Thanks to my mom for this one. PLoS Hats rule.
I spent the last few days at a “retreat” for the Joint Genome Institute and heard about a few things there worth sharing with everyone. I will try and post about some of them in the next few days. Here is one. The JGI and the Center for Integrative Genomics have made a pretty cool tool for comparative analyses of plant genomes. It is called Phytozome and has a variety of simple and nice features. JGI is doing more and more work on plant genomes as part of their energy research and I think Phytozome could turn into a good place to go to get the latest plant genome information. Go to http://www.phytozome.net to see the real thing.
OK – I cannot help it. Whenever I see this little train letters in stores everywhere I spell something related to PLoS. If you support OA, please continue the conspiracy and spell something OA-related wherever you find letters like this. PS – Vaughn this is for your kid.
Tony Trewavas has an interesting review (Redefining “Natural” in Agriculture) in PLoS Biology of my friend and colleague Pam Ronald’s new book “Tomorrow’s Table: Organic Farming, Genetics and the Future of Food.”
I was planning on eventually writing my own review of her book but not sure when I will get to it. I personally like the book a great deal, and enjoy how it switches back and forth between the authors (Pam and her husband Raoul Adamchak) and how it interweaves personal stories with discussion of the science and practice of organic farming and plant genetic engineering.
Trewaras has some things in the review I agree with a great deal like
“The text deals with many of the questions raised by the public about GE crops in a sensible and balanced manner, quoting various sources of reliable information on the concerns about risks to health and environment that often recur. It also mentions Richard Jefferson, who is Chairman of CAMBIA, a non-profit organisation that attempts to make the tools of biotechnology widely and freely available (http://www.cambia.org/). As a scientist, I cannot help but applaud!”
I personally love what CAMBIA is doing and found the discussion of CAMBIA in the book to be interesting. I have gotten to know Richard Jefferson over the last few years and think he is a true pioneer in revolutionizing biotechnology and freeing it from the shackles of over protectionism.
Trewavas also has a very interesting thread about the value of different opinions. Since this was printed in PLoS Biology and is under a CC license I can reprint it here (with acknowledgment of the source – Citation: Trewavas T (2008) Redefining “Natural” in Agriculture. PLoS Biol 6(8): e199 doi:10.1371/journal.pbio.0060199) and it is worth doing so:
The continuing conversation did not resolve the issues between them. It convinced me, however (if I needed convincing), that while everyone is entitled to their opinions, when dealing with detailed technical matters of science or medicine or any subject that requires enormous qualifications and experience, the notion that all opinions have equal validity is simply downright wrong. If you want real information on the safety of heart surgery procedures, do you follow the advice of a qualified heart surgeon or the local butcher? If you want advice on flying a jumbo jet, do you ask the local bus driver or a pilot with 10,000 hours of experience flying jumbo jets? And if you want advice on how to captain a supertanker, do you ask a person whose experience is limited to rowing a dinghy? Mistakes by surgeons are not uncommon, 70% of air crashes result from pilot error, and occasionally supertankers hit the rocks. But relying on rank amateurs instead of professionals would guarantee instant catastrophe. Many branches of science are very complex. However, being a scientist isn’t enough, of course, as being a scientist doesn’t qualify you to advise on any subject except your specialty. To provide advice that can lead to sensible policy requires not only a thorough understanding of the workings and literature of the particular scientific area but many decades of experience in that field.
It is unfortunate that for the past 40 years, agriculture in particular has been damaged by opinionated groups of the public that have forcefully used fear and anxiety and carefully selected information to try and coerce policy makers to adopt their own mistaken and unqualified views. Fear and emotion do not make for good policy. I applaud Ronald’s conclusion that “if citizens vote, it should be for a specific matter on which they are well informed, not because of general concerns about a new technology.”
The corollary is that on most technical matters, the public can never be well enough informed. If scientific knowledge does not form the basis of policy on technology, basing such policy on ignorance can be guaranteed to generate disaster. It was Slovik in his classic Perception of Risk [3] who demonstrated that non-experts overestimate the frequency of death from rare causes while underestimating the frequency of common causes of death, and who established clearly how additional knowledge changed expert understanding. The use of the local ordinance by activist groups to stop GE farming is only too reminiscent of the damage done by Lysenkoism to Soviet farming in the 40s, which took decades to recover from, once it was abandoned.
Basically, he is indirectly agreeing with Ronald/Adamchak that some negative opinions of GE are simply not valid. Here I think I disagree with all of them. I think much of the objection to GE modification of plants is an esthetic objection and thus presenting scientific arguments for why it is OK to do is a bit off tangent. It is kind of like when someone says “that house is ugly.” Do you respond by saying “Well, actually, the shape and color patterns have been shown to appeal to human sensory systems” Not too helpful. I feel that the same is happening with GE plants — if people’s instinctively do not like them, telling them about the science is not necessarily going to help. Nothing wrong with educating about the science, but I think it is a red herring to say that some of the anti-GE folks do not understand the science and therefore their objections must be wrong. I feel similar vibes in the evolution education discussion going on around the world. I think many people latch on to ID and Creationism because it appeals to them in a esthetic sense. And one needs to be really gentle/careful about bringing science into the discussion (except of course, when one is teaching a science class — then you teach the science).
So sure – I have some quibbles about parts of the book. As does Trewavas (he has to raise some objections – any book review that does not have them seems like fan mail and not a review).
PS – For more on the book see Pam’s blog here.
I am starting a new award here — for people or sites that do something silly in regard to the “Tree of Life” but should know better. That is, this is for scientists or sciency sites that do something unseemly with the Tree of Life. And the first award goes to the Salk Institute for their press release relating to a paper on kinases in single celled choanoflagellates (OK – the pres release is a month and a half old but I was out sick – and I drafted this 7/8/08). In the press release, which discusses a PNAS paper by Gerard Manning and colleagues (Manning does some really great comparative work on kinases and helped me look at kinases in a few genomes such as that of Tetrahymena thermophila). I note – it seems Manning or someone has paid the OA fee for this paper so anyone can read it.
The paper seems both sound and interesting. And it has a really really cool tree figure.
But the press release has a few doozies. The worst (or best, I guess, depending on your point of view) is the following:
It commands a signaling network more elaborate and diverse than found in any multicellular organism higher up on the evolutionary tree, researchers at the Salk Institute for Biological Studies have discovered.
Yup that is right. A modern organism, living today is somehow “lower” on the tree of life than we are. Too bad the person who wrote the press release did not read Amy Harmon’s recent Times story on evolution education. Or they could have gotten help from the high school science teacher Harmon featured, who taught his students about how modern organisms did not evolve from other modern organisms.
And for using one of my most hated metaphors in all of evolution (higher and lower organisms), Salk gets my first “Twisted Tree of Life Award”
Quick post here. For those interested in Deep Sea research, you should check out the story by William Broad in the NY Times on building a replacement for Alvin (New Submersible to Expand Deep-Sea Exploration). Alvin is a wonderful little submarine that I and many others have relied upon for much of our research. But it definitely has some issues. And it looks like Woods Hole Oceanographic Institute is in the processof building a replacement.
Not the best resolution (damn that iPhone camera) but just thought I would post the picture I saw at a Starbucks in San Francisco where I was for a DARPA meeting discussion the “laws of biology”. You see – even Starbucks is a fan of the Tree of Life.
Mark Patterson reports in the PLoS Blog some really good OA news (see Max Planck Society covers publication fees for PLoS journals). The Max Planck Society which has always be a strong OA supporter, will now pay the PLoS Publication fee for all papers articles where an author is affiliated with the Max Planck Institute. So now any author from there will not have to think about fees if they choose to publish in PLoS. I hope lots of other institutes follow this (not just for PLOS papers but for all OA journals).
Just a little quick link here. People might be interested to check out the “Are we alone” Radio Show from July 21, 2008 (Are We Alone). A direct MP3 link is here. Here is there summary of the show from that date:
Remember Mr. Potato Head? You changed his look by snapping in plastic mustaches, googly eyes and feet. Now imagine doing the same with a living cell: inserting the genes you want to create the organism you want. Welcome to the world of synthetic biology. It has potential to create new bio-fuels and life-saving drugs. It also ushers in a host of ethical and safety concerns. We examine both when we discuss this emerging science of mix and match genes. Plus, does doing an end run around Mother Nature challenge the essence of life itself?
Guests:
- Jay Keasling – professor of chemical engineering and biological engineering at UC Berkeley and founder of Amyris Biotechnologies
- Jonathan Eisen – biologist at UC Davis
- Jim Thomas – researcher at ETC group in Ottawa, Canada
- Ed Regis – science writer and author of What Is Life: Investigating the Nature of Life in the Age of Synthetic Biology
- Michael Dosmann – curator of Living Collections at the Arnold Arboretum of Harvard University
This show is produced by the SETI institute and has some interesting topics on different science things.
SPARC has a nice set of talks online about Harvard’s move towards a University wide open access system (see Campus Open Access Policies: The Harvard Experience and How to Get There (SPARC))
From the web site
“This spring, Harvard’s Faculty of Arts and Sciences voted to enable open access to their scholarly articles in an institutional repository. This vote granted the university the rights necessary to archive and make freely available on the Internet articles written by Arts and Sciences faculty members. It is the first time the faculty of a U.S. university has voted for an open access directive and the first time a faculty has granted permission to the university to make its articles available through open access. It is because of this vote, and the efforts leading up to it, that the Harvard FAS was named as the SPARC Innovators for June 2008.
The forum offers an exploration of the motivations behind the Harvard policy, the groundwork invested in its creation, reactions and outcomes to date, and the broader implications of this historic step. Headlining the event is Stuart M. Shieber, professor of computer science at Harvard, director of the Center for Research on Computation and Society, faculty co-director of the Berkman Center for Internet and Society, and the key architect of the policy.
Shieber is joined by Catherine Candee, executive director, Strategic Publishing and Broadcast Initiatives, from the office of the president of the University of California, who relates similar activity in the UC system; and by Kevin L. Smith, JD, scholarly communications officer at Duke University, who suggests legal considerations for institutions following the open access policy path.”
Hat tip to Michael Rogawski from U. C. Davis for pointing this out. In particular, he and I are very interested in the discussion by Catherine Candee about why the UC system did not do this before Harvard (we are hoping to get the UC to do something like this). Rogawski has also pointed me in the direction of some nice tools for sharing my publications through the UC system (see his BE Press site here).
Jonathan Eisen's Lab 
