Last night I was reviewing the final draft of the paper as revised in response to comments from reviewers. Then it hit me. This paper will appear in Theoretical Population Biology several months after I signed the boycott pledge. All I can say is that I'm embarrassed. I won't be submitting any new papers to TPB. Sorry Mark & Tulja.
January 2012 Archives
Last night I was reviewing the final draft of the paper as revised in response to comments from reviewers. Then it hit me. This paper will appear in Theoretical Population Biology several months after I signed the boycott pledge. All I can say is that I'm embarrassed. I won't be submitting any new papers to TPB. Sorry Mark & Tulja.
I am not only going to refuse to have anything to do with Elsevier journals from now on, but I am saying so publicly. I am by no means the first person to do this, but the more of us there are, the more socially acceptable it becomes, and that is my main reason for writing this post.Lest you dismiss Tim Gowers as a crank, he's a Fellow of the Royal Society and he received the Fields medal in 1998 for work in functional analysis and combinatorics. He is just one of 1671 scholars who have signed an online pledge neither to submit papers to Elsevier journals, nor to edit Elsevier journals, nor to review papers for Elsevier journals. I made the number 1672 this morning. As Tim Worstall summarized the situation on Forbes.com
Academic publishing is a very good game indeed if you can manage to get into it. As the publisher the work is created at the expense of others, for free to you. There are no advances, no royalties, to pay. The editing, the checking, the decisions about whether to publish, these are all also done for free to you. And the market, that's every college libarary in the world and they're very price insensitive indeed.I invite everyone who reads this blog to add their name to the list at The Cost of Knowledge. It's time to take a stand.
Protea obtusifolia in the De Hoop Nature Reserve, Western Cape, South Africa
Photograph by Kent Holsinger
Click on the image for a high-resolution image in a new window.
Climate change is on your porch and in your backyard and living room--anywhere you bedeck with flowering plants.Head over to the NSF site if you'd like to read the whole thing.
Global warming affects favorite flowers of garden and vase. This is true of plants around the world, including the proteas and the pelargoniums native to South Africa.


Image via Wikipedia
- Levels of factual knowledge of science in the United States are comparable to those in Europe and appear to be higher than those in Japan, China, or Russia.
- In 2010, 69% of Americans said that the benefits of scientific research have strongly or slightly outweighed the harmful results; 9% said the harmful results outweighed the benefits.
- In 2010, 69% of Americans said that the benefits of scientific research have strongly or slightly outweighed the harmful results; 9% said the harmful results outweighed the benefits.
- In 2009, 73% of Americans said spending on basic scientific research "usually pays off in the long run"; fewer than two in ten said such spending was "not worth it." About the same percentage (74%) said spending on engineering and technology "usually pays off in the long run."
- In 2010, roughly equal percentages of Americans expressed "a great deal" of confidence in medical leaders and scientific leaders; military leaders were the only group in whom more Americans expressed a great deal of confidence.
- On science-related public policy issues (global climate change, stem cell research, nuclear power, and genetically modified foods), Americans regard science and engineering leaders as both knowledgeable and impartial--relative to other leaders--and believe they should be influential in decisions about these topics.
- Americans also perceive a considerable lack of consensus among scientists on these issues.

Much about James Franklin Crow, who died on 4 January two weeks short of his 96th birthday, challenges our sense of scale. Over seven decades, he contributed to an astonishing array of topics in genetics, and the list of his students and postdocs reads like a who's who. One of them, the pioneering geneticist Motoo Kimura, wrote that getting Crow as his adviser after a period of uncertainty was such a joy it was like "meeting Buddha in Hell". Crow also played the viola for 45 years with the Madison Symphony Orchestra. He once performed with the great violin soloist Yehudi Menuhin.That's the opening paragraph of Alexey Kondrashov's wonderful piece remembering the life and work of James F. Crow. Please visit Nature and read the whole thing. Jim was a remarkable individual.

Cold-Blooded Cannibals: Extreme Adaptations to Island Life from Day's Edge Productions on Vimeo.
The deadline for the 2012 competition is Friday, 29 June 2012. Visit the NESCent Film Festival site for more information.

Image by Suzie Katz via Flickr
- 29 November 2010: NASA announces a press conference to discuss a finding that "will impact the search for evidence of extraterrestrial life".
- 2 December 2010: At the press conference, Felisa Wolfe-Simon and colleagues announce that a bacterium can substitute arsenic for phosphorous in proteins and DNA.
- 4 December 2010: Rosie Redfield makes a blog post questioning the claim.
- 7 December 2010: Carl Zimmer writes a piece for Slate explaining the skepticism many scientists have about the claim.
Rosie blogged about her efforts to replicate the Wolfe-Simon results at her research blog, RRResearch, and last Friday, NatureNews published an article entitled Study challenges existence of arsenic-based life.
There are a couple of interesting things about this article.
- Rosie hasn't been able to replicate Wolfe-Simon's findings, in spite of her best efforts to do so. While there remains a slim possibility that Wolfe-Simon is right, "[o]ther researchers who published critiques of the arsenic-life paper say that Redfield and her collaborators have produced a reasonable refutation of its findings." #arseniclife appears to be dying, though it may be a slow death, and it may be awhile before it is completely dead.
- "Redfield and her collaborators hope to submit their work to Science by the end of the month. She says that if Science refuses to publish the work because it has been discussed on blogs, it will become an important test case for open science." There may be good reasons for Science not to publish Rosie's paper. The details of the work are sufficiently technical and sufficiently far removed from my expertise that I wouldn't presume to judge that. But the wide-open discussion of her work on her blog should be seen as strengthening her work, not as a reason for rejecting it. Because she has worked in the open, documenting her successes and failures, accepting advice from colleagues, and debating approaches and protocols, the paper Science receives is likely to be far more thoroughly vetted than most they receive. The editors of Science should ask themselves this question if they have any doubts:
Would we refuse to publish the paper describing faster than light neutrinos just because an early version appeared in Arxiv?

That description is cut and pasted from the text at thomas.loc.gov. So far so good. We're all in favor of ensuring that peer-reviewed research continues to be published, and we're all in favor of integrity. But not so fast. Read a little further.A BILL To ensure the continued publication and integrity of peer-reviewed research works by the private sector.
SEC. 2. LIMITATION ON FEDERAL AGENCY ACTION.Sound harmless? Maybe even reasonable? Well, consider this:No Federal agency may adopt, implement, maintain, continue, or otherwise engage in any policy, program, or other activity that--
(1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher of such work; or
(2) requires that any actual or prospective author, or the employer of such an actual or prospective author, assent to network dissemination of a private-sector research work.
The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication, to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.The Research Works Act would invalidate the requirement for peer-reviewed NIH-supported research to be deposited in PubMed Central.
CAMEL is a free, comprehensive, interdisciplinary, multi-media online resource for faculty members and other educators to enable them to effectively teach about climate change causes, consequences, solutions, and actions.For more information, visit the CAMEL website or watch the video below.
You can upload resources, build your own website, collaborate on curricular materials, teach a course, give an exam or implement a survey at: www.camelclimatechange.org.
The resource types include: Articles, Risk Assessment Tools, Assignments, Audio/podcasts, Case Studies, Correlation Views, Datasets, Glossary, Field Exercises, Games, Images, Lab Exercises, Lectures, Modules/Units, PowerPoints, Reports, Simulations, Syllabi/Lesson Plans, Videos, Websites, White Papers, Blogs, and Discussion Boards.
CAMEL connects educators through Facebook, LinkedIn, and Twitter (@camelclimate).
Please join the climate educators community at www.CAMELclimatechange.org. You may join CAMEL here.
CAMEL Introductory webinars will be presented:
Tuesday Jan 24, 3:00 PM - EST
Wednesday Jan 25, 2:00 PM - EST
Tuesday Jan 31, 3:00 PM - EST
Thursday Feb 2, 4:00 PM - EST
To participate, please contact Virginia (Ginny) Brown, Project Director, ginny@ncseonline.org and let us know which webinar you want to register for. Upon registration you will receive call in and log on instructions.
Martha Anderson describes efforts at the Library of Congress to archive the website, but as she points out:
[W]e try to get as much of a site we can, and retain functionality as much as possible, but many things do not function the same as on a live site. Anything requiring input to bring up content won't function in the archive.There is also an archive version at the Internet Archive, but we have lost a valuable resource.
The National Center for Science Education has long been an effective advocate for the teaching of evolution. But look at their logo and you'll see something new in their tagline.Defending the teaching of evolution & climate science (emphasis added).That's right. NCSE is now defending the teaching of climate science. As NCSE puts it in its announcement,
Like evolution, climate change is accepted by the scientific community but controversial among the public. As a result, educators trying to teach climate change, like their counterparts trying to teach evolution, are often likewise pressured to compromise the scientific and pedagogical integrity of their instruction.I am delighted that NCSE has taken on this new role. Reasonable people can disagree about what policies should be adopted to respond to climate change. There is no reasonable doubt that the planet is getting warmer and that our emissions of carbon dioxide contribute significantly to heating it up.

Carl Zimmer gets it just right (not surprisingly):
Berry's TEDx talk is more satisfying because it's a talk. You look at the mesmerizing images, and Berry explains what you're seeing. What's really interesting is how he-no doubt unconsciously-uses words that switch on the mental eye. When he zooms in on a chromosome, he points out structures passing through it that look "like whiskers," which act as the "scaffolding" for the cell (the microtubules). He then zooms into the place where the chromosome and microtubule meet, the kinetochore. What you see looks like a supercomputer's acid trip. But you can make sense of what you see because Berry uses metaphors. He calls it a "signal broadcasting system." Now all the molecules jittering around aren't totally random. We can see how molecules come together to make life possible.
There's no question that people like Berry are going to be making the movies that fill our heads in our future when we think about what's going on in our bodies. But those movies will need good soundtracks.
This colloquium will survey the state of the art of empirical social science research in science communication and will focus on research in psychology, decision science, mass communication, risk communication, health communication, political science, sociology, and related fields on the communication dynamics surrounding issues in science, engineering, technology, and medicine with five distinct goals:The first day, May 21, begins with an overview of individuals responses and of social dynamics in science communication and continues with a discussion of emerging technologies and their likely impact. The lunchtime address sounds particularly intriguing:
- To improve understanding of relations between the scientific community and the public
- To assess the scientific basis for effective communication about science
- To strengthen ties among and between communication scientists
- To promote greater integration of the disciplines and approaches pertaining to effective communication
- To foster an institutional commitment to evidence-based communication science
Why We Can't Trust Our Intuitions: Communication as a Science, Arthur Lupia, Michigan
The Sackler lecture will be presented that evening by Daniel Kahneman. I wish I could be there to here what he has to say. I finished reading Thinking, Fast and Slow. It's the most interesting book I've read in a long time, I learned a tremendous amount, and I can see many ways its insights can be applied to improving science communication. But Kahneman is also extremely creative. He is certain to share insights that go well beyond any I can infer. I wish I could be there to hear them.
David Pogue of the New York Times and NOVA will give the lunch address on the second day, May 22:
Lost in Translation? Journalists as Conduits Between Science and the Public
Registration is $150 before 7 May.
First, the University of Connecticut has been good to me. When I joined the faculty in August, 1986, I didn't expect to stay in Connecticut more than a few years. Even though I've now lived here more than a quarter of a century, I still think of myself as a westerner, born and bred. I was born in Oregon City, Oregon, but other than one very dim memory of Sacramento, California when my father was in his medical internship, all of my memories growing up are from the small town of Burley, Idaho. I went to college at the College of Idaho (in Caldwell), received my Ph.D. from Stanford and did post-doctoral work at UC Berkeley and UC Davis. I'd spent a grand total of two weeks east of the Mississippi before moving here, and most of that was on job interviews. But Connecticut is home. I have many wonderful colleagues in this department, and I've been able to grow and develop professionally here in ways I don't think I could have elsewhere.
So when Peter Nicholls asked me to step up and serve the University in this positon, how could I refuse? I owe the University at least this much.
Second (quoting from my earlier post),
As I've told a few close friends, I think of myself as mediocre in research. My record of external funding is pitiful compared to those I regard as leaders in evolutionary biology, and my intellectual contributions have occurred at the margins of important topics, not at the center. In contrast, I think of myself as a talented and effective leader.That's the comment that needs some clarification.
The past 4-5 years have been the most productive and satisfying years for research of my entire career -- thanks largely to the extremely talented group of people I've been fortunate to work with. But I think I might be even more effective as a dean. I think I have an ability to work with other people that's unusually strong (at least for an academic). I seem to be able to identify the strengths and weaknesses people have, to feed their strengths and starve their weaknesses, to mediate disputes, to foster collaborations, to remain even-tempered when situations get tense, to defuse tensions when they arise, to ensure that all people are treated fairly, and to make connections for myself and others. In short, I think I'm more talented at helping others get real work done than I am in doing real work myself. Now I have a chance to find out.

"this is not even a tempest in a teapot, it's a fuss in a thimbleful of spit."
That's an example courtesy of one Professor Zwicky and Johnson, a blog at The Economist devoted to English usage. Johnson reviews evidence from the Merriam-Webster Dictionary of English Usage that (a) good writers used comma splices freely in the 18th century, (b) cited examples only in personal letters of good writers in the 19th century, and (c) guidebooks commonly warned against comma splices.1
Johnson concludes:
MWDEU, which often debunks sticklerish rules with massed evidence from indisputably great writers, says "uncorrected examples are so hard to find in print" that "You should not try the device [of the comma splice] unless you are very sure of what you want it to accomplish."And I agree with Johnson. But just to beat a dead horse, let me point out that Garner's Modern American Usage advises that:
I agree. Editors have made the comma splice so rare that they leap off the page (unpleasantly so, for me) when I spot one. The comma splice is unnecessary; a brief pause between two related thoughts can be accomplished by a semicolon like the one in this sentence. A full stop separates two thoughts more cleanly. Unless you're being aphoristic ("Man proposes, God disposes") or intentionally seeking a loose-knit style, beware that a comma splice is probably not worth the readers it will irritate.
[M]ost usage authorities accept comma splices whenIf you know anything about manuals of English usage, it won't surprise you that Fowler2 dismisses comma splices as simple error.3
- the clauses are short and closely related,
- there is no danger of a miscue, and
- the context is informal.
I listened to a bit of A rose from the dead, and I can't claim to like it.2 I am pleased to see that in an artist takes botany seriously. The titles of his songs include "Convolvulus altheoides", "Quercus lamellosa", "Echinocereus", "Monstera's lair", "Sanguinaria", "Dodecatheon", "Asclepias currasavica", "Trillium recurvatum", "Cypripedium", and "Nephrolepsis". Botanist knows his plants. Here are the lyrics to "Nephrolepsis".
Sword fern
Thriving in humid oppression
Lomariopsidaceae
Alternate pinnae leaflets
Deltoid fronds serrated edge
Damocles sword of green
Above your head doomlike dangles
Head over to NPR if you'd like to hear A rose from the dead.

If you happen to be anywhere near Hartford today and you have any interest in contemporary music, call the Hartford Symphony box office (860-244-2999) right now or go online and buy tickets for their concert this afternoon, Brahms and beatboxing. Shodokeh performs "Fujiko's Fairy Tale", a work by Finnish composer Jan Mikael Vainio that had its world premiere in 2010. It is unlike anything you've heard with a symphony before. Shodokeh's vocal abilities are beyond belief, and Vainio's score is the perfect complement.
We saw last night's performance of "Fujiko's Fairy Tale" at the Bushnell. It was among the two or three most memorable musical performances I've ever seen.1
The overture to "Die Fledermaus", which opens the concert was brilliantly played, but Brahms' First Symphony was disappointing. It lacked the fire and precision that Carolyn Kuan usually brings out of our orchestra. It's the first piece I've heard her conduct in which I've been disappointed.

The January issue of Genetics began a series of articles, "Honoring Our Colleague James F. Crow, an Outstanding Gentleman, Citizen, and Scientist".
Why honor Jim? The answer is obvious to the many who have the privilege to know him: a gentleman and scholar of the highest order, he represents the best of our field. (source)John Hawks sums up the feelings of those who knew him the best, his colleagues at the University of Wisconsin.
Several years ago, colleagues from several departments here at the University of Wisconsin-Madison succeeded in a long-time ambition of Jim's to found an Institute for the Study of Evolution. He had envisioned that the institute should be named for Sewall Wright, who had been important to Jim himself and forms a major part of the legacy of genetics and evolution. But the future institute's members insisted instead to name the new entity in honor of Jim. It is a fitting legacy for a great evolutionary geneticist.Jim was a treasure, and he will be greatly missed.

Meeting recently in South Africa, representatives from 194 countries agreed to the Durban Platform, the latest effort to put the world on a path to cut greenhouse gas emissions that scientists say are driving climate change.
One crucial question is whether the Durban conference was even addressing a real issue. For many conservatives, the answer is no. Global warming, it's said, is a (flawed) theory, not a fact. The idea that human activity is in any way responsible for higher temperatures is false. Advocates of global warming are relying on doctored data. Indeed, global warming is a manufactured crisis being used by environmentalists to impose their left-wing agenda on America. Or so the argument goes.
Having looked into this matter a bit, I've settled on several judgments which are open to refinement and amendment, including these: The world is getting warmer. The warming is almost certainly caused, at least in large part, by human activity. And rising temperatures could pose a future risk, though how significant of a risk is open to interpretation.
Here's what we do know. According to a report by the National Academy of Sciences, the average temperature of Earth's surface increased by about 0.8 degrees Celsius during the past 100 years, with more than half occurring during the past three decades. During one recent 12-year stretch (1995-2006), 11 of those years ranked among the 12 warmest years in the instrumental record of global surface temperature. Richard A. Muller, a professor of physics who once counted himself a skeptic about global warming, re-examined the data through the auspices of the Berkeley Earth Surface Temperature Project and came to this conclusion: "Global warming is real." And the preponderance of the scientific evidence points to human activity as the most likely cause for most of the global warming that has occurred over the last half-century. Gregg Easterbrook, an environmental commentator who has a long record of opposing alarmism, put it this way: "All of the world's major science academies have said they are convinced climate change is happen[ing] and that human action plays a role." ("Conservatives and climate change - Part I", by Peter Wehner, Commentary, 19 December 2011)
When you're reading that, you're probably thinking to yourself, yet another commentary on climate change by a left-wing environmentalist. Or that's what you were thinking until you got to the end and noticed the source -- if you recognize the name Peter Wehner or the magazine in which the article appeared, Commentary. Commentary, by its own description, "emerged as the flagship of neoconservatism in the 1970s." Peter Wehner is a Senior Fellow at the Ethics and Public Policy Center. He served in the Reagan and George H.W. Bush administrations before becoming deputy director of speechwriting for President
George W. Bush in 2001. In 2002, he was asked to head the Office of
Strategic Initiatives. In short, Wehner is a strong conservative, and the magazine in which his piece is published is strongly conservative.
As Tom Smerling (from Skeptical Science) puts it:
Climate hawks will find plenty to argue with, but these caveats are worth considering because a) most have some merit, and b) they clarify exactly where many conservatives get stuck. If we don't address conservative reservations and fears directly, we're failing to get at the roots from which science denial stems.More importantly, Wehner explicitly separates the question "Is it happening?" from "What should we do?" -- in itself a major step forward -- and for the most part he accepts the science.
It's beyond time to accept the science. The earth is getting warmer because of carbon dioxide we are producing. It's time to talk about "What should we do?"

Drawing Inspiration from Wesley Louis on Vimeo.
Drawing Inspiration is a charming animated modern-day fable about serendipity and the deep desire to transcend aimlessness. It tells the story of a man all too enslaved by his routine who one day finds some mysterious sketches on the park bench he visits daily. The drawings prompt him to reconsider the world and his place in it, as he encounters a young boy whose innocent hunger for the world helps peel away those layers of protection and reclusion. (source)
January: The scale of the universe
February: Climate change and extreme weather
March: The sixth mass extinction
April: Remembering Sally Richards
May: I'm a climate scientist
June: GFAJ-1 arrives
July: The theory that would not die
August: Which type of scientist are you?
September: Evolution travel award for ScienceOnline
October: The Jackson Lab comes to Connecticut
November: Google Scholar citations
December: #arseniclife links
If there's a pattern there, I can't see it. All I can say is thank you for stopping by. I hope to "see" you again in 2012.


