In 2010 I ran just over 1000 miles. I went to the gym this morning1 for my last run of 2011: 32 minutes a 7.8mph or 4.16 miles. My total for this year was over 1100 miles. The difference is partly that I ran more (256 times in 2011 vs. 227 times in 2010, 148 hours in 2011 vs. 135 hours in 2010), but it's also because my pace was faster (7.7mph in 2011 vs. 7.4mph in 2010). In 2010 my average pace was 8:06 per mile. In 2011 it was 7:49 per mile. That's not fast enough to win me any races (even local races in my age category), but I still feel pretty good about it.
OR-7 crossed the state line and entered northern Siskiyou County earlier this week. It's the first time there's been a wild gray wolf in California in nearly 90 years. He probably won't stay too long. According to the biologists tracking him, he's establishing a home range and looking for a pack. But since he's the only wolf for several hundred miles in any direction, he's not going to find a pack nearby. I suspect that means he'll be leaving soon.
But still he made it. It's a great day when a wild wolf can wander into California.
"Whether one is for it or against it, the entry of this lone wolf into
California is a historic event and result of much work by the wildlife
agencies in the West," said Department of Fish and GameDirector Charlton
H. Bonham.
...
"I go to the Rockies every year, to Idaho," Stopher said. "The place
where I hunt has wolves. It's really quite something to come across
their tracks in the snow. It changes the air. It adds a wildness. This
is why we are in this business." ("Lone wolf crosses into California from Oregon", by Julie Cart, Los Angeles Times, 29 December 2011.)
Skeptical Science is an extraordinarily valuable resource for those of us who are concerned about human impacts on the global climate but aren't climate experts. It provides easy-to-read and authoritative analyses of recent discoveries, and it provides excellent summaries of what we do and don't know. It was started by John Cook in 2007.
A physics graduate from the University of Queensland who majored in
solar physics in his postgraduate honours year, Cook launched the
Skeptical Science website in 2007 after becoming frustrated at lies and
half-truths surrounding global warming. The site provides a
scientifically accurate database of climate information and is the
engine room of Cook's campaign to use the web, smartphone apps and
social media tools to disseminate climate information.
Having
received international acclaim within the science world, the Skeptical
Science website receives more than 500,000 visits per month, while the
iPhone app has been downloaded more than 72,000 times. (source)
Cook's work was recognized this year with the 2011 Eureka Prize for the Advancement of Climate Change Knowledge from the Australian Museum. The Eureka Prizes are the most prestigious awards in Australian science.
I bring this all up because just a few days ago Skeptical Science updated its Climate Big Picture, which provides a broad overview of what we know. You should follow that link and read the whole thing, but here's a quick summary:
The earth is warming.
Global warming continues.
Humans are increasing atmospheric greenhouse gases.
Human greenhouse gases are causing global warming.
It sounds crazy, but it might just happen. The last gray wolf was killed in California in 1924. Now there's a lone male in southwestern Oregon that might just make a visit.
"I can't think of another
species that was completely extirpated in California that has returned,"
said Michael Stopher, who has been monitoring the wolf for the
California Department of Fish and Game. "As a scientist, seeing the
possible restoration of our historic mega fauna thrills me."
...
In three months, he has
zigzagged for 730 miles across the Blue Mountains and high desert
plains, killing at least one elk along the way. He ended up outside of
Medford on Mt. McLaughlin in the Cascades, 300 crow-fly miles away from
home.(source)
It would be wonderful to have wolves in California, and one wandering male would be a start. I hope this guy makes a visit.
Next August, the Astronomical Society of the Pacific will sponsor a conference on science education and public outreach. I wish I could attend, but it's very likely that I'll be in South Africa for the second season of fieldwork on our Dimensions of Biodiversity project.
Here's a bit of information about the conference from the conference web site:
Join us in the beautiful setting of the American Southwest for a
three-day symposium on the joys and challenges of communicating our
understanding of the universe and science in general--whether in the
classroom, in a museum or nature center, to general and specific
audiences, through books and magazines, on the web, via festivals and
fairs, on radio and television, or through the social media. Preceding
the symposium will be a two-day workshop: In the Footsteps of Galileo, a
national workshop of educators in grades 3-12 and in informal settings.
I am a professor in the Department of Ecology & Evolutionary Biology at the University of Connecticut. I received my B.S. from the College of Idaho and my Ph.D. from Stanford University. After post-doctoral work at the University of California,1 the University of California - Davis, and Stanford, I moved to Connecticut and I've been there ever since.
I've taught introductory biology, evolutionary biology, philosophy of science, population genetics, and conservation biology since joining UConn, and much of my current research focuses on understanding the evolutionary mechanisms responsible for the great diversity of plants in the Cape Floristic Region of South Africa, with a particular emphasis on the genera Protea and Pelargonium. That work is part of a large, multi-investigator Dimensions of Biodiversity project funded by the National Science Foundation. I am also interested in developing statistical methods for analysis of genetic diversity in geographically structured populations and for demographic analysis of perennial plant populations. Until about 10 years ago, my research focused on the evolution of plant mating systems.
If you're really interested, you can get a better sense of the kind of research I've done by looking at my Google Scholar page. And if you're really interested, you can download a PDF of my curriculum vitae.
In yesterday's Nature, the editors identified ten people (scientists) who mattered this year. They include Dario Autiero, who headed the International Oscillation Project with Emulsion-Tracking Apparatus (OPERA) at CERN. If that doesn't ring a bell, maybe faster than light neutrinos will. OPERA is the experimental group with evidence that seems to indicate neutrinos can move faster than the speed of light.
I was delighted to see that Rosie Redfield (pictured to the left) was one of the other people featured. If you followed the #arseniclife saga at all, you'll recognize Rosie as the microbiologist and blogger whose blog post kicked off a firestorm of criticism about claims that a strain of bacteria had been identified that could substitute arsenic for phosphorous in biomolecules -- including DNA.
Nature uses Rosie and her role in the #arseniclife saga to talk about open science and the new role of social media in science.
To Redfield, the exercise has shown how social media tools are binding
science into a community closer than it has been since the early
twentieth century, when it was possible for scientists to personally
know everyone in their field. "Scientists are much more able to
communicate with people we don't know, and to learn from people we've
never met," she says.
I agree with Ford Doolittle.
Ford Doolittle, a biochemist who hired Redfield for her first faculty
job and is now at Dalhousie University in Halifax, Canada, says that
Redfield's work has proved a point by showing how science is supposed to
work. "Science is way too uncritical of itself," says Doolittle. "We
need more Rosies out there."
Congratulations Rosie, and keep up the great work.
If you've never heard of Strunk & White, this video won't be nearly as much fun as it could be -- and you should run out and buy yourself a copy. Joseph Williams writes in Style: Toward Clarity and Grace that "Telling me to 'Be clear' is like telling me to 'Hit the ball squarely.' I know that. What I don't know is how to do it." Strunk & White lay down the rules, and Williams tells you how to follow them. Come to think of it, if you don't already own a copy of Strunk & White and a copy of Williams, run out and buy both.
I learned on Tuesday that the National Biodiversity Information Infrastructure (NBII) will be taken offline in January.
January 15, 2012, will see the end of a long-term project to empower
users of biological resources data and information. The National
Biological Information Infrastructure, or NBII, was begun in 1994 within
what was then the National Biological Service (NBS) of the Department
of the Interior. Its purpose and mission were to ensure that scientists,
resource managers, decision makers, and concerned citizens could go to a
single place on the Web and find biological resources data and
information from vetted sources--whether in government, academia,
non-governmental organizations, or the private sector. (source)
I was very sorry to learn the news. I am not a heavy user of NBII data, but I know that many others are. It has been a vital resource for many as a gateway to data maintained by federal, state, and local governmental agencies and by non-governmental organizations. Those who manage our nations forests, grasslands, and waterways will now have an even more difficult task. An important part of the data on which wise decisions depend will no longer be available to them.
What have we done to ourselves? We will be flying with blinders.
The University of Connecticut Board of Trustees held a special meeting yesterday. At that meeting, the Board not only adopted tuition rates for 2012/2013, it laid out a plan for tuition rates through 2015/2016, with the proviso that "[i]f the State appropriation decreases or the current fiscal climate worsens, the University may revisit the approved tuition increase amounts."1
For in-state undergraduates that will mean their tuition and fees
will climb to $11,290 next fall -- $620 more than this year's charge of
$10,670. By 2016, the charge will be $2,676 more than this year, or
$13,346.
That's assuming the state
does not increase funding to the university; if the state does boost
funding by 0.5 percent in each of the next four years, the board
approved a slightly scaled-back series of tuition hikes, starting with
5.5 percent next year and ending in 2016 with 6.3 percent. ("UConn trustees approve 6% tuition hike," Kathleen Megan, The Hartford Courant, 19 December 2011)
Under this plan, the University will hire approximately 290 new tenured or tenure track faculty, reducing the student:faculty ratio from 18:1, where it stands now, to 15:1. Not only will the additional faculty help the University ensure that students can enroll in the courses they need, but they will further enhance the University's contributions research, economic development, and creative activities. By laying out a plan for four years, the University can plan its course strategically. Most importantly, students and their families can plan their own finances to ensure that every student who wants to attend the University of Connecticut can afford to do so.
Click through to read the statement I presented at the meeting on behalf of the University Senate Executive Commitee.
That's what Daniel Kahneman calls the shortcuts we use that often lead to conceptual errors. I haven't finished reading Thinking, Fast and Slow, but I am learning a lot, and I highly recommend you buy or borrow a copy for yourself and read it. System 1 is responsible for many of our biases, and the only thing we can do to correct those biases is to engage System 2. Unfortunately, System 2 is lazy and slow.
Nikki (at Science and Nature) has collected 20 common faults in reasoning, first her top 10, then 10 more. Many are biases I've encountered in reading Kahneman. Until you have time to read Kahneman for yourself, read Nikki.
You might also want to watch this video in which Kahneman describes the difference between memory and experience.
A year and a half ago we lost Charley Heiser, one of the giants of 20th century botany. Although he is best know for his work on sunflowers and hybridization, he and his students also devoted themselves to the study of cultivated plants, some well known (chile peppers), some less well known (pepino, naranjilla, and quinoa), and some unusual (like the gourds worn as penis sheaths in New Guinea and South America).1
Two of his students, Barbara Pickersgill and Greg Anderson, have written a biographical memoir that is now available as a free PDF download from that National Academy of Sciences.
[A]lthough new techniques have necessitated modification of some of charley's interpreta- tions, others still stand. his publications are still much cited and remain a monument to a professional lifetime spent on what a former ph.d. student described as "never work--more like a full-time hobby."
Regular readers will remember that I spent most of July and August in South Africa measuring plants and collecting specimens as part of a large, NSF-funded Dimensions of Biodiversity project. The project focuses on the plant genera Protea and Pelargonium, and we seek both to understand functional trait variation within these and to relate it to the community context in which the plants are embedded.
We are now seeking new post-doctoral research associate to join us on the project. The person we hire will be required to spend a long period of time in South Africa starting in June or July 2012 and will be responsible for design, implementation, and analysis of field and greenhouse experiments that explore the relationship between leaf traits, leaf physiology, and leaf longevity. (See the job ad for a more detailed description of the position and the project web page for more information about the project. Click on the "Dimensions of biodiversity" tag at the bottom of this post or in the tag cloud for some blog posts about the project.)
We'll start reviewing applications in late January. Please pass this ad along to anyone you know who might be interested.
Three statisticians go deer hunting. They see a large buck. The first one fires and misses one meter to the left. The second one fires and misses one meter to the right. The third one exclaims, "We got him!"
If you're reading this blog, you're probably already familiar with statistics. You probably regard linear regressions and ANOVAs as simple, even if you don't know all of the mathematical details behind them. If that describes you, you may not find Nathan Green's new series on statistics at The Guardian all that useful,1 but if you have friends or relatives who don't understand the difference between the mean of a sample and the mean of the population from which it was drawn or why the difference is important, you might want to encourage them to follow his series.
The first one outlines the challenges associated with sampling. The second one describes different measures of central tendency (mean, median, and mode).2
I've been a member of the University Senate since some time in the mid-1990s, except for a year here and there when our bylaws required me to step off for a year. For a year and a half I've served on the Executive Committee (SEC). Since July I've served as Chair of the Executive Committee. While I've met some faculty members who think the Senate, and the SEC in particular, are "yes people" who don't challenge the administration aggressively and who have been co-opted by those on the "dark side", I think the Senate serves effectively to share governance with the administration. There have been many times when the administration has made a decision contrary to the advice of the Senate, but that's not entirely unexpected. We give advice. They make the decisions.
Why do I mention all of this now?
Because our by-laws require that I step down from the SEC when I take up my new duties in January. I'm moving to the "dark side". I will become an ex-officio, non-voting member of the Senate. I will miss that relationship with my colleagues -- faculty, staff, and students. I hope that in my new role I am able to build a new relationship with them that is as satisfying as the one I've had for a decade and a half.
Yesterday afternoon was the last Senate meeting at which I presented a report for the SEC. After my report, I was touched when Jack Clausen rose from the floor to offer his thanks for my service on behalf of the SEC. I especially liked the limerick with which he finished:
There once was a professor named Kent. To chair the SEC he was sent. Now he's a dean, Vice provost and mean. Let's all wish him a rapid ascent.
On the 13th of January I take up a new position, Interim Vice Provost for Graduate Education and Dean of the Graduate School at the University of Connecticut. Our Provost, Peter Nicholls, asked me to serve when the person for whom I am serving suffered a serious illness. The most difficult part of agreeing to serve was reconciling myself to the awful circumstances that made my service necessary. I am very, very grateful that in spite of his serious illness, the person for whom I am serving is in good spirits, and he is his usual helpful self. He's even volunteered to chat on the phone once or twice a week about issues facing the Graduate School. Knowing that he's so willing to help is an enormous relief, even though I will bother him as little as I possibly can.
Some of you know that about 5 years ago I served as Acting Head of the Department of Ecology & Evolutionary Biology. When the dean decided it was time for a permanent head to be appointed, I was one of two candidates for the position. He selected the other candidate on the basis of the search committee's recommendation and the recommendation of my department. That decision was very painful for me.
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. Others in organizations for which I've served as president (the American Genetics Association, the American Institute of Biological Sciences, and the Botanical Society of America) or in board leadership positions (the Connecticut Chapter of The Nature Conservancy, BioOne) seem to have greatly valued my service. It cut me to the quick when my closest colleagues didn't agree.
Now I have an opportunity to redeem myself and serve a broader set of colleagues at the University of Connecticut. I hope I do not disappoint them.
In 2002, Paul Crutzen1 published an article in Nature entitled "The geology of mankind." In it he argued that the human influence on the global environment has been so large that were we suddenly to go extinct, the record of our activities would be recorded in earth's geology. He coined the term "Anthropocene" to refer to the geological stage in which we are now living. The International Commission on Stratigraphy even has a working group on the Anthropocene within its division of Quaternary Stratigraphy whose purpose is "to examine the status, hierarchical level and definition of the Anthropocene as a potential new formal division of the Geological Time Scale" (http://www.quaternary.stratigraphy.org.uk/workinggroups/). To most people who have heard the term Anthropocene before, it conjures up a world of degraded ecosystems, a world in which humans have depleted resources, poisoned airs and waters, and cuased extinctions of many plants and animals.
Emma Marris, Peter Kareiva, Joseph Mascaroa, and Erle C. Ellis have a different view:
The Anthropocene does not represent the failure of environmentalism. It is the stage on which a new, more positive and forward-looking environmentalism can be built. This is the Earth we have created, and we have a duty, as a species, to protect it and manage it with love and intelligence. It is not ruined. It is beautiful still, and can be even more beautiful, if we work together and care for it. (source)
The government [of the UK] has signalled a revolution in scientific publishing by
throwing its weight behind the idea that all publicly funded scientific
research must be published in open-access journals. ("Results of publicly funded research will be open access - science minister," Alok Jha, The Guardian, 8 December 2011)
I've written before that open access (and its variants) is one way to ensure broad publicaccess to the results of scholarly research. And ensuring the broadest possible access ought to be a primary goal of any scholarly society involved in publishing. Those societies exist to enhance the work of scholars and to enhance the contributions scholars make to society. Both the work scholars do and the contributions that work makes to society depends on ready access to published scholarly work. The more widely available that work is, the greater the contributions to scholarship and the greater the contributions to society.
My concern about immediate open access has always been how to pay for the cost of publishing. In some fields, grants may be large enough to absorb the cost of authors fees, and some funders have made arrangements to ensure that funds are available to support immediate open access publication of work they support. That appears to be the approach that the government of the UK is taking. The science minister, David Willetts, seems to understand that.
We want to move to open access, but in a way that ensures that peer
review and publishing continues as a function. It needs to be paid for
somehow. One of the clear options is to shift to a system from which
university libraries pay for journals to one in which the academics pay
to publish. But then you need to shift the funding so that the academics
could afford to pay to publish. (emphasis added)
The proposal represents a fundamental change in the way scholarly publishing has been funded for a century or more, and there are deeply entrenched forces that will oppose it. But if the change can be made to stick, and if it can be made to stick in a way that promotes wide public access to scholarly research in all fields, not just heavily funded biomedical fields, it is a change all scholars should embrace.
Freshlyground is a wonderful South African musical group.1 They've rewritten they're hit, "Doo Be Doo", for a special concert in Durban today (7:00pm local time). (If you haven't seen or heard the original, be sure to click through to the full page.)
Zolani Mahola, lead
singer of Freshlyground, and Leigh Wood, Producer of the youth program
"It's Up to US" on 50/50, co-wrote a new version of "Doo Be Doo" called "Doo Be Doo - Take a Stand" as
a tribute to the youth and the environment for COP 17 - (The 17th
Conference of the Parties) to the UN Framework Convention on Climate
Change. The conference takes place 28 November to 9 December in Durban
and will assess progress in dealing with climate change.
The song performed by Freshlyground
also features a talented children's choir from Soweto. The message of
the song is directed toward the World Leaders, asking them to consider
the voice of the youth whose generation will be the most affected by
decisions made at the Climate Change talks.
Zolani and Freshlyground are
passionate ambassadors for the environment and conservation. The song
also supports the "Consider US" campaign, which is a youth movement for
children to voice their opinions on Climate Change in 20 words.
The 20 words that the kids write are put into a beautifully bound book
and buried in a time capsule with an air and water sample for the next
30 years. The book will be buried on 8 December in the Durban Botanical
Gardens just before the Freshlyground concert.
If you can't make it to Durban for the concert, please enjoy the video, and do something kind for the planet.
The massive increase of atmospheric CO2 concentrations since
pre-industrial times would, in fact, have caused substantially more
surface warming were it not for the cooling effects of atmospheric
aerosols such as black carbon (source)
Climate negotiators in Durban are trying to hammer out a successor to the Kyoto protocol that expires at the end of next year.1 Now I read2 that global carbon dioxide emissions climbed dramatically in 2010.
Emissions rose 5.9 percent in 2010, according to an analysis released Sunday by the Global Carbon Project, an international collaboration of scientists tracking the numbers. Scientists with the group said the increase, a half-billion extra tons of carbon pumped into the air, was almost certainly the largest absolute jump in any year since the Industrial Revolution, and the largest percentage increase since 2003.
The increase solidified a trend of ever-rising emissions that scientists fear will make it difficult, if not impossible, to forestall severe climate change in coming decades. ("Carbon Emissions Show Biggest Jump Ever Recorded," by Justin Gillis, The New York Times, 4 December 2011)
It's past time for us to find a way to deal with climate change. I fear that we'll keep kicking the can down the road and leave our children and grandchildren with a greatly impoverished world.
Rush Limbaugh and those like him claim that the earth stopped warming in 1998. Wrong!
A new analysis confirms that global warming actually shows no sign of slowing down. That's according to Stefan Rahmstorf of the Potsdam Institute for Climate Impact Research in Germany, and his colleague Grant Foster.
Focusing on 1979-2010, the pair compared the five most important
databases of global temperature: three based on surface weather
stations, and two based on satellite measurements of temperatures in the
lower troposphere. All of them show warming of 0.014-0.018 °C per year. (source)
The world is getting warmer, and we're largely responsible for it. That's about as certain as anything we get in science. What we should focus on is what we're going to do about it.
Skeptical Science, the website that "gets skeptical about global warming skepticism", has released The Debunking Handbook. It's available as a free PDF download, and I encourage you to download a copy and read it.
Perhaps the most important message is in a callout box on the first page: "It's not just what people think that matters, but how they think." Here's a blurb about the booklet from the Skeptical Science website:
The Handbook explores the surprising fact that debunking myths can
sometimes reinforce the myth in peoples' minds. Communicators need to be
aware of the various backfire effects and how to avoid them, such as:
It also looks at a key element to successful debunking: providing an alternative explanation. The Handbook is designed to be useful to all communicators who have to deal with misinformation (eg - not just climate myths).
I haven't finished Thinking, Fast and Slow yet, and I've only skimmed this short PDF, but the advice from Skeptical Science seems completely consistent with Kahneman's survey of how we think.
We have a new faculty position available in my department. Here is the text of the job advertisement:
University of Connecticut
PLANT ECOLOGICAL OR EVOLUTIONARY GENOMICS
The Department of Ecology and Evolutionary Biology at the University of Connecticut seeks applicants for a 9-month tenure-track position to begin in August 2012. Although targeted at the Assistant Professor rank, an appointment at a higher rank may be possible for a candidate who exceptionally enhances the diversity elements of our academic mission.
We seek a creative individual employing genomic approaches to address key questions in the ecology and evolutionary biology of plants. Research on non-model organisms is preferred but appropriate research foci involving model organisms will also be considered. Experience in bioinformatic and statistical analyses is desirable.
The successful applicant will have a Ph.D., preferably with postdoctoral experience. They will be expected to supervise an independent research program that will attract extramural funding, teach at the undergraduate and graduate levels, and provide research training for graduate and undergraduate students. Teaching duties are expected to include participation, on a rotating basis, in a) our introductory biology curriculum, b) an upper-level botany, evolution, or ecology course, and c) a graduate course in the candidate's specialty. Preferred qualifications include the ability to contribute to the diversity and excellence of the learning experience and academic community through research, teaching or service.
Submit a curriculum vitae (with links to your top 3 publications), a summary of research accomplishments and future research objectives, a brief description of teaching experience and philosophy to: Husky Hire (http://jobs.uconn.edu).
Please have letters from three referees sent to: (EEB.Search@uconn.edu). Review of applications will begin January 6, 2011. Questions regarding this position may be addressed to kathleen.tebo@uconn.edu
Evaluation of applicants will be made by assessment of: 1) graduate and post-doctoral experience; 2) research accomplishments, productivity and extramural funding; 3) statements of teaching and research objectives; 4) professional references; and 5) expertise in ecological or evolutionary genomics.
Information about the Department of Ecology and Evolutionary Biology can be found at http://hydrodictyon.eeb.uconn.edu/eebwww/
The University of Connecticut houses state of the art genomics instrumentation and computational facilities.
The University of Connecticut encourages applications from under-represented groups, including minorities, women, and people with disabilities.
About a year ago the U.S. Fish & Wildlife Service published a rule in the Federal Register (75 FR 77801 77817) proposing the dunes sagebrush lizard for listing as endangered under the Endangered Species Act. In April, they announced re-opening of the comment period and the holding of public hearings (76 FR 19304 19305). In June, Sen. John Cornyn (R-TX) and Rep. Steve Pearce (R-NM) introduced a bill to prevent the listing.
The ESA requires that FWS take one of three actions within one year of publishing a proposed listing: (1) propose a final rule making the listing, (2) withdraw the listing, or (3) extend the final decision by no more than three months. They chose option 3.
On December 5th,
2011, the U. S. Fish and Wildlife Service (Service) will publish in the
Federal Register a 6-month extension of the final determination of
whether to provide protection under the Endangered Species Act (Act) for
the dunes sagebrush lizard (Sceloporus arenicolus) (lizard).
The Service is taking this action in order to solicit additional
scientific information and public comment before making any final
listing determinations regarding the agency's proposal. Publication of
this announcement will reopen the comment period on the proposed rule to
list the species for 45 days. ("Service Announces a 6-Month Extension of the Final Determination for the Proposed Listing of the Dunes Sagebrush Lizard to Allow for Additional Public Comment and Discussion", 1 December 2011, press release from Region 2 available at http://onlinepressroom.net/fws/)
I am participating in a seminar involving undergraduate journalism students and graduate students from my department (Ecology & Evolutionary Biology) and the Department of Natural Resources and the Environment. Its purpose is to give journalism students a chance to practice their interviewing skills and to give science students practice at communicating their work to reporters. For our last meeting this year, we decided to talk about the #arseniclife episode. What I've collected below are links and resources we'll use in our discussion.
Participants: All of the resources linked to below are relatively short and easy to read (except for Rosie Redfield's posts -- just try to get a sense of her objections, don't worry about the details). Scientists will especially want to ponder the question of how peer review works in very public science, and journalists will want to think about Carl Zimmer's take on Tom Clynes' Popular Science piece about the controversy and Clynes' response. The Deepak Singh video gives a non-biologist, non-journalist take on the role of Twitter in the controversy (hence the hashtag in the title of this post).
Media advisory from NASA announcing an astrobiology discovery (29 November 2010)
WASHINGTON -- NASA will hold a news conference at 2 p.m. EST on
Thursday, Dec. 2, to discuss an astrobiology finding that will impact
the search for evidence of extraterrestrial life. Astrobiology is the
study of the origin, evolution, distribution and future of life in the
universe.
NASA press release accompnaying news conference (2 December 2010)
Researchers conducting tests in the harsh environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components.
"The definition of life has just expanded," said Ed Weiler, NASA's associate administrator for the Science Mission Directorate at the agency's Headquarters in Washington. "As we pursue our efforts to seek signs of life in the solar system, we have to think more broadly, more diversely and consider life as we do not know it."
Rosie Redfield's blog post criticizing the paper1 (4 December 2010)
Here's a detailed review of the new paper from NASA claiming to have isolated a bacterium that substitutes arsenic for phosphorus on its macromolecules and metabolites. (Wolfe-Simon et al. 2010, A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus.) NASA's shameful analysis of the alleged bacteria in the Mars meteorite made me very suspicious of their microbiology, an attitude that's only strengthened by my reading of this paper. Basically, it doesn't present ANY convincing evidence that arsenic has been incorporated into DNA (or any other biological molecule).
Some scientists are left wondering why NASA made such a big deal over a paper with so many flaws. "I suspect that NASA may be so desperate for a positive story that they didn't look for any serious advice from DNA or even microbiology people," says John Roth of UC-Davis. The experience reminded some of another press conference NASA held in 1996. Scientists unveiled a meteorite from Mars in which they said there were microscopic fossils. A number of critics condemned the report (also published in Science) for making claims it couldn't back up. And today many scientists think that all of the alleged signs of life in the rocks could have just as easily been made on a lifeless planet.
The controversy over the Martian meteorite still sputters on today because they contain only a few alleged fossils, rather than living bacteria. There are only a limited number of tests that scientists can run on the rocks, and their results remain murky. Fortunately, that's not the case for GFAJ-1. Critics say that a few straightforward tests on the bacteria would show whether they really do have arsenic-based DNA once and for all. And the NASA scientists say they're ready to hand out GFAJ-1 to researchers who want to study it. This controversy may be burning brightly at the moment, but it probably won't burn for long.
Last December, Felisa Wolfe-Simon announced the discovery of a microbe that could change the way we understand life in the universe. Soon she found herself plunged into a maelstrom of bitter backlash and intemperate criticism. A dispatch from the frontiers of the new peer review.
Carl Zimmer's blog post commenting on Clynes' article (20 October 2011)
It's a good article. I won't be forgetting the opening scene anytime soon, when Wolfe-Simon is ambivalently posing for a television crew, and she sinks into the mud of Mono Lake, where she first encountered GFAJ-1.
But I do share some of the reservations that science writer David Dobbs expresses over at his blog Neuron Culture. As a genre, the profile is one of the most addictive and enjoyable of all. It doesn't matter if the profile is of a hero or a scoundrel; the story is good as long as it's full of human nature in all its extremes. But profiles of scientists are tricky, because science transcends any single individual scientist. To do the science justice, you may need to pull the spotlight away and get into the less human stuff, like chemical reactions and pH levels.
To that end, I'd like to add a bit of context to a paragraph that you quote, regarding the storm of criticism and the paper's authors going "underground." You follow the excerpt with your comment that "Clynes has us believe that this barrage of extraordinary, brutal criticism (or perhaps questions from journalists) forced Wolf-Simon and her colleagues to go into witness protection."
Actually, I don't believe that, nor would I have my readers believe it. I think it would have been useful to your readers for you to have included my next paragraph, which makes it clear that I am in fact spotlighting both sides of a polarized dialogue regarding this particular point:
Microbiologist Jonathan Eisen of the University of California at Davis called the lack of response "absurd" and told Carl Zimmer from Slate, "They carried out science by press release and press conference. They are now hypocritical if they say that the only response should be in the scientific literature."
Though I didn't state my opinion in the story (better for readers to decide for themselves), I will here: I think that Eisen is on the money here.
I'm not going to do any more work on this - not going to do experiments to find out why arsenate stimulates growth, unless the mass spec shows that there really is arsenic in the DNA of arsenate-grown cells. The growth stimulation I'm seeing isn't a replication of Wolfe-Simon et al's report that their cultures grew with arsenate but not without it, but it might reflect the same biological process.
Deepak Singh3 provides a video overview. Read the posts above before you watch the video. The video won't make much sense without that background.
If you really can't get enough of #arseniclife, here are some more links:
The version of the Wolfe-Simon paper as it originally appeared on ScienceExpress: (2 December 2010) The version of the Wolfe-Simon paper as it finally appeared in Science: (3 June 2011) Table of Contents for Science (scroll to the bottom for the technical comments): (3 June 2011) Links from The Guardian through the end of December 2010: (Story Tracker) Various blog posts I made in which I mentioned arsenic-based life (Uncommon Ground) Bora Zivkovic' comprehensive collection of #arseniclife links (A Blog Around the Clock) A one-year anniversary update (Cosmic Log)
The difference is partly that I ran more (256 times in 2011 vs. 227 times in 2010, 148 hours in 2011 vs. 135 hours in 2010), but it's also because my pace was faster (7.7mph in 2011 vs. 7.4mph in 2010). In 2010 my average pace was 8:06 per mile. In 2011 it was 7:49 per mile. That's not fast enough to win me any races (even local races in my age category), but I still feel pretty good about it.
On the 13th of January I take up a new position, Interim Vice Provost for Graduate Education and Dean of the Graduate School at the 
