Tag: Misc.

Lack of neutrality in bacteria and where pseudogenes go when they die

ResearchBlogging.org

Pseudogenes, which are in essence regions of the genome that used to be genes but no longer able to produce a functional unit, have long been considered to be models of the genetic equivalent of Switzerland’s neutrality. With this assumption of neutrality in hand, researchers have used studies of pseudogenes to better understand what happens to DNA when it is not visible to any form of natural selection. That is, pseudogenes have been thought to be neither harmful (as in, they are not under negative selection) or helpful (i.e., they are not under positive selection).

And from this assumption we have supposedly learned about mutation rates and patterns (because if they are neutral then the changes in pseudogenes should be reflective of mutational processes, not selection) as well as all sorts of other features of genome evolution.
Over the years, some have challenged the assumption of neutrality of pseudogenes (e.g., see here) like many have questioned whether Switzerland is really neutral. But overall, the feeling that pseudogenes were mostly neutral seems to have stuck. However, that may change a bit with a new paper from Chih-Horng Chu and Howard Ochman in PLoS Genetics (PLoS Genetics: The Extinction Dynamics of Bacterial Pseudogenes).
In their paper they report: (this is their authors summary)

Pseudogenes have traditionally been viewed as evolving in a strictly neutral manner. In bacteria, however, pseudogenes are deleted rapidly from genomes, suggesting that their presence is somehow deleterious. The distribution of pseudogenes among sequenced strains of Salmonella indicates that removal of many of these apparently functionless regions is attributable to their deleterious effects in cell fitness, suggesting that a sizeable fraction of pseudogenes are under selection.

Basically, what they did was the following
1. Compare Salmonella genomes. Identify putative pseudogenes and trace their evolution onto a phylogeny of the species.
Figure 1. Distribution of pseudogenes among Salmonellagenomes.
The phylogenetic tree was inferred from 2,898 single-copy genes shared by all fiveS. enterica subsp. enterica strains and the outgroup S. enterica subsp. arizonae.

doi:10.1371/journal.pgen.1001050.g001


2. Carry out a variety of analyses of the pseudogenes such as
  • looking at ratios of Ka/Ks (this is in essence a ratio of amino acid changes – aka non synonymous substitutions to “silent” synonymous changes which occur when the DNA sequence changes but the same amino acid is encoded).
  • examining the types and frequencies of gene inactivating mutations
3. Then they looked at the “ages” of pseudogenes – with age being estimated by the position in the tree in which the pseudogenes appear to have arise.
4. Finally the examined the age class distribution of pseudogenes as well as whether there were other differences between pseudogenes of different ages. And what they found was inconsistent with a neutral model. Instead, what they conclude is that something is making it advantageous to delete pseudogenes more rapidly than one might expect.
What explains this? After testing multiple possibilities the authors conclude that their is some negative selection against pseudogenes (or I guess positive selection for deletion of pseudogenes).
They conclude by suggesting this is likely to be pervasive across all bacteria and even in archaea. And furthermore make a connection to possible selection on intron size in eukaryotes. Anyway – the paper seems quite interesting and worth a read. Still pondering what it all means, so I would welcome comments.

Kuo, C., & Ochman, H. (2010). The Extinction Dynamics of Bacterial Pseudogenes PLoS Genetics, 6 (8) DOI: 10.1371/journal.pgen.1001050

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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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Human genome project oversold? sure but lets not undersell basic science

Well, the piling on the human genome project continues, it seems at an accelerating pace.  I think most of this comes from the fact that we are in the range of the 10 year anniversary right now.   Here are some examples of recent stories suggesting the human genome project (or projects, if you count the public effort and Craig Venter’s effort as separate) have had little benefit:

  • 7/31/10: The Human Genome Project: 10 Years Later, Progress but Still a Puzzle – WNYC. Interesting piece by Sarah Kate Kramer discussing the limited clinical value of the HGP.  Includes some criticisms of personalized genomic medicine. 
  • 7/29/10: Spiegel interview with Craig Venter with the headline “We have learned nothing from the genome”.  Has lots of interesting tidbits.  Love the Venter line “Well, nobody likes to be beaten — by superior intelligence, planning and technology. That gets people upset.”  But I note Craig emphasizes the basic science value of human genome data.
  • 7/6/10: Public Radio mini story about Mike Mandel’s article on the failure of the human genome project.
  • 6/12/10: Nick Wade’s NY Times article on “A decade later, genetic map yields few new cures“.  In this Wade discusses many of the issues with both the sequencing of the human genome and some of the spinoff projects (and also butchers some evolutionary biology for which I gave him a twisted tree of life award). 
These are but a small sampling of the many many blogs, articles, and other reports that either directly state or suggest that much of the money spent on the human genome project was a waste.

Certainly, contrary to the suggestion of some of these articles, there have been some practical benefits that have come directly or indirectly from human genome sequencing.  But equally certainly, these critiques have a segment of truth to them in that the practical benefits have been few and far between.

Normally, one would not expect too many direct practical benefit to come from this kind of science project.  But alas, the problem here is that many of the key players (e.g., Eric Lander, Francis Collins, Craig Venter) in the sequencing of the human genome(s) oversold the potential benefits that could come from the sequencing.  In a way, it was their job to oversell the sequencing, since each was a cheerleader in ways for getting others to do a lot of work.

Many people knew at the time that this overselling was going on.  It was talked about extensively at various genome conferences and even occasionally in the press and scientific literature (boy do I wish I had had a blog then, because I was one of those people at conferences practically begging people to not oversell the benefits of the project – I now even give out an “overselling genomics award” on my blog ).  The cautionary voices were mainly saying that there was no need to oversell the project and that we should stick to the benefits of “knowing” ourselves and not guess about how it will lead to immediate cures for diseases.  And many said “If you oversell this now, it will come back to bite you“

And thus it is not surprising to me that there is somewhat of a backlash now.  But there is a very dark side to the backlash that has potential to hurt science for many years to come.  If there is a need in the future for large scale science / medical projects, I can guarantee that some critics will step up and say things like “Well the war on cancer failed.  And the human genome project failed.  Why should we trust you now?”

The problem here is that the human genome project should never have been sold as a means to a series of practical ends.  It should have been sold as a massive basic science project, much like going to the moon or building a giant linear accelerator.  That is, the human genome project was, and still really is, about knowledge.  It is about knowing ourselves.  It has enormous potential benefits in all sorts of areas, like human medicine.  It should greatly aid and abet studies of human biology and genetics and disease.  But given that benefits that come from such studies are impossible to predict, the human genome project should have been presented in a different way.  We need to discuss more in public why basic science is important even if one cannot predict what the benefits are.

In many ways, this is very much like the “war on cancer” which some have argued failed because we still have cancer killing a lot of people.  But this is off base because in fact the war on cancer has provided us with an incredible baseline of information about the biology of cancer.  We need to do a better job in all of these cases of defending the need for knowledge, and discussing how fighting cancer and curing diseases is not the same as building a big bridge or road.

The best person discussing this issue for the last ten or so years in my opinion has been Harold Varmus, who was once the head of NIH and is now the new director of the National Cancer Institute.  I have heard him repeatedly defending the “war on cancer” in terms of its basic science benefits.  For example see his comments on Science Friday 1/30/2009 and 7/16/2010.  There just have not been too many people doing a good job of this with genomics.  Venter and Collins have been OK here and there.  But we need more.

On a related note, we probably should have more discussion about how the money spent on the genome project and the war on cancer pales in comparison to money we spend on other things (e.g., interest on the national dept, wars, etc) but perhaps that is a side discussion.

Most importantly, we need to bring out to the public more of a discussion of the benefits from basic science. Here are some useful resources if you want to try and help:

I also encourage people to look at the National Academy of Sciences report A New Biology for the 21st Century: Ensuring the United States Leads the Coming Biology Revolution.  I note, I was one of the coauthors.  You can download the PDF of the whole document after giving your email address.
I am going to start a new series here on this blog called “Benefits of basic science” where I will be discussing these issues.  I encourage others out there to also bring more to the forefront discussions of the need for basic science.

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UPDATE

Also see

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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.

——–

Twisted tree of life award #6: Scientific American Origins piece for dissing microbes

There is an interesting series of mini articles in the August 2010 Scientific American tracing the origins of various concepts and things: Origins: Going Back to Where the Story Really Starts: Scientific American
Not open access mind you, but if you have a subscription it is worth checking out. They track the origins of the following:

  • swiss cheese
  • paternal child care
  • computer viruses
  • animation
  • sexual reproduction
  • malaria
  • fireworks
  • barbed wire
  • hand washing in hospitals
  • human morality
  • electric cars
  • the influenza virus
  • wheeled vehicles
  • black holes
  • zero
  • biodiversity
  • noodles
Many of the discussions are interesting.  Some are a bit trite.  But that is not what I am here to report on.  I am here to complain about one aspects of the article series: too much emphasis on humans and multicellular organisms as “higher” creatures.  There are various subtle phrases here and there that I did not like too much but the parts that really grate on me are the two below:
  • In the article on biodiversity Melinda Moyer discusses the remarkable possibility that single celled creatures might have in fact had some diversity in them “Today we think of biodiversity in terms of multicellular life, but flowering plants and animals didn’t arrive until relatively recently” she writes.  And ends with “It is no comfort to know that the worst catastrophe would still preserve some biodiversity — even if only for the lowly cell.“
  • In the mini article on sex, Brendan Borrell writes “The truth is, nobody really knows why people — and other animals, plants and fungi — prefer sex to, say, budding.”  This of course leaves out all the other eukaryotes that are not plants, animals and fungi that have sex.  
And though these are certainly subtle small issues, I feel that Scientific American should do better.  So for directly and indirectly dissing the microbes on the planet – I am giving them my coveted Twisted Tree of Life Award #6.  Previous winners are listed below:
——–
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.

——–

Testing, testing – why we need more testing like this in genomic informatics & annotation methods

Just got an announcement regarding this challenge:

Automated Function Prediction SIG 2011 featuring the CAFA Challenge: Critical Assessment of Function Annotations | Automated Function Prediction 2011 July 15-16 2011, Vienna, Austria

Here is a description:

CAFA is a community-driven effort. We call upon computational function prediction groups to predict the function of a set of proteins whose true function is sequestered. At the meeting, we will reveal the functions, and discuss the predictions. The CAFA challenge goals are to foster a discussion between annotators, predictors and experimentalists about methodology as quality of functional predictions, as well as the methodology of assessing those predictions. Registration for CAFA starts July 15, 2010 and the CAFA challenge will take place September 15, 2010 through January 15, 2011.See here for more details on how you can enroll in CAFA.

This is near and dear to my heart as I have been working on methods to predict gene function from sequence for some 15 years now.  My first paper on this was in 1995 in which I showed that for genes in multigene families, phylogenetic trees of the gene family could help in predicting functions of uncharacterized members of the gene family.  More specifically, I suggested that the position of an uncharacterized gene in a gene tree relative to characterized genes could be used to predict its function.  I did this for one family in particular – the SNF2 family – but argued that it could be applied to other families.  (I think perhaps it was the first time someone had made this specific argument about using trees to predict function, but am not sure)

I then formalized this idea with a few papers (e.g., here and here) describing a “phylogenomic” approach to predicting function (alas, this is when I invented my first omics word).  And for many years since, I continued to work on functional prediction methods and continue to do so.  When I was at TIGR for eight years I did this both in my own research and helped others with their functional predictions.  I firmly believe that evolutionary approached approaches are critical in such functional prediction and have laid this out in a series of talks and papers (e.g., see this more recent one).

Anyway, enough about me.  I can argue all I want about how brilliant I am and about how evolutionary methods are the best approach.  But arguing is alas not science.  What we need are tests and experiments.  And that is where things like CAFA come in.  In CAFA one can test how well various functional prediction methods work.  And the people involved in CAFA (including organizers  Iddo Friedberg, Michal Linial, and Predrag Radivojac and others such as Amos Bairoch, Sean Mooney, Patricia Babbitt, Steven Brenner, Christine Orengo and Burkhard RoshRost)) are to be commended for putting this together because we do not have a lot of these activities and need more in all aspects of genomics (and metagenomics too).  Others have discussed doing tests of functional prediction methods before, but I am not sure if any have happened per se.

Have a favorite functional prediction method?  Enter it in the competition or give a talk on it.  And if you are feeling inspired, organize a similar activity in your area of science – testing is a good thing.

See also Iddo Friedberg’s post 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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What is not getting any love at this #metagenomics meeting

Well, Here I am for day 2 in Snowbird at a meeting/workshop discussing the potential for “Terrabase metagenomics”. The main point of the meeting is to discuss whether there would be value in massive massive Metagenomic sequencing in one way or another. I note I have enjoyed this meeting so far greatly – nice and small with some really good people.

Yesterday i gave a talk on microbial evolution and a few others talked about other topics (Rob Knight talked about microbiomes, Jeroen Raes discussed multiple Metagenomic projects, and Rachel Mackelprang discussed permafrost metagenomics). I will write more i hope soon about the science side of this meeting. But that is not what I am here to write about today. I am going to tell you what topics were not getting any love so far at this meetings. And this is not a completely snarky thing here – what people complain about does give some feel for what people are thinking about. In no particular order, here are some examples.

  • The human microbiome project (well, some parts of it)
  • The CAMERA metagenomics DB (significant disappointment in their progress )
  • NCBI (or specifically the short read archive)
  • Bureaucracy (and how it impedes science)
  • Lack of support for informatics
  • Lack of air (we are at 8000+ feet)
  • Large meetings
  • Jet lag
  • IRBs
  • Lack of RAM (many Metagenomic analyses require massive amounts RAM)
  • Bad alcohol (as in drinks)
  • Plants and animals (this is a meeting focusing on microbes)
  • Lack of cooperation among funding agencies
  • Pathogens (most people here are interested in either human commensals or environmental organisms)
  • Difficulty in founding joint projects between US and Europe
  • Projects that don’t collect metadata
  • Software tools that don’t work with each other
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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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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.
——–
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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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.
——–
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.

——–

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.

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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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