The Tree of Life: June 2010

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

By Jonathan Eisen .. 6/28/2010 11:33:00 AM

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

By Jonathan Eisen .. 6/23/2010 10:30:00 AM

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

By Jonathan Eisen .. 6/21/2010 02:17:00 PM

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

By Jonathan Eisen .. 6/20/2010 09:13:00 PM

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

By Jonathan Eisen .. 6/12/2010 03:52:00 PM

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"

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

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

By Jonathan Eisen .. 6/11/2010 07:47:00 AM

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

John Timmer: California libraries gearing up for fight against Nature
SFist: UC Librarians Get Politely Vicious About Being Gouged for Subscriptions
Chronicle for Higher Ed: U. of California Tries Just Saying No to Rising Journal Costs
Times Higher Education: Librarians at the gate over licensing rate
UCLA: UC libraries, faculty protest planned price hike by Nature publisher
Nature Blog UC threatens 'systemwide boycott' of Nature Publishing Group
Chronicle for HIgher Ed: Nature Publishing Group Defends Its Price Increase for U. of California
Support for UC-Nature ban - The Scientist
Sandwalk: Nature vs. The University of California
UC librarians urge boycott of Nature journals - ContraCostaTimes.com
Christina's LIS Rant: Nature Publishing Group and the University of California – Some ...

Electronic lab notebook systems update 2

By Jonathan Eisen .. 6/08/2010 01:46:00 PM

Some more suggestions on electronic lab notebooks (see previous post for more detail).

The friendfeed discussion is extensive so check there for more information too.

Possible electronic lab notebook systems - update

By Jonathan Eisen .. 6/07/2010 08:38:00 PM

Well, I opened up a great can of worms today with a Twitter/Friendfeed post:

"Am looking for systems for my lab to make electronic lab notebooks - suggestions? wiki? OWW? software?"

And have gotten some great responses so far from my various social networking circles and I thought I would centralize them here. At the bottom I will post some of the raw responses. Here is a current summary

Suggested things to look at so far

Basecamp
Evernote
Word documents in notebook layout
Circus ponies notebook
Google docs and Dropbox
WordPress blogs, versioned, subscribe to RSS feeds of your student's work, HUGE GPL community.
Ontowiki
Open Wet Ware
SmartPens such as ones from LiveScribe
Google wave

------------------------------------
From Twitter:

iddux @phylogenomics basecamp
srhymes @phylogenomics have you tried Evernote? I use that for a lab notebook and love it! And it syncs across home, work, iphone, iPad...
MeadGal @phylogenomics I like a word document in notebook layout. I tried labassistant from mekentosj and i see it working for some, just not me.

iGenomics @phylogenomics Depends on what you want. We've developed a software -BioRhythm to track Bioinformaics project progress like twitter a msg.
kbradnam @phylogenomics How important is sharing, cross-platform accessibility, and offline access?
phylogenomics @kbradnam #1 = ease of use, #2 = sharing, #3 = cross platform
kbradnam @phylogenomics Evernote would work well in some ways (cross platform, desktop + phone clients etc), but it stores data in its own format…
kbradnam @phylogenomics But the exporting options for Evernote are a bit weak. See http://bit.ly/zRx1
jobadge @phylogenomics @kbradnam @richardbadge uses a wiki on our VLE Blackboard as lab book http://ff.im/lDrSf
rachelss @phylogenomics Try Circus Ponies' Notebook
kbradnam @phylogenomics Here is a list of many online notebook tools (http://bit.ly/8jK9), though I think a wiki or Evernote would also work well.
kbradnam @phylogenomics We use Google Docs & Dropbox a lot in our lab. I'm hoping that HTML5 will eventually bring syncing of docs to a local DB.
jrmiller2 @phylogenomics google wave seems ideal
Miss__Tina @phylogenomics I'm on a internal review committee for this kind of stuff for one of my pharma clients. It's a nightmare.
phylogenomics @Miss__Tina Couldn't agree more; been looking at this for years & nothing jumps out at me yet
Miss__Tina @phylogenomics We also have 2 separate US docs from rest of world docs when they use the cmputr kiosks. Not allowed 2 read the same stuff.