
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.
Eisen Lab Blog
Redefining Tomorrow’s Table
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.
Twisted Tree of Life Award #1: Salk Institute Press Release on Kinases
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”
Building a new Alvin
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.
Tree of Life Imagery at Starbucks

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.
Open Access Pioneer Award #2: R. Preston McAfee
Great article in the LA Times on August 18 by Gale Holland about “Free digital textbooks.” (see Free digital texts begin to challenge costly college textbooks in California)
The article discussed some issues in open source textbook publishing including in particular R. Preston McAfee’s work on creating a free online economics textbook. McAfee is a professor at Caltech and is a self described right winger.
“I’m a right-wing economist, so they can’t call me a communist,” McAfee said.
And he goes on to say
“What makes us rich as a society is what we know and what we can do,” he said. “Anything that stands in the way of the dissemination of knowledge is a real problem.”
The article discussed other open source educational materials including:
- Merlot, from Cal. St. Universities which is a “a searchable collection of peer-reviewed, online multimedia materials.”
- Connexions, from Rice University , which “stores free, open-licensed educational materials in fields such as music, electrical engineering and psychology.
- OpenCourseWare from MIT which includes “virtually its entire curricula online — video lectures, problems sets and exams for more than 1,800 courses in 33 disciplines.”
- Wikibooks, a collection of editable textbooks
- The Digital Marketplace, from Cal. St. U. which is a “website for selecting, comparing, sharing, approving and distributing both open-source and commercial online educational materials.”
Hat tip to Jeremy Peterson and Eilleen Hamilton for pointing this out.
Update – required evolution reading/ Harmon story/ Mickey Mouse
He started with Mickey Mouse.
On the projector, Mr. Campbell placed slides of the cartoon icon: one at his skinny genesis in 1928; one from his 1940 turn as the impish Sorcerer’s Apprentice; and another of the rounded, ingratiating charmer of Mouse Club fame.
“How,” he asked his students, “has Mickey changed?”
Natives of Disney World’s home state, they waved their hands and called out answers.
“His tail gets shorter,” Bryce volunteered.
“Bigger eyes!” someone else shouted.
“He looks happier,” one girl observed. “And cuter.”
Mr. Campbell smiled. “Mickey evolved,” he said. “And Mickey gets cuter because Walt Disney makes more money that way. That is ‘selection.’ ”
Required evolution education reading – Amy Harmon on Florida Evolution teaching
Amy Harmon has done it again. First it was the series on the “DNA age” which had a suite of interesting pieces on the more personal side of DNA and genomics and won her one of those little pulitzer thingamajiggers. And now she has published a piece on the personal side of evolution education. This piece “A Teacher on the Front Line as Faith and Science Clash“, which I think will be in tomorrow’s Sunday New York Times, is really a must read for all interested in evolution education and evolution in general.
In the article, Harmon details the story of a Florida high school science teacher, David Campbell, and his efforts to teach evolution in a Biology class. I find the whole story fascinating in many ways. First, despite thinking I was paying attention, I was not really aware that Florida now required evolution to be taught in high school biology classes. Harmon details some of the history of how this came to be including how Campbell founded Florida Citizens for Science and helped push for new standards in biology teaching. Campbell’s efforts to put science at the front of science teaching and to keep religious beliefs out is inspiring.
Harmon also details the trials and tribulations of Campbell actually trying to teach about evolution to high school students, many of whom come armed with anti-evolution ideas and literature. And Campbell does a great job with some subtle details — in fact he seems to have a better grasp of evolutionary biology than many active biologists. For example, he does a good job with emphasizing that humans did not evolve from chimps but instead both evolved from a common ancestor. This is something many many biologists do not always get accurately.
I think the whole piece should be required reading for all evolutionary biologists, all biologists, and all science teachers. I confess, Harmon did ask me to glance the piece over a few days to give some feedback on a few sections, so I am perhaps a bit biased. But I am really hoping Harmon stays on this topic and does for evolution what she did for the DNA age, with a whole series on the personal side of things. This is so desperately needed with too much of the debate focusing on an argument about facts and faith and too little about the people in the trenches.
Good Open Access News from Max Planck
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).
Some outdated webpages of mine need external links
Here are some links to some very outdated webpages of mine. I want them to come up in Google Searches and this seemed the best way. I am back posting this a year to hide it from the front of my blog.
