Eisen Lab Blog

A must read for anyone interested in #OpenScience: Peter Suber’s review of 2010

Some ego surfing (i.e., searching for my own name) led me to discover a very useful resource / summary of open access advances from 2010.  The resource is a posting from Peter Suber from the SPARC Open Access newsletter from 1/2/2011.  I found out about the posting from here: BioSharing: Top 10 openness advances of 2010 – BioTorrents because they noted that something from my lab was one of the picks …

Suber, if you do not know, is one of the sages of Open Access having been promoting and discussing and working on Open Access for many many years.  In the post, he discusses what he calls “a
feast of the OA highlights from 2010″.  The whole post is worth reading are here is a summary:

Top 10 advances

  • (1) Open access policies at funding agencies
  • (2) Open access policies at universities
  • (3) Some growth numbers
  • (4) Open access archiving (green OA)
  • (5) Open access journals (gold OA)
  • (6) Data
    • I note in this section he says “The most exciting new open-data platform in 2010 was BioTorrents from Morgan Langille and Jonathan Eisen, a P2P data-sharing service for biology using BitTorrent.  Something like this will be needed in every field where researchers need to share not just megabytes or gigabytes, but terabytes and petabytes.”
    • That made my month – see our PLoS One paper on it here. 
  • (7) Books and digitization
  • (8) Copyright and licensing
  • (9) Effects of the recession
  • (10) Some highlights of the highlights

The last section is particularly entertaining as he discusses the worst and best of 2010

  • Worst includes 
    • James Murdoch objecting to the British Library opening up its archives;
    • English Heritage for claiming to own the copyright on Stonehenge,
    • Todd Platts, Republican representative from Pennsylvania for an inane copyright idea
    • Supposedly OA journals not using actual OA licenses
    • BP, for a very non open contract for research relating to the oil spill
  • Best includes
    • Biotorrents
    • Obama White House
    • UC standing up to Nature
    • many new OA mandates around the world
    • many others
He also posts links to his discussions from previous years.  Anyone interested in OA really should read his full post …
——–
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.

——–

Word clouds of Obama State of the Union speech and Republican Response

I love word clouds.  Here are ones from tonights State of the Union speech and the Republican response:

Obama:
Wordle: Obama State of the Union 1_25

Resopnse
Wordle: Republican_Response_1_25

——–
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.

——–

DOE JGI Microbial Genomics & Metagenomics Workshops 2/7-11; 5/9-13, 9/26-30

Want to learn about microbial genomics and metagenomics. Here is a good way – sign up for one of these DOE JGI workshops:

DOE JGI Microbial Genomics & Metagenomics Workshops

——–
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.

——–

Metagenomics/bioinformatics/microbiology job of the week: Chisholm lab at MIT

Good at bioinformatics? Looking for a job? Check out this one in Penny Chisholm’s lab at MIT:

Chisholm has done some incredible work on marine microbes. Here are some of her “Open Access” papers to browse:

Sure she does publish in some other places but does publish a lot in PLoS and other Open Access journals. If you get the job, maybe you can convince her to move more towards publishing everything in Open Access journals — her stuff is very cool — the more of it that is Open Access the better …
——–
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.

——–

Phylogeny rules:


I am a coauthor on a new paper in PLoS Computational Biology I thought I would promote here.  The full citation for the paper is:

The paper discusses a new software program “phylOTU” which is for phylogenetic-based identification of “operational taxonomic units”, which are also known as OTUs.   What are OTUs?  They are basically clusters of closely related sequences that are used to represent something akin to a species.  OTUs are used a lot in environmental microbiology b/c one key way to study microbes in the environment is through extraction and sequencing of DNA.  Traditionally this has been done through PCR amplification and sequencing of one particular gene (ss-rRNA).  Now it is also being done through random sequencing of all DNA from environmental samples (so called metagenomics).

Anyway – the paper is (of course) fully open access and you can read it for more detail.  Just thought I would post a little here about it.  The paper / project was led by Tom Sharpton, a post doc in Katie Pollard‘s lab at UCSF working on a collaborative project between Katie’s lab, my lab, and Jessica Green‘s lab at U. Oregon (and recently Martin Wu’s new lab at U. Virginia – he was in my lab previously).  This collaborative project even has a name “iSEEM” which stands for integrating statistical, evolutionary and ecological approaches to metagenomics.  This project has been generously supported by the Gordon and Betty Moore Foundation (via a grant for which I am PI).


Some little tidbits of possible interest about the project

Sharpton, T., Riesenfeld, S., Kembel, S., Ladau, J., O’Dwyer, J., Green, J., Eisen, J., & Pollard, K. (2011). PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data PLoS Computational Biology, 7 (1) DOI: 10.1371/journal.pcbi.1001061

——–
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.

——–

Microbiology curators – coming to a museum near you – and about time

Just another mini-post here.  I find it very very interesting that some serious museums out there are looking to start up “microbiology” curator positions.  The latest is the American Museum of Natural History (see job posting here Assistant Curator and Professor of Microbial Systematics : Central Park West at 79th St., New York, NY 10024 : Naturejobs).  And recently, the California Academy of Sciences has been interested in hiring a microbiologist too (see recent ad here).  All I can say is – about time – after all – microbes kind of run the planet and represent the bast majority of the phylogenetic and biological diversity. 
——–
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.

——–

It drives me crazy when the term "open access" is used for anything free of charge

Just a semi quick one here …
There is a new article in Science Now reporting “Quandary: Scientists Prefer Reading Over Publishing ‘Open Access’ Papers – ScienceInsider“. It discusses a new report from the SOAP (study of open access publishing) project. The reports coming from SOAP are very important and can be very useful. That is not what drives me crazy here.
What drives me crazy is that this article and an almost uncountable number of other articles and discussions I see about “open access” publishing throw around the term “open access” inappropriately. This term is now used for basically any of the diverse array of array of journals or articles within journals for which there is no charge to read (the articles). The problem here is that the term “open access” really should be reserved for material that for which the term “free” applies not just to how much you pay for it (i.e., free of charge, like free beer) but “free” as in “freedom” (i.e., Braveheart free or Statue of Liberty free).
Here is a good definition of “open access” from Peter Suber “Open-access (OA) literature is digital, online, free of charge, and free of most copyright and licensing restrictions.”
To me, more important the “free of charge” is “free of most copyright and licensing restrictions”. This aspect of open access frees up the scientific literature to be reused and redistributed by anyone and has the potential to truly revolutionize scientific knowledge. Free of restrictions allows material to be used in textbooks and web resources (e.g., PLoS Hubs) and databases, remixed and remashed and whatever. No restrictions allows bloggers and other writers to take figures and post them and reuse them and spread knowledge. Free of charge simply allows people to read the paper at no cost – useful – important – but not all that “open access” is about.
If you want to learn more about the difference between “open access” and “no charge to access” the best place to look is Peter Suber’s “Open Access Overview.” And please, don’t fall for all these new journals calling themselves “open access” when all they do is make material available for no charge. Look at the restrictions the journals place on use of the material. What is the license used for the article? Does it allow any type of reuse or are there commercial or other restrictions? What is the copyright policy? And so on. In other words, just how “open” are they really?
——–
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.

——–

Nature new PLoS One like journal "Scientific Reports"

Just a quick post here. Interesting news from Nature on the Open Access front: Press release archive:
Nature is starting a new open access journal “Scientific Reports”. Some detail from their press release:
All articles published in Scientific Reports will be open access and subject to an article-processing charge (APC). The 2011 APC rate will be US$1350/GB£890/ EURO1046 per accepted manuscript*
…
NPG will make an annual donation to Creative Commons equivalent to $20 per APC paid for publication in Scientific Reports
…
Scientific Reports will publish original research papers of interest to specialists within a given field in the natural sciences. It will not set a threshold of perceived importance for the papers that it publishes; rather, Scientific Reports will publish all papers that are judged to be technically valid and original. To enable the community to evaluate the importance of papers post-peer review, the Scientific Reports website will include most-downloaded, most-emailed, and most-blogged lists. All research papers will benefit from rapid peer review and publication, and will be deposited in PubMed Central.
Wow – sounds remarkably like PLoS One, even though they do not mention PLoS One in the announcement. Good news all around I think – the more OA we have out there the better.
H/T to Tom Sharpton and Katie Pollard for pointing this out.
——–
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.

——–

Taking a much needed blogging/twitter/etc break for a few weeks

Well, am on Winter Break here at Davis and am going to be taking at least a few weeks off of blogging/twitter/etc.  And trying to ignore email too.  I know – probably some irony in posting about taking a break, but whatever … am really taking a break.

Best wishes to all out there and see you next year ….

——–
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.

——–

NASA arsenic story – let’s lay off the personal attacks on all sides

I have many thoughts about the recent NASA – arsenic – microbe story.

Quick summary

  1. NASA announced a major press conference
  2. at the conference they discussed a new Science paper claiming to show the discovery of a microbe that could replace much/some of its phosphate with arsenic
  3. initial press coverage of the paper was very positive and discussed the work as having profound implications for understanding of life in the universe – though some scientists in some of the stories expressed skepticism of the findings
  4. subsequently many science bloggers further critiqued the paper and/or the press coverage
  5. NASA and the scientists have now refused to discuss the criticisms of their work and press interactions
  6. News stories have now come out summarizing the blogger criticisms and also discussing the unwillingness of NASA / the authors to discuss their work
As I said above I have some strong opinions about the published paper and about the actions of many of the people involved.  For example I think NASA handled this whole thing very poorly.  And I think the unwillingness of the authors and NASA to discuss the work by saying such discussion should be done only in the “peer reviewed literature” is really unwise.  
But that is not what I am here to write about today.  I am here to beg for people to calm down on the personal criticisms and attacks of any of the players involved.  I have seen so much out there about the failings of the paper reviewers, about the intelligence of the authors and the bloggers critiquing the authors, and a whole lot of uneducated guesswork about why some of the things associated with this story happened the way they did.  I think it is perfectly fair to express opinions about the original paper, about the press releases and conferences and about the actions of any of the players here.  But I do not think it is reasonable to go beyond that and to attack the people themselves.  Let’s try and make this an open discussion of science and science reporting and not a venue to spout derogatory comments about the people involved 
——–
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.

——–