Uncommon Ground

Academics, biodiversity, genetics, & evolution

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Getting organized in 2018 – Evernote as a research tool

Introduction to the series

Last week I described how I get pen and paper notes into Evernote so that I have copies of notes associated with meetings in an easily accessible electronic form regardless of whether I’m working on my MacBook, my iPhone, my iPad, or my iMac.1 This week I’ll describe how I use it as a “research” tool. I put research in quotes, because I don’t use it systematically for scholarly research the way some people do.

Scanning or typing notes into Evernote is very straightforward, but what do you do if you are investigating a topic (or simply reading some news) in your web browser and you find an article you want to save?

If you’re on a laptop or desktop and working in your browser, you’ll want to install the Evernote Web Clipper for your browser.2 Once you have the web clipper installed it’s very easy. When you’re on a web page you want to save, just click on the little elephant head icon in your menu bar, and a login screen will pop up where you enter your e-mail address or username, followed by one that will ask for your password. Once you’ve signed in, you’re good for 30 days. Then you’ll have the option to save the article, a simplified article, the full page, a bookmark, or a screenshot. The web clipper remembers your last choice. I typically use the “simplified article” option. It saves all of the text and relevant images without all of the “cruft” that’s on most pages. You’ll see an example from Sunday’s New York Times on the left. You’ll notice that you can also specify which notebook you want the clipping saved in and you can add any tags that you want.3 You can also add your own text notes about what you’re saving before the note is saved (or you can add them later if you call it up again in Evernote and want to add something then).

The process is much the same on my iPhone or iPad. If I’m on a web page that I want to save, I just hit the little icon that I’d use to send a link by e-mail or text message and select Evernote instead. Again I can select a notebook and add tags. I can also add a note if I want. What I can’t do4 is save the page in a “simplified article” format. As a result, web pages I save from my iPhone or iPad often have a lot of “cruft.” They’re legible, but cluttered. If that really bothers me, though, I just open up that note in Evernote on my laptop or desktop, use the embedded link in the note to visit the webpage again and use the webclipper in my browser to get a simplified article.

I probably clip half a dozen articles per day from things I’m reading. They might be articles from the Chronicle of Higher Education or Inside Higher Ed that I want to hang on to because they may have information or ideas that could be relevant to my work as Dean of The Graduate School, they might be an article from a scientific journal that I want to save somewhere in addition to or instead of my bibliographic software,5 or they might be a blog post on a topic that is interesting or important that I don’t want to lose.

I have more than 20,000 notes in Evernote now, and because they’re all searchable, I can easily find notes I’ve collected on a variety of different topics, whether they’re tagged by a particular topic, stored in a particular notebook.6, or simply in the body of the note.

I should point out that these abilities aren’t unique to Evernote. I have used OneNote only a little, but it seems to provide many of the same features. If you have it available to you as part of an Office 365 subscription, you might want to investigate its features before trying Evernote. I use Evernote because I’ve been using it for 10 years, I’m happy with it, it’s familiar, and it’s integrated into my workflow. If I were starting from scratch, I’m not sure it would be my application of choice, but it’s served me very well, and I don’t have plans to change. (more…)

Getting organized in 2018 – Evernote and meetings

Introduction to the series

Last week I described how I combine my new Everything notebook with my electronic task manager, OmniFocus. In looking over last week’s post, I realized that I only described how OmniFocus integrates with my Everything notebook. I didn’t describe how I use it to organize and track projects. That’s worth a post (or two) in itself, but it makes more sense for that post to come near the end of this series, since the way I use it depends heavily on the other applications I use.

Today I’m introducing Evernote, which I’ve been using since February 1st, 2009. The only other applications I’ve used that long are Emacs (a very powerful text editor I’ve been using since the late 1980s), gcc (the GNU compiler collection), Firefox, Thunderbird, and the Microsoft Office suite.

Evernote is, as its name suggests, is an application in which to store notes, but that barely scratches the surface of what it can do. Not only does it synchronize across all of my devices – the laptop I’m writing this on, the desktop that’s my primary machine in the office, my iPhone, and my iPad -, but the notes can include images (imported or snapped with the camera on my iPhone or iPad) and documents in a variety of formats (including Word and PDF). Evernote indexes all of these notes for easy searching, and it even indexes text inside images or PDFs (in the premium version).

So what does this have to do with meetings? I find it very distracting when others bring a laptop or iPad to a meeting and use it to take notes. They seem distracted by the technology rather than being engaged in the meeting. I may simply be projecting my own behavior, but I found early on with my iPad that I couldn’t focus on the meeting and take notes on my iPad at the same time. Instead, I take notes with pen and paper (now in my Everything notebook), but for any meeting where I am likely to want the original notes, I scan them (using my iPhone now) and incorporate them into an Evernote note (or put them on Dropbox – more on Dropbox vs. Evernote in a couple of weeks). Once in Evernote I can put them into an appropriate notebook and tag them to make it even easier to find them in the future.

When I’m leading a meeting, I also make notes ahead of time (typically with Ulysses) and sync the notes to Evernote so that I can refer to them. Then I can add notes from the meeting to the pre-meeting notes,1 or I can use the “link” feature in Evernote to provide links from each note to the other.

I find that this approach gives me all of the advantages of an electronic notebook – portable, accessible, searchable – and all of the advantages of pen and paper – ease of use, lack of distraction, reliability. Your mileage may vary, but it works for me.

  1. I’m typically not organized enough to call my notes an agenda.

Getting organized in 2018 – Tracking tasks

Introduction to the series

Last week I described the approach to an Everything notebook that I’m trying this year. With another week under my belt, I can report that it’s going very well. I have a few small things to add to last week’s entry:

  1. I’m using two different fountain pens in my notebook. I use the Rotring I mentioned last time when I’m working at my desk, but I use a fine-point Namiki Vanishing Point (with a blue carbonesque finish, image above from Fahrney’s Pens) when I go to meetings.1
  2. I make it a habit to review my notebook at the end of every working day so that I can transfer any notes I have to one of my electronic applications, including the task manager I’m about to describe.
  3. I use a Moleskine Classic Notebook (Black, XL) for my notebook.2

I first started tracking my tasks more than 30 years ago when I was a Miller Fellow at UC Berkeley. For some reason, I received a catalog from DayTimer, and it struck me as a good way to keep track of my appointments, which were few in those days, and the things I needed to do. I used a 1-page-per-day compact planner for several years before switching to a journal-sized planner. I mention this because it shows that long before I read Getting Things Done, I was following David Allen’s advice: Write everything down in a place where it won’t be lost. As I told many people, the great thing about my DayTimer was that if it went into my DayTimer, I wouldn’t forget about it.3

When DayTimer came out with an electronic organizer in the mid-1990s, I started to use it. I even printed my own pages through the software. By the late 1990s or early 2000s, the redundancy made even less sense than it did when I started, and I stopped using paper. I’ve been through several different electronic task managers since then, and I’ve settled on OmniFocus as the best fit for me, at least for now. Here’s why:

  • I always have a complete inventory of everything I’m committed to doing,4 including dates by which projects (or components of projects) are do. It synchronizes across my MacBook, iMac, iPad, and iPhone, so no matter what device I happen to have handy, I can add an item or cross one off when it’s completed.
  • It provides a convenient way of grouping tasks into projects, and to making subtasks within tasks. As a result, it works as a lightweight project manager. For example, if I am working on a grant proposal, I’ll construct a preliminary list of all of the things that need to get done before it’s submitted with target dates for completion (e.g., outline proposal, develop budget, share initial draft with collaborators/colleagues, get letters of support, submit budget to Sponsored Programs for approval, submit final draft). The outline approach to organizing makes a lot of sense.
  • It lets me know when I haven’t completed a task by the time I said that I would. Its icon even tells me how many tasks are behind schedule, which makes me feel exceedingly guilty when I see it. My only options are: (1) finish the task, (2) decide that I can re-schedule (delay) the due date beyond what I originally planned, or (3) decide that I no longer need to complete it, so that I delete it from the list.
  • It works with Siri. If I’m walking across campus or driving somewhere and a task occurs to me, I simply say “Hey, Siri. Remind me to XXX at YYY” and a new task shows up in OmniFocus that I now won’t forget.
  • It has a nice “Review” option that I use every Sunday to review the status of all of my tasks.5

There are a lot of other electronic task lists out there, and I haven’t tried most of them. OmniFocus is moderately expensive, and it may be more complicated than you need, but if you have a smartphone or tablet and a laptop or desktop, you probably would benefit from using one of the many cross-platform task managers.

One thing I haven’t described is how my everything notebook, paper and pen, integrates with OmniFocus. It’s very simple. At the end of every day I review notes I’ve written in my everything notebook. If there are any notes that require some action, I create a task in OmniFocus. If there’s information in my everything notebook that’s relevant to the task, I use the “Notes” field in OmniFocus to make a note of how to find that information again.6
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Getting organized in 2018 – Trying an everything notebook

Introduction to the series

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…)

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
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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 8th 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…)

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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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.

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.