Uncommon Ground

Author Archive: kent

Remembering Mimi

Seventeen years ago a driver at Bill’s company was headed south on Route 2 towards Glastonbury. He swerved to miss a paper bag in the road and because he didn’t want anyone else to damage a tire running over a bag of beer bottles, he pulled over and retrieved the bag. Instead of beer bottles, he found two tiny black kittens inside. He was late for a delivery, but he returned to the office and left them there. What follows is a very long story, but at the end of the day Bill took them to our veterinarian. They were so tiny he didn’t know what they could eat. The vet gave Bill some kitten formula, and he brought them home. They were so close to starvation that their bodies shook as they lapped up the formula. They were so small that I could easily hold both of them in the palm of one hand. It was several weeks before they were big enough to climb the stairs to the second floor of our house.

By Sunday night we had named them. Mimi because she was so sweet and kind, as in Puccini’s La Botheme. Maxwell (“Max”) because he is a lovable and ungainly like Maxwell Smart.

Yesterday we lost Mimi. Her health had been declining for more than a year, but in the past week and a half the decline became precipitous. There was a sadness in her eyes, and she was happy only when one of us held her. She passed away peacefully a little after 4:00pm. Max is still healthy, but the three of us, including Max, are heartbrokn. Our house feels empty, but Mimi’s suffering is over. She lives on in our memories, and we will hold her close to our hearts forever.

Championing the Success of Women in Science, Technology, Engineering, Maths, and Medicine


In honor of Ada Lovelace Day, the second Tuesday in October, Digital Science released a report entitled Championing the Success of Women in Science, Technology, Engineering, Maths, and Medicine. I encourage you to read it, and not only because Lauren Kane (COO of BioOne1) is a co-author of one of the chapters. Here how the report is described on its Figshare page.

This report explores the role of women in STEM and the challenges they face, looking at areas of gender inequality, exploring potential causes of this inequality and offering solutions. Women’s reluctance to step into leading roles, their tendency to suffer from “imposter syndrome” and their career breaks as a result of motherhood, are just some of the contributory factors holding them back, as well as the outdated, sexist attitudes they sometimes have to face in the workplace.

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Plants, People, and the Mother City

Tanisha Williams, Fulbright 2015-2016, South Africa, at Boulders Beach visiting the penguins.

Some of you know that Carl Schlichting and I co-advise Tanisha Williams. If you know that, you almost certainly know that Tanisha spent the 2015-2016 academic year as a Fulbright Fellow in South Africa. She was based at the Cape Peninsula University of Technology, and she used her time not only to collect seeds of Pelargonium and establish experimental gardens at Kirstenbosch Botanical Garden and Rhodes University but also to work with two non-profit environmental organizations. She posted an article about her experience on the blog of the Fulbright Student Program. Here’s an excerpt to whet your appetite:

Among the many experiences I had, I must say the residents from the Khayelitsha township have taken a special place in my heart. This is where I taught girls and young women math, science, computer tutoring, life skills, and female empowerment through a community center program. It was such an impactful experience, as these girls are growing up in a community with high rates of unemployment, violence, and other socioeconomic issues. It was empowering for me to see the curiosity and determination these girls had for learning and changing their community. They thought I was there to teach them from my own experiences being raised in a comparable situation and now working on my doctorate as a scientist, but I know I was the one that gained the most from our time together. I learned what it truly means to have hope and persevere. These lessons, along with the ecological and evolutionary insights from my academic research, will be ones that I always remember.

Exploring mixed models in Stan

I am about to begin developing a moderately complex mixed model in Stan to analyze realtinoships among anatomical/morphological traits (e.g., leaf thickness, LMA, wood density), physiological performance (e.g., Amax, stem hydraulic conductance), and indices of fitness (e.g., height, growth rate, number of seedheads). One complication is that the observations are from several different species of Protea at several different sites.1 We’re going to treat sites as nested within species.

Before I start building the whole model, I wanted to make sure that I can do a simple mixed linear regression with a random site effect nested within a random species effect. In stan_lmer() notation that becomes:

stan_lmer(Amax ~ LMA + (1|Species/Site))

I ran a version of my code with several covariates in addition to LMA using hand-coded stan and compared the results to those from stan_lmer(). Estimates for the overall intercept and the regression coefficients associated with each covariate were very similar. The estimates of both standard deviations and individual random effects at the species and site within species level were rather different – especially at the species level. This was troubling, so I set up a simple simulation to see if I could figure out what was going on. The R code, Stan code, and simulation results are available in Github: https://kholsinger.github.io/mixed-models/.

The model used for simulation is very simple:

\(
\begin{equation}
y_k \sim \mbox{N}(\mu_k, \sigma) \\
\mu_k = \beta_0(species|site) + \beta_1x \\
\beta_0(species|site) \sim \mbox{N}(\beta_0(species), \sigma_{species|site}) \\
\beta_0(species) \sim \mbox{N}(\beta_0, \sigma_{species})
\end{equation}
\)

Happily, the Stan code I wrote does well in recovering the simulation parameters.2 Surprisingly, it does better on recovering the random effect parameters than stan_lmer(). I haven’t completely sorted things out yet, but the difference is likely to be a result of different prior specifications for the random effects. My simulation code3 uses independent Cauchy(0,5) priors for the standard deviation of all variance parameters. stan_lmer() uses a covariance structure for all parameters that vary by group.4 If the difference in prior specifications is really responsible, it means that the differences between my approach and the approach used in stan_lmer() will vanish as the number of groups grows.

Since we’re only interested in the analog of \(\beta_1\) for the analyses we’ll be doing, the difference in random effect estimates doesn’t bother me, especially since my approach seems to recover them better given the random effect structure we’re working with. This is, however, a good reminder that if you’re working with mixed models and you’re interested in the group-level parameters, you’re going to need a large number of groups, not just a large number of individuals, to get reliable estimates of the group parameters.

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Announcing the BioOne Career Center

BioOne logos
BioOne is a collaboration between libraries and non-profit scholarly publishers in organismal and environmental life sciences. It was founded in 1999 to help publishers obtain the revenue they need to support their publishing program while ensuring affordable access to scholarly journals for libraries and their patrons. I am proud to have served as Chair of the BioOne Board of Directors since 2000.

BioOne’s primary service is to provide BioOne Complete, a database of 207 journals including many open access titles. As the title of this post suggests, BioOne is now offering a new service, the BioOne Career Center. Anyone looking for an opportunity can create a free account, set up a job aloer, and post their CV. Employers can post jobs on the site for free until the end of October (you’ll find the necessary code in the announcement), and posting for internships, volunteer opportunities, and conferences will always be free. We hope that the BioOne Career Center will become a valuable resource.

A crack in creation

In August, 2012 a paper entitled “A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity” appeared in Science (doi: 10.1126/science.1225829). I probably saw the title in the table of contents of the August 17th issue and skipped right by. Bacterial immunity isn’t a topic a pay a lot of attention to. OK. Let’s be honest. I don’t pay any attention to bacterial immunity.

Not too long after that paper appeared, I started hearing about something called CRISPR-Cas9. I didn’t know what it was or what it might be useful for, only that a lot of people who were interested in molecular genetics were paying attention to it, especially those who were interested in using molecular tools to edit genomes of complex, multicellular organisms. I started to see newspaper and magazine articles talking about how this new technology would revolutionize biology and medicine in the same way that the discovery and use of restriction endonucleases had revolutionized them in the mid-1970s.

Some of the most ambitious projections suggested that we could be entering an era of designer genes in which gene therapy might be used not only to modify or replace genes that lead to diseases like sickle cell anemia, but in which it might be used to enhance “normal” functions. Not too long after that I started hearing about biologists who realized that CRISPR-Cas9 could be used to build gene drives that might be used to control pest populations. A lot of people began worrying about the ethical issues associated with use of CRISPR-Cas9 (e.g., doi: 10.1093/bmb/ldx002).

In June, two pioneers in the work leading to development of CRISPR-Cas9 published a book outlining the history of the work and exploring some of the ethical implications. I am a little less than halfway through A crack in creation, but so far I have found it very readable and informative. Reading this book is the only reason I know about the Science paper from 2012. Only now, 5 years later, am I taking the time to learn about this new technology. I had an inkling of its power and utility before I started reading, and I was (am still am) uneasy about some potential applications. Since so much of the basic science is very distant from my expertise and experience, I can’t judge the historical accuracy of the story Douda and Sternberg tell, but they seem generous in giving credit to other scientists who made contributions and very aware that their creative insights depended on previous work by many other people. That makes me think that if there are inaccuracies in the story, they are inadvertant and unintentional.

If you’ve been waiting for a good time to learn more about CRISPR-Cas9, your wait is over. Click on the image above, go to Amazon, and buy yourself a copy of A crack in creation or check it out from your library. You won’t be disappointed.

(In case you’re wondering, I don’t know either of the authors, and I won’t get any Amazon affilliate credits if you buy the book from Amazon. I’m endorsing the book only because I’ve found it very informative. It’s also written very clearly, clearly enough that I think your non-biologist friends and relatives would find it interesting and informative, too.)

BioOne has a new look

BioOne logos

The new organizational logo for BioOne (left) and the new logo for the BioOne Complete collection (right)

Some of you know that I have chaired the BioOne Board of Directors since a year after its initial incorporation in 1999. In the last 17 years, BioOne has seen many changes. The most recent is an updated set of logos for BioOne, the not-for-profit organization that supports innovative approaches to scholarly publication in organismal and environmental life sciences. BioOne is a collaboration between not-for-profit publishers and libraries, both of whom share an interest in ensuring that scholarly research is widely accessible and that not-for-profit publishers can recover the revenues they need to support their publishing operations. BioOne Complete is BioOne’s core product, “a database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences.”

A week ago BioOne and BioOne Complete launched the new logos above. More information about the new logos is available at http://www.bioonepublishing.org/news/1412/.

Revitalizing Graduate STEM Education for the 21st Century

The National Academy of Sciences has a committee that is leading a study of graduate education in science, technology, engineering, and mathematics (STEM). The goals of the study include:

  • Identifying policies, programs and practices that could better meet the diverse education and career needs of graduate students,
  • Identifying strategies to improve the alignment of graduate education courses, curricula, labs and fellowship/traineeship experiences for students with the needs of prospective employers
  • Identifying policies and effective practices that provide students and faculty with information about career paths for graduates holding master’s and Ph.D. degrees and provide ongoing and high quality counseling and mentoring for graduate students.
  • Creating a set of national goals for graduate STEM education that can be used by research universities.

The committee released a discussion document describing a set of competencies that might form core educational elements for both master’s and PhD programs in STEM fields. It seeks community input on the discussion document. The deadline for comment is 22 September 2017 and may be submitted either by a web form at http://nas.gradedinput.sgizmo.com/s3/ or via e-mail to STEMGradEd@nas.edu. If you are interested in STEM graduate education, I encourage you to read the document and submit comments.

Disclaimer: I was part of the Council of Graduate Schools Committee that developed the Alignment Framework for the Master’s Degree that the document uses to describe core educational elements for STEM master’s degrees.

Rediscovering Adonis cyllenea

Adonis cyllenea

Adonis cyllenea – Photographed at the 8th International Alpine Conference, Nottingham, UK. Photo by Todd Boland (from the North American Rock Garden Society)

Adonis cyllenea was described in 1856 from a specimen collected in the Peloponnese Mountains of Greece (http://bit.ly/2xgG1lS). It was thought to be extinct in the wild until 1976 when it was rediscovered (https://en.wikipedia.org/wiki/Adonis_cyllenea). It was recorded in the Giresun province of Turkey in 1867 and was just rediscovered there (http://bit.ly/2vfDPcO). Occasionally, there is good news about plants that were thought to be extinct. Mostly when they disappear, they are gone for good.

The solar eclipse at UConn

Solar eclipse

Solar eclipse prediction for Storrs from Wolfram

This afternoon at 2:45pm EDT the solar eclipse will reach its maximum in Storrs, about 70%. The figure above is a screenshot from my iPhone of the Wolfram Precision Eclipse Computation for Storrs. Follow that link to get the results for your location. The Physics Department at UConn will be hosting an eclipse viewing party on Horsebarn Hill. There will be solar telescopes and a short public lecture in addition to other activities. Unfortunately, I won’t be able to attend. I will be welcoming the new class of graduate fellows from 2:00-3:00pm and welcoming all new and continuing fellows and their faculty advisors at an ice cream social from 3:00-4:00pm. We will be meeting in the Alumni House, so we should see the darkening outside, and I may suggest that we take a short break a little before 2:45pm to go outside.

It’s almost certainly too late to get eclipse glasses, so if you don’t have them already you’ll have to find welder’s goggles or a solar telescope. If you can’t find any of those, you can still build yourself an eclipse viewer with a cardboard box and a few simple tools. Whatever you do, don’t look at the eclipse without protection for your eyes. A man in Portland, Oregon looked at an eclipse for no more than 20 seconds when he was in high school in 1963. It burned a holed in the retina of his right eye. Don’t let that happen to you.