Human evolution prize – Congrats to Spencer Wells

Kyung M. Song in the Seattle Times reports that Spencer Wells has won a relatively unknown but quite lucrative prize ($100,000) for his work on the human Genographic Project (see this article in the New York Times by Amy Harmon for more information on this project)

I love the lead in to the story

“Nearly half of all Americans reject the theory of evolution, with many believing instead that humans were created by a higher power. But for more than a decade, a little-known nonprofit based in Bellevue has promoted scientific research into the evolution of the human genome — and dispensed money to spread the knowledge.”

Apparently the “Foundation For the Future” is big on human evolution having awarded their Kistler Prize (named after the Foundations founder Walter Kistler) to the likes of Richard Dawkins, E O. Wilson, etc. Congratulations to Spencer, who I still owe for giving me some excellent advice (when I was an undergraduate and he was a graduate student) about people to work for in graduate school (which I ignored, but it was still excellent advice).

Enough about Spencer — The Times reports that

the foundation wields its $25 million endowment to support an array of scientific endeavors, awarding prizes for books, documentaries and teaching.

Hey – what about for blogs?

Evolution for Goodness Sake

Generally, I like the articles Nick Wade writes for the New York Times on science. In fact, I like them so much that I used his work as a template for my April 1 joke about Craig Venter sequencing his own microbiome. But I cannot help but feel that he really punted a bit in his article today entitled “Is ‘Do Unto Others’ Written Into Our Genes? ” The article is mostly about new work by Jonathan Haidt, who has written about “evolutionary views of morality”

I will skip for now discussing my opinions on the meat of the article Haidt’s work. But what irked me about Wade’s article was the beginning. The article opens with

“Where do moral rules come from? From reason, some philosophers say. From God, say believers. Seldom considered is a source now being advocated by some biologists, that of evolution.

At first glance, natural selection and the survival of the fittest may seem to reward only the most selfish values. But for animals that live in groups, selfishness must be strictly curbed or there will be no advantage to social living. Could the behaviors evolved by social animals to make societies work be the foundation from which human morality evolved?”

I have two problems with this lead in. First, it implies that altruism and related behaviors evolved “to make societies work.” This of course is not accurate. Yes, their existence allows societies to work, but they did not evolve to make societies work. Evolution does not have a drive to make societies work. It is a subtle distinction perhaps but an important one.

Second, and more important to me, the introduction could be interpreted as implying that the evolution of altruism itself is not well studied and/or is being debated. This does not appear to be what Wade means (when he says “Could the behaviors evolved by social animals to make societies work” he means in part, “Given that altruism and other social behaviors evolve …”).

However, in discussions I have had with many people about this article they thought Wade was saying the evolution of altruism itself is under debate. If many people are coming away from Wade’s article with this impression that is too bad since the evolution of altruism is well studied (there is a great book on this topic called “The Altruism Equation” by Lee Alan Dugatkin – a good blog about the book is one by Jason Rosenhouse here).

The evolution of altruism is one of my recent pet peeves since it was treated so poorly by Francis Collins in his recent book “The Language of God.” In his book, which has some good discussion of how science and religion should be considered separate areas of study, Collins says that since evolution has been unable to explain altruism, therefore God must exist. This not only contradicts his own discussion in the book on how one should not use a “God is in the gaps argument” as evidence for religious beliefs , but it is simply wrong – evolutionary theory can explain altruism (see the Dugatkin book for more detail).

Note I am not saying anything here about whether I think God or gods exist. I personally believe religion and science can and should be separate fields. But certainly, one cannot use misleading references to non-existent gaps in evolutionary biology as evidence for the existence of one’s own personal view of God/gods.

So – to sum up a way to long blog — altruism can be explained by evolutionary biology and if people say otherwise (i.e., Collins) or could be interpreted as implying otherwise even if they do not mean to (i.e., Wade), don’t believe it.

Faculty Position in Quantitative Phylogenetics/Comparative Methods in the Section of Evolution and Ecology at U. C. Davis

To all evolutionary biologists or people working on phylogenetics/comparative methods. There is a faculty position available in the Section of Evolution and Ecology at U. C. Davis. U. C. Davis was ranked #1 in the country for graduate programs in Evolution and Ecology in 2006. It is a great school with lots of cool stuff going on in evolution and ecology as well as all aspects of the life sciences. The posting is below:

Quantitative Phylogenetics/Comparative Methods

Quantitative Phylogenetics/Comparative Methods, UNIVERSITY OF CALIFORNIA, DAVIS — The College of Biological Sciences, University of California, Davis invites applications and nominations for a tenure-track position in the Section of Evolution and Ecology at the ASSISTANT PROFESSOR level. Candidates must have a Ph.D. (or equivalent) in the biological sciences or related fields. Candidates should have a strong record of research applying phylogenetics to problems in evolution and/or ecology. We will give particular attention to applicants who are both developing and applying quantitative phylogenetic methods. The successful candidate will be expected to teach in the section’s undergraduate program and the graduate program of the Population Biology Graduate Group. Applicants should submit materials online at http://www2.eve.ucdavis.edu/jobs/. These should include: curriculum vita, description of current and projected research, summary of teaching interests and experience, and up to five publications. Applicants should also arrange to have three referees submit supporting letters online at the above website. Closing Date: Open until filled, but all application materials, including letters of recommendation, must be received by October 15, 2007, to assure full consideration. Administrative contact: Barbara Shaneyfelt (bashaneyfelt@ucdavis.edu). Faculty contacts: Bradley Shaffer and Peter Wainwright. The University of California is an Equal Opportunity/Affirmative Action Employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and respect for differences.

An Anti Anti-Evolution Petition to reclassify non-science books from science categories in bookstores and libraries

Just got forwarded this email that I thought would be worth posting

All:

The graduate students at my institution (Portland State) have created an online petition
to reclassify non-science books from science categories in bookstores
and libraries. To quote from the first paragraph of their petition:

“As scientists, we feel strongly that categorizing Intelligent Design
(“ID”) as science is both inappropriate and misleading. Local bookstores
and libraries unintentionally exacerbate this misleading categorization
when they shelve ID books and legitimate science texts in the same
section . Our goal is to convince the U.S. Library of Congress to
re-classify ID books into sections other than the science section.”

If this is something about which you feel strongly (or even are
lukewarm!), I urge you to support their petition. Check URL:
http://www.sciencea2z.com/z_etomite/

Quick bite – Recent interesting evolution papers in PLoS Journals

There have been a slew of interesting evolution papers recently in PLoS journals. Here are some

RNA based metagenomics – bee CCD study suggests a way to survey all microbes at once

After being reprimanded justifiably by one of the authors of the recent paper on bee colony collapse disorder (for a blog I posted and then removed) I have come to realize they used a very interesting approach to metagenomics that I have not seen used extensively before.

Their paper can be found here.

Here is the problem they were faced with – how to survey an sample for ALL the microbes present including both viruses and cellular microbes. The challenge to this is that some viruses have RNA genomes and thus if one simply extracts DNA and sequences it one will not sample any of the RNA viruses. One approach to such a challenge would be to isolate RNA and make cDNA and sequence to sample the RNA viruses. And then to separately isolate DNA and then sequence it either directly (using shotgun sequencing) or indirectly by first amplifying genes with PCR.

They chose a different approach – to isolate RNA and make cDNA and then sequence it. In doing this they in fact do get a sample of both RNA viruses AND cellular organisms. For cellular organisms, since most of the RNA in a cell is ribosomal RNA they get a sample of that organisms rRNA which can be used to say what type of organisms are present. Thus in one fell swoop they in essence sample ALL the microbes present in a sample. I had blogged about this and criticized them because they did not explain in the paper or in the press releases all of this logic, but one of the authors set me straight so I deleted my blog. Then I started thinking about it and realized that this seemed to be a relatively novel approach to metagenomics.

Now – I am not sure if this method is quantitative or exactly how robust it is, but it does provide an alternative to rRNA PCR (which has all the biases of PCR) and also provides an alternative to separately sequencing RNA and DNA from a sample. Certainly many have used RNA to cDNA and then sequencing to survey RNA viruses before. But usually they do this in material in which the cellular organisms have been first removed so that one does not get overwhelmed by the RNA from those organisms. But here, they used the power of massively high throughput sequencing and turned this “problem” of getting RNA from cellular organisms on its head and used it to sample RNA viruses and cellular organisms at the same time.

I do not know if this has been done before — maybe other out there know of examples. But whether or not it has been done before, it is an important approach that should be considered in metagenomic surveys and it also suggests that ANYONE doing metagenomic surveys of microbes might want to purify RNA and save it form samples even if one is going to first focus on DNA.

Retraction – I was buzzing off about bees before my time

Recently I wrote a post about the recent study on bees associated with colony collapse disorder. After receiving a well thought out email from one of the authors on the study I have decided to retract my blog and apologize to the authors of the bee study. I rushed out my blog without really considering the evidence and the data very carefully and accept that I screwed this one up big time. The study is much more complex and comprehensive that I led people to believe. In part this was due to lack of detail in the actual manuscript but alas most of the fault lies with me – in not trying to contact the authors for more detail before mouthing off.

So I am giving myself a new award – the genomic jerk award. Hopefully there will be no more recipients.

Metagenomics 2007 presentations available

For those interested in metagenomics, the Metagenomics 2007 meeting (also see Konrad’s blog) has posted video and pdf’s of most of the presentations. You can get everything at the CAMERA web site here. I have posted links and titles below:

Larry Smarr [video] [PDF]

Masahira Hattori, Tokyo University/RIKEN
Length: 56:30 [video] [PDF]

Paul Gilna, UCSD
Length: 5:55 [video]

Jed Fuhrman, University of Southern California
Length: 1:04:01 [video] [PDF]

Dawn Field, Oxford Centre for Ecology and Hydrology

Length: 27:05 [video] <!–[video]–> [PDF]

Janet Jansson, Swedish Univ of Agricultural Sciences
[PDF]

James M. Tiedje, Michigan State University
Length: 27:09 [video] [PDF]

Breakouts:

Medical Metagenomics
Human Biology
Chair: Trevor G. Marshall, Autoimmunity Research Foundation
Speaker: Peter J. Turnbaough, Washington University
Length: 49:32 [video] [PDF]

Computational Metagenomics
Ontology and Standardization
Chair: Jonathan Eisen UC Davis
Length: 44:18 [video]

Discovering opportunity for Bioenergy
Chair: Phil Hugenholtz, JGI
Speaker: Yuri Gorby, JCVI

Length: 50:45 [video] [PDF]

Modeling the natural world
Chair: Trina McMahon, Univ. of Wisconsin-Madison
Speaker: Patrick Schloss, UMass Amherst

Length: 1:00:36 [video] [PDF]

Evolution and population
Chair: Francisco Rodriguez-Valera, Universidad Miguel Hernández in Alicante

Length: 1:00:36 [video]

John Wooley, UCSD (Moderator); various speakers
Length: 40:47 [video]

Metagenomic analyses of corals
Forest Rohwer, San Diego State University
Length: 21:15 [video] [PDF]

Population structure of microbial communities in the world’s oceans
Mitchell Sogin, Marine Biological Lab, Woods Hole
Length: 41:20 [video] [PDF]

Structural metagenomics: Lessons from the first experimentally characterized GOS proteins
Adam Godzik, Burnham Institute
Length: 46:35 [video]

Detailed view of the architecture and implementation of a metagenomics server
Philip Papadopoulos, UC San Diego/SDSC
Length: 24:27 [video] [PDF

Metagenome sequence data management and analysis
Victor M. Markowitz, Lawrence Berkeley National Lab
Length: 34:25 [video] [PDF]

Developing a software workbench for marine ecological genomics
Frank Oliver Gloeckner, Max Planck Institute for Marine Microbiology
Length: 32:39 [video] [PDF]

The Metagenomics RAST server: Automated analysis of Sanger and 454-type metagenomes
Folker Meyer, Argonne National Laboratory
Length: 17:00 [video] [PDF]

Technologies for metagenomics selection and sequencing
Gautam Dantas, Harvard University
Length: 33:30 [video] [PDF]

Micro-Mar: A database for dynamic representation of marine microbial diversity
Ravindra Pushker, University College Dublin
Length: 32:00 [video]

Conclusion
Kayo Arima, UC San Diego
Length: 2:16 [video]

Calling for a Boycott of of AAP – Association of American Publishers

If you have not seen the wonderful news about the latest anti Open Access initiative called PRISM, well you should surf around the blogosphere a bit. PRISM is a group started by the AAP – the Association of American Publishers that – there is no nice way to put this – is a sad stage in the evolution of publishing. Basically, it is a Macarthy-Era ripoff where Open Access is the new evil that communism once was. And everything wrong with the world is in essence blamed on the Open Access movement. For more detail on PRISM, and what is wrong with it, including the pirates use of copyrighted material, see some of these links:

I think academics and the public need to fight back against this attempt to mislead the public about the issues surrounding Open Access publishing. And one way to fight back is to recommend that the members of AAP drop out or request termination of the PRISM effort. So here is a list (see below for the full list) with links of the members of AAP. If you are involved or have connections to any of these groups, consider writing or calling them and suggesting they reconsider involvement in AAP. Look, for example at all the University presses. If they do not back out of PRISM we should consider launching a boycott of AAP members.

Full list of AAP from the AAP web site:

Absey & Company, Inc.

Academic Innovations

Academic Learning Company, LLC

Academy 123, Inc.

Academy of Management

Aequus Technologies Corporation

Al-Basheer Publications and Translations

Algora Publishing

American Academy of Pediatrics

American Academy Ophthamology

American Association of Cancer Research

American Association of Pharmaceutical Scientists

American Chemical Society

American Foundation for the Blind

American Geophysical Union

American Institute of Aeronautics and Astronautics

American Institute of Physics

American Mathematical Society

American Medical Association

American Psychiatric Publishing, Inc.

American Psychological Association

American Scholars Press, Inc.

American School of Classical Studies at Athens (The)

American Scientific Publishers

American Society of Clinical Oncology

Ames On-Demand

Apex CoVantage

Apex Learning, Inc.

Appalachian Trail Conference

Ardor Scribendi, Ltd.

ASIS International

Association for Computing Machinery (ACM, Inc.)

Association of Research Libraries

Athena Media, Inc.

Atypon Systems, Inc.

AV Book Publishers, Inc.

Avon Books/Harpercollins Publishers

Banta Company

Barnhardt & Ashe Publishing, Inc.

Barricade Books, Inc.

Baseline Development Group

Baydell & Brewer, Inc.

BBC Motion Gallery

Beacon Group, The

Beacon Publishing Services

Berkery, Noyes & Co.

Berkshire Publishing Group, LLC

Black Dome Press Corp.

Blackwell Publishing

Bloomberg Press

Booklight, Inc.

Books International, Inc.

Booktech.com

British American Publishing

Brookings Institution (The)

Brown Publishing Network, Inc.

Cadmus Professional Communications

Cambridge University Press

Capitol Books

CAST

Castle Connolly Medical Ltd

Caxton Printers

CFA Institute

Children’s Book Press

City Lights Books

Cold Spring Harbor Laboratory Press

Colorado Independent Publishers Association

Columbia University, DKV

Consumer Reports

Cornell Maritime Press

Cornell University Press

Council on Foreign Relations Press

Council on Library and Information Resources

Cover Publishing Co.

CQ Press

CrossRef

D2B Group, Inc.

Dana Press, The

Douglas & McIntyre

Eaglemont Press

Earthquake Engineering Research Institute

Educational Concepts

Element LLC

Elsevier Science Inc.

Emida International Publishers

Ernst & Young, LLP

F.A. Davis Company

Federation of American Societies for Experimental Biology

Feminist Press (The)

Focus Publishing/R. Pullins Company, Inc.

Fordham University Press

Fulcrum Publishing

Gallaudet University Press

Genesis Press, Inc. (The)

Gival Press, LLC

Globe Pequot Press, Inc.

Great River Technologies

Grolier Educational

Grove/Atlantic, Inc.

Grove’s Dictionaries/Holtzbrinck

Hachette Book Group USA

Haiduk Press

Hammond, Inc.

Hampton-Brown Company, Inc. (The)

Hannacroix Creek Books, Inc.

Harcourt, Inc./Reed Elsevier

Harlequin Enterprises Ltd.

HarperCollins Publishers

Harvard Business School Press

Harvard University Press

Harvest House Publishers

Health Affairs/Project Hope

Hearst Book Group

Heinz Center (The)

Henry Holt & Co.

Hispanex, Inc.

Houghton Mifflin Co.

Howard University Press

Human Factors and Ergonomics Society

Hyperion

Impact Publishers, Inc.

Info Sys Technologies, Ltd.

Ingram Book Company

Institute for Electrical and Electronics Engineers, Inc. (IEEE)

Institute for International Economics

Institute for Scientific Information

Institute of Physics Publishing

Instrumentation, Systems, and Automation Society (The)

iUniverse

The Institute, Inc.

J. Paul Getty Trust Publications

James A. Rock & Company Publishers

John Wiley & Sons, Inc.

Johns Hopkins University Press (The)

Jordan Publishing House

Journal of Rehabilitation Research Development

Keene Publishing

Key Education Publishing Company LLC

KidBiz 3000

Kirchoff/Wohlberg, Inc.

Knovel.com

LAD Publishing Company

Lattice Press

League of American Poets

Leapfrog Enterprises Inc.

Learning.com

Liberty Fund, Inc.

Library of Congress Publishing Office (The)

Lidenmeyr Book Publishing Papers

Lippincott Williams $ Wilkins Journals

Literary Architects

Little Moose Press

Lousiana State University Press

Love Publishing Company

Luxury Travel Books

Lynne Rienner Publishers, Inc.

MacAdam/Cage Publishing Inc.

Mage Publishers, Inc.

Mark Logic Corporation

Market Data Retrieval

MarketingWorks, Inc.

Markus Wiener Publishers

Massachusetts Medical Society/New England Journal of Medicine

Math Teachers Press, Inc.

Mazer Corporation (The)

McGraw-Hill Companies (The)

Medical Group Management Association

Melville House Publishing

Meta Comet Systems

MG Taylor Corporation

Microsoft Corporation

Midland Information Resources

Minnesota Historical Society Press

MIT Press (The)

Modern Language Association of America

Momentum Books, LLC

Mondo Publishing

Mooring Field Books, Inc.

Morgan & Claypool Publishers

Morgana Press LLC

Moseley Associates, Inc.

Music Together, LLC

National Academy Press

National Computer Systems/Pearson

National Education Standards

National Geographic Society

National Learning Corp.

National Publishing Co.

National Science Teachers Association (NSTA)

Nature America

New England Journal of Medicine

New Press (The)

New York Botanical Garden (The)

New York University Press

Newmarket Press

Oak Knoll Press

Overlook Press (The)

Oxford University Press

P. H. Glatfelter Company

Pan American Health Organization

Pangaea

Paratex, LLC

Parmenides Publishing

Pearson Education

Pelican Publishing Co., Inc.

Penguin Putnam, Inc.

Pennsylvania State University Press (The)

People’s Publishing Group

Peter Li Education Group

Posterity Press, Inc.

Pillsbury Winthrop Shaw Pittman, LLP

Posterity Press, Inc.

Princeton University Press

ProQuest Information

Pub Smarts, LLC

Publish America, Inc.

Publisher’s Group Incorporated

Publishing House Research

Publishing Illuminations

Publishing Works

Quarasan Group, Inc. (The)

R R Donnelley

R.R. Bowker

Rainbow Books, Inc.

Rand

Random House, Inc.

Ray of Light Publishing Company, Inc.

Reader’s Digest Association

ReadHowYouWant.com

Recording for the Blind and Dyslexic

Red Rock Press

Reed Reference Publishing

Resolve Corporation

Resources for the Future/RFF Press

Rockefeller University Press

Rosetta Solutions, Inc.

Rowland Reading Foundation

Saferock USA, LLC

Sagaponack Books

Sage Publications, Inc.

Scholastic, Inc.

Scholatic Testing Services, Inc.

Scientific American/St. Martin’s College Publishing Group

Sea Hawk Publishing

Seven Locks Press

SGI-USA

Sheridan House, Inc.

Simon & Schuster

Six Red Marbles LLC

Soft Skull Press

Springer Publishing Co.

Springer-Verlag New York, Inc.

St. Martin’s Press

Stanford University Press

Stoeger Publishing

Swan Isle Press

Teachers College Press

Thames & Hudson, Inc.

Thieme New York

Thomson Learning

Tichenor Publishing

Tighe Publishing Services, Inc.

Too Far

Tribune Education

Tupelo Press

Turtle Books

The University of Hawaii Press

UAHC Press

University of California Press

University of Chicago Press

University of Illinois Press

University of Tennessee Press

University of Texas Press

University Press of Kentucky

van Tulleken Company (The)

Vantage Press, Inc.

Veronis, Suhler & Associated, Inc.

Victory Productions, Inc.

Virginia Museum of Fine Arts

Viz Media, LLC

Von Hoffmann Corporation

Walford Press

Wesleyan University Press

Western Economic Association

White Rhino Press

Whitston Publishing Company, Inc.

Wiggin and Dana LLP

William Morrow & Co., Inc./HarperCollins Publishers

Willow Creek Press, Inc.

Wooster Book Company

Words & Numbers.com

Workman Publishing

World Bank Group

Worth Publishing, Inc.

Xerox Corporation

Yale University Press

PRISM – Partnership for Research Integrity in Science and Medicine – Seems like a spoof but it is real, and sad

I just came across this web site for something called the “Partnership for Research Integrity in Science and Medicine.” I looked through it an thought – this must be a spoof. A good April 1 joke about the dinosaurs of the publishing industry. The reason it seems like a joke is well, the stuff there is so incredibly inane as to make one laugh. In essence the whole site is an anti Open Access site. They are against Open Access to publications it seems because Open Access does things like

  • “undermines the peer review process.” Yes that’s right. If an article is freely available for all to read, that must mean that peer review has been compromised. Nevermind that openness in other areas (e.g., politics, law, etc) is well established to promote critical review (anyone heard of freedom of the press). But apparently in science, openness is bad.
  • “opens the door to scientific censorship”. Yup. Making publications freely available apparently means that you will stifle communication. Again, the logic here is completely silly – how on earth is openness connected to censorship?
  • “undermining the reasonable protections of copyright holders.” Yup, the publishers of scientific articles, who do not deserve the copyright to articles in the first place, are now saying that because they have stolen the copyright from many scientists, now we should defend them because they have the copyright. Kind of like saying that someone who steals some money should not give it back because of finders keepers rules.

I could go on and on about the silly stuff there … but lets just say that everything on the site seems like a spoof. But alas, it is not. PRISM is for real. It is the last gasp of a dying breed – publishers who refuse to do what is the right thing for science and society. Yes, I understand there are some issues with Open Access that still need to be solved. But this McCarthy like tone of PRISM – basically equating openness with evil and godlessness is ridiculous. I think this is a sad day for the people behind PRISM – the AAP (Association of American Publishers). I am sure they have done some good things over the years. This is certainly not one of them and a good sign that anyone out there with any common sense who might be involved in AAP should get out or fight for change within the institution.

For more on Prism see