Eisen Lab Blog

Is it time to refer to mitochondria as bacteria?

Any time a scientific article has in the summary a sentence like the one below, I am attracted to it:

“Here, I playfully explore the arguments for and against a phylogenetic fundamentalism that states that mitochondria are bacteria and should be given their own taxonomic family, the Mitochondriaceae.”

So how could I not want to read this: Trends in Microbiology – Time to recognise that mitochondria are bacteria?:

Well, one reason is that it had been unavailable outside of the TIM paywall. However, the author, Mark Pallen, with a little prodding from me, managed to get the Editors to feature it as a “free” article on their website for at least some time. So everyone, download this paper and distribute it to as many as you can (legally). Oh, and read it, it is definitely worth a read.
In the article Pallen argues for giving mitochondria their own family w/in bacteria. I think that would be a good idea as they are really just a highly reduced form of bacteria. We give endosymbionts, even those with tiny genomes, their own groups. So why note organelles that are derived from bacteria? After all – phylogenetically they are bacteria.
Pallen even goes so far as to suggest rethinking of mitochondria as bacteria will help with efforts to engineer mitochondria in various ways. That is an interesting notion.
I suppose one could push this to an extreme position and argue that the nucleus and all the genes associated with it are really just a shell around a mitochondrial core. And then I guess all eukaryotes could be considered bacteria. But I do not want to confuse the issue too much here. Overall, I really really like this paper. I wish it were in an OA journal, but since it is free for now I think it is worth checking out. In the long run, it would be better (hint hint Mark Pallen) to publish such thought provoking pieces in places everyone can access ….
So I guess this paper, along with all the “microbiome” stuff means that humans are really just carrying vessels for bacteria.
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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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Alternative Real Time Twitter Feed for #AGBT #Experiment

http://widgets.twimg.com/j/2/widget.js
new TWTR.Widget({ version: 2, type: ‘search’, search: ‘#AGBT’, interval: 6000, title: ‘Marco Island AGBT Meeting tweets’, subject: ‘Genomics Live’, width: 250, height: 300, theme: { shell: { background: ‘#8ec1da’, color: ‘#ffffff’ }, tweets: { background: ‘#ffffff’, color: ‘#444444’, links: ‘#1985b5’ } }, features: { scrollbar: true, loop: false, live: false, hashtags: true, timestamp: true, avatars: true, toptweets: true, behavior: ‘all’ } }).render().start();

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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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Tracking Advances in Genome Biology & Technology meeting w/ Twitter Widget: #AGBT

Just a little experiment here seeing if this twitter widget tracks #AGBT tweets in real time …

http://widgets.twimg.com/j/2/widget.js
new TWTR.Widget({ version: 2, type: ‘search’, search: ‘#AGBT’, interval: 6000, title: ‘AGBT Meeting’, subject: ‘Genomics Live’, width: 250, height: 300, theme: { shell: { background: ‘#8ec1da’, color: ‘#ffffff’ }, tweets: { background: ‘#ffffff’, color: ‘#444444’, links: ‘#1985b5’ } }, features: { scrollbar: false, loop: true, live: true, hashtags: true, timestamp: true, avatars: true, toptweets: true, behavior: ‘default’ } }).render().start();

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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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Valentine’s Special: Dating in the 21st Century: 2/8 Berkeley #BABS

Posting this email I received:

Bay Area Biosystematists Meeting

Tuesday evening, February 8th, 2011
at UC Berkeley, 2063 Valley Life Sciences Bldg.

Valentine’s Special:
“Dating in the 21st Century:
Theoretical and Empirical Issues in Putting Dates on Phylogenies”

Featuring a Diverse and Distinguished Panel of Discussants
Followed by vigorous audience discussion

Panel members representing different approaches will give short informal presentations (10 minutes each), to be followed by active audience participation (this all following traditional pizza and beer, of course!).  
Confirmed Panel Members:
Tracy Heath
Pat Holroyd
Nick Matzke (moderator)
Sarah Werning

The venerable Biosystematists group (http://www.biosystematists.org/), operating since 1936 (see the history on the website), is the only inter-institutional seminar/discussion group on evolution for the Bay Area, so we encourage everyone to join in.

Schedule and venue:
    5:30 – social gathering with beverages (beer and soft drinks) and informal pizza dinner:  cost ca. $10, to be collected at door, 2063 Valley Life Sciences Bldg., UC Berkeley campus.
    7:00 – talk followed by discussion, in same room.
Reservations required for beverages and dinner (but not the talk).  Please email reservations to your host, Brent Mishler, at by Sunday, Feb. 6th  

For a map of campus and view of VLSB, use the link below.

All are welcome, members or not.  If you want to join the Biosystematists, sign up for our mailing list at: 

See you all there!
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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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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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#Badomics word of the day (or even month): Culturomics

Omics omics omics. The suffix is everywhere. And this paper has one of the worst ones I have seen in a while: Quantitative Analysis of Culture Using Millions of Digitized Books. paper came out right when I started winter vacation, which is why I am getting to it now …
In this paper, which is pretty cool, the authors make use of digitized books to track and study cultural trends. The data is f#*$#$ impressive. The results are very very interesting. The press coverage was very positive. The word, however, was and is awful. Did they really really have to call it culturomics, thereby contaminating their fascinating work with all the baggage of genomics? Really? Really? For that you get a Bad Omics Word of the Day Award.
Anyway – here are some links to coverage of the culturomics work, which as I said, is quite impressive. Just wish they had come up with their own non omicy word:
Hat tips to many people including Morgan Langille, Elizabeth Pringle, Michael Dunn, Nick Matzke, Mihai Pip and Sergios-Orestis Kolokotronis for calling my attention to culturomics.
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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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I get complaints; and I want more (plus other comments) about #PLoS Biology

Many out there may know that I have a nice lofty title at PLoS Biology. I am the Academic Editor in Chief there. With this title I get a lot of complaints about PLoS Biology.

Alas, despite my lofty title, I do not actually run PLoS Biology. You see, PLoS Biology is a hybrid journal with both Professional editors and Academic Editors. The way it actually works is that the Professional Editors, under the direction of Theo Bloom, run the journal. As part of their running of the journal, they consult with Academic Editors (AEs) to get help in deciding if papers should be reviewed; if they are reviewed the AEs help suggest reviewers; and once reviews are back the AEs help in making decisions about the fate of the papers. They also consult AEs about a variety of other topics.

In the end, you could view the AEs, including the AEIC (that is, me) – as having an advisory role at PLoS Biology. Generally, decisions are made in a collaborative manner with the AEs but in the end, it is the professionals who make the “final” decisions regarding the journal. But they do listen when I tell them about what the community likes and dislikes about PLoS Biology.

Anyway, the reason I am writing is that in two weeks there is a meeting in San Francisco of the EICs of the various PLoS Journals and I will be going to this meeting. So here is my request:

I WANT YOUR COMMENTS ABOUT PLOS BIOLOGY.

What do you like?
What do you not like?
What new things would you like to see?
What would you like to get rid of?

Please either post your comments here, on twitter, or friendfeed or wherever. Or send them to me by email. And I will try to communicate them to the powers that be …

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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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