Recently in Shoptalk Category

I am sure we all read it in the papers several weeks ago: Two-thirds of all cancers are caused by bad luck. The New York Times said so. Science magazine, which published the original article said so too.

Only problem, the original article did not say that, and to her credit, Jennifer Couzin-Frankel, the Science reporter who “said so too,” corrected the record in a sort of meditation on the difficulty of getting difficult scientific concepts correct while working on deadline.

In fact, the authors did not say that “[r]andom mutations may account for two-thirds of the risk of getting many types of cancer, leaving the usual suspects—heredity and environmental factors—to account for only one-third, …” as the Times put it. What they said was more subtle, that two-thirds of the difference in cancer rates between different tissues could be explained by random bad luck. That is, “[s]ome tissues are overtaken by cancer more readily than others, and mutations accumulating in stem cells explained two-thirds of that variability,” in Couzin-Frankel’s words.

It is good to know that Science is self-correcting.

A report this morning on NPR asks, “Is collecting animals for science a noble mission or a threat?” The question is left unanswered, but the reporter notes that collecting specimens from small, isolated, and endangered species can be counterproductive, at best. Ben Minteer, an author of the Science article that inspired the NPR report (not to mention a rebuttal by around 120 other scientists), recommends photographs and DNA samples in lieu of specimens, but other researchers challenge that approach as impractical.

Also this morning, Mark Bekoff, a professor emeritus of evolutionary biology at the University of Colorado, takes the Boulder Daily Camera to task for using the term “euthanasia” when black bears or cougars are killed for venturing into an urban environment. The animals are not euthanized, says Bekoff; they are killed. I might add that laboratory rats, for example, are not sacrificed; they are killed.

All of which raises the question: Are we too ready to kill nonhuman animals?

Expanding the genetic alphabet


By Gert Korthof.

“It is a very, very hard problem. Getting all the pieces to work means re-engineering 3.5 billion years of evolution. It’s so ambitious.” These are the words of a scientist 14 years ago [1]. He was talking about the project of inventing new bases to include in DNA and let the new DNA function in a living cell. Now an important milestone has been reached towards that goal. Scientists have succeeded in adding a new base pair, d5SICS (call it X) and dNaM (call it Y), to the DNA of the bacterium E. coli and let it replicate its DNA [2]. Furthermore, the growth rate of the bacterium was not significantly slowed down, and the DNA-repair system did not remove the new bases. These results give us hope for realistic answers to the so far speculative questions as to why evolution settled on only two base pairs in DNA. Could there be superior bases and superior DNA?


Plasmid, modified from Wikipedia. The yellow dot is the new base pair.

By Brianne Fagan.

This column by Brianne Fagan, a senior majoring in chemical engineering at the Colorado School of Mines, is a response to a recent New York Times column on women in science. It was prepared as part of a class on Explorations in Science, Technology, and Society. The class is co-taught by physics professor Lincoln Carr and Toni Lefton of the Liberal Arts and International Studies department. The course is offered through the McBride Honors Program.

During a class presentation about Kate Kirby, one of my peers brought up some statistics about girls in math and science while sharing her own motivations for pursing environmental engineering. During a related discussion, the two female Physics students both discussed their mostly positive experiences as women in the Physics Department at the Colorado School of Mines. The question always seems to remain, though: Why do so few girls pursue degrees in STEM (science, technology, engineering, and math) fields?

Well, I was perusing the articles on my New York Times app this morning, and what did I find?

Troy Britain joins the Thumb crew


Troy Britain has joined the Panda’s Thumb crew. Troy is a long-time veteran of the creationism wars. He blogs at Playing Chess with Pigeons. He is a TalkOrigins Archive volunteer, was a co-founder of the McLean v. Arkansas Documentation Project, and is a member of both NCSE and the Skeptics Society.

Welcome, Troy! We look forward to your posts.

Late last night, I got word from Ed Brayton that Panda’s Thumb blogger Skip Evans was found dead at his Madison, Wisconsin home. Skip had been having problems with his cardiovascular system, and so far as we know now those problems appear to have been the cause of his death.

Skip should be well known to most of our readers, either by his posts here or by some of the contributions that he made to advancing science education and countering the socio-political machinations of the creationism movement. A couple of the high-profile things Skip did included much of the concept of NCSE’s “Project Steve” and its naming, plus taking on (now convicted felon) “Dr.” Kent Hovind concerning his “doctoral disssertation”. Skip personally requested a copy of Hovind’s dissertation from “Patriot University”, and they shipped Skip the original, including taped-in graphics Hovind had scissored out of science magazines.

I’ll plan to add some photos later, but I wanted this news to go out soonest to our community. Skip was a friend of mine, and I appreciated his good humor. I already miss him.

His colleague posted this comment on Facebook:

To ease the pain of Skip’s dear friends, please know that he has so many people who loved him here. He was only with our company a year, but brought more life and energy to us in that short time than most people do in a lifetime. I went to a presentation on the fallacies of creationism a few weeks ago, where Skip gave an irreverent and poignant and funny talk. Over 150 people were in stitches. We were lucky to know him.

At Evolution2012 in spirit


Evolution 2012 is starting tomorrow! This time it’s in Ottawa, representing the First Joint Congress on Evolutionary Biology – a meeting of the American Society of Naturalists (ASN), the Canadian Society for Ecology and Evolution (CSEE), the European Society for Evolutionary Biology (ESEB), the Society for the Study of Evolution (SSE), and the Society of Systematic Biologists (SSB).

Sadly, though, I can’t go this year. A good friend of mine is having her wedding right in the middle of the meeting. There’s only one wedding in someone’s life (well, hopefully!) and there are a lot of meetings, so I picked the wedding. I guess the wedding won’t be entirely evolution-free, seeing as the bride studies extinct giant sloths.

But at the moment I’m looking over the program for Evolution 2012 and experiencing a few missing-the-conference blues.

Ah, but here’s something to cheer me up. After you’ve been in science for awhile, you discover that you don’t even have to be at a meeting for your name to get into the program, due to the collaborations you are involved with! Here are the papers I’m a coauthor on:

Eat dirt


A recent article in Natural History magazine does not exactly advise eating dirt, but rather examines what the author calls “the hygiene hypothesis,” that is, the hypothesis that the increasing prevalence of asthma and other autoimmune diseases is the result of excessive cleanliness. Along the way, the author, Druin Burch, illuminates in some detail just how good science works.

Note: This topic is outside of my specialty, so it may be that I have missed some important points. I think I’ve got the basics correct, but this is a very complex topic. I will be interested in critical but constructive posts in the comments.

Update: required reading, which basically confirms my points I think:

Weiss, K. M. and J. C. Long (2009). “Non-Darwinian estimation: My ancestors, my genes’ ancestors.” Genome Research 19(5), 703-710.

Nievergelt, C. M., O. Libiger and N. J. Schork (2007). “Generalized Analysis of Molecular Variance.” PLoS Genetics 3(4), e51.

On Monday, Jerry Coyne at Why Evolution is True posted on “Are there human races?” While acknowledging the very bad history of the race concept in human history, and noting some of the problems with applying the concept to humans, Coyne concluded, basically, that the answer was yes, there are human races. While reviewing Jan Sapp’s piece which concluded that human races did not objectively exist, Coyne wrote:

Teaching real science


Under that headline, Bruce Alberts, the editor of Science magazine, announced the first of 15 winners of the Science Prize for Inquiry-based Instruction. The first winner, An Inquiry-Based Curriculum for Nonmajors, describes “an inquiry-based curriculum designed to increase the scientific literacy of those who are not science majors and to impart a fundamental understanding of the nature of scientific investigation.” The curriculum uses a series of independent modules in which the students design their own experiments. The curriculum described in the paper is Light, Sight, and Rainbows. It Includes a scattering experiment and a solar oven experiment designed by the students, and looked to my (optical) eye like very sound pedagogy.

Guardian Science Blogs


Another group (or as self-styled, “network”) of science blogs is being set up at the Guardian newspaper in order to “entertain, enrage, and inform.” According to the announcement, to start with there will be four blogs covering “evolution and ecology, politics and campaigns, skepticism (with a dollop of righteous anger) and particle physics…”. A fifth will be more generic, and “…will hopefully become a window onto just some of the discussions going on elsewhere. It will also host the Guardian’s first ever science blog festival - a celebration of the best writing on the web.”

We start tomorrow with the supremely thoughtful Mo Costandi of Neurophilosophy. You can also look forward to posts from Ed Yong, Brian Switek, Jenny Rohn, Deborah Blum, Dorothy Bishop and Vaughan Bell among many others.

The Guardian’s science blogs join a growing array of aggregations of science bloggers, most of which are well known to PT readers.

Comment on access to publicly funded research


I got this announcement from AAAS today:

Make your voice heard!

We have been asked to relay to the broad scientific community the following opportunity to advise US government policymaking deliberations.

You can read the latest updates at:

The Obama Administration is seeking public input on policies concerning access to publicly-funded research results, such as those that appear in academic and scholarly journal articles. Currently, the National Institutes of Health require that research funded by its grants be made available to the public online at no charge within 12 months of publication. The Administration is seeking views as to whether this policy should be extended to other science agencies and, if so, how it should be implemented.

The Office of Science and Technology Policy in the Executive Office of the President and the White House Open Government Initiative are launching a “Public Access Policy Forum” to invite public participation in thinking through what the Federal government’s policy should be with regard to public access to published federally-funded research results.

To that end, OSTP will conduct an interactive, online discussion beginning Thursday, December 10. The discussion will focus on three major areas of interest:

* Implementation (Dec. 10 to 20): Which Federal agencies are good candidates to adopt Public Access policies? What variables (field of science, proportion of research funded by public or private entities, etc.) should affect how public access is implemented at various agencies, including the maximum length of time between publication and public release? Add your comments

You will want to read the Terms of Participation and will need to register a new account and log in using the link at the bottom of the page to comment. Tips on how to comment and moderate posts are listed in the right-hand column. * Features and Technology (Dec. 21 to Dec 31): In what format should the data be submitted in order to make it easy to search and retrieve information, and to make it easy for others to link to it? Are there existing digital standards for archiving and interoperability to maximize public benefit? How are these anticipated to change?

* Management (Jan. 1 to Jan. 7): What are the best mechanisms to ensure compliance? What would be the best metrics of success? What are the best examples of usability in the private sector (both domestic and international)? Should those who access papers be given the opportunity to comment or provide feedback?

Each of these topics will form the basis of a blog posting that will appear at and will be open for comment on the OSTP blog at

Sincerely, Alan I. Leshner, CEO, AAAS and Executive Publisher, Science

Blogging Batholiths


I am currently in British Columbia, Canada, participating in the Batholiths Onland experiment.

Nominally, this large group effort involving over 50 scientists and grad students is for “a seismic refraction and wide-angle reflection survey across the Coast Mountains batholith of British Columbia, Canada.”

This rather terse description does not really do justice to the project, which has the purpose of discovering why continental mountain ranges are often made of granite instead of basalt.

Relevance to the Panda’s Thumb? (1) Real science involves real work; when is the last time you saw a creationist actually measure something, or use a shovel? (2) Real scientists think the earth is billions of years old. You just can’t scientifically reconcile these batholiths with a 10,000-year old earth without being more than a little schizophrenic.

Oxford University’s previous Charles Simonyi Professor for Public Understanding of Science, Richard Dawkins, visited Michigan State University in East Lansing on March 2nd and 3rd. Prof. Dawkins gave a lecture on “The Purpose of Purpose” to a sold-out crowd at the Wharton Center on the evening of the 2nd, and held an hour-and-a-half question and answer session at the Fairchild Theater on campus in the morning of the 3rd.

(Original post at the Austringer)

A Video Birthday Card

I got this from Rob Pennock:

Society for Study of Evolution has created a video birthday card to wish Charles Darwin a Happy 200th Birthday. You can view the YouTube birthday greetings at the following link:

Other details of the SSE Darwin 200 outreach projects are or soon will be posted at:

Please help SSE extend this outreach project, by forwarding the links broadly to your other professional societies, departments, groups and friends.

Happy Darwin Day!


It’s not just General Motors

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While this may seem off-topic for PT, it’s an important issue that is directly relevant to science education and research. In the midst of the current severe economic downturn, all segments of our society are feeling knock-on effects. College and university endowments have taken substantial hits. We hear about the big ones: Harvard’s $36 billion endowment taking a 25% (at least) hit, and Yale taking (at least) a similar loss. I say “at least” because a significant proportion of those endowments are invested in illiquid instruments for which pricing is at best chancy and at worst blind guesswork. The “Yale model” of endowment portfolio management has been adopted by a number of institutions, and they have to be in similar trouble.

Smaller private institutions whose operating budgets are more heavily dependent on tuition are also having significant problems. Beloit College has axed 40 positions because of a 36-student enrollment shortfall. My own institution, Kenyon College in Ohio, has suspended construction on several projects and has frozen hiring. More pain is likely to come as donors retrench and parents redirect their childrens’ college choices based more on cost and less on perceived educational advantage. And while public universities have a temporary economic advantage, that will not last as state aid is inevitably cut as a consequence of decreasing tax revenues.

The problems extend beyond that. Nature News reports that the Chicago Field Museum’s endowment has fallen by at least 36%, and it is cutting positions and reducing research support. Its unrestricted operating budget is being cut 15% and early retirement packages are being offered to 68 people, including 15% of its scientists. Neil Shubin’s position as provost has been eliminated. The same is happening elsewhere, I’m sure.

It’s tempting to imagine that with the massive amounts of federal bailout money already poured into financial institutions and the prospect of even more massive amounts being spent in an economic stimulus package under the incoming Obama administration, there will be a return to the good old days of the 1990s and early 2000s sometime in the not-too-far-distant future. I think that’s a fool’s hope. Recent U.S. economic growth has been built on a string of bubbles over the last two decades, the most recent the real estate and mortgage debt bubble, and I do not believe that there is the prospect of another stretch of bubble-based growth in the foreseeable future. If the last two decades are interpreted as “normality,” we will not return to normality for years, if not decades. The good times will not roll again in my lifetime.

As a consequence we need to carefully think through how we will fund both science education and basic scientific research in a considerably straitened economic context. It is not clear to me when we will have once again have the resources that we have had for the last several decades. Nor is it clear how our research and educational institutions will adapt without cutting to the bone. But we need to think about it and talk about it, and scientists and science supporters must be actively and effectively involved in that conversation. We can’t sit back and passively hope for better times.

Oh, and Happy Monkey to all.

PT needs a video…


…as you can see by looking at the cool video of science bloggers at the American Society of Microbiology meeting. You do get to meet fellow PT blogger Tara Smith there, as well as our buddy Larry Moran.

December Animalcules is up

The latest edition of Animalcules, a monthly carnival of microbiology blogging, is up over at Aetiology.

The early word is that PT contributor Reed Cartwright (real webpage) (alter ego) has, despite being a PT poster, helping to construct the PT blog, and spending his time annoying creationists, managed to PASS his dissertation defense. Watch out world, here comes Dr. Cartwright.

I believe Prof. Steve Steve is planning the all-night bash in Athens as we speak. I wonder how spatially explicit population genetics sounds after a few pints of bamboo beer?

by Kevin Padian, Professor, Department of Integrative Biology; Curator, Museum of Paleontology; University of California at Berkeley.

Last Tuesday William Dembski began posting diatribes on his weblog accusing me of racism. He based them on a second- or third-hand report that he received from one of his acolytes who got the basic facts wrong. Dembski didn’t bother to check them before jumping to his accusation.

But worse things have happened in the world. I could have responded to Dembski immediately, because I was sure of my facts, and I’m happy to stand on my record. But I wanted to wait until I could get a tape of the talk, and to be sure that no one could reasonably interpret my comments as Dembski and his acolytes did.

That took until Friday afternoon, at which point I immediately sent an e-mail to Dembski’s Discovery Institute address. On Monday morning I received an apology from him, which he posted on his website. I consider the matter closed.

However, I would like to clarify the record on several additional points that have come up:

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