2008 for the second year as a
mentoring organization in the Google Summer of Code (http://
code.google.com/soc). Through this program, Google provides
undergraduate, masters, and PhD students with a unique opportunity to
obtain hands-on experience writing and extending open-source software
under the mentorship of experienced developers from around the world.

Our goal in participating is to train future researchers and
developers to not only have awareness and understanding of the value
of open-source and collaboratively developed software, but also to
gain the programming and remote collaboration skills needed to
successfully contribute to such projects. Students will receive a
stipend from Google, and may work from their home, or home
institution, for the duration of the 3 month program. Students will
each have one or more dedicated mentors with expertise in
phylogenetic methods and open-source software development.

NESCent is particularly targeting students interested in both
evolutionary biology and software development. Project ideas (see URL
below) range from visualizing phylogenetic data in R, to development
of a Mesquite module, web-services for phylogenetic data providers or
geophylogeny mashups, implementing phyloXML support, navigating
databases of networks, topology queries for PhyloCode registries, to
phylogenetic tree mining in a MapReduce framework, and more.

The project ideas are flexible and many can be adjusted in scope to
match the skills of the student. If the program sounds interesting to
you but you are unsure whether you have the necessary skills, please
email the mentors at the address below. We will work with you to
find a project that fits your interests and skills.

INQUIRIES:
Email any questions, including self-proposed project ideas, to
phylosoc {at} nescent {dot} org.

TO APPLY:
Apply on-line at the Google Summer of Code website
(http://code.google.com/soc/2008), where you will also find GSoC program
rules and eligibility requirements. The 1-week application period for
students opened on Monday March 24th and runs through Monday, March
31st, 2008.

Hilmar Lapp and Todd Vision
US National Evolutionary Synthesis Center

=====
URLs:
=====

2008 NESCent Phyloinformatics Summer of Code:
http://phyloinformatics.net/Phyloinformatics_Summer_of_Code_2008

Eligibility requirements:
http://code.google.com/opensource/gsoc/2008/faqs.html#0.1_eligibility

Stipends:
http://code.google.com/opensource/gsoc/2008/faqs.html#0.1_administrivia

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