Month: July 2010

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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PZ Myers will reveal his decision on free blogagency on live TV

Morris, MN — For the final act of the drama that has captured the imagination of science blogging fans around the world, PZ Myers of Pharyngula plans to announce his decision live on the Discovery Channel at 9 on Thursday night.

The arrangement, first reported by Discovery, was confirmed by a person close to Myers, who requested anonymity because he was not authorized to speak on Myers behalf.

Yesterday, Myers met with representatives of Discover, Google, Wired, and many others to discuss his plans in regard to the ScienceBlogs free blogagency diaspora. Now, they and everyone else will soon find out Myers’ highly anticipated plans. Thursday marks the first day that free bloggers can sign new contracts that have been verbally agreed upon. Starting yesterday, bloggers and blog hosts were allowed to negotiate, but not consummate new deals.

The most-hyped free blogagency diaspora in science blogging history has so far been mostly bluffs, whispers and hypothetical situations. Prominent bloggers like Sharon Astyk of Casabaun’s Book, David Dobbs of Neuron Culture, Chris Rowan of Highly Autochthonous, Dave Bacon of The Quantum Pontiff, Scicurious, Blake Stacey of Science After Sunclipse, Alex Wild of Myrmecos, PalMD of the White Coat Undergound, Dr. Isis of On Becoming a Domestic and Laboratory, GrrlScientist of Living the Scientific Life, Janet Stemwedel of Adventures in Ethics and Science, Brian Switek of Laelaps, and many others are all reportedly on the move, but the details remain murky.

But one player has emerged who may be a key factor in the decisions of Myers and other prominent soon to be ex-ScienceBlogs bloggers: Ed Yong of Not Exactly Rocket Science.  Yong blogs at the highly respected Discover blog site with other stars like Carl Zimmer of the Loom. Yong, regarded as one of the most sought after free bloggers is reported to be happy at Discover but also is considering his options.

“The days are passing by a lot quicker now,” Yong wrote Wednesday on his Twitter page. “It’s always like that when you have to make a BIG decision.”

Myers and Bora (of Blog Around the Clock), Brian Switek (of Laelaps) and Scicurious all reportedly want to co-write a blog with Yong, according to multiple news reports. Myers has never blogged directly with an science blogger as talented as Yong, although Yong was at Scienceblogs for some time before moving to Discover. Bora paired with others to win a blog championship in 2006.  Switek has blogged with a variety of support personnel, but none enough to carry him to the blogging championship. In turn, Yong, according to news reports, has shown interest in blogging with Myers, Bora, Switek, Scicurious or all of them.

Last week, Yong, who shares an blogging agent with Switek, posted a picture on Twitter of the two of them at dinner. The caption ended “although it feels like someone is missing……” in a reference to Myers.

Discover Blogs General Manager Diana Scover conceded before free blogging began that Yong would probably sign with another team. If Yong does, he will lose the sixth year on his guaranteed blogging contract and earn less money under the so-called Rebecca Skloot rules rules that offer perks to free bloggers who remain with their organization.

Therefore, Yong would need Discover to facilitate a sign-and-trade deal with his preferred blogging site to maintain those benefits.

In a text message, Joe Eisen, the agent for Yong and Switek, confirmed that ScienceBlogs had inquired about landing Yong in a sign-and-trade deal. Eisen did not say if Yong would be interested in blogging for ScienceBlogs should Myers return. ScienceBlogs would be over the blogging cap and would not be able to sign Yong outright. Given the recent controversy at ScienceBlogs it seems highly unlikely Yong would go there whether Myers remained or not.

A sign-and-trade deal with Discover would almost certainly cost the ScienceBlogs a prominent blogger like Dr. Isis, and Discover would also probably use any deal to try to free itself of one of their expensive contracts like that of Carl Zimmer, which extends another four years.

A Discover official, speaking on the condition of anonymity because he was not authorized to discuss blogger movement publicly, said Discover had “nothing imminent” with a sign-and-trade deal for Yong. A deal between Discover and ScienceBlogs appears improbable.

Flush with blogging-cap space, Wired and Google who also met with Myers and Bora and Switek, have sought ways to land Yong. ScientificBlogging, the first site that met with Yong when free blogging started, are hopeful they can obtain Yong, a Sacramento native, in a sign-and-trade deal.

Google meanwhile, can offer Myers, Bora, Scicurious, and Switek a talented blogging support staff and massive exposure, even if they have no prominent science bloggers to speak of currently.

On Wednesday, Myers, Bora, Scicurious, and Switek retreated to their blogging camps. None met with reporters, and Bora canceled a scheduled news conference at his youth event in North Carolina.

Myers arrived nearly four hours late at his evolution academy in his hometown with a contingent that included his business manager, Chaz Darwin, the prominent atheist scientist Richard Dawkins, and others.

Myers walked onto the floor and watched while some of the country’s top high school science bloggers writing for a second day. He playfully wrote twitter posts from the floor during a break and then retreated through a side door.

Anticipation mounted that Myers would use social media outlets as a conduit to release the news of his destination. After recently activating his dormant MySpace page, Myers created a Twitter account Wednesday that gained more than 85,000 followers before his first message, which broke his public silence from the start of free blogging.

But those who hoped his first message would deliver the big news were vastly disappointed:

“Hello World, the Real PZ is in the Building ‘Finally,’ ” it read, before crediting Dr. Kiki for motivating him to join.

Still, Myers had attracted nearly 150,000 followers by 7 p.m. Richard Dawkins, confirmed that the account belonged to Myers but said that Myers would probably not use Twitter to release his decision.

Instead, he’ll use Discover

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With apologies to the New York Times and Jonathan Abrams to leveraging an article of theirs.

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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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Anyone else getting lots of China-Conference SPAM recently?

Anyone else out there getting a ridiculous amount of conference SPAM recently relating to conferences in China? I keep getting invited to speak at or chair sessions at various meetings of little relevance to what I do. For example, consider a recent email I got that starts with

Dear Dr. Jonathan A. Eisen,
You are cordially invited, on behalf of the organizing commission, to Chair a Session or give a Keynote Speech at Session 9-3: Protein Biomaterial Design and Applications of BIT’s 4th Annual Protein and Peptide Conference (PepCon-2011). The theme of this upcoming conference is “New Leaders in Protein and Peptide Science”. The conference will be held at China National Convention Center, Beijing, China from March 23-25, 2011.

This is relating to this meeting: BIT Life Sciences’ 4th Annual PepCon-2011 which has little relevance to what I do. I have been getting many many emails like this over the last few weeks. Not sure what led to the uptick in getting these emails but they are starting to annoy me …

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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.

——–

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.

——–

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.

    ——–