Eisen Lab Blog

#UCDavis Becomes Smoke and Tobacco Free January 1, 2014

Just got this email and thought it would be of interest to some out there:

I am highly skeptical of the CHORUS system proposed by scientific publishers as an end run around PubMed Central

Just read this news story … Scientific Publishers Offer Solution to White House’s Public Access Mandate – ScienceInsider

It reports on an effort by various scientific publishers to create something they call “CHORUS” which stands for “Clearinghouse for the Open Research of the United States.” They claim this will be used to meet the guidelines issued by the White House OSTP for making papers for which the work was supported by federal grants available for free within 12 months of being published.

This appears to be an attempt to kill databases like Pubmed Central which is where such freely available publications now are archived.  I am very skeptical of the claims made by publishers that papers that are supposed to be freely available will in fact be made freely available on their own websites.  Why you may ask am I skeptical of this?  I suggest you read my prior posts on how Nature Publishing Group continuously failed to fulfill their promises to make genome papers freely available on their website.

See for example:

We need to make sure such papers are freely available permanently and the only way to do this is via making them available outside of the publishers own sites.  Pubmed Central seems to be a good solution for this.  I would be happy to hear other possible solutions – but leaving “free” papers under the control of the publishers is a bad idea.

UPDATE 6/27/2013

Saw this Tweet

//platform.twitter.com/widgets.js Seemed potentially really interesting. Read the story and got pointed to a new Nature paper on the ancient horse genome. I guess not so surprisingly, despite the fact that they report a new genome sequence, it is not openly available. We really cannot trust Nature on this can we? They could say “Well, this is a draft genome, and we did not mean to apply our policy to draft genomes.” Well, that would be weird since, well, they have applied this to draft genomes before. And then I decided to search for other examples … and in about ten minutes I found a few. See

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

——–
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.

——–

Lab meeting June 4th 2013

Sima Tokajian will be presenting for this week’s lab meeting. The talk is titled “Molecular Epidemiology of Community Acquired Staphylococcus aureus”
We will meet in the Genome Center in room 4202 from 1:30 to 3pm.

Guest post from Jake Scott: Building trust: a sine qua non for successful acceptance of preprints in the biological sciences

Today I am happy to have a guest post from my friend and colleague Jake Scott.  The topic of the day is preprints in biology and medicine.



Hi – I’m Jake Scott.  I met Jonathan last year when he and I spoke at TEDMED 2012. Both Jonathan and I have posted recently about the need for, and (slowly) growing movement in the biological sciences to post #preprints of manuscripts in openly accessible fora to circumvent some problems associated with standard academic publishing.  Most worrisome are the issues surrounding #openaccess and the length of time it takes to get information from one’s brain to the literature – drastically slowing down the pace of science.

This has worked GREAT in the physics community, where this trend really began quite some time ago when the high energy physicists started the arXiv.  Now, the precedent is set, and no one in physics bats an eye about sticking their paper on the arXiv, and cite other works presented there as standard publications.

The climate in biology, sadly, is much different. Whether this is because of a more competitive climate for funding, or just a field diluted by more talented scientists, I don’t know.  But there is a pervasive attitude of fear and mistrust around the idea of preprints.

Before you read on (and become biased by my opinions) take a few second (really, probably 1.5 minutes) and take this quick survey:

When I preach to my biological colleagues about the virtue of pre-print servers, I most often, I hear:

Why should I post my papers on a pre-print server where anyone can see it before it is published!?  They could scoop me!

I honestly don’t understand this argument, but I hear it all the time.  By nature of pre-print servers, like the arXiv, the idea is yours! Time and date stamped. And, better yet, it is completely #openaccess, free of charge, and helps move science along at a better pace.  Only a very few journals have problems with posting of pre-prints before they get their (greedy) hands on the results of all your hard work, but most are totally OK with it.

The arXiv isn’t really interested in shopping its (free) service out to the biological sciences, not because they don’t think it would be of value, but because it just doesn’t have the infrastructure to support it.  This is a problem that is being with newly created repositories like Nature Precedings, PeerJ and soon, the bioRxiv.  So, the only thing holding us up is, IMHO, trust.

How can we rectify this?

I think the way forward is to create something that we are all missing now, except when we are at our home conference, among friends or if we got into a time machine and went back 100 years – community.

Science is such a juggernaut now that putting your work onto a pre-print server where anyone in the world can see your as of yet unvetted work can be daunting.  Worse, the idea of commenting on it is a tough sell when the world is a witness.  I think we need to (re)create micro-communities of our specialist peers where these initial discussions can be held.  Two examples of this are Haldane’s Sieve and more recently created, an initiative I’m involved with, Warburg’s Lens.  These two sites are micro-communities where population and evolutionary biologists, and mathematical oncologists (respectively) congregate to discuss pre-prints culled from any repository but necessarily of interest to the micro-community.

This does two things: it allows a common place for easy browsing in topics of interest to a specialist (like reading your favorite journal), and increases the chances that the readers and commenters are your (at large) peers.

So, those are my two cents. #Openaccess for all is coming, and preprints are a part of the wave.  The sooner we all adopt an open science attitude, the sooner we’ll come to the conclusions and make the discoveries that make doing science AWESOME.  There is no better job than science, and sharing and communication are central to it

So START SHARING your science.  Commit to this – when you are ready to submit your next paper, put that version on a pre-print server as you start the submission process. Then tweet about it, G+ about it, blog about it, do whatever, but let your peers know!

Anyone else interested in starting a micro-community discussion forum, or to just discuss this issue further, please contact me.

If you are against it – please leave some comments about why, I’d love to try to convince you otherwise!  If you are a biologist (or know one) who DOES post pre-prints, weigh in and share your good experiences!

About me: I am a radiation oncologist and I approach the understanding of cancer like my original training in physics taught me – from the ground up, using the descriptive language of mathematics.  Using established mathematics in new ways, guided by the principles of evolution, I hope to better understand (and maybe treat!) cancer.  I am a proud member of the Integrated Mathematical Oncology group at the Moffitt Cancer Center and the Centre for Mathematical Biology at Oxford University.  You can follow me on twitter @CancerConnector or read my blog Connecting the Dots.

——–
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.

——–

Learning How to Work Qiime

So we’ve done our data collection, we’ve done more PCR than we could ever imagine, and we finally got our sequences. Now what? We analyze our data using Qiime, a software that will help us see connections between our microbe data. Qiime is useful since it can handle the large amounts of data we’re throwing at it, something most other programs would crash just thinking about. As someone with average knowledge of computers, it’s entirely intimidating learning something based on programming from scratch, but it has also been a great learning experience. Now off to play with terminal and find some meaning in these strings of letters…

More bio preprint discussion sites …

Another Bio-related preprint discussion site has popped up: Connecting the Dots: Warburg’s Lens: A pre-print discussion forum for the mathematical oncology community.  From my friend and colleague Jacob Scott.  A good addition to Haldane’s Sieve.  Seems to me preprints are the next wave in open access in biology …

——–
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.

——–

Re-reading this on "Why women leave academia and why universities should be worried"

Been reading some somewhat old material out there on women in academia.  I am getting more and more interested in this issue especially as I have become more involved in the UC Davis ADVANCE Program.  The ADVANCE program from the National Science Foundation “aims to increase the participation and advancement of women in academic science and engineering careers.”

I was pointed to this Guardian article from 2012 today based on “The chemistry PhD: the impact on women’s retention”: Why women leave academia and why universities should be worried | Higher Education Network | Guardian Professional.   This Guardian article has a lot of detail and links to other information.  Definitely worth checking out if you had not seen it or forgotten it.

——–
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.

——–

At #UCDavis Eric Schadt 6/4 – Leveraging the digital universe of data to construct predictive models of disease

—

Eric Schadt flyer.pdf

The human microbiome never looked so good

Another week, another microbial art project — this one is from Erno-Erik Raitanen who is creating self portrait “bacteriograms” using his own microbiome.  See stories at Petapixel: Photographer Erno-Erik Raitanen Creates ‘Self-Portraits’ Using His Own Bacteria and CoCreate: INSTAGERMS: SEE A PHOTOGRAPHER’S STRANGELY BEAUTIFUL PORTRAITS OF HIS OWN BACTERIA. 

From CoCreate

“The process itself is pretty much a replication of the processes used in microbiology to cultivate bacteria on agar in petri dishes,” Raitenan says. “Instead of agar, I just used the film gelatin as my growth medium. As the bacteria grows, it consumes the gelatin layers that together make all the colors in a color photograph, and creates all these random patterns and colors.”

The human microbiome never looked so good …

——–
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.

——–

Is the New York Times microbial diversity centric?

The answer to the question in the title – I think – is yes.  Here are some recent stories in the Times on topics of relevance to microbial diversity.

Plus – of course – there is a continuous stream of information on microbes from Carl Zimmer who writes frequently for the NY Times.  Perhaps the best example of this is his coverage of the Human Microbiome Project papers: Studies of Human Microbiome Yield New Insights June 18, 2012.  But there have been and I am sure will be others. 
Sure – the NY Times is not the only place with a bunch of stories about microbial diversity and microbiomes. But they do seem tto have a good ratio of “diversity” themed coverage vs. germoophobia themed topics which are common in many other places.
——–
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.

——–