Uncommon Ground

Academics, biodiversity, genetics, & evolution

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Getting organized in 2018 – Evernote and Dropbox

Getting organized in 2018 – links to the series

I’ve mentioned Evernote in two previous posts (here and here). It and OmniFocus (posts here and here) are two of the three software applications I use most frequently. The third isn’t an application that I use in the traditional sense of “use.” I don’t start it up and work with it. It’s just always sitting there in the background silently doing its job. “It” is Dropbox.

Most of you are probably familiar with Dropbox. It stores files in the cloud and keeps them synchronized across computers. I have Dropbox installed on my MacBook, my iMac at work, my iMac at home, my iPhone, and my iPad.1 Any file I save to one of my Dropbox folders on one device is automatically to the same folder on other devices.2 That means when I save a document from my MacBook or anywhere else (whether PDF, Word, Excel, CSV, plain text, or Markup) it is (almost) immediately synced to every other device I have. Since I have versions of Word and Excel on my iPhone and iPad as well as on my other computers, it means I can read virtually any document I save on whatever device I’m working with at the moment.

That’s my key to going paperless to meetings. For meetings I organize, I prepare notes (in plain text or Markup – more on that in next week’s post). For regular meetings (like staff meetings in The Graduate School) that I want to have accessible and easily searchable, I’ll write in Markup and export the result to Evernote using Byword. For other meetings, I’ll write in plain text, save the result in an appropriate folder in Dropbox and open the note on my iPad directly.3

The key to all of this is that everything I do that’s related to my main duties, Vice Provost for Graduate Education and Dean of The Graduate School, finds its way into an electronic document that’s stored in my “Graduate School” folder in Dropbox. I don’t have to think about syncing. I don’t have to designate one machine or device as the “mother” device on which I work. I can work on any of my devices and have the results accessible from any of them – provided that I have Internet connectivity.

For my MacBook and iMacs, that’s not a problem. They have local copies of everything. I can work on the local copy even without an Internet connection. Dropbox will upload the results when I’m connected again. If I happen to work on the same file separately, Dropbox will notify me of the conflict and duplicate the file so that nothing is lost.4

Some of the apps I have on my mobile devices can download files from Dropbox into local storage. If I know before I go to a meeting that I’m going to need a particular document, I’ll download it ahead of time – just to make sure I have a copy if there are connectivity problems during the meeting.

Dropbox isn’t the only way to do this, of course. There’s iCloud (from Apple), OneDrive (from Microsoft), Box, and probably others I don’t know about. I’m not claiming that Dropbox is the best alternative. It’s just the one I’ve been using for 8-10 years, and it works very well for me. There’s a lot more that it can do (including Paper, which I have not investigated), but what I’ve described here are the key functions that I use more than 95% of the time.

  1. With the latest release of iOS I don’t really need to have Dropbox installed on my iPhone or iPad. The builtin Files application can connect directly to Dropbox.
  2. It’s a little more subtle than that. You can choose which folders you’d like to sync to any particular device. I’ve chosen not to sync any of my work files to my home iMac, for example.
  3. Since nearly every meeting I go to is associated with work, the Markup files that are exported to Evernote sit in one of my Dropbox folders. I end up with two copies, but that’s OK. Some times it’s easier simply to open the file from Dropbox. Other times it’s easier to open them in Evernote. Either way, I know that they’ll show up in an Evernote search if they’re relevant.
  4. Except for the time I lose reconciling the changes.

Trait-climate evolution in Protea

Protea compacta

If you’re reading this post, you know that my colleagues and I have been studying Protea for more than a decade. A lot of our work has focused on documenting and understanding trait-environment associations. We’ve studied those associations both among populations within species (Protea repens: https://doi.org/10.1093/aob/mcv146), among populations within a small, closely related clade (Protea sect. Exsertae: https://doi.org/10.1111/j.1558-5646.2010.01131.x and https://doi.org/10.1111/j.1420-9101.2012.02548.x), and across the entire genus (https://doi.org/10.1086/680051). But all of those studies look at the relationship between the climate as it is now (as reflected in the South African Atlas of Agrohydrology and Climatology). They haven’t examined how traits have evolved in response to changes in climate.

Our latest paper, begins to address that shortcoming. We use the highly resolved phylogeny of Protea that Nora Mitchell constructed as part of her dissertation (http://darwin.eeb.uconn.edu/uncommon-ground/blog/2017/01/23/a-new-phylogeny-for-protea/ and https://doi.org/10.3732/ajb.1600227), and we reconstruct estimates of how traits changed over evolutionary time in concert (or not) with climates. Our reconstructions depend on particular models of evolutionary change, and we explore several alternatives. Here’s the abstract:

Evolutionary radiations are responsible for much of Earth’s diversity, yet the causes of these radiations are often elusive. Determining the relative roles of adaptation and geographic isolation in diversification is vital to understanding the causes of any radiation, and whether a radiation may be labeled as “adaptive” or not. Across many groups of plants, trait–climate relationships suggest that traits are an important indicator of how plants adapt to different climates. In particular, analyses of plant functional traits in global databases suggest that there is an “economics spectrum” along which combinations of functional traits covary along a fast–slow continuum. We examine evolutionary associations among traits and between trait and climate variables on a strongly supported phylogeny in the iconic plant genus Protea to identify correlated evolution of functional traits and the climatic-niches that species occupy. Results indicate that trait diversification in Protea has climate associations along two axes of variation: correlated evolution of plant size with temperature and leaf investment with rainfall. Evidence suggests that traits and climatic-niches evolve in similar ways, although some of these associations are inconsistent with global patterns on a broader phylogenetic scale. When combined with previous experimental work suggesting that trait–climate associations are adaptive in Protea, the results presented here suggest that trait diversification in this radiation is adaptive.

Mitchell, N., J.E. Carlson, and K.E. Holsinger.  2018.  Correlated evolution between climate and suites of traits along a fast–slow continuum in the radiation of Protea. Ecology and Evolution 8:1853–1866. doi: 10.1002/ece3.3773.

Getting organized in 2018 – Tracking tasks revisited

Getting organized in 2018 – links to the series

I was planning to finish my discussion of Evernote this week by describing how I use it and Dropbox to keep archives. The system I have isn’t a system at all. It’s haphazard and inconsistent. In spite of that, once I have notes or a document in one of them, I can find them wherever I am, since both sync to all of my devices. But I’m getting ahead of myself. For more on Evernote and Dropbox, you’ll have to come back next week.

Instead, I’m returning to tracking tasks and my everything notebook. Why? I happened to see a post on Cal Newport’s blog, On simple productivity systems and complex plans. Earlier he’d described his ideas for a modified Bullet Journal into a Bullet Journal Pro that fit his ideas about weekly and daily plans, time blocks, etc. In his more recent post, he reports that his Bullet Journal Pro system didn’t work. He’s returning to a system that has a notebook for daily plans, printouts of text files for weekly plans (printed multiple times per week as plans change), and a collection of e-mails to himself. His system clearly works for him, but it wouldn’t work for me.

As I described earlier, I tried a Bullet journal last year. Like Cal Newport, I like the analog flexibility of paper and pen. What I don’t like about the Bullet journal, is that it would only work for me if I always had it with me. Ideas about things I need to do or ideas I need to follow up on occur to me at all sorts of times in all sorts of places. If I’m wearing a suit jacket or sport coat, I’ll have a couple of fountain pens with me in one coat pocket and a Levenger pocket briefcase in the other pocket. I can whip out the pocket briefcase and make a note on a 3”x5” card that I transfer to OmniFocus when I have time. That’s less distracting to anyone I’m with than making the same note directly into OmniFocus on my iPhone or iPad. So why not just transfer that note to a Bullet journal instead?

Because I don’t have my Bullet journal with me all of the time.

At any one time I probably have a couple of hundred tasks, maybe more, sitting in OmniFocus waiting for my attention. They’re not all waiting for my attention right now or even today. Some of them won’t need my attention for several months, but all of the tasks I know of that I’ll need to do – ever – are in there. Since they’re there, I don’t have to worry about forgetting them.

But the only reason I can have all of my tasks stored somewhere and know that I won’t forget them is that (a) the “somewhere” is electronic and accessible from all of my electronic devices and (b) I always have one of my electronic devices with me. That means that I can always check what needs doing now (or today) wherever I am and whenever I need to. I probably lack imagination, but I can’t imagine how I could set use a Bullet journal, or an Everything notebook for that matter, to keep a record of everything that I need to do and have that record current and accessible wherever I am and whenever I want it.

What’s working well for me is a modified Everything notebook, a notebook in which I keep notes from every meeting I attend. Not only is pen and paper more flexible than my iPad, iPhone, or laptop, I find that they are less distracting, both to me and to those I’m meeting with. For me electronic devices take me away from paying full attention to the people in the room. Pen and paper don’t. To maintain the electronic advantage of accessibility and comprehensiveness, I simply transfer any to-do items to OmniFocus and scan any notes that I need ready access to into a PDF for Evernote or Dropbox.

That’s what works for me. Your mileage may vary. As I said in the introduction to this series,

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. 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.

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

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

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…)