Category: Misc.

Calling on AAAS to Deposit all Archives of Science in Pubmed Central

Much has been written recently about a call to boycott Elsevier due to their outrageous policies regarding academic publishing.  I support the boycott but I also agree with many others who have said it perhaps unnecessarily singles out one publisher over others who also have publishing policies that could, well, use a bit of work.  And one such publisher is AAAS – the American Association for the Advancement of Science.

Today, the annual meeting of AAAS begins today in Vancouver.  I was supposed to be there by now, but thanks to some technical problems at Alaska Airlines, I am back in Davis for the day.  AAAS has some policies regarding openness that I believe are unnecessary and not in the general interest of scientific progress.  One is the strange “talk embargoes” I have written about recently.  Another, which is much more problematic, is the fact that Science Magazine (published by AAAS) does not deposit archival content in Pubmed Central.  Now, mind you, I think all scientific publishing funded by taxpayer money should be openly and freely available immediately. But that is not going to happen immediately.

One helpful tool in making scientific literature freely available is Pubmed Central.  Most scientific societies I know of deposit published material in Pubmed Central after some initial delay of 3-6-12 months.  But for reasons that are not entirely clear (to me at least, or to a Google search), AAAS clings to their archival material making it only available through their own web site.  Sure – they do allow authors to deposit their version of their manuscripts in Pubmed Central after a delay.  But most alas do not do this.  And I note – this option is only open to NIH and Wellcome Trust funded work.  So much material cannot be deposited anyway.

AAAS’s policy seems unnecessarily closed accessy and limits the impact and spread of the knowledge contained within papers in Science.  I note – this policy is yet another reason to not publish in Science and to instead choose either fully open access journals or ones that at least release their stranglehold on the papers after a short delay.

Today I call on AAAS to make archival literature from Science Magazine available in Pubmed Central.  And I call on others out there, such as those at the AAAS meeting, to pressure AAAS to do this.  Write blog posts.  Call and email AAAS members and leadership.  Email AAAS.  And so on.

Ideally everyone would just publish in fully open access journals and the journals would deposit material in archives.  But until that happens, we need to make every effort to increase the amount of literature getting into Pubmed Central and other archives.  So – pressure AAAS.  And while everyone is at it, please deposit whatever you can in preprint servers, in various repositories and in Pubmed Central.  Every little bit helps.

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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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Calling all phylogeneticists: Encyclopedia of Life Phylogenetic Tree Challenge

Just got an email from Todd Vision about this. Definitely seems worth checking out: EOL Phylogenetic Tree Challenge – Encyclopedia of Life
The challenge is summarized on their web site and I quote it here
“A prize is offered to the individual or team that can provide a very large, phylogenetically-organized set(s) of scientific names suitable for ingestion into the Encyclopedia of Life as an alternate browsing hierarchy.

  • Names must be provided in Darwin Core Archive1 format.
  • Extinct organisms may be treated but are not required.
  • Ranks are not required for names but may be included.
  • Internal nodes need not all have formal Linnaean names but require a label which can be arbitrary. Leaf nodes also need not have formal names but ideally most will overlap with current EOL species pages.
  • For the purpose of this contest, metrics and source of node support, branch lengths, vernaculars, and synonyms are not required. These may be included; not all are currently displayable on EOL.
  • Trees must be rooted. Multiple, overlapping hierarchies may be submitted as a set (e.g. to handle reticulation)
Among other factors, the total number of uniquely named nodes, node/leaf ratios and tree height may be used to compare entries so contestants should consider how they wish to trade off strict consensus versus other methods of reflecting the state of phylogenetic knowledge.
Problems to solve include 1) how to assign labels to unnamed nodes, 2) how to fill in gaps so that the set of taxa included is as comprehensive as possible, even if trees are not fully resolved or all taxa have not been analyzed, 3) how to handle competing hypotheses, 4) how to update the hierarchy at least annually.
The winning submission must be available to EOL and others under an acceptable CC license if it is under copyright. The tree need not be previously published in peer-reviewed form.
Questions about the challenge may be asked in the Phylogenetic Tree Challenge community on EOL.”

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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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Meta-Omics and Phylogenetics Journal Clubs

If you’re looking to catch up on your reading, come to journal club!

The Meta-omics journal club is run weekly on Tuesdays, from 11-12 in 5202 GBSF (organized by the Facciotti Lab, papers are sent around via an e-mail list).

There is also a bi-weekly Phylogenetics journal club run by the Center for Population Biology, 4-5pm every other Friday in Storer 5343 (The Treehouse). Regardless of journal club, there is always a 5pm Happy Hour at CPB every Friday – although be warned there are always are a substantial number of vertebrate biologists in attendence.

Paper out from the "Evolution in the Deep Biosphere" workshop I went to #OpenAccess

Just picked up this paper in one of my automated Google searches for, well, my own name: Prospects for the Study of Evolution in the Deep Biosphere.
The paper is the result of a workshop I went to at the USC Wrigley Marine Station on Catalina Island. See my notes on the trip here: A “work” trip to Catalina Island: USC, Wrigley, C-DEBI, dark energy biosphere, Virgin Oceanic, Deep Five, & more. I note – the group of people at the meeting worked on their paper after the meeting and invited me to be a co-author on it. However, I was busy and I felt like I could not contribute to it in a way that would qualify for authorship. So I sent them comments here and there and had also given them some ideas while at the meeting. And now I am happy to report their paper is out.

I note – the paper is in “Frontiers in Extreme Microbiology” one of the new Open Access journals in the Frontiers series.  Not sure yet what to think of all these Frontiers journals.  But they do have a suite of journals in “Microbiology” so I will keep an eye on them …

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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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Cool paper from DerisiLab on viruses in unknown tropical febrile illnesses #metagenomics #viroarray

Quick post:

Figure 3. Circovirus-like
NI sequence coverage and phylogeny.

Cool new paper from Joe Derisi’s lab: PLoS Neglected Tropical Diseases: Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing

Full citation: Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, et al. (2012) Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing. PLoS Negl Trop Dis 6(2): e1485. doi:10.1371/journal.pntd.0001485

They used a combination of a viral microarray and metagenomic sequencing to characterize viruses in various samples from patients with febrile illness.  And they found some semi-novel viruses in the sample.  Definitely worth a look.

Note – here are some other posts of mine about Derisi:

See some follow up discussion on Google+ 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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Trolls and flames discuss #NotSoFunny satire at the Scholarly Kitchen

Bit of a tiff going on over at the Scholarly Kitchen over a “satire” someone named Ken Anderson wrote related to the Research Works Act. The piece was about the “Restaurant Works Act” — Someone pointed me to the post and I found the satire to be, well, unfunny so I chose to ignore it. My brother alas could not ignore it, nor could some others and there is some discussion going on there now.

I will skip commenting on the discussion itself – go read it. But a few things there annoyed me. One of these is that Anderson has resorted to criticizing the punctuation of some of his critics there. That is pretty lame.  See start of thread below

Alex Merz wrote 

The inappropriateness of the analogy was clear by the end of paragraph 2. For the rest: TL;DR

To which Anderson responded

For those of us not as hip as Alex, TL DR means “too long, didn’t read.” I won’t comment on the inappropriateness of the semicolon in his Urban Dictionaryesque construction. The post is about 850 words, by the way

To which Alex re-responded

It is sad when an overly serious someone attempts a grammar or usage flame, and fails. 

“Too long; didn’t read” is both proper usage and a more effective construction than “too long, didn’t read.” 

Bryan Garner: “Fourth, the semicolon sometimes appears simply to give a weightier pause than a comma would. This use is discretionary. A comma would do, but the writer wants a stronger stop—e.g.: “There is never anything sexy about Lautrec’s art; but there also is never anything deliberately, sarcastically anti-feminist in it.” Aldous Huxley, “Doodles in the Dictionary” (1956), in Aldous Huxley: Selected Essays 198, 206 (1961).” 

Don’t be sad, though. Like you, a lot of smart people don’t know their way around a semicolon. 

If you’re too timid to wade into Fowler, Strunk & White, or Garner, there is help:
http://theoatmeal.com/comics/semicolon

 

To which Anderson responded

Nice try, but you don’t have any reason to use a semicolon there. In any event, I think you’re just covering up a typo with sophistry, so let’s move on.

To which Merz responded

You attempt a punctuation flame. When your own-goal is pointed out (with reference to authoritative sources) you mumble that your flame was correct (though it wasn’t), and you indicate that we should drop the discussion of punctuation that *you initiated.* 

Do you have *any* idea that makes you look? 

I’m guessing that you don’t: http://en.wikipedia.org/wiki/Dunning–Kruger_effect

and so on …

And before the folks at Scholarly Kitchen accuse me of having no sense of humor about such things – I suggest they look at my history of making fun of EVERYONE in publishing all the time.  The key to me is to be funny first and if you have some political comments you want to make, make them in that context.  I found the cooking / food RWA story to just not be funny so I did not pay any attention to its other messages.  Though clearly those messages bothered some folks, like my brother.

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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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Storification of Fake Science Publishing @fakeelsevier @fakeplos @realelsevier @fakeeisen @closedaccessj

So – I have been enjoying all the Fake Scientific Publishing Posts on Twitter from @fakeelsevier @fakeplos @realelsevier @fakeeisen @closedaccessj and others.  Now I understand why some people think I am behind some of these (e.g., here are some of my Fake Science News posts).  But alas though I WISH I was behind some of these accounts, I am not.  Anyway – I created a storification of the beginning of some of these postings if you want to see some of the origins of the fakery.

http://storify.com/phylogenomics/fake-scientific-publishing.js[<a href=”http://storify.com/phylogenomics/fake-scientific-publishing” target=”_blank”>View the story “Fake Scientific Publishing” on Storify</a>]

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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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Hmm … City of Davis definition of microorganism needs work

From City of Davis Guide to Composting

MICROORGANISM microscopic plants and animals.They exist in soil for the purpose of breaking down organic matter into basic mineral elements.They include bacteria, fungi, actinomycetes, algae, protozoa, yeast, germs, ground pearls, and nematodes.

Gonna have to get them to work on this …

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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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Microbial metaomics discussion group this week: metatranscriptomics and biogeography

A visiting student at my lab Lea Benedicte Skov Hansen will be leading our “metaomics” discussion group this week.  We will be discussing a combination of metatranscriptomics and biogeography and the papers of the week are:

Metatranscriptomics paper:

Microbial community gene expression in ocean surface waters. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF. Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3805-10. Epub 2008 Mar 3.

Some related papers of potential interest from DeLong

We are also discussing:

Drivers of bacterial beta-diversity depend on spatial scale. Martiny JB, Eisen JA, Penn K, Allison SD, Horner-Devine MC.
Proc Natl Acad Sci U S A. 108(19):7850-4.  (NOTE I am an author on this one – but the meat of the ideas/work was done by Jen Martiny, Claire Horner-Devine and others).

Related papers of possible interest by Jen Martiny and Claire Horner-Divine include:

Will let everyone know how the discussions go.  
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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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New publication from members of my lab (e.g., @ryneches) & lab of Marc Facciotti on ChIP-seq based mapping of archaeal transcription factors

New publication from members of my lab and the lab of Marc Facciotti on a workflow for ChIP-seq based mapping of archaeal transcription factors. The paper includes a description of new software from Russell Neches in my lab called pique for peak calling.

See: A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq

Russell’s pique software is available on github here: https://github.com/ryneches/pique.
Figure 3.
The Pique software package processes ChIP-seq coverage data to predict protein-binding sites. Strand-specific coverage data are output as tracks for the Gaggle Genome Browser, and putative-binding sites (peaks) are output as ‘bookmark files’. (A) Screenshot of data browsing in the Gaggle Genome Browser. Green box outlines the navigation window for clicking through bookmarks of predicted binding sites. Details of each site can be displayed (inset). The Gaggle toolbar (shown with black arrow) can be used to broadcast selected data to other ‘geese’ in the gaggle package, programs such as R, cytoscape, BLAST or KEGG. (B) Schematic overview of bioinformatics workflow.

ResearchBlogging.org Wilbanks, E., Larsen, D., Neches, R., Yao, A., Wu, C., Kjolby, R., & Facciotti, M. (2012). A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq Nucleic Acids Research DOI: 10.1093/nar/gks063

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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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