Category: Misc.

CA scientists – time to rally for a good rock (serpentine)

I have been spending much more time on Twitter recently than on my blog, though I am trying to get back into the blog more and more. And today I am posting a mini post here that is more like a twitter post but I just have to at least put this on the blog. Sheril Keirshenbaum is calling for all Californians to DO SOMETHING in regard to this inane attempt to remove serpentine as the State Rock of California. See here recent post here:

Calling on Californians: West Coast Represent! | The Intersection | Discover Magazine

Really not much more to say than she has said, but I call on everyone in CA to do something about 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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Evolution diet for pets. Why not for people? Oh wait, of course that has been thought of before

Yup, that is right.  There are evolution based diets for pets.  Do you think people will use them if they don’t believe in evolution?  Do pets believe in evolution? Is an evolution based diet better than other diets? Actually, for the last question, it seems plausible that evolution informed diets could be of some use, but still seems funny to see it in pet food. 
Why isn’t there an evolution diet for people yet? Oh wait, there is. 
And there is all sorts of stuff out there about evolution and diet including
Just goes to show you, with google you can find that just about everything you can think of already exists. 
——–
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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Summary of #iEVOBIO Day 2, #phylogenetics #informatics #opensource #biodiversity #evolution

This is a continuation of notes on iEVOBIO meeting.  Much of this comes from twitter.  Additional comments will be posted over the next few days.  See notes on Day 1 here. Note – thanks to the people who answered my query on twitter about how to remove spurious html code from pages – I wrote this post a few days ago but somehow the copying and pasting I did from twitter broke blogger with some weird html.  I ended up using Zubrag which was suggested by brendanwlocke.

Day 2. Beginning.

Since I was leaving that PM I could not borrow a hotel bike and bike over again.  So I walked from the hotel, along the river 2 or so miles, after getting coffee.  I got to the meeting a bit late and thus missed much of the opening Keynote, which was a bummer since it seemed very good.  But I find if I do not get some exercise every day at a meeting I go crazy so it was worth it.  Here are some notes on Day 2.

Day 2. Part 1. Keynote

Alas, I missed much of the keynote.  But what I caught was good.  Here are some notes, mostly from twitter. And also see Rob G’s slides below

RPG iEvoBio 2010 Keynotehttp://static.slidesharecdn.com/swf/ssplayer2.swf?doc=ievobiokeynote3-100630154451-phpapp02&stripped_title=rpg-ievobio-2010-keynote

Rob Guralnick: Biodiversity Discovery and Documentation in the Information and Attention Age

    Day 2. Part 2. Short talks.

    Day 2. Part 3. Lunch

    Went to lunch with a small group to the People’s Sandwich of Portland.  Took the light rail over the river.  Portland has some really nice features – like free light rail in the city.

    Day 2. Part 4. Lightning Talks

    Day 2. Part 5. Birds of a feather


    Then there were breakout sessions which were called “Birds of a feather”  I went to one discussing open access and fair use issues. 

    Day 2. Part 6. Wrap up and other general information

    And then I had to go home.  The meeting wrapped up as I was leaving. Here are some ending tweets:

    Some other general info tweets:

    Post meeting posts and blogs
    ——–
    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.

    ——–

    Summary of #iEVOBIO Day 1 #evolution #phylogenetics #informatics #opensource

    Well, just getting around to writing up some thoughts on the iEVOBIO meeting I went to earlier this week.  It was really quite excellent so here are some thoughts/notes.  Today I am writing about the background and Day 1.  Most of this is simply a catalog of what happened along with some twitter details … In a few days I will write up a post on what I think it meant ….

    The background: how I heard about iEVOBIO (skip to below if you just want to know about what happened in the meeting)  

    The first I heard about regarding the meeting was Dec 7, 2009, in a Direct Message on Twitter from @rdmpage.  That would be Rod Page, who I had never met, but followed remotely via twitter, his blog, his software and his papers.  He wrote

    Hi Jonathan, hope you got my email about speaking at iEvoBio in June. No pressure, just checking that it made it into your in box.

    I had known about Rod for a long time since I had used his software since I was in grad school.  For example, I used to use Treeview for all phylogenetic tree viewing/drawing etc.  It seems from the history, it has been available since 1996.  Not 100% when I started using it, but it was around then.  Then I switched over to using Treeview X a few years later.  And I have used on and off some of his other software.  More recently I have followed his blog/tweets/web sites closely.

    When Rod invited me, I was on a mini vacation in Monterrey and I had not actually seen his email yet (I am ALWAYS behind in reading email).  So I found the email, inviting me to give a Keynote at this cool sounding iEVOBIO meeting focusing on informatics for phylogenetics, evolution and biodiversity.  Sounded great actually.  Especially the part about Open Source:

    iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software developmentand reuse within the research community. For this reason, if a submitted talk concerns a specific software system for use by the research community, that software must be licensed with arecognized Open Source License, and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial

    I also liked the notion of a challenge – in this case there was a challenge for new visualization methods for evolutionary data. In summary the challenge was:

    From phylogenetic trees to population networks, whether on printed pages or in GoogleEarth, visualizing evolution is a key part of our discipline. Inspired by the challenges and opportunities visualizing presents for our field, the first iEvoBio challenge is “To create a new visualization tool or platform to support evolutionary science”.

    Alas, since I was on vacation I did not have all my schedule information with me, so I said I was not sure. Fortunately, when I got back, it looked like good timing with the Evolution meeting just before so I said sure.

    Going to iEVOBIO (skip to below if you just want to know about what happened in the meeting)

    Anyway – jump to last week, skipping over some of the preparatory stuff for the meeting. I was planning on being in Oregon for almost a week, including the SSE meeting just before iEVOBIO and a meeting for my iSEEM project in Eugene before that.  But I just could not deal with being away for that long including over the weekend, after having not really taken any time off in a while.

    So I went home and skipped SSE2010 and then headed back to iEVOBIO on Monday the 28th. I flew on Southwest from Sacramento to Oregon, took the light rail into the city, and walked the last bit to my hotel.  I arranged to have dinner with Aaron Darling, a Research Scientists working in/with my lab who was at SSE.  We had a good dinner and then I went back to my room and stayed up until about 3:30 AM working on my keynote talk.

    I really wanted to include some new stuff and also include some background on microbes and microbial diversity and so worked very late making new slides, piecing together slides from multiple talks, and then trying to delete slides since my talk was way way way too long.  The final project I did not finish that night.

    I set my alarm on my phone and asked for a wake up call and got about 3 hours sleep. I got up around 6:30 worked on my slides for an hour, and then took a showed and heading downstairs where I borrowed a hotel bike (god, I love Portland – free bikes at my hotel) and biked along the river, over the bridge, and after a little hunting around found where I could park and lock the bike.  And I went in.

    I worked on my talk for another 30 minutes in an isolated corner and then went over to the main part of the conference center. Finally I was done.  I was amazed at how crowded it was.  Were all of those people there for iEVOBIO?  Alas, no – SSE2010 was still going (I did not realize it would still be on).

    After asking around I found the meeting room and met the one and only Rod Page (we had never met).  I made sure my laptop would connect with their system and then headed out to get coffee – there was a Starbucks in the hallway outside the meeting room.  Alas there was a giant line and my talk was in 25 minutes.  Fortunately, Aaron Darling was in the line and he agreed to purchase a latte for me.  I went back in, made sure everything was set, and paced around until I got my coffee from Aaron and then it was time for the meeting to start.

    The meeting itself: Day1 part 1: keynote by me 

    The meeting kicked off with a few details from some of the organizers including Rod Page and Todd Vision.  We found out who the other organizers were (Rod Page (University of Glasgow), Cecile Ane (University of Wisconsin at Madison), Rob Guralnick (University of Colorado at Boulder), Hilmar Lapp (NESCent), and Cynthia Parr (Encyclopedia of Life).  We also found out who helped fund the meetings (US National Evolutionary Synthesis Center (NESCent), and the Society of Systematic Biologists (SSB). I am no longer sure exactly what else they said.  But there seems to have been at least one tweet about the intro:

    • toranaga Todd Vision mentions how computational biology is a guild, full of people that take great pride in their craft.

    And then Rod introduced me.  Pretty funny actually.  He gave me grief for writing about bad omics words and yet inventing and then using phylogenomics for everything.  And then my talk was on.  Here it is on slideshare.

    Jonathan Eisen talk at #ievobio 2010http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=eisen-100629132410-phpapp01&stripped_title=eisen

    Also – there were a few tweets about my talk including the following:

    I got asked some great questions afterwards including one by Joe Felsenstein, one by Arlin Stoltzfus, and one by James McInerney (well, McInerney mostly gave me grief about how he disagreed with me about the extent of lateral gene transfer).

    Day1 part 2:  Short talks 

    After my talk, thankfully for all involved, there was a coffee break.  And then we were back with short, ~15 min talks. These are listed below with some information, most of it from Twitter.

    Day 1: part 3: Lunch – here are some tweets that came out around that time …

    Day 1 part 4: Challenge talks

    And then the post lunch challenge talks began.  These related to visualization tools entered into the meeting challenge mentioned above and described here.

    Day 1. Part 5. Lightning talks.   

    • dgaston83 Now time for the lightning talks. Gives me a good idea what to expect for mine tomorrow. Glad I’m on day 2!#ievobio
    • toranaga #ievobio lightening talks! 5 minutes and then the gong goes off

    Day 1. Part6. Software bazaar and demos

    Then there were was the software bazaar and challenge demonstrations, which alas, I skipped most of because of the lack of sleep the night before.  It seemed quite packed in there and I was just exhausted. So I went back to my hotel, riding the bike I had borrowed from the hotel back, slowly, along the river.

    Here is what I missed:

    • Software bazaar
      • W. Berendsohn: The EDIT Platform for Cybertaxonomy
      • R.J. Challis: Pipefinder – semantic pipelines made easy
      • B. Gemeinholzer: DNA Bank Network Ð a virtual linkage of natural history collections’ voucher specimens and documentation with physical DNA, sequences, and publications
      • M.J. FavŽ: eFECTIV: Shape analysis using elliptical harmonics
      • T.M. Keesey: Names on Nodes: Automating the Application of Taxonomic Names within a Phylogenetic Context
      • S. Lewis: Functional Gene Ontology Annotation across Species using PAINT
      • S. McKay: GBrowse_syn
      • M. Porter: iBarcode-nextgen: tools for next generation biodiversity analysis
      • D. Rosauer: Biodiverse, a tool for spatial analysis of biological diversity
      • R. Scherle: The Dryad Digital Repository
      • C.L. Strope: indel-Seq-Gen version 2.0
      • M. Youngblood: mt-tRNA-Draw
    • Challenge demonstrations
      • M. Porter: GenGIS
      • K. Urie: VoLE (Viewer of Life in EOL)
      • V. Gopalan: Nexplorer3
      • A. Hill: PhyloBox
      • S. Smits: jsPhyloSVG

    Summary of Day 1. 

    Here are some tweets summarizing Day 1:

    • oatp Open science and data sharing at Evolution 2010 andiEvoBio: Posted by petersuber to oa.notes oa.biology oa.new oa… http://bit.ly/bOocHh
    • chrisfreeland @rdmpage @cydparr sounds like #ievobio is going well & interesting. v. sorry I couldn’t work it in!
    • trinaeroberts Demos of Biodiverse, GenGIS, various tree visualizers… very cool stuff at #iEvoBio today!
    • justsayinnn someone explain to me how the ievobio wants open source yet they charged for registration???
    • justsayinnn data visualization stuff was way cool today at #ievobio

    At the end of the day, I had dinner with Steven Kembel and Tom Sharpton (@toronaga) who I work with on a Gordon and Betty Moore Foundation funded project we call iSEEM.  Dinner and conversation were great.  I then went for a walk along the river and went back to my room.

    ——–
    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.

    ——–

    Twisted tree of life award #5: Nicholas Wade & use of higher, lower, ladders, etc

    Nicholas Wade has a new article in the New York Times critiquing some aspects of the human genome project (A Decade Later, Gene Map Yields Few New Cures – NYTimes.com)

    Whether one agrees with his critiques or not, I hope that everyone can recognizes that one section on evolution is, well, awful. Wade writes

    First was the discovery that the number of human genes is astonishingly small compared with those of lower animals like the laboratory roundworm and fruit fly. The barely visible roundworm needs 20,000 genes that make proteins, the working parts of cells, whereas humans, apparently so much higher on the evolutionary scale, seem to have only 21,000 protein-coding genes.

    While Mr. Wade may want to believe he and humans in general are somehow “higher” on some evolutionary ladder than other species, I have some news for him

    THERE IS NO FU*$ING EVOLUTIONARY LADDER.

    Humans are neither higher nor lower than any other organisms. This is an antiquated and inane view of evolution. Sure, humans are smart. Sure we are more complex in some aspects than, say, some bacteria. But new features evolve on ALL branches in the tree of life. And some organisms lose features present in their ancestors. The evolution of complexity is, well complex, sure, but please, “higher” and “lower” organisms? An evolutionary ladder? Uggh.

    I do not pay much attention to human GWAS studies, but if Wade’s understanding of them is akin to his understanding of evolution, well, I would then infer that GWAS studies have revolutionized all of medicine. For his butchering of evolution, I am giving Nicholas Wade my 6th coveted “Twisted tree of life award”

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    More on this topic can be found at:
    Larry Moran’s Sandwalk
    Larry Moran has a good discussion of the genes in the human genome issue (from 2007)
    PZ Myers at Pharyngula Chimes in

      ——–
      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.

      ——–

      Scooped in a good way by my own brother re Nature-UC dispute

      Well, I so wanted to write a piece about the Nature-UC dispute going on right now. In summary, a group from the University of California (University Committee on Library and Scholarly Communication (UCOLASC) including librarians and scientists and various others circulated a letter a few days ago to UC faculty suggesting a possible boycott of Nature journals due in large part to impending price increases. The letter became public (see for example here). Some News stories were written. Some blogs and many tweets were posted (including mine, wondering why I had not heard anything about the whole issue before). Nature responded. UC responded back. More news stories were written (e.g., SJ Mercury news here) and more blogs and tweets came out.
      But something was missing in the whole thing from my point of view. What was missing was a discussion of how this whole discussion should not really be about UC vs. Nature.  It should be about how the publishing systems right now is broken – about how we should expect commercial publishers to want to make money and how what we need to do as scientists is to take control of publishing to make it more open and to save taxpayer’s money because we do not really need many of the broken parts of the publishing system.

      And it should not have really been about Nature vs. UC – Nature to me is not the issue here.  I personally would not have gone after Nature in the way the UC library group did.  Nature does some good things and some bad things.  As do many, if not all publishers, even, God forbid, PLoS.  Nature in fact has been doing some useful experimenting with some nice web/open science features.  We should neither expect them to do good things or bad things.  What we need to do is think about the whole system of publishing, not just go after one publisher.

      Fortunately, before I wrote this up, I found a blog post that covers many of my feelings on the issue. And it just happens to be by my brother, Michael (CoFounder of PLoS), who is traveling on the East Coast and who I have not had a chance to talk to at all about the Nature-UC issue. So I recommend people go to his post: The Nature kerfuffle: boycott the business model not the price

      I am not saying I agree with every sentiment in his post but the key part to me is:

      “It’s time for UC to follow suit. Rather than haggling over prices, the faculty, students, staff and administration of all ten UC campuses should unite to end the business practices that empower NPG and other publishes to regularly attempt to extort money from our chronically cash-strapped library system.”

      I have little to add to this so will leave it there.   Read his post for more.
      ——————————————–
      Here are some links about the UC-Nature dust up

      ——–
      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.

      ——–

      Slides and audio from my talk at #ASMGM

      Slides and audio from my talk at ASM General Meeting

      Jonathan Eisen talk at ASM General Meeting 2010http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=eisen-asm-opdf-100525171216-phpapp02&stripped_title=jonathan-eisen-talk-at-asm-general-meeting-2010

      View more webinars from Jonathan Eisen.
      ——–
      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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      Archaea in the news – a growing trend

      Archaea, the so-called “third” branch in the tree of life, don’t get in the news much but good when they do and for some reason, they are getting in the news more and more these days.  See below for some links to news stories.

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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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      Request – information on the fraction of microbes that can be cultured

      To all – I am looking for some information on the fraction of microbes that can currently be cultured from different environments. If you know of any good review papers or databases or other information on this topic, it would be very useful.


      Here are examples of some information I have found:
      • From Jo Handelsman’s review on metagenomics in 2004: “One of the indicators that cultured microorganisms did not represent much of the microbial world was the oft-observed “great plate count anomaly” (135)—the discrepancy between the sizes of populations estimated by dilution plating and by microscopy. This discrepancy is particularly dramatic in some aquatic environments, in which plate counts and viable cells estimated by acridine orange staining can differ by four to six orders of magnitude (66), and in soil, in which 0.1 to 1% of bacteria are readily culturable on common media under standard conditions (138, 139).”
      • From Phil Hugenholtz’s review in 2002: “under aerobic conditions, at moderate temperatures. Easily isolated organisms are the ‘weeds’ of the microbial world and are estimated to constitute less than 1% of all microbial species (this figure was estimated by comparing plate counts with direct microscopic counts of microorganisms in environmental samples; it has been called the “great plate-count anomaly” [1]). ” Reference 1 is Staley JT and Kanopka 1985.

      But what I am looking for is some sort of review or database that has information for lots of different ecosystems.
      Anyone know of anything like this?

      http://friendfeed.com/treeoflife/51f698e2/request-information-on-fraction-of-microbes?embed=1

      ——–
      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.

      ——–

      Holy lateral transfer batman; amazing story on fungal to aphid transfer from Nancy Moran

      As many know, I generally do not write a lot about papers in non open access journal because I like readers to be able to access all the papers which I write about. But this is one of the exceptions to my normal rule. An amazing paper was published a few days ago in Science by Nancy Moran and Tyler Jarvik. Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids — Moran and Jarvik 328 (5978): 624 — Science
      I first found out about this from Ed Yong’s blog post here (just a note – his Not Exactly Rocket Science is such a frigging incredible blog). He really does the whole story on this so I am just posting a bit here.
      Anyway Moran and Jarkiv paper focuses on genes in the aphid genome that encode enzymes for carotenoid synthesis. These enzymes are involved in red and/or green coloring seen in the pea aphids. Recently the pea aphid genome was sequenced (a paper about this was published in PLoS Biology ) and it was analysis of the genome data that helped lead Moran and Jarvik to the study reported in the recent issue of Science.
      In their study they report a detailed evolutionary and phylogenetic analysis of the carotenoid synthesis genes found in the aphid genome and show quite convincingly that these genes do not appear to be of “normal” descent. That is, they seem to have an ancestry separate from many of the “normal” animal genes in the genome. Instead, these genes are related to genes from fungi. In fact, these genes are embedded in an evolutionary sense, in a group of genes which are all from fungi and thus Moran and Jarvik conclude the most likely explanation is that some time in relatively recent pea aphid evolutionary history, these genes were acquired from some fungus.
      About to have some eye drops put in my eyes so gotta go for now, but just wanted to get something out there about this fascinating work. For more on this story – there is lots out there, such as the following:

      Moran, N., & Jarvik, T. (2010). Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids Science, 328 (5978), 624-627 DOI: 10.1126/science.1187113

      . (2010). Genome Sequence of the Pea Aphid Acyrthosiphon pisum PLoS Biology, 8 (2) DOI: 10.1371/journal.pbio.1000313

      ResearchBlogging.org

      ——–
      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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