Uncommon Ground

Monthly Archive: October 2017

Universitas 21 3-minute thesis competition winners announced (@U21News)

Universitas 21 is a global network of research intensive universities, founded in Melbourne in 1997. It aims to enhance global citizenship and institutional innovation. Since 2012, Universitas 21 has sponsored a Virtual 3-minute thesis competition in which videos of local 3-MT competition winners are judged against one another for a network-wide prize. Last year, one of UConn’s own PhD students, Islam Mosa, won the People’s Choice award. This year First Prize and the People’s Choice award went to Samuel Ramsey of the University of Maryland. Here’s his presentation.

Here’s how a press release from U21 describes his award:

In his winning presentation, Samuel described his research which has focused on the parasitic mite, varroa destructor, which is one of the main reasons for the decline in the honey bee population. Samuel’s research has centred on finding out how this parasite is so destructive; focussing on what the parasite is eating and where on the honey bee they feed. His results have shown that the parasite only feeds on one specific part of the honey bee, the fat body tissue, an important tissue that controls nine major functions within the organism, including the storage of nutrients, the detoxification of pesticides and the production of the immune response. Now he knows what they are feeding on, he is investigating whether it is possible to introduce an agent into this fat body tissue that can disrupt the reproductive cycle of the parasite and eliminate this pest once and for all.

Samuel spoke of his experience of taking part in the 3MT® competition: “I would characterize this experience as challenging but in the best way possible. Ph.D. programs teach us complex technical terms and opaque jargon. Reliance on them can make our entire field inaccessible to the people most in need of our insight. Being forced to explain your work simply, forces you to approach it differently; to understand it better.

So many ground-breaking scientific discoveries never move beyond the pages of journals to public consciousness or public policy, partly because it’s difficult to explain things briefly without sacrificing accuracy. That’s why I’m so glad that I entered this contest. It forced me to refine this skill; one that I’m certain will serve me well throughout my career in science.

I’m so grateful to the University of Maryland for encouraging us to be a part of this competition! I think I’m a better communicator and a better researcher as a direct result. I want to thank everyone who participated in the contest by watching and sharing the videos. I also have to thank my advisor Dennis van Engelsdorp for all of his support, my mentors Kathy and Dr. Kevin Hackett, and my incredible parents who have constantly encouraged my interest in science and who are always so interested to hear what I’m up to in the lab. I had no idea at the time but dinner with them was the best possible practice for this competition.”

Dr Steve Fetter, Interim Dean of the Graduate School and Associate Provost for Academic Affairs at the University of Maryland, spoke of the university’s delight in Samuel’s achievement: “We are thrilled that Sammy Ramsey won both the U21 3MT® Judge’s Prize and the People’s Choice Prize in this year’s competition.  Sammy’s presentation is a wonderful example of how researchers can describe their work to a general audience in a clear, compelling, and engaging manner.”

The international judging panel noted that Samuel’s presentation was really engaging, that Samuel presented clearly and with confidence, and that he articulated his research very well. The general public clearly agreed with the judges and voted Samuel’s presentation top in the People’s Choice competition which took place online during mid-October. With around one third of the overall votes, Samuel clearly impressed the public with his research on the how the parasitic mite, varroa destructor, is affecting the honey bee population and how this could be stopped. Entrants from the University of Nottingham and University of British Columbia were second and third respectively, in the public vote.

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.


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:

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})

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.


Announcing the BioOne Career Center

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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.