Category: Misc.

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

——–
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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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

——–
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.

——–

Overselling Genomics Award #2

Well, all I can say is “Aaaaargh” again. So I am awarding my second overselling genomics award to a Press Release from U. Florida entitled “Conquest of land began in shark genome” relating to a paper in PLoS One on shark development . The press release centers on a reported finding that

Using molecular markers to study the formation of skeletal cartilage in embryos of the spotted catshark, UF scientists isolated and tracked the activity of Hox genes, a group of genes that control how and where body parts develop in all animals, including people.

Now admittedly, this is not genomics here – but the press release just had to use genomics in the title so my automated google search for “genome” and “evolution” picked it up. So – why do they get the overselling award? Read more in the press release:

The finding shows what was thought to be a relatively recent evolutionary innovation existed eons earlier than previously believed, shedding light on how life on Earth developed and potentially providing insight for scientists seeking ways to cure human birth defects, which affect about 150,000 infants annually in the United States.

Yes that is right, this genome-ish gene expression study in sharks is going to help cure human birth defects (note the paper in PLoS One seems entirely reasonable … this is another case of press releases being disconnected from the science – and is another reason to support OA publications because here you can actually all go and read the paper and ignore the press release).

In addition, the press release says

“We’ve uncovered a surprising degree of genetic complexity in place at an early point in the evolution of appendages,” said developmental biologist Martin Cohn, Ph.D., an associate professor with the UF departments of zoology and anatomy and cell biology and a member of the UF Genetics Institute. “Genetic processes were not simple in early aquatic vertebrates only to become more complex as the animals adapted to terrestrial living. They were complex from the outset. Some major evolutionary innovations, like digits at the end of limbs, may have been achieved by prolonging the activity of a genetic program that existed in a common ancestor of sharks and bony fishes.”

Now I accept that the specific details of Hox gene expression here might have been surprising but what friggin evolution textbook are these people reading if they are surprised that there is not a chain of life going from less complex to the pinnacle of complexity in humans? Hopefully not mine.

——–
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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Check out Eye-On-DNAs Grand Rounds

Just a little post here suggesting people check out the Medical Blog Carnival Grand Rounds at Eye on DNA here.

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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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Why all medical professionals need to study evolution

As an evolutionary biologist with a 50% appointment in a medical school (in the Med. Micro. and Immunology department at U. C. Davis – my other 50% is in the Section of Evolution and Ecology on the main campus) I am somewhat dismayed by the lack of attention evolution receives in Medical Schools.

So I am starting a new thread here on my blog about why medical professionals need to understand evolutionary biology. First, there is a great site out there for people who want to learn more called the “Evolution and Medicine Network” which has links to courses, articles, books, etc.

Here are my top 10 picks for reasons medical professional need to understand evolution

  1. Antibiotic resistance. The emergence and spread of antibiotic resistance is one of the most vexing issues in medicine right now as well as one of the best studied topics in the evolution of microorganisms. Understanding how antibiotic resistance originates and spreads is fundamentally a question of evolution. The more medical professionals understand this issue the better they will be at preventing spread in hospitals and in convincing patients and the community to stop abusing antibiotics in human and animal care.
  2. Origin and spread of virulence. Not all pathogens are equal. Some are minor annoyances. Others produce really nasty outcomes. And importantly, organisms can change these virulence properties on the short term. Even more importantly, behavior of medical personnel can both influence the spread of virulent strains (can anyone say – wash your *$&% hands) and can unintentionally select for more virulent strains. Understanding the evolution of virulence is critical for making sure health care does not make things worse (see papers by Ewald for example).
  3. Vaccine use and development. Vaccines involve altering the evolutionary arms race between pathogens and hosts. It is not an intelligent design arms race. If you do not get the difference, stay out of vaccine work.
  4. Cancer origins. Cancer is in essence a analog of natural selection operating among cells within the body. Unfortunately for us, the “winners” of this selection process are those that have uncontrolled growth. Thinking of cancer in this way can help understand how to both prevent and treat it.
  5. The human microbiome. Beneficial microbes are all over us and play fundamental roles in human health. Unfortunately they are very hard to study because, well, they are small, and many cannot be grown in culture in the lab. The current ways to study them primarily involve indirect DNA based assays involving evolutionary and ecological analyses of the data.
  6. Understanding the human genome. The human genome is done (well, almost, but close enough for most uses). Now what? Well, the best way to learn about the genome sequence itself is through “phylogenomic” analyses comparing to other genomes.
  7. The relevance of animal and other models. Mouse is a useful model for some aspects of human biology but not all. Drosophila too. And even yeast and E. coli? Which aspects of human biology can be modelled by each model organism? Understanding their evolutionary history and evolutionary processes helps figure this out.
  8. Aging. Aging is in essence an unfortunate side effect of natural selection maximizing fitness by futzing with health and reproduction in the early years. Since there is little fitness cost to mutations that lead to deleterious effects when we are old, well, we are kind of screwed. But understanding the ailments associated with aging is best done with this knowledge of the efficiencies and inefficiencies of selection.
  9. The immune system. See #3 above. But this is bigger than that. The whole process of how the immune system (both the innate and the adaptive components) works both at the level of an individual and at the level of a population is an exercise in population genetics and natural selection.
  10. Pluses and minuses of high mutation and recombination rates. Many medical professionals know HIV has a high mutation rate. And some might know that recombination rates are high in some pathogens. What are the consequences of this on the pathogen biology? Read Evolution 101, or my new textbook.
  11. A bonus one. Epidemiology of infectious diseases. One of the best tools in studying the spread of infectious diseases is phylogenetic analysis – which can show how different strains are related to each other.

Just a brief tour of some of the areas that evolutionary biology informs medicine. More on this later.

——–
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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The human genome war from a fun perspective

So I was browsing around Amazon because I have a new Evolution Textbook that just came out. And when I searched for “genomics” and “evolution” up popped a “Listmania” list (which I had never heard of before) for Books about J. Craig Venter. And then I saw a new book by Craig – his autobiography “A life decoded: my genome: my life” coming out in October. And that’s when I discovered that the people who bought his book (even though it has not come out yet) also bought

So people apparently link Craig to atheism and Einstein. So I said to myself – what about other books by the genome-war folks? What else did people buy when they bought them? This is where the fun began.

Francis Collins: The Language of God.

So apparently, Francis has the religious readers on his side but nobody seems to link him to science in much of any way.

John Sulston’s a Common Thread

So it seems Sulston has gotten all the people interested in science history.

Michael Ashburner’s Won for All

So I guess Ashburner gets the people interested in the science itself.

I am sure there is more fun to be had here with these. And as my brother pointed out – the Amazon function here of listing what other people bought does not say it is representative in any way (that is, they are trying to sell books so perhaps they list the most popular other books not the ones most commonly linked to the book in question). But it is kind of voyeuristic and fun to see the types of books people are buying in association with these books.

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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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Metagenomics Based Discovery Highlight: Novel Photosynthetic Organism Discovered

Normally I avoid writing about discoveries in non Open Access journals. But I cannot help myself here. On Friday a wickedly cool paper was published in a journal that I will not name here. In this paper they describe a new bacterium: “Candidatus Chloracidobacterium thermophilum.” It is REALLY rare for a new bacteria to be described in a journal like this one. How did they get it in this journal? Well this organism represents the first new photosynthetic lineage of organisms discovered in many many many years. The bacterium is in the phylum Acidobacteria and can carry out aerobic photosynthesis. Prior to this discovery, photosynthesis was only known in five evolutionary lineages – all of them bacteria: Cyanobacteria, Chlorobi, Chloroflexi, Proteobacteria and Firmicutes. Photosynthesis in plants, algae and other eukaryotes all came from symbioses with cyanobacteria to these five groups represented the only “primary” photosynthetic lineages. Thus it is a big deal to find a sixth lineage having photosynthesis.

And – here is the fun part. How did they find this? With the help of metagenomics.

Only five bacterial phyla with members capable of chlorophyll (Chl)–based phototrophy are presently known. Metagenomic data from the phototrophic microbial mats of alkaline siliceous hot springs in Yellowstone National Park revealed the existence of a distinctive bacteriochlorophyll (BChl)–synthesizing, phototrophic bacterium. A highly enriched culture of this bacterium grew photoheterotrophically, synthesized BChls a and c under oxic conditions, and had chlorosomes and type 1 reaction centers. “Candidatus Chloracidobacterium thermophilum” is a BChl-producing member of the poorly characterized phylum Acidobacteria.

That is, they saw the first hints of this through analysis of metagenomic data which was generated by isolating DNA from a Yellowstone hot spring and sequencing the snot out of it. Anyway – as some might have guessed – my only lament about this paper is that it is in a non Open Access journal (I tried to convince the lead author to submit elsewhere but was not convincing enough I guess). It really is too bad – it would be nice to post some of their figures here for others to look at and it this paper would make a great one to use for educating the public about metagenomics. But alas the public cannot get this from Science for at least 1 year and bloggers and other news sources cannot really run with the story because of the copyright limitations. So – great science and great example of the power of metagenomics but restricted public use.

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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 Science like the start of Apple?

I know a lot has been written in support of Open Access publishing and Open Science but I must say this paragraph (from MungBeing magazine by Andrew Hessel) is one of my favorites is more over the top than I initially realized,

Garage Biology and Open Source Biology: Twenty five years ago, kids flocked to computers, pushing the limits of what they could do. Similarly, the next generation of genetic engineers won’t need laboratories or even PhD: they’ll have laptops, cheap mail order DNA synthesis, and, thanks to Google and Wikipedia and open journals like PLOS Biology, access to mountains of free biological data. They’ll work in basements, garages, and cafes, and they’ll trade ideas and collaborate on genetic designs the same way open source programmers now write computer code. Keep in mind that it was only 30 years ago that a little company called Apple started out of a California garage.

Thanks to Bill Hooker’s blog response for calming me down a bit about how brilliant this quote is. The main issue I have is that there are risks associated with genome engineering that are different and more substantial than those associated with piecing together computers here and there.

——–
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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The pope is committed to evolution

Well, in my last post I asked if people were committed to “Evolution” and I confess I got a bit worried that this might be misinterpreted by some as “We believe in evolution regardless of the facts.” And in fact there was one flame-like comment posting that I deleted from the comments.

But now apparently the Pope has read my blog (or maybe someone told him about it) and he has come out in full support of evolution as a science and the facts of evolution as we evolutionary biologists know then (i.e., natural selection, macro and microevolution, etc).

As reported on MSNBC the Pope said

the debate raging in some countries —particularly the United States and his native Germany — between creationism and evolution was an “absurdity,” saying that evolution can coexist with faith.

In addition, he said

They are presented as alternatives that exclude each other,” the pope said. “This clash is an absurdity because on one hand there is much scientific proof in favor of evolution, which appears as a reality that we must see and which enriches our understanding of life and being as such.

Furthermore, and more importantly, the Pope has re-stated his belief that everyone must do something about global change and environmental destruction:

“We cannot simply do what we want with this Earth of ours, with what has been entrusted to us,” said the pope, who has been spending his time reading and walking in the scenic landscape bordering Austria.

I know I said recently that biology had a good day in the Bush administration. Unfortunately, that was mostly genetics and biochemistry. Evolution and environmental stewardship never seem to have good days there. Maybe just maybe, the Pope will have some impact around the world on both issues even as the U.S. sticks its head in the sand. NOTE – SEE COMMENTS – THE POPE IS PRETTY CLEARLY NOT DOING EVERYTHING HE COULD TO PROTECT THE ENVIRONMENT.

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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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Are you committed to Evolution? Prove it!

Peggy Farnham at the U. C. Davis Genome Center sent me this picture. apparently of a real tattoo. After a google search I found at least an early source for it here.

This inspires me to ask everyone out there – are you committed to Evolution? What have you done to show your commitment?

What have I done? I think the biggest example of my commitment, though boring, is that I worked six years on a new evolution textbook which was just published a few weeks ago (which you can find out about here or order from Amazon here).

Less boring – I once stood on a street corner in New Orleans with Owen White and handed out altered forms of a pamphlet someone else was handing out in which we added some information about evolution.

So – rather that spout off about what I have done .. what has anyone else done? Are you committed?

——–
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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