Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

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. 
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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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Freeing my father’s publications part 2

http://picasaweb.google.com/s/c/bin/slideshow.swf

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.

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http://friendfeed.com/treeoflife/895d1026/freeing-my-father-publications-part-2?embed=1

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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

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

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

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

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

THERE IS NO FU*$ING EVOLUTIONARY LADDER.

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

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

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

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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.

    ——–

    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.
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    Here are some links about the UC-Nature dust up

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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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    Electronic lab notebook systems update 2

    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.

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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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    Possible electronic lab notebook systems – update

    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

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    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.


    FriendFeed had a wealth of useful information:



    http://friendfeed.com/treeoflife/f9791f25/am-looking-for-systems-my-lab-to-make-electronic?embed=1


    Also got some useful feedback from Eric Alm on Facebook who said they use Smart pens from LiveScribe.com

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    Slides and audio from my talk at #ASMGM

    Slides and audio from my talk at ASM General Meeting

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

    View more webinars from Jonathan Eisen.
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    Archaea in the news – a growing trend

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

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    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

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

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


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

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

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

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

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

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

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

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

    ResearchBlogging.org

    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

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