Uncommon Ground – Page 9 – Academics, biodiversity, genetics, & evolution

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Getting organized in 2018 – Trying an everything notebook

If you know me or if you read later entries in this series, you’ll see that I’m a bit of a tech geek. Most of what I do to keep myself organized I do electronically with a series of different applications that work across the electronic platforms I use (MacBook, iMac, iPhone, iPad),¹ but I am also a fountain pen afficianado. I carry 6-7 different fountain pens with me in my briefcase, even when I travel. I also find it much easier to take notes with pen and paper when I’m in a meeting. Since I’m in meetings so much as a result of serving as a Vice Provost and Dean, I use pen and paper a lot. Let’s start with how I use them, or more accurately how I am planning to use them in 2018. I’ll describe how I integrate the paper with my electronic platforms in a couple of weeks.

Last year I tried using a Bullet journal. The idea is appealing. It provides a simple way to organize to-do lists, meetings, and notes from every day into a single notebook. If I were working solely analog, I would almost certainly be using a Bullet journal. But I depend heavily on my interconnected electronic devices. I suppose I could carry my Bullet journal with me everywhere and record everything there, but it just doesn’t fit the way I work. I always have my iPhone with me, and if I’m at home or in the office, my iPad and MacBook (and iMac if I’m at the office) are never far away. I can add something to my to-do list if it occurs to me when I’m at the grocery store.² I can even use Siri to add something if it occurs to me when I’m driving to or from work. For me a paper Bullet journal is just duplicated effort, and after a year of trying it, it’s clear that it won’t work for me.

This year I’m trying an Everything notebook. I don’t remember how I ran across the idea, but I think it’s going to work very well. There have only been 4 working days to try it out so far this year, but so far it fits my work patterns much better. There are a few differences between the way I’m setting up my Everything notebook and the way that Raul Pacheco Vega set his up.

My notebook will be strictly black and white. I’ll be using a Rotring fountain pen that I’ve had for a little over 20 years, because its nib is fine and inflexible, so that my notes will be as neat as they can be with my lousy handwriting. I can’t tell you the exact model of the pen, because Rotring no longer makes fountain pens so far as I can tell.
I will be using index pages in the front of the notebook, an idea borrowed from the Bullet journal, instead of labeled plastic tabs.

At the end of every day, I’ll quickly review my notes and transfer to my electronic platforms as needed. The only difference between this and what I’ve done in the past (ignoring the Bullet journal for the moment) is that in the past I used notepads that didn’t leave a permanent record (other than what I transferred to my electronic systems). I expect this to work well for me, and it will provide a physical backup should that become necessary. (more…)

kent January 8, 2018 Productivity 6 Read more >

The origin of a bipolar moss (i.e., one that occurs in the far North and the far South)

One of the great pleasures of serving as an associate advisor on PhD committee is that sometimes you contribute enough to the analysis and interpretation of the data that you end up being a co-author on a paper. That’s why I have papers on New Zealand cicadas, deer mice, and tapeworms, among other things. Now I’ve added another group to my list – moss. Lily Lewis finished her PhD at UConn in the spring of 2015 working with Bernard Goffinet. I was a member of her committee, and now a chapter of her dissertation on which I was able to help has appeared in the American Journal of Botany.¹ Here’s the title and abstract. You’ll find the DOI and a link to the paper below.

Resolving the northern hemisphere source region for the long-distance dispersal event that gave rise to the South American endemic dung moss Tetraplodon fuegianus.

PREMISE OF THE STUDY: American bipolar plant distributions characterize taxa at various taxonomic ranks but are most common in the bryophytes at infraspecific and infrageneric levels. A previous study on the bipolar disjunction in the dung moss genus Tetraplodon found that direct long-distance dispersal from North to South in the Miocene–Pleistocene accounted for the origin of the Southern American endemic Tetraplodon fuegianus, congruent with other molecular studies on bipolar bryophytes. The previous study, however, remained inconclusive regarding a specific northern hemisphere source region for the transequatorial dispersal event that gave rise to T. fuegianus.
METHODS: To estimate spatial genetic structure and phylogeographic relationships within the bipolar lineage of Tetraplodon, which includes T. fuegianus, we analyzed thousands of restriction-site-associated DNA (RADseq) loci and single nucleotide polymorphisms using Bayesian individual assignment and maximum likelihood and coalescent model based phylogenetic approaches.
KEY RESULTS: Northwestern North America is the most likely source of the recent ancestor to T. fuegianus.
CONCLUSIONS: Tetraplodon fuegianus, which marks the southernmost populations in the bipolar lineage of Tetraplodon, arose following a single long-distance dispersal event involving a T. mnioides lineage that is now rare in the northern hemisphere and potentially restricted to the Pacific Northwest of North America. Furthermore, gene flow between sympatric lineages of Tetraplodon mnioides in the northern hemisphere is limited, possibly due to high rates of selfing or reproductive isolation.

DOI: 10.3732/ajb.1700144
(more…)

kent January 3, 2018 Botany 0 Read more >

Getting organized in 2018 – Introducing a blog series

Welcome to 2018! This post is different from others you’ve seen if you’ve been here before. Instead of comments on a recent piece of research, on science policy or science communication issues, or on issues concerning conservation, biodiversity, or the environment, this post begins a series that will share how I organize my work. Why? Off and on through my career I’ve had people ask me about how I get things done. Especially since I became Vice Provost for Graduate Education and Dean of The Graduate School at UConn nearly 6 years ago,¹ quite a few people have asked me how I can do that and continue to advise graduate students, teach (a little), and make research contributions. By writing down what I do, I’ll now have a link I can send anyone who’s interested.

Today’s post merely announces the series. The first real post will appear on Monday, January 8^th and there should be another one every Monday morning after that for several weeks.²

Important disclaimer: I am not a productivity expert, and nothing you’ll read in this post or the posts that follow has been validated by empirical research.³ What I’m doing to organize myself may not work for you, and what I’m doing right now may not even be the best way I could organize myself. What you’ll read here is what I’m doing now. Adopt and modify anything that seems like it might be useful. Ignore anything that seems pointless. If you have suggestions for how I could organize myself better, please leave a comment. Not only will you help me, you’ll help other people who read this.

A note on software I’ve been a Mac user since 2009 or 2010. I also use an iPhone and an iPad. I know that some of the software I’ll mention, e.g., Evernote and Scrivener, is available on Windoze and Android. I’m pretty sure that some of it isn’t, e.g., Ulysses and OmniFocus. There are probably Windoze and Android equivalents of anything I mention, but I don’t know what they are so I can’t comment on them. When I am aware of alternatives to software I use, I’ll mention them, but I probably haven’t tried them. That doesn’t mean what I’ve chosen is best. It just means that I’ve found what I use works well for me.

I should also mention that I have no connection with any of the software products I’ll mention other than as a satisfied user. If you decide to purchase any of them, none of the companies will send me a royalty. Just as you should adopt and modify any advice you think might be useful and ignore what isn’t, you should use your own judgment about whether or not to purchase any of the products I use. (more…)

kent January 1, 2018 Productivity 0 Read more >

Climate change and Pelargonium in South Africa

For more than a decade my colleagues Margaret Rubega and Bob Wyss have co-taught a course to graduate students in science and engineering and undergraduates in Journalism.¹ The purpose of the course is to help science students improve their skills in working with journalists and to help journalist increase their skills in interviewing scientists and developing stories from those interviews. One of the projects in this fall’s edition of the course was for the journalism students to interview one of the science graduate students and produce a short video describing the student’s research. Daniela Doncel interviewed Tanisha Williams, a PhD student in EEB whom I co-advise with Carl Schlichting. In addition to interviewing Tanisha, Daniela also interviewed Cindi Jones and me. She assembled a video that explains Tanisha’s work very well. I think Daniela did a very nice job of weaving the disparate interviews into a compelling story, and I think the video looks very good (even though it has me in it). I hope that you agree.

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kent December 29, 2017 Botany, Climate change, Science communication 0 Read more >

AIBS Emerging Public Policy Leadership Award

The American Institute of Biological Sciences works to ensure that the public, legislators, and others have access to the best scientific information available, especially in the fields of environmental and organismal biology. In addition to individual members, more than 100 professional societies are organizational members. One of the most interesting programs AIBS offers is its Emerging Public Policy Leadership Award. Here is the text of an e-mail I recently received announcing this year’s award.

Each year, the American Institute of Biological Sciences (AIBS) recognizes graduate students in the biological sciences who have demonstrated initiative and leadership in science policy. Recipients obtain first-hand experience at the interface of science and public policy.Winners receive:

A trip to Washington, DC, to participate in the AIBS Congressional Visits Day, an annual event that brings scientists to the nation’s capital to advocate for federal investment in the biological sciences, with a primary focus on the National Science Foundation. The event will be held on April 17-18, 2018. Domestic travel and hotel expenses will be paid for the winners.
Policy and communications training, including information on the legislative process and trends in federal science funding.
Meetings with congressional policymakers to discuss the importance of federal investment in the biological sciences.
A one-year AIBS membership, including a subscription to the journal BioScience and a copy of “Communicating Science: A Primer for Working with the Media.”
The 2018 award is open to U.S. citizens and U.S. permanent residents enrolled in a graduate degree program in the biological sciences, science education, or a closely allied field. Applicants should have a demonstrated interest in and commitment to science policy and/or science education policy.

Applications are due by 11:59 PM Eastern Time on 9 January 2017. The application can be downloaded at http://www.aibs.org/public-policy/eppla.html.

kent November 13, 2017 BiologyScience policy 0 Read more >

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.

kent October 31, 2017 Science communicationUConn 0 Read more >

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.

kent October 14, 2017 Personal 2 Read more >

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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kent October 13, 2017 Science 0 Read more >

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.

kent October 11, 2017 Botany, EcologyUConn 0 Read more >

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., A_max, 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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kent October 4, 2017 Statistics 0 Read more >