Unisexual Ambystoma

Unisexual Ambystoma

Sunday, August 24, 2014

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.

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.

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 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 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. 

Thursday, August 7, 2014

First publication from SciFund support

The reason I started this blog two years ago was to connect to those who helped fund my science through the SciFund Challenge. Crowdfunding has come a long way, even since then, and I hope that my funders have been able to check back time and again to see how my PhD is progressing. However, after the t-shirts were sent and the thank-yous were written, I haven't shown much about the salamander for for which I was so graciously supported by a group of science-loving citizens.

One thing that is difficult to appreciate about science: it takes a long time. Creating new knowledge is tough. From generating new ideas to collecting and analyzing large amounts of data to having your work evaluated by your peers, even small projects can take years until the product of all that work is produced. 

I'm thrilled to finally have the first scientific publication resulting from crowdfunded support officially in press. The paper is titled "Evolutionary basis of mitonuclear discordance between sister species of mole salamanders" appeared in volume 23 (issue 11) of Molecular Ecology. If you take a look at the acknowledgements at the end of the paper, there is a specific sentence where I send my thanks to all of those who funded my work through SciFund. How cool is that!

The data that was collected for this project was done while I was in the field working on the Ambystoma dispersal project, and my Scifund support was much appreciated during the associated travel across the state of Ohio.

So, that sounds nice, but what is the science?
One thing we noticed when looking at the salamander samples that we had from all across Ohio: some of the species of salamander were showing up in weird places. Particularly, these two sweethearts:

The salamander above on the left is only found in the very southwest of Ohio and is mostly located in Eastern Kentucky. The reason? The Streamside Salamander loves to breed in small streams that don't have fish. In contrast, the Smallmouth Salamander, which is found over most of Ohio and across a wide part of the central United States, only lays its eggs in ponds and other wetlands that aren't streams. 

Here are some of the areas we find these two salamanders ("sympatry" just means they are found in the same county):

BUT, when we used DNA to identify the samples we had from across Ohio, we identified many animals as Streamside Salamanders that we were almost sure were actually Smallmouth Salamanders. 

See all that green in the middle of Ohio? That didn't seem right.

We found these animals in ponds (not streams) and they were well outside of the above range of Streamside Salamanders. Since we only had DNA samples, how could we figure out what was going on?

Because we were using tiny pieces of DNA from the salamanders' mitochondria, there were three main explanations for this unexpected pattern:

The kidney bean thing is suppose to be a mitochondria!

So, we could be observing 1) a misidentification of the central Ohio salamanders or 2) the presence of mitochondria from one species inside the other species (weird!) or 3) hybridization between the two species.

We used DNA collected from both the mitochondria and nuclear DNA of salamanders from all across the state to show that mitochondria inside of the Smallmouth Salamanders in central Ohio are invaders from the Streamside Salamanders, a biological process called mitochondrial introgression

Mitochondrial introgression happens when two species hybridize at some point in time and the mitochondria that comes from the female of one species becomes abundant in the other species, either by natural selection or random chance. As strange as it sounds, the phenomenon is well-recognized and has been identified in a diverse group of animals. 

So why is our publication important? 
First, we solve the mystery of finding salamanders with strange DNA by using a bunch of different genetic techniques. Our methods show the pros and cons of the different ways that scientists have tried to study mitochondrial introgression in the past and provides a guide for how to use these techniques.

Yellow-Rumped Warbler
Second, we took a look at all of the locations where we find salamanders with mismatched mitochondrial DNA and found that these wetlands are located in places with significantly higher rainfall during the spring and summer. This could be a sign of an adaptive link between the foreign mitochondria and a wetter environment.

Making the links between patterns of foreign mitochondria and their adaptive advantages is important and finally becoming common. Other recent publications like ours have shown both advantages (in Warblers) and disadvantages (in Long-Toed Salamanders) to having an introgressed mitochondria. Using genetic information, scientists are finding out what evolutionary processes are happening hidden from sight inside the animals of our backyards. Pretty neat.

Long-Toed Salamander