Category: Misc.

Indoor Air 2011; Austin, Tx; June 5-10 #microBEnet

Just thought I would give people the heads up – I am helping plan a session on “Microbiology of the Indoor Environment” that will happen at the “Indoor Air 2011” meeting in Austin, TX June 5-10 2011.  The conference itself covers an enormous amount of ground about, well, Indoor Air.  And I am helping the meeting organizer Rich Corsi plan a special session that will try to bring together (1) researchers working on culture-independent studies of the microbes in the indoor environment with (2) scientists and engineers and others who work on the indoor environment.  Will post more about this special session as details come out.  But thought I would give people a heads up …

I note, this is a component of the Sloan Foundation’s New program in Indoor Microbiology – I have received a grant from them to create something called microBEnet (“microbiology of the Built Environment network”).  In this microBEnet project we will be working to foster communication, collaboration, research and other related activities for the Sloan Program.  More coming on microBEnet soon but if you want a little taste (a very preliminary taste) – see our blog 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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IQ Test for bacteria

ResearchBlogging.org

Social IQ of bacteria

Another quick one here.  Interesting paper out in BMC Genomics: Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments

The paper is from Eshel-Ben Jacob and colleagues from many institutions around the world.

Here is a summary of the article (from the paper)

Background

The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae) have been sequenced. However, no genomic data is available on the Paenibacillus species with pattern-forming and complex social motility. Here we report the de novo genome sequence of this Gram-positive, soil-dwelling, sporulating bacterium.

Results

The complete P. vortex genome was sequenced by a hybrid approach using 454 Life Sciences and Illumina, achieving a total of 289× coverage, with 99.8% sequence identity between the two methods. The sequencing results were validated using a custom designed Agilent microarray expression chip which represented the coding and the non-coding regions. Analysis of the P. vortex genome revealed 6,437 open reading frames (ORFs) and 73 non-coding RNA genes. Comparative genomic analysis with 500 complete bacterial genomes revealed exceptionally high number of two-component system (TCS) genes, transcription factors (TFs), transport and defense related genes. Additionally, we have identified genes involved in the production of antimicrobial compounds and extracellular degrading enzymes.

Conclusions

These findings suggest that P. vortex has advanced faculties to perceive and react to a wide range of signaling molecules and environmental conditions, which could be associated with its ability to reconfigure and replicate complex colony architectures. Additionally, P. vortex is likely to serve as a rich source of genes important for agricultural, medical and industrial applications and it has the potential to advance the study of social microbiology within Gram-positive bacteria.

The organism is certainly interesting.  See http://en.wikipedia.org/wiki/Paenibacillus_vortex for more detail (Eshel-Ben Jacob told me he updated the site).

But perhaps more interesting is the concept that Eshel-Ben Jacob has been pushing on bacterial social intelligence.  See for more detail:

The main idea behind this is to look at social communication strategies as a measure of intelligence.  And from a genomics point of view one can measure the genetic diversity of genes likely involved in these processes.  Such counting of genes is not the most useful thing in the world but more important, these organisms really have some fascinating behaviors and in the end we should measure behavior diversity not genomic diversity of putative social genes to measure “bacterial IQ”. 

Sirota-Madi, A., Olender, T., Helman, Y., Ingham, C., Brainis, I., Roth, D., Hagi, E., Brodsky, L., Leshkowitz, D., Galatenko, V., Nikolaev, V., Mugasimangalam, R., Bransburg-Zabary, S., Gutnick, D., Lancet, D., & Ben-Jacob, E. (2010). Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments BMC Genomics, 11 (1) DOI: 10.1186/1471-2164-11-710

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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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More and more books focusing on #metagenomics these days …

A friend/colleague Peter Turnbaugh just sent me a note about a new metagenomics book which he contributed to (see Metagenomics: Current Innovations and Future Trends). So I sniffed around Amazon and found a collection now of books that focus heavily on metagenomics. I do not know much about the quality of them but some look interesting. So I created a mini-Amazon collection of them: Metagenomics Books. Yet another sign metagenomics is still hot I suppose …

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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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Nature’s publishing machine really wants you to pay for stuff, even if it is supposed to be free #OA #fb

Well, this is annoying. I recently published a paper in Nature for which I was senior and corresponding author on “A phylogeny driven genomic encyclopedia of bacteria and archaea.” Though I did not want to submit it to Nature, the project involved a large large large number of other people and in fairness to their contribution to the project I agreed to submit it to Nature. However, the reason I agreed in the end was that Nature said they would use their Genome Paper open license for it. For papers reporting genome sequence data, Nature claims to make the papers available at no charge and supposedly uses a Creative Commons license for publishing the paper. In addition, I note, that as the work was done my many US Government employees, we did not sign over Copyright to Nature.

On the html version of the paper, this “semi-openness” of the paper is described:

“This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.”

Other than the strange spelling of license, this seems good. However, Nature’s machine seems to not be set up to make the copyright/license issues clear in every place/way. For example: if you go to the Nature site for my paper, it seems Nature is now claiming Copyright for the paper. For example see the PDF here.

And then if you click on the “Rights” link from the paper you get this which makes no mention of the Creative Commons license:
But wait. It gets better. If you go through the rights page and fill out the form asking to use the paper in an academic setting, you find out it will cost hundreds of dollars to use, according to this:

I suppose you could say that this all could be part of the Nature publishing machine just making a mistake here or there.  In fact, I would bet that this is in essence what has happened.  The system is designed for articles for which Nature holds the Copyright and has the rights to sell.  And the papers that do not follow that model get caught up in the machinery.  Nevertheless, it is annoying.  And it  makes me worry a bit about what is going to happen with Nature’s new supposedly “open access” journal “Scientific Reports” which actually is not quite as open as it might seem. (The journal uses a somewhat restrictive Creative Commons license which does not fit the standard definition of “Open Access”).

This seems to be YARFOA – Yet another reason for (full) open access.  If you set something free, even if someone claimed they had rights to it, it would seem more obvious to everyone out there that such a claim would be inappropriate.

I note – I am not saying Nature is trying to steal rights here.  In fact, in the past Nature has done a decent job at making sure that papers that were supposed to be available at no cost were.  For example, I looked into papers I published in Nature that Nature told us would be freely available for ever more?  This is what we were told for papers reporting genome sequence data years ago.  It was a very nice policy of Nature’s that helped spread knowledge about genome papers and also helped convince me publishing in Nature was not so bad in terms of openness while I was starting to become a more openaccess advocate.  So I decided to take a look at some of the papers that I was an author on that were supposedly made freely available forever.  Here is a sampling:

Every once in a while, I had noticed in the past some of these papers were not freely available and Nature quickly corrected this so I do think they are trying not to violate their commitments.  But again, in their system, buying access is a key component and alas if the switch is going to be set wrong, it seems that it is set on “you have to pay for this” as a default.  I hope they use a different default setting for their new semi-open journal ….  
Meanwhile, if you want to do something non -commercial with our paper, feel free to do so, regardless of what the Nature website says.  
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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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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 …
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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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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

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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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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

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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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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 …
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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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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

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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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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?
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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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