Friday, August 29, 2008

Sarah Palin on EvolutionCreationism

Well, it seems McCain has further embraced an anti-science agenda with his pick as Sarah Palin as his running mate.

The Science Bloggers are a bit up in arms over this. I think there is some hope that she/McCain will drift back to the middle on this at some point but they both now seem to fall in the camp of the Intelligent Design supporters. It is the "independent" streak both do seem to show occasionally that gives me hope that if they do get elected, they will not be as tied to the ID supporters as they will be during the election.

Anyway, here are some things I found on the web about Palin's evolution views:

NewMiner.Com: in response to written questions in a 2002 election ...
Q: The education section of the Republican Party of Alaska’s platform states “We support giving Creation Science equal representation with other theories of the origin of life. If evolution is taught, it should be presented as only a theory.” Do you support this position? Why?

A: I support this plank in the Republican Party’s platform. I believe society can have healthy debates on scientific theories, so equal representation of creation and evolution shouldn’t be an offense.
Anchorage Daily News in 2006 reported
The volatile issue of teaching creation science in public schools popped up in the Alaska governor's race this week when Republican Sarah Palin said she thinks creationism should be taught alongside evolution in the state's public classrooms.

Palin was answering a question from the moderator near the conclusion of Wednesday night's televised debate on KAKM Channel 7 when she said, "Teach both. You know, don't be afraid of information. Healthy debate is so important, and it's so valuable in our schools. I am a proponent of teaching both."
Most other thigns I have seen are rehashing these two stories in some way. If anyone has any other detail I would love to see it.

Examples of blog posts on this issue include:

Thursday, August 28, 2008

I see PLoS in everything #2


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.

Wednesday, August 27, 2008

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).

Despite my quibbles here and there, the book really is a must read for those interested in GMOs and/or the organic farming movement as well those thinking about "slow food" and other related topics. In addition it is a wonderful personlized story, with a mixture of recipes, stories of research, discussions of teaching about organic agriculture, and some minor family drama. For the same reason that I like Amy Harmon's New York Times stories (such as the recent one on evolution) I like this book - it personalizes what is frequently a boring impersonal discussion.

And of course it does not hurt that the heart of the story / discussion is good. Ronald/Adamchak present an overall idea I have a hard time arguing against - GE and organic growth practices both have a lot to offer the world and if we took the good parts of both, a "GE-Organic" system might be highly beneficial to all. For example, in principle, GE plants can lead to a reduction in the use of pesticides and fertilizer. Similarly, they could lead to a reduction in water use and higher crop yields. Since it seems unlikely that the current organic movement will embrace the benefits of GE crops, it will probably require a whole new movement to merge the two. It will also require the companies and organizations that push GE to do it with the environment and health of people and the planet in mind. To me, the biggest problem with GE food and farming is that it seems to be used more to help the farmers and the companies selling stuff than the consumers and the public. If that changed, I can see people embracing GE plants in much the same way they embrace GE medicines.

PS - For more on the book see Pam's blog here.

Tuesday, August 26, 2008

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"

Monday, August 25, 2008

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.







------------------------------------------
Follow up.  After Laura wrote in asking about the origins of this picture I have searched around and found many others interested in it.  I note - the caption says "The Deeper the Roots - the Higher the Reach".  I have not found the origins of the print but here are some other discussions

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."
Now, I am not saying here there is not a place for textbooks in the normal model (I have one).  Unlike basic science papers, for which the cost of making a presentable paper is relatively low, the cost of producing a textbook can be very very high.  Thus I think publishers are welcome to work with authors to come up with their own models for how to publish the texts.  But nevertheless, the more we can get good open source textbooks out there, the better off we will be.  And thus, for his role in promoting the release of what seems to be a high quality open source textbook, I am giving R. Preston McAfee my second "Open Access Pioneer Award.

Hat tip to Jeremy Peterson and Eilleen Hamilton for pointing this out.

Update - required evolution reading/ Harmon story/ Mickey Mouse

Yesterday I posted about Amy Harmon's excellent story in the NY Times about evolution education.  For more on it see my post - Required evolution education reading - Amy Harmon on Florida Evolution teaching

I just wanted to give an update here as I have seen a few postings out there discussing the Mickey Mouse example in the story.  In the story, Harmon described how David Campbell, the Florida high school science teacher uses the evolution of Mickey Mouse as an  example of natural selection.  

From the Times article:

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.’ ”

Some bloggers have questioned using this example (see john hawks weblog for example as well as Bora's excellent post about this story here) because it seems more like Intelligent Design than natural selection.  I disagree and wanted to point out that this is a classic Stephen Jay Gould teaching case study which he detailed (see A BIOLOGICAL HOMAGE TO MICKEY MOUSE Stephen Jay Gould).  

In fact, when I was an undergrad at Harvard and was taking Gould's class, we played around with a cool new computer program called MacClade to track the evolution of Mickey Mouse. Little did I know I would still be using Macclade and its descendants today.

Saturday, August 23, 2008

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.

Addendum: Clearly lots of other bloggers liked this.  Here are some:

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).

Thursday, August 21, 2008

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.

Monday, August 11, 2008

Shameless Self Promotion # 200: Are We Alone

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:
This show is produced by the SETI institute and has some interesting topics on different science things.

Saturday, August 09, 2008

Campus Open Access Policies: The Harvard Experience and How to Get There (SPARC)

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).

Friday, August 08, 2008

Happy Birthday Anna Eisen 8-8-8 at 8:08 PM

Happy Birthday Anna Eisen (my niece)
8/8/08 at 8:08 PM

New Yorker on Superbugs

Still catching up after being out sick with an antibiotic resistant infection. But I had to post on this one. The New Yorker has new piece by Jerome Groopman on, well, antibiotic resistant bacteria. See Medical Dispatch: Superbugs: Reporting & Essays: The New Yorker

Thanks to Saul J for pointing this out.

I particularly like the ending
No one, Moellering said, has developed a way to disarm bacteria sufficiently to allow the human body to naturally and consistently defend against them. I asked him what we should do to combat these new superbugs. “Nobody has the answer right now,” he said. “The fact of the matter is that we have found all the easy targets” for drug development. He went on, “So the only other thing we can do is continue to work on antibiotic stewardship.” Meanwhile, new resistant bacteria, Moellering asserted, aren’t going to go away. “We can temper things, we might be able to slow the rate of emergence of resistance, but it’s unlikely that we will ever be able to conquer it.”

Friday, August 01, 2008

Open Metagenomics Highlight: Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

OK - it is not quite metagenomics, but there is new paper in PLoS One worth looking at if you study uncultured organisms. This paper (Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing) reports on a slightly new twist in carrying out deep rRNA surveys of uncultured microbes using one of the "next" generation sequencing methods.

Open Metagenomics Highlight - PloS Biology paper reporting more from Banfield lab on the Acid Mine Drainage

Just a quick "Open Metagneomics" posting here. There is a very interesting paper in PLoS Biology that just came out reporting more detail from Jill Banfield's lab on their studies of an Acid Mine Drainage (AMD) site. This paper is ostly a population genomic study of the microbes living in the AMD. See the paper at PLoS Biology - Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation.

Closed Access Award #2: Andrey Rzhetsky, Michael Seringhaus and Mark Gerstein

Just got pointed to a new paper by someone near and dear to me. In this paper (Seeking a New Biology through Text Mining), Andrey Rzhetsky, Michael Seringhaus and Mark Gerstein seem to argue for the importance of text mining for the future of biology research. Text mining is indeed an important new tool in biology. Of course, it works best if you have access to the text. Alas, I would tell you more about their paper, but I have been out sick and stuck at home, and I do not have access to their paper, which was published in Cell. And thus, even without seeing their paper, I am giving them my second "Closed Access Award" for apparently outlining a path for a new biology that will be only available to some, not all.

Open Anthrax: Open access publications for those writing about B. anthracis

Well, I am sure there are going to be a million news stories and blogs over the next few days about the anthrax letters. That is because of the recent death of someone who appears to have been the latest suspect in the anthrax mailings (see for example CNN Report: Anthrax suspect kills self as FBI closes in). (Also see the LA Times, which broke the story). I must say, after the disastrous handling of some of the previous suspects, I think we should reserve judgement on this case until some of the evidence is made public.

In the interest of helping out some of those interested in the science of studying the organism that causes anthrax I am posting here some links to fully open access articles on B. anthracis.

PLoS One papers
PLoS biology Papers
Biomed Central Journals