Category: Misc.

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.

——–
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.

——–

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

——–
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.

——–

Research council of UK gives additional thumbs up for open access publishing

The RCUK (Research Councils of the UK) has published a new report on open access (see RCUK publishes report on open access study):

The purpose of the study was to identify the effects and impacts of open access on publishing models and institutional repositories in light of national and international trends. This included the impact of open access on the quality and efficiency of scholarly outputs, specifically journal articles. The report presents options for the Research Councils to consider, such as maintaining the current variation in Research Councils’ mandates, or moving towards increased open access, eventually leading to Gold Standard.

…

In response to the study, the Chief Executives of the Research Councils have agreed that over time the UK Research Councils will support increased open access, by:

  • building on their mandates on grant-holders to deposit research papers in suitable repositories within an agreed time period, and;
  • extending their support for publishing in open access journals, including through the pay-to-publish model.

Hat tip to Karla Heidelberg for pointing this out.

——–
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.

——–

Public Lecture on Population Genomics at Davis Today

Once each year the Davis Division of the Academic Senate selects a Faculty Research Lecturer, who gives a public lecture under the auspices of the Chancellor and the Chair of the Davis Division. The lecturer is singled out for the distinction of their scholarly research, chiefly for efforts carried out while a member of the Davis faculty.

The Faculty Research Lectureship is the highest honor the Davis Division of the Academic Senate accords its members.

Please join us this evening as the campus honors our distinguished colleague

Charles “Chuck” Langley

Distinguished Professor

&

2009 Faculty Research Lecturer

Wednesday May 6, 2009

4:00 – 5:00 p.m.

A reception sponsored by Ken Burtis, Dean of the College of Biological Sciences, and

Maureen Stanton, Chair of the Department of Evolution and Ecology will follow the lecture.

Activities & Recreation Center (ARC) Ballroom

BioSci_Sig_Horizontal_emailsig (2)

Events Coordinator Office of the Dean

202 Life Science Davis, CA 95616

phone 530.752.2358 fax 530.752.2604

——–
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.

——–

Public Lecture at Davis Today – Chuck Langley on "Population Genomics"

Once each year the Davis Division of the Academic Senate selects a Faculty Research Lecturer, who gives a public lecture under the auspices of the Chancellor and the Chair of the Davis Division. The lecturer is singled out for the distinction of their scholarly research, chiefly for efforts carried out while a member of the Davis faculty.

 

The Faculty Research Lectureship is the highest honor the Davis Division of the Academic Senate accords its members.

 

Please join us this evening as the campus honors our distinguished colleague

Charles “Chuck” Langley

Distinguished Professor

&

2009 Faculty Research Lecturer

 

Wednesday May 6, 2009

4:00 – 5:00 p.m.

 

A reception sponsored by Ken Burtis, Dean of the College of Biological Sciences, and

Maureen Stanton, Chair of the Department of Evolution and Ecology will follow the lecture.

 

Activities & Recreation Center (ARC) Ballroom

 

 

 

BioSci_Sig_Horizontal_emailsig (2)

Events Coordinator   Office of the Dean

202 Life Science   Davis, CA 95616

phone 530.752.2358   fax 530.752.2604

——–
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.

——–

Seeking information on undergraduate programs/majors in genomics and/or genome biology?

I am looking around to find examples of undergraduate programs/majors in genomics or genome biology.  I got a couple of potential examples from a post I made on friendfeed but am looking for more.  What I am looking for is not just courses in genomics but majors/programs in genomics … do they exist and if so, where and what do they look like.  Any information would be helpful.  Here is what I have found so far:

——–
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.

——–

Francis Collins Launches Biologos – a strange re-working of theistic evolution

Biologos.  All I can say is, well, I am just really baffled by the whole thing. I am all for trying to have discussions about science and religion. But I do not think the two topics are really compatible in the sense of merging them together. Science (and medicine) should be about, well, science. And religion can be about whatever it wants to be. And when we can get religious and scientific leaders together to talk about the implications of each area on the other and on the world, fine too.  But merging the two together into one hybrid such as Christian Science and Creation Science?  Not for me.
Thus it is with some horror that I have been browsing the web site for Francis Collins’ new The BioLogos Mission | The BioLogos Foundation (f0r some other discussions of it see e.g., Larry Moran’s discussion here, and PZ Myers here and Time Magazine here and US News here). BioLogos appears to be Collins attempt to promote a slight variant of “theistic evolution” which he has been discussing for years and is also in his recent book.
And whatever you may think of theistic evolution, the Biologos version of it is just icky in many ways in my mind. For example, the site has many many links and pointers to books authored by the members of the Foundation (e.g., the front page says “Among other resources, this website posts responses to many of the questions received by Collins, Giberson, and Falk since the publication of their books, including: The Language of God; Saving Darwin; and Coming to Peace With Science.”) There are also other links to this page with ads for their books. Not that there is anything wrong with selling ones books, but to have a foundation whose purpose seems in a large part to promote one’s books really seems distasteful. 
And the details of Collins attempt to merge science and religion into a version of theistic evolution are really unclean.  Basically, he is trying to argue that on the one hand science and religion are completely separate activities (I support this) but at the same time argues that God can intervene in the setting up of natural laws and in providing some guidance here and there in order to, for example, produce human beings in his image.  
The web site repeats some things from Collins book that are equally illogical – such as saying that altruism can be explained by science (and even specifically saying that science is the way to explain the natural world) but then turning around and saying that science cannot explain extreme forms of altruism (and therefore implying that actually, the natural world cannot be explained by science).  Which is it?  Is science for the natural world or not?
What one wants to believe in terms of faith/religion is a highly personal issue.  But trying to both say that science and religion are completely separate but also that they are not is just completely illogical.  
UPDATE: See also:

——–
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.

——–

Worst new omics word award: ethomics

Well, look at what I just saw on twitter:

tlemberger omics mania: ‘ethomics’ http://is.gd/wOcg – should be added to http://omics.org/ but perhaps also nominated for this http://is.gd/g2Bc

That is from Thomas Lemberger and so I followed the last link first, since I thought I might be to, well me. And indeed it was a link to my “Worst new omics word award” for museumomics.

And so then I went to the link on ethomics: High-throughput ethomics in large groups of : Drosophila : Abstract : Nature Methods.
And indeed they use “ethomics” – what is clearly a quite new omics word (only 62 google hits as of this PM). I confess, I stopped reading at the abstract because it was just too much:

We present a camera-based method for automatically quantifying the individual and social behaviors of fruit flies, Drosophila melanogaster, interacting in a planar arena. Our system includes machine-vision algorithms that accurately track many individuals without swapping identities and classification algorithms that detect behaviors. The data may be represented as an ethogram that plots the time course of behaviors exhibited by each fly or as a vector that concisely captures the statistical properties of all behaviors displayed in a given period. We found that behavioral differences between individuals were consistent over time and were sufficient to accurately predict gender and genotype. In addition, we found that the relative positions of flies during social interactions vary according to gender, genotype and social environment. We expect that our software, which permits high-throughput screening, will complement existing molecular methods available in Drosophila, facilitating new investigations into the genetic and cellular basis of behavior.

For trying to extend omics to ethogram and beahvioral plots I am giving my second coveted “worst new omics word award” to Kristin Branson, Alice A Robie, John Bender, Pietro Perona & Michael H Dickinson. Here is a prediction – ethomics will not become widely used – not soon – not ever. Thanks for pointing this one out Thomas.

——–
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.

——–

Worst new omics award: ethomics

Oops – posted this to the wrong blogspot blog.  Please go to my Tree of Life blog to see this post here.  
——–
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.

——–

Oops. Seems like Davis, CA does not have the swine flu, yet.

See :
Probable swine flu cases in Yolo County found to be human flu – Daily Democrat Online
and News 10 and KCRA

——–
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.

——–