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 FriedbergMichal 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

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

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.

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.

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 PontiffScicurious, Blake Stacey of Science After SunclipseAlex 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.

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 ...

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. 

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


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

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.



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).


Freeing my father's publications part 5: many PDFs added

I made some major updates to this page where I am posting information about my father's publications: The Tree of Life: Freeing my father's publications

This is part of my ongoing effort on Freeing my father's publications

Today I added PDFs for about 10 more of his papers to the list of papers which I am posting here. Still more to add, but making progress.

Freeing my father's publications part 4

Well, the saga on "Freeing my father's publications" continues.  I am now experimenting with posting papers by my father on a "personal" website dedicated to this task, since most/many journals allow one to post one's papers this way.

Since I am about to head out to a meeting, I am going to do the simple part first.  Making a collection of as many of his papers as I can.  I am posting these on a "Page" associated with this blog here, at least for now.

Here is the first:

Eisen HJ, Goodman HM. Growth hormone and phosphorylase activity in adipose tissue. Endocrinology. 1969 Feb;84(2):414-6. PMID: 4303531.  I have a printed copy I made 10 or so years ago.  I scanned it with my Fukitsu ScanSnap S1500M scanner and used the "convert to PDF with text" option.   And this is what came out.  Not perfect but not so bad.

More coming.  And thanks to David Williams, a friend from my youth, who knew my dad, for helping inspire me to keep at this.

Freeing my father's publications part 3

Well, continuing on with what I started two years ago and posted about yesterday. I am trying to make scientific publications by my father (Howard J. Eisen) freely available on the web somehow.

For more see
And alas things did not start out well today.  At the suggestion of Linda Avey I looked at Academia.Edu to see if I could create a page there for my father.  I guess I could have lied, but they ask for current institution/affiliation so I could not do that. 

So I decided to start to try to download his papers from journal sites to use when I create some web site for him... not getting very far I note ... and getting a bit pissed off. 
  • Paper #1: 
    • Growth hormone and phosphorylase activity in adipose tissue. Eisen HJ, Goodman HM. Endocrinology. 1969 Feb;84(2):414-6. 
    • Available online apparently here.  Published by The Endocrine Society which makes papers from 12 month old back to 1997 available for free online.  But it does not make older papers available.  What an inane policy.  So I cannot (legally) get a PDF of this paper without paying for it?  F*$cking brilliant. Glad though, that UC Davis is not paying for this as it should be available for free to everyone.
  • Paper #2 : 
    • Horm Metab Res. 1971 Sep;3(5):331-5.The effects of hypophysectomy on phosphorylase activity in adipose tissue and muscle. Hellman DE, Eisen HJ, Goodman HM.
    • Seems to be available via Thieme Journals here.  But then alas, it is not available for free. Great.
  • Paper #3 :
    • Endocrinology. 1973 Feb;92(2):584-8. Effect of insulin on glycogen synthesis in fetal rat liver in organ culture. Eisen HJ, Glinsmann WH, Sherline P.
    • Any guesses anyone?  Yup, some thing from Endocrinology
  • Paper #4 :
    • Proc Natl Acad Sci U S A. 1973 Dec;70(12):3454-7. Regulation of hepatic glycogen synthesis during fetal development: roles of hydrocortisone, insulin, and insulin receptors. Eisen HJ, Goldfine ID, Glinsmann WH.
    • Hooray. Kudos to PNAS for doing the right thing and making older papers available for free via Pubmed Central
That is where I am stopping for now.  Will keep working on this over the next few weeks. 

Freeing my father's publications part 2




Well, it is Father's Day.  And inevitably I end up thinking about my father, who passed away in 1987.  As part of wanting to keep the memories of my father alive, every Father's Day I end up thinking at least a little bit about my father's scientific work.  He was an MD who did research at the NIH, focusing mostly on glucocorticoid receptor's and related topics.

In 2008 I wrote a post about how I was struggling to "free" his publications so at least people could see them, if they wanted to.  See Freeing My Father's Scientific Publications and then an update here Freeing My Father's Scientific Publications Update

But inevitably, as with most things in life, I got busy and never ended up finishing this activity.  And so I am back to it again in 2010.  And I am still struggling to do this.  The fact that papers by my father, published some 20-40 years in the past, are still not all available is indicative in part of the broken state of scientific publishing.  For example, many of his papers are available electronically, but are behind some pay wall from a publisher that limits access (I made a list of many of his papers here: CiteULike: Group Papers by my father, Howard J. Eisen)

I do not think that this is what NIH or taxpayers envisioned when they supported his work -for it to basically be lost due to greed.  And as my brother pointed out in a comment on one of those posts from 2 years ago - since my father worked for the NIH his publications should be free anyway, in terms of government employees not being allowed to sign over copyright.

So I am going to at least do what I can to free them up and make them known.  My main plan is to get PDFs of all the papers (some I can download, others I will have to scan myself),  and create a "personal" website to distribute all of them.  Hopefully these will get picked up by Google Scholar.  And I am going to explore whether there are better ways to get these papers in the public domain.  I am also going to try to do whatever else I can to get his work into the public domain - it seems like the least I can do to honor his memory.

-----------------------------------------

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:

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