Category: Misc.

Archaea get no respect from the New York Times

There was kind of funny and certainly interesting article in the New York Times on June 4: Greening the Herds – Trying to Limit Cows’ ‘Emissions’

The article by Leslie Kaufman discussed how there are attempts in some dairy farms in the US to change the diet of cows to reduce their methane output. The methane is a strong greenhouse gas and in total cows make a surprisingly large global contribution to greenhouse gases. The article states:

Cows have digestive bacteria in their stomachs that cause them to belch methane, the second-most-significant heat-trapping emission associated with global warming after carbon dioxide.

Alas, this is not correct. Yes, bacteria in the cow rumen contribute to the production of methane. But they do not make the methane. The methane is made by archaea (for those not in the know, archaea are a distinct group of organisms relative to bacteria – they resemble bacteria in many ways but are a separate branch on the tree of life). For those of us who study archaea this is a major slight. A diss. A taunt. A sad day. And all those other things. Not sure how we archaea fans will have our revenge but I swear we will. Too bad Carl Zimmer does not think that this is important enough to go on one of his newspaper fact chekcing investigations.

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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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David Byrne on Bicycling and Davis in the New York Times

For those of you who are obsessed with bicycling (like me), and live in bicycling heaven Davis, CA, and occasionally look at the New York Times, you may have noticed this already. But for others who have not I want to call your attention to a book review in the New York Times this past Sunday by David Byrne Book Review – ‘Pedaling Revolution – How Cyclists Are Changing American Cities,’ by Jeff Mapes – Review – NYTimes.com.

Amazingly this is indeed the same David Byrne of them Talking Heads. It turns out he has a book coming out in the fall called “Bicycle Diaries.” Anyway he reviews this book on the effect of bicyclists on American Cities and right there in the review are some props for my town, Davis, CA. The article is worth checking out and I will both be buying this book and awaiting Byrne’s. Maybe we can have a reading here in Davis when the Bicycling Hall of Fame opens its doors.

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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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Junk mail and trash associated with science

Just got back from the ASM Meeting that was in Philly last week.  It was good and bad – and will write more about it soon.

But what I am writing about now relates to an annoying part of the meeting.  It seems ASM has sold my name/address to various entities since I have been receiving a significant amount of junk/trash advertising things associated with microbiology.  I am sure ASM gets some $$$ out of this, but at what cost to the world?  The last thing I want is more trash and there seems to be no way to say no to this.  
And on top of it, many science related publications also seem really keen on wrapping themselves in plastic.

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

In this case I am showing Nature Methods and the ASM Microbe and even the HHMI magazine  wrapped in plastic. Bad Nature. Bad ASM. Bad HHMI.  Sure there may be reasons for this (e.g., maybe they have an insert), but there must be non plasticy solutions.  And fortunately the news from the JDRF has no plastic. Good JDRF.  Here’s to sciency publications getting a little greener.

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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 science education resource: HHMI Cool Science

Just a quick one here. Was reading the HHMI Bulletin and saw a note about this web site they have set up on science education (see Cool Science: Home). It has all sorts of goodies for educators, kids, and others. Some of my favorite things there in looking so far include material from the Genome Consortium for Active Learning (GCAT) and the Biointeractive page. YAGTFH (Yet another good thing from HHMI).

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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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Got phylogeny?

For an obsessed evolutionary biologist, it is always good to see “Need phylogeny” on the blackboard while sitting through a faculty meeting.
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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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Very strange "permission" form to use my name in a story

I just got a request from a fact checker for a publication who wanted to reference my April 1 joke on Brain Doping in a story (I was not interviewed for the story).  And they wanted me to sign over some rights associated with them using my name.  The text of the form is below.  I have been quoted and written about and even had my picture in places like the Scientific American, the New Yorker, US News and World Report, USA Today, PLoS Biology, Nature, Science, blogs, etc and not once has anyone sent me such a form.  Anyone seen anything like this?  

For good and valuable consideration, the receipt of which is hereby 

acknowledged, I, ___________________________ (“Subject”), hereby irrevocably grant 

to XXXXXXXXXXXX, and YYYYYYYYYYYYYY , the absolute right 

and permission to publish my name and/or photograph or likeness and/or statements 

(either in part or in their entirety) in: (a) the publication, ZZZZZZZZZZZZZZ, that ,

 (including all print and digital versions), (b) reprints of the article, including excerpts thereof, 

in which Subject’s name and/or photograph or likeness 

and/or statements originally appeared (including all print or digital versions) and (c) 

promotional materials relating to ZZZZ, YYYY, XXXXX, in any and all media. 

  

In the event this Consent & Release cannot by signed by the Subject, the undersigned represents that 

he/she is fully authorized by Subject to grant the rights herein.  

 

Subject agrees that electronic signatures shall have the same force and effect as original signatures. 

  

________________________________________________ 

Print Name 

________________________________________________ 

Signature 

________________________________________________ 

Address 

________________________________________________ 

City/State/Zip Code 

________________________________________________ 

Telephone 

________________________________________________ 

Email 

________________________________________________ 

Date 

 

 

he/she is fully authorized by Subject to grant the rights herein.  


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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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Is it a faux pas to wear the same T-shirt as another professor when you like the shirt?

No plans to wear the same shirt as Marc Facciotti who is another faculty in the UC Davis Genome Center (who by the way does brilliant stuff on gene regulatory networks in yeast and halophilic archaea). But there we were in our Hamsters Love PLoS shirts. And rather than run away in shame, I begged Lizzy Wilbanks, a grad. student, to take this picture (and note the picture of Harold Varmus, Pat Brown and my brother Michael Eisen from the Genome Technology cover in the background …)

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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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New Web Resource on Evolution … EvolverZone

Looks like T. Ryan Gregory, who writes the GenoMicron blog has evolved … he has released a new web resource on evolution – Evolver Zone. Clearly still a work in progress, it has some good collections of links to videos, journals, books and other materials about evolution. Worth checking 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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Must reading for those interested in Open Science – Michael Nielsen on "Doing Science in the Open"

Not much for me to add here other than to tell everyone interested in Open Science that you should look at Michael Nielsen’s article: Doing science in the open – physicsworld.com. It covers a wide range of topics from secrecy to journals to the internet to online commenting to wikipedia to collaboration to FriendFeed. It has lots of interesting points in there. Hat tip toDavie Bacon / The Quantum Pontiff.

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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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Elsevier, fake medical journals, and yet another reason for #openaccess

For those of you not in the loop on this there is a bubbling story going around the web and in some news sources about Elsevier publishing fake science/medical journals for hire. First reported by The Scientist (as far as I can tell), the story just seems to get worse and worse. Basically, it seems one branch of Elsevier published a series of journals that were little more than advertisements for Merck products while pretending to be independent journals.

The whole thing is pretty sad. The head of Elsevier as well as multiple people that have worked at Elsevier seem to have not been aware of that these were being used to pretend they were real journals. But I think one this is abundantly clear – we can cross of the list of criticisms of Open Access publishing that the costly non open access journals and publishers are protecting the world from bad science. Instead, it seems like they are in fact explicitly and purposefully pushing bad science and medicine in order to make extra money. Lovely.

For more informaiton on the story see for example, Kate McDonald in the Australian Life Scientist (see Elsevier published fake medical journals – Elsevier Australia, Merck, Vioxx – Australian Life Scientist). In this article she reports:

The CEO of Elsevier’s Health Sciences division in the US, Michael Hansen, has now issued a statement admitting the company’s Australian office published six journals paid for by pharmaceutical companies.

Also see for example Forbes (via AP). The best source on this has been the Bloggosphere where there were a large number of discussions including

My favorite source so far has been Bill Hooker at Open Reading Frame who did some really useful digging into the details of what was being published. After his posting there has been an interesting discussion on FriendFeed (see embed below)

http://friendfeed.com/billhooker/6907bac6/no-bottom-to-worse-at-elsevier?embed=1

There also has been some other discussion on FriendFeed including the following from a Graham Steel posting:

http://friendfeed.com/mcdawg/9b919af7/statement-from-michael-hansen-ceo-of-elsevier?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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