Friday, August 31, 2007

Too eager for ethanol?

Just a quick one here along the lines of my biofools series. Anyone interested in biofuels should take a look at the LA Times Editorial from Aug 20 titles "Drunk on Ethanol" which discusses many of the negatives of growing corn for ethanol and of other aspects of the crop to ethanol pipeline. Also check out the letters to the editor following up on the piece (one of them by my sister, Lisa Coffman, Executive Director of the California Water Impact Network). My personal biggest concern is the environmental damage that could come from increased use of plants to produce ethanol. Such damage includes the conversion of rainforests into sugar cane plantations, the use of more and more pesticides and herbicides and fertilizers to go onto less useful land, and the excessive use of an already limited resource - water. Yes, if you do the calculations in certain ways, ethanol seems like a great idea. And it is certainly true that if we are going to make ethanol from crops we could do it more efficiently. But the way it is being done now - with corn sucking up water like their is not tomorrow we are heading down a bad path.

What would make more sense is to first make better use of all the wasted biomass from various agricultural systems and from solid waste. Lots of material is still being burned on farms for example (see pictures below of a fire near Davis --- these are going all the time, even on "spare the air" days). Sure - one can make lots of money from corn to fuel right now. But that does not make it the right thing to do when there are plenty of sources of biomass being wasted all around us. Lets hope that more of the biofuels projects work on converting leftovers not new crops.


Thursday, August 30, 2007

Adaptationomics Award #1 - Wolbachia DNA sneaking into host genomes

Well, I have decided to start a new award. For years I have been fighting against the tide on the tendency for people doing genomics work to resort to silly adaptationist arguments for observations. The argument goes something like this. We sequenced a genome (or did some type of genomics). We made an observation of something weird being present (take your pick - it could be a gene order or a gene expression pattern or whatever). We conclude that this observation MUST have an adaptive explanation. We have come up one such adaptive explanation. Therefore this explanation must be correct.

Gould and Lewontin railed against this type of thing many years ago and others have since. Just because something is there does not mean it is adaptive (e.g., it could be neutral or detrimental). And even if something is adaptive, just because you can think of an adaptive explanation does not mean your explanation is correct.

And this is so common in genomics I have decided to invent a new word - Adaptationomics. And I am giving out my first award in this to Jack Warren Werren and colleagues for their recent press release on their new study of lateral transfer in Wolbachia (plus it lets me plug their new study which is pretty ^$%# cool).

Basically, in their study (led by a past colleague of mine from TIGR, the brilliant up and coming Julie Dunning Hotopp) they showed that there have been multiple lateral transfers of DNA from Wolbachia (which are intracellular parasites that can infect germ cells) into invertebrates. Furthermore they showed that that the DNA transfered to the host genome is not completely transient and that in many cases it is passed on to future generations. This is interesting because it is the first report of strong evidence for such "stable" transfers from bacteria into multicellular species. Of course, one could say that this finding is not that surprising given that Wolbachia infect germ cells and given that DNA transfer from organellar genomes to nuclear genomes is quite common. But Wolbachia are not organelles and since it appears that their DNA can readily move into genomes of multicellular species, this opens up a new window into our understanding of gene transfer.

This of course does not mean that the DNA is anything but "junk" in terms of functions in the host genome. And this is where the adaptationomics comes in. One of the press releases associated with the paper has a bit of an outrageous adaptationomics claim that I would like to counter. In response to their finding of a nearly complete Wolbachia genome in the nuclear genome of a fly Warren Werren says
The chance that a chunk of DNA of this magnitude is totally neutral, I think, is pretty small, so the implication is that it has imparted of some selective advantage to the host.
And Dunning Hotopp in a Nature article says:
The discovery also hints that the bacterial genome must have provided some sort of evolutionary advantage to its host. "You're talking about a significant portion of its DNA that is now from Wolbachia," says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. "There has to be some sort of selection to carry around that much extra DNA."
This notion that the DNA MUST have an beneficial function is pure adaptationomics. Consider the movement of DNA from organellar genomes into the nucleus. Such movement occurs at an incredibly high rate and the DNA seems to be maintained in the host genomes for millions of years. For example, when we were sequencing the Arabidospsis genome, we found at least one if not more whole copies of the mitochondrial genome embedded in the nuclear genome and we concluded this was likely a non adaptive event. That is, the mt DNA was not conferring some advantage on Arabidopsis plants. There is extensive work on what are called "numts" (nuclear mitochondrial DNA) in humans and other species that makes similar conclusions - the mtDNA in the nucleus is basically junk but it is maintained for long periods of time. Sure, occasionally, the DNA confers some selective advantage. But this is a very rare event and one cannot infer that some DNA is advantageous simply because it is present. This is especially the case for eukaryotes which are generally more able than bacteria to maintain DNA that confers little selective benefit.

So I would argue that WarrenWerren and colleagues appears to have fallen for the adaptationomics trap - they want to believe these Wolbachia DNA inserts confer some selective advantage. But there is no need to assume this simply because the DNA is there.

Anyway - as is the case more and more. Read the paper. Ignore the interviews and the press releases.

Tuesday, August 28, 2007

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

Saturday, August 25, 2007

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

Thursday, August 16, 2007

Anyone else having gmail spam filtering issues?

Over the last week I have had a sudden increase in missing email messages, both from me and to me. Only by luck did I figure out that at least the missing incoming messages are being placed into the spam folder by gmail, which I run all my messages through since in the past their spam filter has been phenomenal.

The incoming messages included diverse messages - some with the word "FWD" in the subject line but some appearing as normal as can be.

Anyone else out there experiencing a sudden increase in missing email?

Wednesday, August 15, 2007

Save the Bay Delta

Just a quick one here. I am appalled by some of the discussions of water resources out here in the Central Valley in California. I know there is a long history here relating to the allocation of water but we are risking destroying an incredible ecosystem in the Bay Delta by dishing out water rights like they are candy (not to mention the pollution, pesticides, antibiotics and other crap (literally) we allow to flow into the Delta. So here is a plug for a petition being circulated relating to one of the latest US Bureau of Reclamation activities in this area.

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.

Monday, August 13, 2007

SciFoo Camp - The End and New Beginnings

Well, I am finally getting around to writing about the last day of SciFoo camp (see here for my other blogs on the topic).

For Day 3, I got up early, packed up my bag, and then polished up my presentation for a session on "The Human Microbiome." This was particularly difficult for me since I do not really at this time work on the human microbiome much (although I want to). But I figured, of all the things microbial I know about, this would be the one that would be most fun to talk about to scifooers and would catalyze the most interest. So I searched around for slides and figures and ideas on the web for a while and then said "WTF - I can do a chalk talk if I need to" and I headed downstairs to the lobby in the hopes of getting over to Googleplex and enjoying the last bits of scifoo.

There was quite a crowd in the lobby and I ended up talking to a few other evolutionary biologists which was good and then finally got a bus ride over to camp. At Google, I had a bit of breakfast and then went inside to sit at a table to do the last bits of preparation for my talk. If I had been at a normal conference I would have simply skipped the first two sessions to prepare for my talk at 11:30 (the last session of the meeting). But I said this would be silly and decided to go to a session at 9:30. My choices were:

Golem: Data Mining for Materials (and Non-Programmers): sketching information systems (Andrew Walkingshaw) --AND-- Searching the Edges of the WebNovel Biofuels, smart materials in energy production, the energy mix in the short term.Genome Voyeurism -- Let's poke through Jim Watson's genomeInternational polar year, an opportunity to... (Dave Carlson)
Simplifying citation linking (Dan Chudnov)Would You Upload? (Melanie Swan)


Future health care delivery and transport models: When "science" is not enough, benefit of new research vehicles (Berman and Neelagaru)Reforming Patent Systems, patent informatics and innovation5 mins on your favorite science website / tell us your dream science web tool (Richard Akerman)How to Celebrate Darwin in 2009 (Phil Campeck)Innovation is Not Pointless...But It's So 20th Century (Bingham)

And again, the choosing was brutal. Though I really wanted to go to Lincoln Steins Genome Voyeurism session, I followed my rule of going to things I did not know a lot about and went to the session on the International Polar Year. This was one of those sessions in a giant room and I expected a huge crowd. Instead, there were about seven people. But boy did the others miss something brilliant. Dave Carlson not only told us about the whole IPY project but proceeded to tell us about how their project was completely Open Science. That is, everyone involved was required to post their data on the web for anyone to use. OK - well apparently they are allowed to publish in non Open Access journals, which seems counter to their whole philosophy, but their openness about data is brilliant (Note - I just found out from a Google search that a childhood friend of mine, Thomas Nylen, is participating in the IPY project -- see this blog here for some of what Tom has been up to).

Unfortunately, I missed the next session due to my computer having issues and me freaking out about whether it would work for my presentation at 11:30. The choices for the session I skipped were:

Incorporating science into social networks (Josh Koarer and Jon Durant)
Assessing the risks of tech innovation, ethics of synthetic bio. Do we have any choice? (Caruso)Tree of Life: Fractal Data Problem (Sereno)
Provenance analytics: illuminating science trails. Future of scientific publications, dynamic and evolving papers. (Juliana Freire)Planetary Defense Against Asteroids (Pete Worden)




Science Blogging
Towards an open source science learning collaboratory (Ted Kahn Design Worlds)Opening the scientific literature: OpenLibrary, Google Scholar (Aaron Swartz)21st century medicine: electronic medical records, privacy, and data mining (Erez L. and Kevin F.)

Then it was time for the final session. And I was up -- the Human Microbiome. Here is what I was up against

Social limits of scientific knowledge - can too much information impede science? (Dalton Convoy)Culture of Fear: Scientific Communication and Young Scientists

(Alex Palazzo, Andrew Walkingshaw)

Towards DataWiki (Hugh Rienhoff, Alan Littleford)Do systems organize themselves to produce entropy at the maximum rate? (Ralph Lorenz)

Science on the Stage, "science-in-theatre" (Djerassi)Human Microbiome, microbes in and on us (Jonathan Eisen)Science fiction: what is it for? (Henry Gee)

It would have been funny if I had gone to someone elses session and skipped mine, but I am glad I did not as actually quite a few people showed up to mine. I started by saying I had a presentation but would prefer if people just asked questions along the way. And the great part was - did they ever. This included some by Freeman Dyson - kind of cool to have the guru asking me questions about microbial colonization of babies. Finally, after I had spent too much time on background - Drew Endy said something to the effect of "Lets get to the technically hard stuff" and I briefly discussed using genome sequencing to study microbes that live in and on humans. And then - we just had to stop.

I decided to linger for the wrap up session after lunch so I had lunch, made some phone calls, and then we had a wrap up which was mostly an open mike for comments and this ended up being a bit too much of "It was great" and not enough of "How could we make it better." But hey - it was great so I guess I understand. I went around saying thanks to the Google team and the Nature and O'Reilly folks and then moseyed on to the train back to Davis.

Some brief notes about the end and the new beginnings:
  • I got lots of ideas for new projects and new things to do from this meeting as with the last one.
  • Over the next few weeks I will be posting about some of the other things I saw there and discussing why/how they are interesting.
  • I think this "un-conference" style would be really good to emulate for other gatherings. Not sure how to pull it off though.
  • I know I will get in trouble from some of my Open Access colleagues, but I definitely came away from the meeting being really impressed with some of the things Nature Publishing group is doing. They really seem to be trying to move into the Web 2.0 area for science communication with Nature Preceedings, and the Nature Network and Scintilla and Connotea and Podcasts and of course Scifoo. Sure there were probably too many people from Nature at Scifoo, but hey, they were sponsoring it so why shouldn't they send them? Here's hoping that they continue to experiment with Open forums and Open material and that they change to OA for all their publications as a way to bring in more people to their Web services. And lets hope other publishers, especially truly open ones build similar resources for the community.
  • Thanks to Timo Hannay, Tim O'Reilly, and all the folks at Google, Nature, and O'Reilly for organizing this and inviting me.
Some interesting scifoo collections and follow up discussions:

Saturday, August 11, 2007

New Textbook on Evolution

From Egghead, U. C. Davis' research blog:

Jon Jonathan Eisen FoE (Friend of Egghead) is coauthor of a new college-level textbook on evolution that incorporates recent developments in genomics and molecular biology alongside traditional evolutionary principles. Evolution (Cold Spring Harbor Laboratory Press, 2007) is intended for undergraduate courses in evolution and for biologists looking for a guide to the current state of evolutionary science.

The authors are Nicholas H. Barton, University of Edinburgh, U.K.; Derek E.G. Briggs, Yale University; UC Davis’s Eisen; David B. Goldstein, Duke University Medical Center; Nipam H. Patel, UC Berkeley. Eisen holds appointments at the Section of Evolution and Ecology and the Department of Medical Microbiology and Immunology at UC Davis.

An accompanying website, http://evolution-textbook.org/, contains supplemental illustrations, additional online chapters, class problems and other material, all freely available

From Cold Spring Harbor

Public release date: 10-Aug-2007
[ Print Article | E-mail Article | Close Window ]

Contact: Ingrid Benirschke
benirsch@cshl.edu
619-275-6021
Cold Spring Harbor Laboratory

New textbook illuminates the close links between evolutionary and molecular biology



Cover of Evolution. The images, from left to right, are of (1) a map of the genome of the bacterium Deinococcus radiodurans R1, (2) a mineral skeleton of a radiolarian...
Click here for more information.

COLD SPRING HARBOR, N.Y. � In an innovative approach to the subject of evolutionary biology, a new book, Evolution, combines the contemporary fields of genetics and molecular biology with traditional evolutionary theories to provide an elegant, cohesive view of biology. The book, which was recently released by Cold Spring Harbor Laboratory Press (www.cshlpress.com), is geared toward all biologists seeking a clear, current, and comprehensive account of evolutionary principles and processes. It is a new and innovative choice of textbook for undergraduate courses in evolution.

�It is the most comprehensive book out there, with an admirable and clear presentation of the facts,� wrote Trevor Price, Ph.D., in a pre-publication review of the text. �I personally learnt a great deal...the book as a whole would be useful for workers in the field as a source of reference and to give them breadth.�

The branches of biology concerned with molecular events and evolutionary principles have developed independently of one another. But with recent breakthroughs in fields such as genomics, developmental biology, human genetics, and biochemistry, it has become yet more evident that evolutionary principles guide biological phenomena at all levels, and are essential to a practical understanding of these phenomena.

The authors, who are world-renowned experts from diverse biological backgrounds, illustrate how basic processes such as natural selection, optimization, and conflict occur at the molecular level as well as the organismal and ecological levels. They illuminate evolutionary principles and mechanisms with examples from across the spectrum of life�from �jumping genes� and RNA molecules, to populations of yeast and E. coli reared in the laboratory, to dung flies, lizards, and deer in their natural habitats.

�Evolutionary biology underpins all our knowledge of the living world,� write the authors. �[It] is a synthesis of Darwinian natural selection and Mendelian genetics. It allows us to ask not just how life evolved, but why it is as it is: Why do organisms develop from a single cell? Why is the genetic code as it is? Why is there sexual reproduction?�

The book is divided into four sections. The first three sections detail the history of evolutionary and molecular biology, describe the origin and diversification of life over the past 3.5 billion years, and explain the fundamental mechanisms underlying evolutionary change. The final section is devoted to human evolution and diversity, merging recent insights from molecular techniques with paleontological evidence. For a complete table of contents, see http://www.cshlpress.com/link/evolutn.htm.

The supplementary Web site (www.evolution-textbook.org) will be useful to biologists who incorporate Evolution into their undergraduate- or graduate-level courses. The site includes two Web-only chapters, downloadable figures and tables from all chapters, a glossary, author notes with complete reference lists, discussion questions, chapter problems, links to useful Web sites, and other material, all of which are freely available.

###

About the book: Evolution ISBN 978-087969684-9, � 2007 Cold Spring Harbor Laboratory Press Hardcover, 833 pp., 8.5� � 11� trim size, 1200 color illus., glossary, index http://www.cshlpress.com/link/evolutn.htm, www.evolution-textbook.org

About the authors: Nicholas H. Barton�s early research was on narrow zones of hybridization that subdivide many populations, with work on a variety of species, including grasshoppers, butterflies, and toads. More recently, his research, which has been mainly theoretical, is attempting to understand the influence of selection on complex traits, models of speciation, the evolution of sex and recombination, and the coalescent process. He is professor of Evolutionary Genetics at the Institute of Evolutionary Biology, University of Edinburgh.

Derek E.G. Briggs works on preservation and the evolutionary significance of exceptionally preserved fossils, including those of the Cambrian Burgess Shale of British Columbia. His current research focuses on the chemical changes that occur during the transformation from living organism to fossil. He is Frederick William Beinecke Professor of Geology and Geophysics at Yale University and Director of the Yale Institute for Biospheric Studies.

Jonathan A. Eisen uses a combination of genomic sequencing and evolutionary reconstruction methods to study the origin of novelty in microorganisms. Previously, he applied this phylogenomic approach to cultured organisms, such as those from extreme environments. Currently he is using phylogenomic methods to study microbes in their natural habitats, including symbionts living inside host cells and planktonic species in the open ocean. He is Professor in the Department of Medical Microbiology and Immunology and the Department of Evolution and Ecology at the University of California, Davis.

David B. Goldstein�s principal interests include human genetic diversity, the genetics of neurological disease, population genomics, and pharmacogenetics. His laboratory currently investigates how human genetic variation influences the response to drug treatments for common neurological and cardiovascular disorders. He is Director of the Center for Population Genomics and Pharmacogenetics at the Duke University Medical Center.

Nipam H. Patel initially studied the development of several model and nonmodel species, including cows, chickens, grasshoppers, and Drosophila melanogaster. His research group studies the evolution of development, with a focus on the evolution of segmentation, neurogenesis, appendage patterning, and gene regulation. He is Professor in the Department of Molecular and Cell Biology and the Department of Integrative Biology at the University of California, Berkeley and an Investigator of the Howard Hughes Medical Institute.

About Cold Spring Harbor Laboratory Press: Cold Spring Harbor Laboratory Press is an internationally renowned publisher of books, journals, and electronic media, located on Long Island, New York. Since 1933, it has furthered the advance and spread of scientific knowledge in all areas of genetics and molecular biology, including cancer biology, plant science, bioinformatics, and neurobiology. It is a division of Cold Spring Harbor Laboratory, an innovator in life science research and the education of scientists, students, and the public. For more information, visit www.cshlpress.com.

Wednesday, August 08, 2007

SciFoo Camp Day 2 - Afternoon

OK - More on Scifoo Camp - Day 2.

Session 4: Here were the choices:
  • Collecting More Data Faster Can Make an Organization Dumber (Jeff Jonas) 
  • Skepticism and Critical Thinking in an Age of Marvels (Guido Nurez) 
  • Computable Data/Mathematics (Theodore Gray) --AND-- $100 laptop demo (Ted Kaehler) 
  • Evolutionary robotics (Lipson Olliver) 
  • Ocean Exploration
  • why a mouse? Multi-touch, physical and social interfaces for manipulating data (Philip Tiongson)
  • Scientific Communication in 2030 (Kurte-Bilder) --AND-- The selfish scientist (Carole Goble)
  • Universe or Multiverse? (Martin Rees, Frank Wiligat, Lee Smolin) 
  • Reuse of Sewage to Grow Food and Provide Sanitation (Frank Rijsbertian) 
  • Is Collaborative Policy Making Possible? (think wikipedia, economic/government simulation games) (TimHubbard, Beth Noveck) 
  • Viral Chatter (Nathan Wolfe)
And here was definitely my first big mistake of the meeting. I went to the one on Ocean Exploration -- even though I had sworn to not go to things I knew a lot about unless I felt like I had to go. Here I did not have to go. But I went and though I am sure others in there found it very interesting, it was mostly stuff I knew a lot about (I have on and off done studies of microbial diversity in the oceans and deep sea). I guess the one highlight for me was discovery of Earthbrowser.
    Session 5: Here were the choices (which I pulled from the Scifoo web site - but one was left off - we had planned a session for the second half on Terraforming).
    • Sessions
      • Freebase Demo 
      • Biodiversity on the Web: Science Publishing 
      • Prioritizing the World's Problems 
      • Display of Greater than 2D Data or Lots of 2D Data All at Once Tamara Munzner. 
      • E-Science Beyond Infrastructure /RichardAkerman/ 
      • Implantable Devices and Microchips for Healthcare --AND-- Diver Assistance Devices 
      • Using Evolution for Design and Discovery 
      • Stem Cells (a.k.a. How to Get Scientists to Care about Web 2.0 
      • Machine Reading & Understanding Science 
      • Science & Fundamentalism (Durant) 
      • Biological Data & Research --AND-- Open Source Biomedical Research for Neglected Diseases 
      • My Daughter's DNA: Hacking Your Genome / Towards a Data Wiki 
      • Network-Centric Biomedicine (Ken Buxton) 
      • Squishy Magnets, Talking Paper and Disapearing Ink: How can inventables.com open its doors to kids for free?
    • Since I was planning to go to a session half way through I was not sure which to do for the beginning and so I went to "Prioritizing the Worlds Problems" - a discussion led by Bjorn Lomborg about a new book he is working on. Basically the deal is - he and a bunch of economists thought a bunch and picked 10 world problems that might be solvable: climate change, communicable diseases, conflicts, education, financial stability, corruption in government (or something like that), malnutrition and hunger, sanitation and water access, and subsidies and trade barriers. And then they did an exercise basically asking - if you could spend some money in the next five years, could you solve any of these problems.
    • He had some skeptics in the audience (which is not surprising given the semi-controversy over his book the Skeptical Environmentalist). For example Richard Jefferson of CAMBIA said that these were symptoms not problems and someone else said that it was bad to encourage governments to think on short time scales like a few years.
    • I had to leave early for my Terraforming session and wished I had stayed. Not sure what I thought about the exact details of what he was presenting, but he was certainly not the demon some people implied he would be.
    • A bunch of us met up outside the room where we were to have our Terraforming session only to find out that the occupants of the room were apparently circling the wagons and would not let us in. So we did the scifoo thing and took over the lobby area - doing an excellent job of sofaforming and chairforming.
    • Then we had a discussion of Terraforming with SciFi writers and scientists and technology folks and reps from NASA. It was a pretty good discussion.
    • In the end we concluded that if there is to be a Terraforming effort it should be on a near Earth asteroid encosed in some type of shell to retain gases. Sort of Biosphere 4 or something like that. Now we just need an asteroid.
    Session 6: Here the choices were:
    • Give us your Data! Google's effort to archive and distribute the world's scientifcic datasets. (Noel Gorelick) 
    • Personal Impact Factor: Measuring Scientific Contributions Outside the Literature --AND-- Sensible organizations of sociometric badges 
    • Kids, Science, Math & Rational Thought 
    • Where are the aliens? (David Grinspoon, Steve Benner) 
    • Visual communications, graphics gesture (Barbara Teresky) 
    • Godel and the draft board (George Dyson) 
    • Micro-UAVs 
    • Dinosaurs, ancient humans, expedition science (Paul Sereno, Gabrielle Lyon) 
    • Machine Learning in the Natural Sciences 
    • why does science suck on TV, and what can we do about it? (Adam Rutherford) 
    • Hunch Engines /Eric Bonabeau/

    • For this one I was completely torn. I really wanted to go to Noel Gorelicks discussion of Google's efforts to collate scientific data. But then I remembered my vow to stay away from things I might know something about.
    • So I went to a session on MicroUAV. That is, small unmanned aerial vehicles. Holy *$%$. This was the best session I went to. Simply put - it was incredible. The leader (who I found out later was Chris Anderson the editor in chief of Wired) showed the evolution of his attempts to make cheap small UAVs.
    • Here is the deal. He started off with trying to figure out all the things he would need to make robust small UAVs - and originally pieced together multiple various gizmos to control the planes and do things like communicate with ground and get GPS signals and take pictures. And then he realized he could use a GPS enabled cell phone with a CAMERA for all the functions and this helped reduce the costs of the planes such that one can now make one for < $700. Really. See DIYDrones.com.
    • And then he showed us pics he had taken that AM of a fly over of Google HQ. Friggin' incredible. It was amazing from the fun point of view but also - I hope to use such UAVs to do sampling of microbes in air ...
    • And one of the last things I heard in the session "And the sky will darken with Robots"













    Session 7. Here the choices were:

    • Data Mining the Sky, knoledge extraction and real-time discovery (Tony Tyson) 
    • All-Fluidic Computing, large-scale biological
    • Science vs. Capitalism: Utopian Effots in the Overshoot Century. (KIm Stanley Robinson)
    • Buildings engergy use and behavior change - can the built environment be an interface?
    • The Paperless Home (Martha Stewart)
    • Provenance Analytics: Illuminating Science Trails and the Future of Scientific Publications
    • And here I chose to see what Martha Stewart had to say about the Paperless Home.
    • Just before the session, Bora asked her about whether that meant no toilet paper and she responded by saying everyone should use bidets (really).
    • She started off really well I thought - saying that homemakers are underserved by technology.
    • She also complained about organizers made by other companies including Microsoft and said her plan was to make a better organizer for the homemaker.
    • She also said that people need this because they need time for their families and she mentioned that many men spend less than 15 minutes a day with their kids. She also said she wanted this to help support the family unit, whatever that family was (referring back to her introduction when she said that the family has changed a lot but not saying that she thought new family structures were bad).
    • She made a bunch of digressions that were basically the equivalent of "My magazine is brilliant and perfect" but I guess this did not surprise me since I think it is good that she is a perfectionist
    • She did say she considers herself a typical customer for such an organizer - which made many people literally groan. Yes, Martha, with her 100s of millions of dollars, her boyfriend who pays 30 million to go into space and her many homes and giant houses and teams of assistants, she is the perfect customer.
    • She did make some insightful comments about home technology like "I don't mind my talking to my computer but I do not want my refrigerator talking to me" when she was complaining about all the noise some gadgets make.
    • Then she said nobody wants a drier that buzzes when it is done (I agree with her that this is annoying). She then asked the crowd if anyone wanted the buzzer and Paul Ginsparg said yes. So she skeptically dissed him and asked him why when he could just wait a little bit and put in the load a bit later. So he said "He wants to get another load in as fast as possible so he can spend more time with his kids", referring back to her comment about fathers not spending time with their kids. She knew she had lost this argument and she moved on to another topic.
    • She made a funny reference to "Nature" magazine as though it was about you know, plants and bugs and well, "nature."
    • She also said she wants scents out of the houses, which I agree with too. And she told a bizarre story about some worker who came over to her house with smelly pants because he had used a smelly dewrinkler. And she made him go and change into a new set of clothes because he smelled so bad.
    • In the end, I guess I agree with Anna Kushnir in her brilliant "Letter to Martha" that she missed a chance to get technogeeks interested in helping the homemaker. I felt this was happening and asked her a leading question trying to get her to say something about what technogeeks could do to help but she misunderstood and answered some other question.
    • In the end, I am glad I went to her talk --- it was off the beaten path and memorable even if it was not technogeeky enough for me.
    Then we had another googlelicious dinner. I cannot for the life of me remember what I did but I guess that is OK.

    And finally we had the last session. The choices here were:

    • Reinventing scientific publication (Web 2.0, 3.0, and their impact on science) 
    • Piracy, Murder and a Media Revolution 
    • Engineering Living Instruments, android sensors 
    • Nanohype: The volumnious vacuous vapid world where only size matters. 
    • Biohacking science security society (Greg bear) 
    • The user-generated content I like (anyone can show the content they like on the internet) 
    • Science communication with comics... come turn your science into comic books 
      And here I went to Greg Baer's session on Biohacking. It was quite interesting with a wi
    • de ranging discussion of biohacking, biodefense, biosafety, etc.
    • I am not sure everyone came out with the same conclusion though. I came out thinking -- we should not worry about biohecking compared to normal pathogens. But many other people said later they came out of it scared about hackers making nasty viruses and killing us all. I mean - I think the community should worry a bit about genetic engineering and put into place safeguards against terrorists and accidental released. But I still worry more about MRSA and XTR TB and so on.
    And thus ended the sessions. We had a reception and then at around midnight people went back to the hotel and some continued to linger for many hours ... I only lasted til ~ 1 am.

    Tuesday, August 07, 2007

    SciFoo Day 2 - Morning

    Here is the continuing Saga of SciFoo Camp. It is here that the author describes a portion of Day 2 - specifically the morning through lunch.

    I got up pretty early and headed down to the lobby in the hopes of getting a bus over to Google and getting the good Google food and coffee. But alas the bus was a little behind schedule and so I was forced to hang out with other campers in the lobby area. Eventually a bus came and we went back to Googleplex. We had a lazy breakfast and I got to talk to many interesting folks.

    Session 1.
    • For the first session, the choices were:
    • The Next Big Programming Language /Josh Block & Bob Lee/
      Open Science 2.0 /BoraZivkovic/Digital Data Libraries /Mike Halle/Citizen Science - Where Next? /John Durant/












    • Future of Healthcare /Richard Satava/
      Visual Garage - We'll Fix Your Graphs and Visuals /Felice Frankel/
      Quantum Computing - What, Why, How /Frank Wilczek/Synthesizing Life /Steve Benner/
    • Well, actually, I could not chose as I told Bora I would help with his session on Open Science. This one turned into a passionate conversation about many topics relating to Open Science. There was also quite a collection of people there including young and old. Much of the initial discussion was around the problems and difficulties in doing Open Science (see here and here and here for more detail on this and the session overall - in particular the young scientists, who I felt did not get enough time to talk in this session, had many concerns). I felt Pam Silver expressed the most important and interesting concern which was that she said that students in the Systems Biology program at Harvard seemed most dismayed by the slow pace of publishing). Some other comments by the village elders that were present (e.g., Eric Lander and Carl Djerassi) were not overly encouraging in terms of how people get jobs in the field (I am not sure Eric understood what the young scientist's concerns were completely and I think he may have made them feel worse about things when he was trying to make them feel better).
    • I think I sent the session down the wrong path at the way beginning by talking about the need to identify roadblocks to Open Science and to figure out ways to circumvent them. This is a true need but it made the beginning of the session seem more about problems than visions for the ideal future, which is what most people seemed to have expected.
    • But then Paul Ginsparg and Dave Carlson got us back to talking about the good, positive things about Open Science. Most importantly for me, we got a brief look at Jean Claude Bradley's Open Notebook system which I would like to use in my lab.
    Session 2
    • Here the choices were:
    • Efficient Inverse Control: Through the Users Not the Resources /Wefi Vardi aka Neuman/
      Clinical Problems in Neuroscience / Towards Practical Cognitive Augmentation /Vaughn Bell/ / Towards Practical Cognitive Augmentataion /Ed Boyden/How to Build Intelligent Machines /Jeff Hawkins/
      Why aren't there more Scientists on the Covers of Magazines /Jackie Floyd/Future of Human Space Flight and Ocean Exploration /D Mindell/
      Science and Art /Brian Derbey/




    • 3D Video Applications: How to Publish Science in Video /Steve Silverman/The Nature of Time and Mathematics /Jaren Lanier & Neal Stephenson & Lee Smolin/Alternate terms of Science EducationFuture History of Biology /Rob Carlson/Human Cell and Regeneration Map or is it worth building a cellular resolution database for the whole human body? / Ahila Attila Csordas /

    • I was completely torn here and even ended up being late because I was staring at the bulletin board trying to decide. Finally I went to "the future of human space and ocean exploration" since I thought this was going to be split into space for the first half hour and ocean for the second. Instead they talked about space the whole time I was there and the ocean exploration representative did not get too many words in. But the space discussion was actually really interesting with Pete Worden, the head of the NASA Ames Research Center there discussing future space flights and many other space afficionados present. I thought the most insightful and interesting comments in the session came when everyone was talking about how to better publicize space travel such that it got better attention. And then Larry Page from Google said, basically, that this was simply "marketing" and that the key was to do really cool things in space and not worry about the marketing. This also relates to the safety culture of NASA and other space travel agencies - many of us pointed out that 1000s of people die every day from various causes and that if space travel cannot take risks and accept that some people will die, we have no hope of doing anything interesting in space (e.g., Page pointed out that more people probably dies in the making and moving of the space shuttle than have died in the accidents).
    Session 3. Here the choices were:
    • 3D Printing / Robot Printing / Food Printing / Printer Printing /Lipson, Olliver, Bonabeau/Just When You Thought It Was Safe to Teach Evolution /Eugeinee Scott/Sequencing the Genome: Implications, Ethics, Goals /Linda Avery, Steve Benner/Are Patents Preventing Innovation? /S Patton/Tricoder is Finally Here
      Ethical Implications of the Information Society /Luciano Floridi/






    • Reversible Computation and Its Connections to Quantum Interpretations /Gary Flake/Mapping Science and Other Big Networks /Carl Bergstrom/A Magician Looks at the Irrational and Pseudo-Science /James Randi/Listening to the World: Voices from the Blue Deep /Chris Clark/
      dISSEMINATION AND aCCESS TO dISCOVERY - cOMMUNICATION OF sCIENCE /gABE lYON/

    • And though I promised myself I would go to things I knew nothing about, I simply had to go to this one by Eugenia Scott on evolution education.
    • Here I found the discussion quite varied and interesting. Some people suggested that evolutionary biologists should be careful about what they say because intelligent design supporters might use it for their own good. Henry Gee and I were adamant that one should not temper ones science for such fears.
    • Other interesting things in the session: Dwayne Spradlin did a good job of making everybody justify assumptions that they made about people and Sarah Keller pointed out that it would be useful to have evolution education in chemistry classes
    • Then it was time for a Googlicious lunch (OK - it was not as good as I had expected but it was better than any other conference food I have had). Paul Ginsparg and I went through the line together and decided to sit outside the tent. Good choice as inside the tent was absurdly loud. Really good talking to Ginsparg for a while about PLoS and Open Access. He is one of those people who, when you find out he won a Macarthur "genious" award you are like "well, duh - how could he not win one?"
    • After we sat down Larry Page and Lucy Southworth sat down as did some others who I have already spaced out on. The best part of the conversation at lunch was Larry Page giving Ginsparg grief about some technical annoyances Google found in their early days with the Arxiv preprint archive. Apparently, Google had to shut down some connections/services to Arxiv for a while and this was the first conversation about it.
    • Also interesting was briefly hearing about Lucy's work at Stanford on mouse aging and changes in gene expression. This was particularly interesting to me since I hope to study how microbial populations inside animals change with aging. I unfortunately did not get enough time to interrogate her about her project - the perils of having too many interesting things going on.
    Well, I will have to post more later on the rest of Day 2.

    SciFoo Camp Day 1 - More notes

    Well, I am finally getting around to writing up the rest of my impressions of Day 1 at SciFoo camp. For detail on the camp and the outline of Day 1 go here. For those too busy or lazy to go there, SciFoo camp was a 2.5 day un-conference at Google HQ organized by Nature and O'Reilly publishers.

    Some more comments on Day 1.
    • Paul Serano and colleagues had a display of dinosaur fossils in the main reception area. They announced that they did not want anyone publishing pictures of the fossils since they were unpublished, following the big trend among paleontologists to not be too open about anything. Funny since Serano also gave some lip service to the idea of openness and sharing --- clearly what he meant was different from what many others meant.
    • I talked to Eugenia Scott for a bit before the sign ups and gave her the lowdown on SciFoo, and encouraged her to have a session on Evolution education, which thankfully she did.
    • The three words I chose for my introduction were "Microbes Rule Planet, " which of course is true.
    • Tim O'Reilly was the grandmaster of introductions. He was running around introducing as many people as he could to others he thought they would find interesting. He introduced me to Jim McBride (who is currently I think working with Howtoons). We had a good conversation about how the best way to attract good mathematicians to something in biology is to make sure the math is really hard (and why in general it is fun to work on something hard).
    • Martha Stewart gave a brief summary of how she made food for Charles Simonyi's space flight and trip to the International Space Station.
    • The food, as always at Google, was quite good.
    • I hope Felice Frankel would be happy that my notes for her talk on "Envisioning Science" are all drawings and no words. Her key point was "Representation clarifies scientific thinking." I could not agree more.