Required reading: What are we going to do about saving salamanders?

The fungi are coming for all the animals I love.

Frogs have declined across the world. Bats are disappearing from North America. Even snakes! From the outside looking in, our American biodiversity is a hodgepodge of invasive species surrounding smaller and smaller pockets of protected native flora and fauna. 

And now, you may be able to add salamanders to the list. Nooo!

Eastern Newt in red eft phase (Notopthalmus viridescens)

A recent publication in the journal Science describes the threat of a skin fungus that causes massive die offs of salamanders in Europe. Like the fungal pathogens that have caused declines in frogs and bats, this fungus has been introduced into areas where the local wildlife has no evolutionary history with the pathogen, and therefore lacks a natural defense with no time to develop one. In this case, the salamander fungus has an Asian origin and has recently been introduced to naive European salamanders.

So this fungus isn't even in North America? Right, not yet. However, the danger is a real one. North America is THE place for salamanders. We are the Amazon for these animals. You can walk across a few hills in Georgia and see more salamander species than you could find in a coast-to-coast trek across Costa Rica.

Credit to Clinton Jenkins

Here is your required reading if you want to know how to help and potentially make a difference:

1. This news article from the New York Times
2. This excellent editorial by Drs. Karen Lips and Joe Mendelson

Cumberland Plateau Salamander (Plethodon kentucki)

How We Work: Dr. Tyler Smith talks standing desks, cranberries, and coding to the Tron soundtrack

Our next guest for the How We Work series is Dr. Tyler Smith. Tyler is currently a research scientist for the Canadian government, but we first me while he was a faculty member in the department of biology at Eastern Kentucky University. 

Prepped and ready for sedge hunting in turkey season

Location: Agriculture and Agri-food Canada, Ottawa, Canada

Current Position: Research Scientist, Taxonomy of native crop wild relatives

One word that best describes how you work: Inertia would work. Reactive would be accurate too much of the time as well. I aspire to be a more mindful and deliberate in my approach. I struggle with the bad kind of perfectionism, which can be crippling when you get a manuscript 90% done. At that point it becomes irresistibly tempting to start something new, rather than complete something that won't live up to your aspirations. That's a real productivity killer.

Current mobile devices: Nexus 5

Current computer(s):
Personal Laptop: Debian GNU/Linux on a Thinkpad x201 with 4GB RAM and 320GB HD
Work Laptop: Debian GNU/Linux on a Standard Issue HP Elitebook
Both computers run the same operating system with the same suite of programs. I sync my important configuration and documents via BitBucket.

Digital Ocean Droplet with 512MB RAM, 20GB HD for my website and Owncloud storage
If you like tinkering with computers, Digital Ocean provides really good value. $5/month gets me my own virtual server. So far, other than serving a static Jekyll-generated website, I use it to host my OwnCloud instance. Owncloud is a Free Software replacement for Google Drive or Dropbox. It offers the same sort of features, but you control the whole system. Nobody is mining it for ad revenue, and I know the owner (me!) isn't in cahoots with the NSA or CSEC.

Another cool thing about Digital Ocean is that you can rent servers by the hour. So if you need to do some computationally intensive simulations and don't have access to a cluster, you can set one up for a few dollars a day, and shut it down as soon as you're done.

I expect I'll eventually install my own version control repositories, but until then I use both BitBucket and GitHub. Github is more popular, but BitBucket provides unlimited private repositories for free, so all of my manuscripts and coding projects go there.

High-performance clusters for simulation projects and next-gen sequencing projects.
My post doc was working on spatially-explicit community simulations, which introduced me to cluster computing. I'm gearing up to start working on next-generation sequencing data, so I'll be putting that experience to use as a taxonomist in future.

What apps/software/tools can't you live without?

Debian GNU/Linux
Debian provides a huge collection of Free Software, maintained by a chaotic but dedicated community of volunteers. Other than the programs I describe below, I use the i3 tiling window manager and spend a lot of time in Bash shells.

Emacs
It's not just a text editor, it's a lifestyle choice. The learning curve is steep, but in return you get an infinitely customizable workhorse.

R
It has its rough spots, but the enormous user/developer community means there's very little analysis I need to do that I can't either find a package for, or write my own scripts/packages to accomplish. Of course, my preferred interface is Emacs, via the ESS (Emacs Speaks Statistics) add-on. The knitr R package provides almost seamless integration of data analysis and manuscript preparation.

LaTeX
Writing manuscripts in LaTeX means I get to use the same tools I apply to coding (Emacs, version control with git or mercurial) to my manuscripts. And the integration of code and text in the same document with knitr is a game-changing approach to organizing manuscripts.

That said, Emacs and LaTeX are steep hills to climb. A more approachable version of the same workflow is using RStudio and Markdown. When I teach R workshops, this is the combination I recommend.

Distributed Version Control
git is the most popular option, but I find mercurial a little simpler to use. Either one provides a very powerful way to track changes in multi-file projects, share code with others, and sync files between computers. Having just finished collaborating on a manuscript with 'track changes', I wish all my peers were using one of these systems. 

Preparing a manuscript with Emacs, R, knitr, Inkscape and a PDF reader

What is your best time-saving shortcut/life hack?

For biologists, make your research Reproducible Research: 

"Reproducible research involves the careful, annotated preservation of data, analysis code, and associated files, such that statistical procedures, output, and published results can be directly and fully replicated" (from ropensci.org)

This can be a bit overwhelming, as there are a whole ecosystem of tools available, including text editors, programming languages, development tools and version control systems. But the pay-off is immense when it comes to sharing, revising and extending your work.

Other resources:
My brief overview
Software Carpentry
Roger Peng

How do you organize all the stuff you have to do?
I maintain my project outlines and to-do lists with the Emacs extension org mode. The data is stored as human-readable plain text files, but with lots of handy features for sorting and prioritizing tasks, tracking progress and scheduling. I also use it to clock my work on different tasks (inspired by tweets from Rob), to see if that helps keep my effort more focused and deliberate. So far I like it, although it takes a bit of concerted effort to stick with the habit.

Tyler's homemade standing desk

Besides your phone and computer, what gadget can't you live without and why?

In the field, my GPS. An important part of field trip prep is loading it up with all the maps and herbarium data I need ready access to.

In the office, I love my standing desk. I've had lots of neck, back and arm issues, and working upright is a big relief.

What do you listen to while you work?
Repetitive, atmospheric stuff. Nothing too melodic or lyrical, it needs to settle into the background. Other than that, I'm pretty eclectic: Persian sufi music, baroque, Arcade Fire. My current geeky pleasure for coding is the Tron soundtrack.

What are you currently reading?
So good they can't ignore you. This is a very contrary approach to building a career. The author argues strongly against the notion that you should follow your passion. His antidote is to build up a set of rare and valuable skills, and use them to carve out a rewarding niche for yourself. It's an interesting read, especially for a scientists considering a career outside academia.

Are you more of an introvert or an extrovert?
Introvert

What is your sleep routine like?
Horrible. I don't often get a restful sleep. I'm quite thankful I work in a job where I can set my own hours. Life was simpler when I was a professor -- I was so physically exhausted by the workload that I usually collapsed into sleep at the end of the day!

Tetraploid cranberry blooms

Fill in the blank: I'd love to see ___ answer these same questions.
Andrew Hipp (Morton Arboretum), Sally Otto (University of British Columbia)

What's the best advice you've ever received?
When you feel like you've run up against a brick wall, pause to consider if getting through it is really what you need to do. I get pretty attached to my ideas sometimes, and it can be hard to let go of the bad ones.

Also, not so much advice, but my wife is often responsible for getting me outside in my down time for civilian nature hikes. It's easy to get caught up in the abstract intellectual side of science. But just experiencing nature, unburdened by the need to find a target population and acquire more samples, that's an important way to reinvigorate my work and myself.



Thanks Tyler!

Old Man of the Forest

Our department's graduate students took our fall camping trip over the weekend to southern Ohio, and we were treated to a really special animal:

That's a big timber rattlesnake (Crotalus horridus) hiding out under some fall leaves. This endangered species is both secretive and well camouflaged, so you could easily walk right past one of these bad boys even if you were lucky enough to be near one.

This particular snake is part of a long-term study to understand the movements and behavior of these snakes in Ohio. A radio transmitter guided the volunteers who track these snakes directly to this individual, and we were lucky enough to follow along.

My lab mate Matt Holding was asked to get DNA samples from this snake over the summer, and he remembered this individual fondly. Here is a photo of Matt with this same snake so you can get a sense of scale. The volunteers said that their last measurement of this individual was 54 inches, and it could very well be 15-25 years old.

So next time you are hiking around in timber rattlesnake country, keep an eye out and you may get to appreciate one of these incredible animals for yourself.

I mean really keep an eye out!

What's Going On in Science, September 2014

Why student evaluations of teaching are worthless

"The paper compared the student evaluations of a particular professor to another measure of teacher quality: how those students performed in a subsequent course. In other words, if I have Dr. Muccio in Microeconomics I, what's my grade next year in Macroeconomics II?
Here's what he found. The better the professors were, as measured by their students' grades in later classes, the lower their ratings from students."

"This class should start an hour later in the morning. Also, the
teacher shouldn't wear sandals."

This NPR article summarizes a new study that tackles a problem that teachers in academia would love to talk your ear off about: teaching evaluations are horribly broken. If you get high scores from students in teaching evaluations, are you a good teacher? Maybe, but probably not. I've noticed the phenomenon of teaching evaluations (like product reviews on Amazon) consisting of only the most extreme opinions resulting in teachers who just don't care about the feedback.

Wildlife is culture, and culture deserves your tax money

"I mostly write about wildlife. So here is how it typically happens for me: A study comes out indicating that species x, y and z are in imminent danger of extinction, or that some major bioregion of the planet is being sucked down into the abyss. And it’s my job to convince people that they should care, even as they are racing to catch the 7:10 train, or wondering if they’ll be able to pay this month’s (or last month’s) rent."

This lovely New York Times Opinion eloquently states why biologists constantly have a lingering pressure to justify their research in terms of benefits to humans. 

Understanding genetics for the future of medicine

"Various efforts are underway to interpret mutations and compile them in publicly available databases; one of the latest is an online registry to which patients can upload their own data. Eventually, they will be able to see how many other people have the same mutation, and how many get cancer."

Genetic testing is becoming a more and more prominent aspect of individualized medicine. Unfortunately, the pace at which genetic tests are increasingly used is racing ahead of the general understanding of genetic tests and how to interpret them. Until better education about traits, alleles, and heritability can permeate into the public, doctors will continue to be limited by their ability to educate their own patients.

Salamanders: forest vacuum cleaners

"On an average day, a salamander eats 20 ants of all sizes, two fly or beetle larvae, one adult beetle and half of an insect called the springtail. And in doing so, they collectively affect the entire course of life in the forest — and perhaps far beyond."

This article is from back in April of this year, but I can't leave a nice salamander study out in the cold on this blog. You may not see them, but in most woodlands in North America, there are salamanders that make big differences in how ecosystems manage nutrients. While they make look cute and cuddly, salamanders are ultra-efficient, insect-seeking torpedoes:

How We Work: Dr. Paul Hurtado

Throughout my travels around academia, I've always been very interested in how other scientists work. Scientists in particular make for a great study of working habits for two main reasons: they typically juggle a variety of tasks and they largely determine their own work schedules. This results in a huge variety of work habits: night owls, early birds, multitaskers, focus-taskers, and on and on.

I've been a long-time reader of Lifehacker's "How I Work" series, an interview format in which folks from various organizations detail the secrets behind their work habits. I've always loved this idea: getting a peak into the habits of someone who's work you admire. As I've read more and more "How I Work" articles, I began to think that this format would work really well for scientists. So, in the same vein as the previous "Get to know a grad student" series, I'm bringing you a series of interviews that showcase how scientists get stuff done. I'm calling it "How We Work". 

A big thanks go to the inspiration for these questions, and to Andy Orin for giving me permission to use them. Go read Lifehacker for more neat stuff.

The first subject for How We Work is Dr. Paul Hurtado. I met Paul through OSU's Evolution and Ecology Club, and have since learned he is our resident statistics guru, birding expert, and all-around smart guy. Paul's work focuses on using mathematical models and computational techniques to answer large-scale biological questions (see his research page). In simple terms, Paul is a statistics wiz that thinks of new ways to analyze tricky data.

Location: Mathematical Biosciences Institute (MBI), OSU, Columbus, OH

Current Position: It’s complicated. Technically, I’m unemployed, however I just finished a postdoc at OSU in August and I’m currently negotiating a faculty position at a university out west that would start January, 2015. Fortunately my wife has one more year of funding for her postdoc position, which gave me some flexibility in hunting for jobs.

One word that best describes how you work: Inertia. Hard to get started sometimes, and also hard to stop once I get rolling.

Current mobile devices: Galaxy S4 smartphone


Current computer:
1. Desktop: Windows 8.1 (64-bit) 3.1GHz Intel i7 CPU with 8GB RAM.
2. Laptop: An older Dell Latitude D630 with too little storage capacity and speed.
3. I also have access to a multicore linux server through the MBI which I use occasionally.

What apps/software/tools can’t you live without?
Because I interact with biologists and mathematicians, I prefer to use free (or widely used) software so that licensing issues and/or software costs don’t get in the way of communicating and sharing content.

1. R is my go-to platform for data visualization, stats and model simulation.

2. I occasionally use R Studio – a front-end for R – but I tend to prefer the multi-window configuration of R and use Notepad++ to edit and run R scripts via NppToR.
3. Matlab is usually my second-in-line computing platform
4. MatCont (a Matlab add-on; although I really need to try Auto or XPP-Auto).
5. Maple and sometimes the free software Maxima for computer algebra (i.e., symbolic manipulation of algebraic expressions instead of crunching numbers)
6. I also use Python, Perl, and C from time to time, so access to a Linux command line is a must.
7. PuTTY and WinSCP for connecting to remote servers via SSH.
8. TeXstudio is my new favorite editor for writing manuscripts and other documents in LaTeX
9. Google Calendar is my primary means of scheduling everything.
10. “To Do” lists help me keep my days organized, so I also use apps like Google Keep (or emails to myself) to jot down important ideas and to organize and schedule tasks.
11. Facebook and Twitter have proven to be useful platforms for “crowdsourcing” technical problems, and soliciting advice or other information from friends and colleagues (Facebook) as well as people I've never met (twitter).
12. I can’t seem to go without Microsoft Office, despite my preference for using free software.
13. The internet, so I guess that means my web browser belongs on this list!

You need big screens to display big data

What is your best time-saving shortcut/life hack?

Talk with the right people, at the right time. Sometimes, I need to spend a lot of time wrapping my head around a problem and thinking it through carefully. But more often than not, I’m stuck on something mundane. In those cases, it can really pay off to just seek out someone with the right expertise who can either point me towards an existing solution, or who can help bounce around ideas until we figure it out. Especially when it comes to doing research, it pays to be selective in how you spend you time.

How do you organize all the stuff you have to do?
I should first admit that I've never considered myself to be a well-organized person, and over the past few years I've been spoiled by the flexible schedule that comes with being a graduate student and postdoc. That said, I have found some nice ways of staying somewhat organized:

1. Simple “To Do” lists – either in a smartphone app, a text file on my desktop, in an email, or written out on some scratch paper next to my computer keyboard – are a primary tool I use to prioritize and schedule most of my day-to-day tasks.

2. Software helps immensely with scheduling. I rely on Google Calendar and a note taking app on my phone to help with scheduling.

3. When I comes to organizing my work, a lot of it takes place on my computer, so I have a simple system of keeping work projects in their own folders, and using cloud-based software (e.g. Box, Dropbox, etc.) to sync content across my laptop and other computers. I incorporate “To Do” lists in code comments, text files and emails, etc. as needed. I’ve tried using version control software like Git to manage code revisions and manuscript drafts, however I’ve abandoned them in favor of just saving copies (with the date appended to the file name) and keeping those in their respective project directories. 

Besides your phone and computer, what gadget can’t you live without and why?

For work, my phone and computer are pretty much all I need! I suppose my coffee mug is the next most essential gadget in my arsenal. Outside of work, however, I am a fairly serious bird watcher (Rob: Paul is probably being modest here. Check out his birding resources page and note that he is one of the top 50 birders in Ohio). I rarely venture outside or do any traveling without bringing along a pair of binoculars. Especially during spring and fall migration! 

The first Kirtland's Warbler in central Ohio. Spotted by Paul in 2011.

What do you listen to while you work?
It depends. My musical interests are pretty broad, so if I want music I’ll just leave Pandora on and let it play from a mix of different channels. But, I can get pretty distracted by music. I’m usually better off with a lot of silence or a lot of ambient noise that won’t draw my attention away. For example, I used to be most effective at getting my math homework done as an undergraduate by bringing it with me to the Biology Club’s weekly bowling night and working on it one or two problems at a time. It was pretty effective, but definitely a compromise between getting my homework done and hanging out with friends.

What are you currently reading?
I've most recently been trying to finish up Writing Science by Schimel, which was the book the Aquatic Ecology Lab chose to read for the summer.

Are you more of an introvert or an extrovert?
I’m closer to the extrovert side of the spectrum, but definitely somewhere in the middle.

What is your sleep routine like?
I have a two and a half year old who loves to sneak into bed with us in the middle of the night, so lately my sleep has been pretty variable. I probably average around 8 hours a night but often with at least one interruption during late morning, which takes a toll. Now that I’m a parent, I definitely go to bed earlier (and probably sleep about the same or slightly more on average) although the interruptions definitely take their toll.

I’d love to see _____________ answer these same questions.

Libby Marschall (Ohio State), Liza Comita (Yale), Amy Downing (Ohio Wesleyan)

What’s the best advice you've ever received?
Work hard, play harder.

Salamander Snapchats

With the school year starting up again, it means that the undergraduate crew that I work with in the laboratory at Ohio State are back on campus. They are great to work with. Really great. One of my favorite things about them, aside from their work ethic and trustworthiness, is that they have a fantastic collective sense of humor. Because levity is a big part of my own personal work environment, I encourage joking around extensively while doing scientific work. 

One of our salamander caretakers, Paul, is particularly fond of updating me regularly about how the captive salamanders are doing. However, instead of coming to my office or sending me an email, Paul chooses to accomplish this through funny snapchats. If you don't know what Snapchat is, it is a messaging app for phones that allows the sender to create picture messages that are only viewable for a few seconds.

I thought I'd share some of Paul's work (with his permission). These messages are irreverent and silly and very funny to me. I hope you think so too.

Apps for Academia: Let's Talk Tech

A big part of training to be a scientist is training to be productive. Grad students and faculty do a lot of different things in a set amount of time, and that amount of time always stubbornly stays the same or reduces. Improving efficiency not only allows you to have more time for non-work things, but also allows you to devote valuable time to tasks that need creativity instead of efficiency. My advisor often tells us that we are too busy and need more time to sit around and think. 


As much as technology can be a rabbit-hole of wasted time, I love using tech for helping me stay on task. I thoroughly enjoy talking to other grad students and faculty about what programs, devices, and apps they use to organize their work lives, and I've cherry-picked from them extensively.

Here is a summary of the nine apps that I would be lost in academia without, organized from most essential to most expendable. As a warning, most of these are based on Microsoft Windows, Google Chrome, and Android platforms. Have additions or suggestions? Let me know.

Timesheet
Here is my number one productivity tool and secret weapon against wasted hours, and it is the simplest thing to do. I keep track of how much time I spend doing things. I've written about my experience before, and I have continued to keep track of my hours ever since. In fact, I've gotten so used to it, I can't start working on anything until I glance at my timesheet and decide "Ok, what am I doing right now?".

There are a million apps that keep track of time spent on various projects. I use this one, but they all seem similar.

Any.do
This is my checklist app of choice, and it nicely integrates across my web browser and phone. If I have any task to do, it gets quickly jotted down in Any.do and given a priority. I naturally think of tasks in the same way that they are categorized in Any.do: do this "today", "tomorrow", "upcoming (next week", or "someday". Additionally, I really like the daily reminder function of this app. Every morning when I start my work day (usually 8am), Any.do asks me to prioritize what I'm doing that day. Just a few minutes of considering what is important and what can wait can be super helpful when things get busy.

I used to just write down a to-do list on paper at my desk, but going digital allows me to jot something down anytime. What do you carry with you more often, a notebook or a phone?

Google Calendar
When I was an undergrad, I carried a planner everywhere I went. If you tried to schedule something with me, odds are I was going to forget if I didn't write it down. I'm still the same, except now I don't have to carry the planner and I can share my schedule with ease. Important meeting? "Google, remind me 15 minutes before this meeting starts." 

Mendeley + Scholarley
One of the worst parts of writing scientific manuscripts is controlling the references to other papers. There are different formatting guidelines for each journal, and managing huge libraries of PDFs can be a supremely annoying task. The time I was allotting to formatting citations and finding relevant papers was cut down significantly through the use of a citation management software (Endnote, Papers, Zotero are some examples). 

I prefer the free program Mendeley for a few reasons. One, it is free. Two, it is pretty good at finding information about my PDFs on its own. Three, it plays really nicely with a companion mobile app, Scholarley. Scholarley lets me access all of my Mendeley library on my phone, which is helpful when I'd like to read a journal paper away from the computer. Now I just find an interesting paper online and dump the PDF into a folder on my laptop. Mendeley takes that new file, fills in the details about the paper, and organizes it in another directory.

Maybe the most helpful aspect of Mendeley is using the citation plugin for Microsoft Word. When I'm writing and want to insert a citation, I just click Alt+M, search for topic or author keywords, and press enter. Mendeley adds the citation in whatever journal style I specify and builds a literature cited section for me. Easy.

Cloud Storage (Drive + Dropbox)
Sharing files is necessary for any level of collaboration between scientists, and the cloud storage revolution has been a welcome addition to being scientifically productive. Almost all projects I'm working on have an associated folder in Dropbox or Google Drive, where I can add/view/change content in real time. 

Pocket
Pocket is an app for your phone or internet browser that acts as a glorified bookmarks folder. I had no idea why this would be helpful, but I kept seeing it pop up on websites like lifehacker and decided to give it a try. 

The main advantage of Pocket is the ability to store all the things that I don't have time to read on the internet (blog posts, science articles, discussion boards) into a centralized place. Then when I have time, I can go through and quickly figure out what is worth reading and what's not. Very simple and surprisingly efficient. 

Twitter + Tweetdeck + Plume
I'll tell you what scientists are talking a lot about: using social media. "Uggh, do I have to tweet?" say many. No you don't, but it sure can be helpful. For scientists, Twitter can help your work reach farther, let you know what new science is being talked about, and help you connect to other scientists extremely quickly. Here is an example from my experience where I was trying to find someone who has a treadmill for salamanders. The correspondence below would have taken me at least a few emails and plenty of internet searching. Instead, in five minutes I have two prominent scientists volunteering to help little 'ol me out. How cool is that?

In terms of social media, Twitter hits the time-to-benefit ratio perfectly for me. Part of using Twitter effectively is being a little bit organized. To do this, I use a combination of Tweetdeck on my computer and Plume on my phone. I create columns for groups of people that I follow ("OSU scientists", "Herpetologists") and columns for relative hashtags ("#scicomm", hashtags from conferences). 

Spreed
Spreed is a plugin available for the Chrome internet browser that serves a very simple function. It helps me read much, much faster. Spreed works by taking the text on a page, feeding it to you one word at a time, and eliminating all the extra noise in your head when you usually read.

Now, I would never spreed a scientific journal article. I take my time doing things like looking up words and glancing back and forth at figures. However, Spreed is exceptionally useful when reading news articles, blog posts, and other internet text. 

Another potential downside is how strange you look when someones walks into your office as you are staring a words quickly flash one-by-one on the screen.

Google dictionary
Speaking of looking words up, Google Dictionary is my favorite way to look up word definitions while I'm browsing. Double click a word to see the definition. Simple.


So there you have it. Everybody's different, so what I find essential, you may find laughable. What really matters is that I get this paper done in time to watch the hockey game.