Cheatgrass and climate change

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Cheatgrass (Bromus tectorum) is an invasive annual found throughout the United States.1 It is regarded as a noxious weed in most of the Intermountain west and may infest as much as 41 million hectares (101 million acres).2 Now it appears set to spread even further, thanks to our warming of the planet.

We conducted a two-year experimental manipulation of temperature and snow pack to test whether 1) warming increases cheatgrass population growth rate and 2) reduced snow cover contributes to cheatgrass' positive response to warming. We used infrared heaters operating continuously to create the warming treatment, but turned heaters on only during snowfalls for the snowmelt treatment. We monitored cheatgrass population growth rate and the vital rates that determine it: emergence, survival and fecundity. Growth rate increased in both warming and snowmelt treatments. The largest increases occurred in warming plots during the wettest year, indicating that the magnitude of response to warming depends on moisture availability. Warming increased both fecundity and survival, especially in the wet year, while snowmelt contributed to the positive effects of warming by increasing survival. Our results indicate that increasing temperature will exacerbate cheatgrass impacts, especially where warming causes large reductions in the depth and duration of snow cover.3 (doi: 10.12952/journal.elementa.000020)

If you think cheatgrass is a nuisance now, just wait a few years. It's going to get even worse.

Understanding (a bit) about Protea community structure

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Most of the work I've been involved in concerning Protea has focused on evolution and diversification.1 But chapter 3 in Rachel Prunier's dissertation concerned patterns of community assembly in Protea of the Cape Floristic Region. Xun ("Tony") Jiang extended the ideas in that chapter as part of his disseration and developed a new class of link functions for analysis of binary outcomes. The paper describing Tony's work has just appeared in the Annals of Applied Statistics. Here's the abstract:

Understanding the mechanisms that allow biological species to co-occur is of great interest to ecologists. Here we investigate the factors that influence co-occurrence of members of the genus Protea in the Cape Floristic Region of southwestern Africa, a global hot spot of biodiversity. Due to the binomial nature of our response, a critical issue is to choose appropriate link functions for the regression model. In this paper we propose a new family of flexible link functions for modeling binomial response data. By introducing a power parameter into the cumulative distribution function (c.d.f.) corresponding to a symmetric link function and its mirror reflection, greater flexibility in skewness can be achieved in both positive and negative directions. Through simulated data sets and analysis of the Protea co-occurrence data, we show that the proposed link function is quite flexible and performs better against link misspecification than standard link functions.

The Annals paper is behind a paywall, so you may not be able to get to it there. Fortunately, arXiv hosts a reprint of the article. Here's the link:

If you're reading this you probably know the name Michael Mann. If you don't, here's the quick version: Mann is Distinguished Professor of Meteorology and Director, Earth System Science Center at Pennsylvania State University. In 1998, he was lead author on a famous paper (the "hockey stick" paper)showing a dramatic increase in global surface temperature. He's been a target of those who deny a human influence on climate change ever since.

In 2011, Ken Cuccinelli (then Attorney General for the Commonwealth of Virginia) filed suit asking the University of Virginia to turn over documents related to research Mann did while he was a faculty member there (link). The American Association for the Advancement of Science, and the American Council on Education supported the University of Virginia's refusal to supply the documents Cuccinelli requested, and the Supreme Court of Virginia denied the request.

Now I learn that there's a different case pending.

In a case scheduled to be heard on Thursday by the Virginia Supreme Court, the university and several national higher-education groups are arguing that the open-records law should not be construed as giving an advocacy group access to many research-related documents produced Michael E. Mann, the climate scientist, while he was on the university's faculty.

On the other side, the Reporters Committee for Freedom of the Press has joined 17 media organizations in arguing that the records-request exemption being sought by the university is so broad that it would effectively gut the law at issue, the Virginia Freedom of Information Act, hindering journalists' ability to cover public institutions. (source; likely to be paywalled, sorry)

A conservative advocacy group, the American Tradition Institute, filed the initial request for documents, and the University was apparently inclined to agree to much of the request until Mann, the American Association of University Professors, and other groups urged them not to. The case apparently centers on the interpretation of "data, records, or information of a proprietary nature", because such records can be excluded from a freedom of information request. Several media organizations have filed briefs supporting release of the records, arguing that the lower court decisions interpreted the "proprietary nature" clause so broadly that it would effectively gut Virginia's open records law.

I am not a lawyer, so I can't comment on which side of the argument has the better legal case. I can also say that although I don't know the details of this case, I am inclined to think that the American Tradition Institute is on a fishing expedition, seeking to harass and intimidate Mann and to dissuade other scientists from investigating human effects on climate change. If it were only the data that the American Tradition Institute were seeking, they would have a strong case, and Mann probably wouldn't object. My understanding is that he and the entire climate science community have already made much or all of their data freely available in a true spirit of openness and transparency. But the suit seeks access to correspondence between Mann and other scientists. In the end, I agree with the arguments from a brief filed by the American Association of University Professors and the Union of Concerned Scientists that are summarized in the Chronicle of Higher Education:

"Requiring the production of correspondence with other academics will have a particularly strong chilling effect on intellectual debate among researchers and scientists," the brief argues, because the exposure of preliminary, unpublished thoughts to the public eye will "inhibit researchers from speaking freely with colleagues, with no discernible countervailing benefit."

I've mentioned Elementa on this blog a few times before. (Here's a link to posts mentioning Elementa.) In case you've forgotten, Elementa is an open access journal, published by BioOne in partnership with academic editors and librarians at four universities focusing on the science of the anthropocene. It accepts contributions in six knowledge domains: atmospheric science, ecology, sustainability transitions, earth and environmental science, ocean science, and sustainable engineering.

Almost a month ago now, 4 December to be precise, Elementa launched. If you visit the site now, you'll find a series of recent articles that have been posted. One of the articles particularly caught my eye (link).

Online resources for statistics and population genetics

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Several days ago @Graham_Coop pointed out that Lex Flagel has collected a very useful set of free, online resources for statistics, population genetics, and programming. They are, in his words, 

Free Resources I'd Gladly Have Paid For

It's a great set of resources, and I was especially pleased to see that he links to my Lecture Notes in Population Genetics, especially when you consider that the other resources on that list are Graham Coop's notes on population genetics, Joe Felsenstein's Theoretical Population Genetics, and Magnus Nordborg's chapter on coalescent theory. That's a very nice crowd to be part of.

DNLee, BoraZ, #ripplesofdoubt, and me

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If you're seeing this post, you've undoubtedly heard about the series of events that rocked the online science community over the last week. On the off chance that you haven't, here's a quick recap:

  • On Friday, 11 October, Daniel Lee posted an entry to her blog at Scientific American describing a vile incident in which a editor for Biology Online (now a former editor) called her an "urban whore" for declining to contribute to Biology Online when he told her that the site wouldn't compensate her for her writing. (link)
  • On Monday, 14 October, Monica Byrne updated a year-old post describing an incident of sexual harassment and identifying Bora Zivkovic, Blogs Editor for Scientific American (now former Blogs Editor).
  • Soon after that Hannah Waters described a series of incidents involving Bora. 
  • On Friday, Kathleen Raven described another series of incidents involving Bora, and included e-mail excerpts from some of the exchanges.
I read all of these accounts with a mixture of shock and horror. I don't know either Danielle or Bora, although I've seen many of their blog posts and tweets. I was shocked and dismayed that in 2013 anyone would think of calling Danielle an "urban whore" simply because she politely declined to write something without receiving compensation. And I was shocked and dismayed that someone many members of the online science community regarded as the "blogfather" engaged in such reprehensible conduct.

It's that "shock" that I want to say something about.

I'd heard or read many times before this week that it is very likely that every woman I know has suffered some form of sexual harassment, many of them repeatedly. It was a fact that I knew and I'd probably even repeated, but somehow i didn't really know it. Somehow it never really struck home until I started seeing a few of the hundreds of tweets with the #ripplesofdoubt hashtag. That and a conversation with a colleague and it finally became real. I guess I'm revealing how clueless I am most of the time, but I also hope I'm capable of learning and that I'm a little less clueless (about this at least) than I have been.

Then I started thinking...

3-minute thesis @UConn - Results

I mentioned in August that The Graduate School was sponsoring a 3-minute thesis competition. As a reminder, the 3-minute thesis competition

is a research communication competition developed by The University of Queensland which challenges research higher degree students to present a compelling oration on their thesis and its significance in just three minutes in language appropriate to a non-specialist audience.
I'm pleased to announce that we now have our winners:

Vanessa Lovelace, 1st Place (and People's Choice winner)
Title of Presentation: Genealogies of Liberty: An Embodied Black Freedom Trail
Graduate Program: Political Science

Cheryl Bell, 2nd Place
Title of Presentation: Estrogen and the Foreskin: Is Thicker Better?
Graduate Program: Molecular and Cellular Biology

Austin Johnson, 3rd Place
Title of Presentation: Reliability of Data Derived from Time Sampling Methods with Multiple Observations Targets
Graduate Program: Educational Psychology

Here's Vanessa's presentation.

You can see all three on The Graduate School's Vimeo channel. You can also read more about the competition at UConn Today.
From today's Inside Higher Ed:

On Monday, Biology-Online posted a statement that said in part: "We would like to express our sincerest apologies to Danielle N. Lee (DNLee) and anyone else who may have been offended by the way our recently hired employee, Ofek, handled the conversation with her. Ofek's behaviour was completely out of line and after gathering the facts we immediately terminated his employment. Ofek failed to show the respect and prudent behavior expected of him as a contributor to Biology-Online."