Uncommon Ground

Author Archive: kent

2017 Graduate Commencement Ceremonies @UConn

The University of Connecticut celebrated its 138th Commencement exercises last weekend.1 The Graduate School now confers so many degrees that we have two ceremonies, a ceremony for recipients of master’s degrees on Saturday afternoon and a ceremony for recipients of doctoral degrees on Monday evening. Stuart Rothenburg, who received his

Stuart Rothenburg, who received his PhD in Political Science from UConn, addressed the graduating class at the master’s ceremony. If you’d like to see his remarks, follow the link below, click on “Graduate School Ceremony: Masters Candidates, May 6, 2017”, and then click on “Commencement Address” at the left.

I addressed the graduating class at the doctoral ceremony on behalf of Elizabeth Jockusch, this year’s winner of the Edward C. Marth Award for Mentorship, and Takiyah Harper-Shipman was our student speaker. If you’d like to see my remarks, follow the link below, click on “Graduate School Ceremony: Doctoral Candidates, May 8, 2017”,  and then click on “Welcome Remarks” at the left. After a brief welcome from Interim Provost Jeremy Teitelbaum, you’ll see me. If you’d like to see Takiyah’s remarks, click on “Commencement Address” instead. If for some reason you’d like to read my remarks, keep scrolling down (or click through if you’re on the home page).

University of Connecticut Commencement Ceremonies 2017 (from Total Webcasting)

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Happy Birthday Sir David Attenborough

Wildscreen’s photograph of David Attenborough at ARKive’s launch in Bristol, England © May 2003 You are free: to share – to copy, distribute and transmit the work to remix – to adapt the work

Today is Sir David Attenborough’s 91st birthday. If you follow me on Twitter or read this blog, you don’t need me to tell you who he is, but just as a reminder, here is some of his biography from IMDb:

Born 8 May 1926, the younger brother of actor Lord Richard Attenborough. He never expressed a wish to act and, instead, studied Natural Sciences at Cambridge University, graduating in 1947, the year he began his two years National Service in the Royal Navy. In 1952, he joined BBC Television at Alexandra Palace and, in 1954, began his famous “Zoo Quest” series. When not “Zoo Questing”, he presented political broadcasts, archaeological quizzes, short stories, gardening and religious programmes. 1964 saw the start of BBC2, Britain’s third TV channel, with Michael Peacock as its Controller. A year later, Peacock was promoted to BBC1 and Attenborough became Controller of BBC2. As such, he was responsible for the introduction of colour television into Britain, and also for bringing Monty Python’s Flying Circus (1969) to the world. In 1969, he was appointed Director of Programmes with editorial responsibility for both the BBC’s television networks. Eight years behind a desk was too much for him, and he resigned in 1973 to return to programme making. First came “Eastwards with Attenborough”, a natural history series set in South East Asia, then “The Tribal Eye”, examining tribal art. In 1979, he wrote and presented all 13 parts of Life on Earth (1979) (then the most ambitious series ever produced by the BBC Natural History Unit). This became a trilogy, with The Living Planet (1984) and The Trials of Life (1990).

I knew about Life on Earth, The Living Planet, and The Trials of Life (obviously). I didn’t know that he’d introduced color TV to Britain and that he was responsible for “brining Monty Python’s Flying Circus to the world. What an amazing set of accomplishments. His contributions are simply astounding.

More at Wikipedia and Biography

Science, doubt, and the need for action

From Merchants of Doubt, by Naomi Oreskes and Erik M. Conway:

All scientific work is incomplete—whether it be observational or experimental. All scientific work is liable to be upset or modified by advancing knowledge. That does not confer upon us a freedom to ignore the knowledge we already have, to postpone action that it appears to demand at a given time. Who knows, asks Robert Browning, but the world may end tonight? True, but on available evidence most of us make ready to commute on the 8:30 next day.

“A demand for scientific proof is always a formula for inaction and delay, and usually the first reaction of the guilty. The proper basis for such decisions is, of course, quite simply that which is reasonable in the circumstances.” Or as Bill Nierenberg put it in a candid moment, “You just know in your heart that you can’t throw 25 million tons a year of sulfates into the Northeast and not expect some … consequences.”

Amazon.com

Barnes & Noble

A thought on science and public policy

From Merchants of Doubt, by Naomi Oreskes and Erik M. Conway:

if science is about studying the world as it actually is—rather than as we wish it to be—then science will always have the potential to unsettle the status quo. As an independent source of authority and knowledge, science has always had the capacity to challenge ruling powers’ ability to control people by controlling their beliefs. Indeed, it has the power to challenge anyone who wishes to preserve, protect, or defend the status quo.

Amazon.com

Barnes & Noble

A new approach to spam journals?

This is a new one. I’ve received invitations to submit to what appear to be spam journals well outside my field, and I’ve received conference invitations to present at conferences well outside my field. But this is a new one – an invitation to review a paper well outside my field that will (a) make me a member of the Technical Program Committee for a workshop and receive a discount on registration as a result. Keep in mind as you read this that my expertise is in plant evolutionary genetics and population genetics. I know molecular biologists, even some who have worked on membranes, but I am not a membrane biologist, and I don’t even play one on TV.

Dear Kent E. Holsinger,
Due to your innovative findings in the field of Biology, we need your expertise for reviewing one or two papers in a special issue to be published in Molecular Membrane Biology (2015 Impact Factor: 1.983).
This reviewing will entitle you to become a member of the Technical Program Committee of the Workshop on Molecular Biology, and will give you a discount in case you will attend the 6th International Conference on Biomedical Engineering and Biotechnology (Oct.17-20, 2017 Guangzhou, China).

You may also send your report there to be published in the special issue. If you are too busy to attend our conference and/or review the papers, we would appreciate if you recommend us your colleagues or subordinates who can represent your honorable institution in our international cooperation.

Please feel free to contact me on this or related issues.

For more information, please visit
www.icbeb.org

or contact
icbeb@icbeb.org

The debate about new conservation and alternatives

I mentioned a couple of weeks ago that I fall roughly into the camp of New Conservationists. When I took the Future of Conservation survey, I scored relatively strongly on  “means of improving human welfare” and slightly positive on “willingness to embrace markets and capitalism.” In catching up on my reading this weekend, I discovered that the folks behind the survey also surveyed attendees at the 2015 International Congress of Conservation Biology. Here’s the abstract of the paper describing what they found (full citation and link below):

A vibrant debate about the future direction of biodiversity conservation centers on the merits of the so-called new conservation. Proponents of the new conservation advocate a series of positions on key conservation ideas, such as the importance of human-dominated landscapes and conservation’s engagement with capitalism. These have been fiercely contested in a debate dominated by a few high-profile individuals, and so far there has been no empirical exploration of existing perspectives on these issues among a wider community of conservationists. We used Q methodology to examine empirically perspectives on the new conservation held by attendees at the 2015 International Congress for Conservation Biology (ICCB). Although we identified a consensus on several key issues, 3 distinct positions emerged: in favor of conservation to benefit people but opposed to links with capitalism and corporations, in favor of biocentric approaches but with less emphasis on wilderness protection than prominent opponents of new conservation, and in favor of the published new conservation perspective but with less emphasis on increasing human well-being as a goal of conservation. Our results revealed differences between the debate on the new conservation in the literature and views held within a wider, but still limited, conservation community and demonstrated the existence of at least one viewpoint (in favor of conservation to benefit people but opposed to links with capitalism and corporations) that is almost absent from the published debate. We hope the fuller understanding we present of the variety of views that exist but have not yet been heard, will improve the quality and tone of debates on the subject.

Holmes, G., C. Sandbrook, and J.A. Fisher. 2017. Understanding conservationists’ perspectives on the new-conservation debate. Conservation Biology 31:353–363  doi: 10.1111/cobi.12811

Climate change and biodiversity loss in the Cape Floristic Region


Jasper Slingsby is the lead author on a recent paper in the Proceedings of the National Academy of Sciences describing some of the work he, John Silander, and others did as part of our recently concluded Dimensions of Biodiversity project. Here’s the abstract. Follow the links below to find the full paper and a story about it in UConn Today.

Prolonged periods of extreme heat or drought in the first year after fire affect the resilience and diversity of fire-dependent ecosystems by inhibiting seed germination or increasing mortality of seedlings and resprouting individuals. This interaction between weather and fire is of growing concern as climate changes, particularly in systems subject to stand-replacing crown fires, such as most Mediterranean-type ecosystems. We examined the longest running set of permanent vegetation plots in the Fynbos of South Africa (44 y), finding a significant decline in the diversity of plots driven by increasingly severe postfire summer weather events (number of consecutive days with high temperatures and no rain) and legacy effects of historical woody alien plant densities 30 y after clearing. Species that resprout after fire and/or have graminoid or herb growth forms were particularly affected by postfire weather, whereas all species were sensitive to invasive plants. Observed differences in the response of functional types to extreme postfire weather could drive major shifts in ecosystem structure and function such as altered fire behavior, hydrology, and carbon storage. An estimated 0.5 °C increase in maximum temperature tolerance of the species sets unique to each survey further suggests selection for species adapted to hotter conditions. Taken together, our results show climate change impacts on biodiversity in the hyperdiverse Cape Floristic Region and demonstrate an important interaction between extreme weather and disturbance by fire that may make flammable ecosystems particularly sensitive to climate change.

Slingsby, J.A., C. Merow, M. Aiello-Lammens, N. Allsopp, S. Hall, H.K. Mollman, R. Turner, A.M. Wilson, and J.A. Silander, Jr.  2017. Intensifying postfire weather and biological invasion drive species loss in a Mediterranean-type biodiversity hotspot. Proceedings of the National Academy of Sciences USA (early edition) doi: 10.1073/pnas.1619014114

The new game of Russian roulette for fire-prone ecosystems, UConn Today, 17 April 2017

Not every credible interval is credible

Lauren Kennedy and co-authors (citation below) worry about the effect of “contamination” on estimates of credible intervals.1 The effect arises because we often assume that values are drawn from a normal distribution, even though there are “outliers” in the data, i.e., observations drawn from a different distribution that “contaminate” our observations. Not surprisingly, they find that a model including contamination does a “better job” of estimating the mean and credible intervals than one that assumes a simple normal distribution.2

They consider the following data as an example:
-2, -1, 0, 1, 2, 15
They used the following model for the data (writing in JAGS notation):

x[i] ~ dnorm(mu, tau)
tau ~ dgamma(0.0001, 0.0001)
mu ~ dnorm(0, 100)

That prior on tau should be a red flag. Gelman (citation below) pointed out a long time ago that such a prior is a long way from being vague or non-informative. It puts a tremendous amount of weight on very small values of tau, meaning a very high weight on large values of the variance. Similarly, the N(0, 100); prior on mu; may seem like a “vague” choice, but it puts more than 80% of the prior probability on outcomes with x < -20 or x > 20, substantially more extreme than any that were observed.

Before we begin an analysis we typically have some idea what “reasonable” values are for the variable we’re measuring. For example, if we are measuring the height of adult men, we would be very surprised to find anyone in our sample with a height greater than 3m or less than 0.5m. It wouldn’t make sense to use a prior for the mean that put appreciable probability on outcomes more extreme.

In this case the data are made up, so there isn’t any prior knowledge to work from. but the authors say that “[i]t is immediately obvious that the sixth data point is an outlier” (emphasis in the original). Let’s take them at their word. A reasonable choice of prior might then be N(0,1), since all of the values (except for the “outlier”) lie within two standard deviations of the mean.3 Similarly, a reasonable choice for the prior on sigma (sqrt(1/tau)) might be a half-normal with mean 0 and standard deviation 2, which will allow for standard deviations both smaller and larger than observed in the data.

I put that all together in a little R/Stan program (test.R, test.stan). When I run it, these are the results I get:

         mean se_mean    sd    2.5%     25%     50%     75%   97.5% n_eff  Rhat
mu      0.555   0.016 0.899  -1.250  -0.037   0.558   1.156   2.297  3281 0.999
sigma   4.775   0.014 0.841   3.410   4.156   4.715   5.279   6.618  3466 1.000
lp__  -16.609   0.021 0.970 -19.229 -17.013 -16.314 -15.903 -15.663  2086 1.001

Let’s compare those results to what Kennedy and colleagues report:

AnalysisPosterior mean95% credible interval
Stan + "reasonable priors"0.56(-1.25, 2.30)
Kennedy et al. - Normal2.49(-4.25, 9.08)
Kennedy et al. - Contaminated normal0.47(-2.49, 4.88)

So if you use “reasonable” priors, you get a posterior mean from a model without contamination that isn’t very different from what you get from the more complicated contaminated normal model, and the credible intervals are actually narrower. If you really think a priori that 15 is an unreasonable observation, which estimate (point estimate and credible interval) would you prefer? I’d go for the model assuming a normal distribution with reasonable priors.

It all comes down to this. Your choice of priors matters. There is no such thing as an uninformative prior. If you think you are playing it safe by using very vague or flat priors, think carefully about what you’re doing. There’s a good chance that you’re actually putting a lot of prior weight on values that are unreasonable.4 You will almost always have some idea about what observations are reasonable or possible. Use that information to set weakly informative priors. See the discussion at https://github.com/stan-dev/stan/wiki/Prior-Choice-Recommendations for more detailed advice.

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Photos from Bonn

Christmas market in Bonn

Christmas market in Bonn, December 2016. Click on the photo to see the entire album on Flickr.

Late last November I visited Bonn to participate in a small workshop sponsored by the Crop Trust (https://www.croptrust.org/) intended to develop criteria to assess whether germplasm collections of crops and crop wild relatives are sufficient to meet the Millenium Development Goals. I was there not because I know a lot about crop germplasm (I don’t), but because my expertise in analysis of genetic structure in plant populations and my work on plant conservation genetics provided some (I hope) useful context for the discussions.

I didn’t have a lot of time to explore Bonn, but I did have a couple of hours on the afternoon I arrived and most of the morning on the day that I left. If you’d like to see the photos I thought were worth saving, click on the image above to visit a Flckr album where you can see them all.