Tag: Misc.

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.

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    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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    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.
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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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    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

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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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    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

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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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    Open access: getting more & more support incl. from #UCDavis

    Everyone interested in science should take a look at the press release from the “Alliance for Taxpayer Access.” The release discusses how “Major research institution leaders support legislation to ensure public access to publicly funded research”. I am quoting much of the release here because I think it is very valuable:

    The provosts and presidents of 27 major private and public research institutions have voiced their support for the Federal Research Public Access Act in an “Open Letter to the Higher Education Community,” released Friday by the Harvard University Provost. The Act, first introduced in the Senate last year, was introduced in the House of Representatives on April 15. The letter signals expanded support for public access to publicly funded research among the largest research institutions in the U.S.

    The letter reads, in part:

    “As scholars and university administrators, we are acutely aware that the present system of scholarly communication does not always serve the best interests of our institutions or the general public. Scholarly publishers, academic libraries, university leaders, and scholars themselves must engage in an ongoing dialogue about the means of scholarly production and distribution. This dialogue must acknowledge both our competing interests and our common goals. The passage of FRPAA will be an important step in catalyzing that dialogue, but it is not the last one that we will need to take.

    For the full letter see “The Open Letter to the Higher Education Community” is available at http://osc.hul.harvard.edu/docs/FRPAA-open-letter-2010.php.

    I am very very happy to note that UC Davis is one of the signatories (represented by Provost Enrique Lavernia).  This is a good change of pace as one of our previous vice-provosts Barbara Horwitz was an extreme anti-open access advocate.

    And if you want your institution to be added to the list of supporters, talk to your administrators and get them to register their support here.  Seems to me that many should want to get on board.

    Hat tip to Michael Rogawski from the UC Davis Department of Neurology for pointing this out.

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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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    Good kids activity around Davis: Aerospace Museum of California

    Good time today with my kids at the Aerospace Museum of California. Just East of Sacramento – with a nice facility, great outdoor playground, and lots of plances and satellites and rockets and other things. My kids loved it. Here are some pics:

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

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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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    Quick one here: nice pic of "Earth From Mars" from NASA

    Just a wee bit humbling here. H/T to Andy Fell.

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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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    Protect that biodiversity – wear protection

    Here are some pics of some biodiversity protecting devices seen around here ..

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

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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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