T-24 hours til I’m back in the tropics!

Tomorrow, I take off for the OTS course in Tropical Plant Systematics!

The course will be based in San Jose, Costa Rica, with several modules in each of the sites listed in the map below:

The course will include a module each in a mid-elevation rainforest (Las Cruces), a high-elevation forest (Cuericí), a seasonally dry forest (Palo Verde), a lowland rainforest (La Selva), and the herbarium at the Universidad de Costa Rica.

I’ve never had a botany course so far, and definitely not a tropical plant identification course, so I am very much looking forward to a this immersion into the world of plant systematics! The instructors have listed the following objectives for the course:

• identify the main families and genera of tropical Angiosperms, ferns, and lycophytes
• explain the overall patterns of Angiosperm, fern, and lycophyte phylogeny
• explain the basics of phylogenetic theory
• run some commonly used computer programs for cladistic analyses
• interpret and describe vegetative, floral, inflorescence, and fruit structures
• construct dichotomous keys and identify plants with them
• write formal descriptions of plants
• collect and preserve various kinds of plants
• apply the principles of botanical nomenclature
• recognize the major tropical vegetation types found in Costa Rica and their characteristic plants
• use a common floristic inventory method (the 0.1 ha transect)

I’ll try to post updates on how the course is progressing here! I will also post any notes I take digitally online.

And finally, I should thank the University of Maryland CMNS Deans Office, BiSi office, BEES office, and the Kraft lab for financing my attendance. This course will certainly be indispensable for me, and I’m really grateful to be able to go to it early in my education 🙂

The Gap Year was worth it.

Last Friday was my last day in Candice Hirsch’s maize genomics lab at UMN, and with it ends my “gap year” between undergraduate and grad school. In this post, I want to talk about how I spent the past 12 months and what I got out of them.

For some context, I graduated college with a degree in Ecology, Evolution & Behavior and Plant Biology. At the time of graduation, I had a vague idea that I’d like to pursue a career in tropical ecology, but felt completely unprepared to make such a decision. I thought I’d like to be an active researcher pursuing the answers to interesting but esoteric questions; I thought I’d enjoy being in the field, travelling to remote locations to collect plant samples; I thought I’d like to be a plant systematist, learning the names and characteristics of the world’s flora; I thought I’d like to be an ecologist, developing new methods and applying them to tropical forest systems; I thought I’d like to be an academic, constantly applying for grants and writing papers resulting from those grants, …. the list goes on. Point is, there were a lot of aspects of my proposed field that I’d never tried before, and I felt uncomfortable comitting to it.

The gap year was basically a chance for me to work on a few of those things I thought I’d like but had no experience with. So here’s what I did:

May: Travelled to Area de Conservación Guanacaste with Jennifer Powers for a 2-week-ish long field course
June – August: Interned the NHRE REU at NMNH. This was my first experience doing research 40 hours a week, which was definitely a new feeling!
August – September: Travelled to India, hung out with grandmas and cousins :).
September – October: Started writing graduate school application essays
October – December: Attended the AFEC field course at XTBG
December – May: Worked at a maize genomics lab at UMN.

Each of these addressed specific gaps in my knowledge/experiences. Being at ACG with Jennifer gave me my very first field experience, and while there, Jennifer gave me a lot of encouragement to stay in the field. Jennifer also encouraged me to attend the AFEC, which was another fantastic experience. My time at NMNH was brilliant — it was the first time that I did research for 40 hours a week, and really enjoyed it quite a bit (and I liked the area enough to return to it for graduate school!) Finally, by working in a genomics lab, I’ve developed a lot of critical computer scripts, which will help me in more ways than I know now.

So, here’s what I think gap years have to offer:

pros:

  •  I gained exposure to more parts of the field of ecology/academia in general before comitting at least 5 more years to it
  • By participating in a series of distinct activities, I developed specific skills that will probably pay off for a long time yet (and they look good on my CV, which is great too)
  • Saved up some $$
  • Had some to really think about what direction I’d like my career/life to take. So, I’ll be entering grad school with a clearer idea of what I want to get out of it.
  • It was a little easier to work on grad school applications while not also juggling a bunch of classes/school responsibilities. (I actually ended up submitting my grad school and GRFP app from XTBG, when I was attending the course from 8am to 9pm and working on the essays between 10pm and midnight, but you know what I mean)
  • I had a whole lot of time to pursue other interests. I started running, read more books than I did during all of undergrad, etc.
  •  
    cons:
    I spent a lot of time thinking of what I wish would have been different, but couldn’t come up with much:

  • Sometimes, I felt like I wasn’t working towards anything. I have no piece of paper to show for all I learned in the past year — this isn’t a problem per se, but in a society where pieces of paper are Sanctum Sanctorum, it feels weird to not have anything to “show” for the past 12 months (other than my Certificates of Completion from NHRE and AFEC 😉 )
  • I knew everything I was doing was kind of a short-term thing, so I never really invested a whole lot of energy into things. I really like to dive head first into anything I do, so holding back felt weird.
  • The whole gap-year was spent in Academia-related things. I really wanted to get out of the college campus and into the service industry or something, but that never happened. I honestly think that would have been a very useful experience. Maybe I shouldn’t be complaining about this…!
     

    If you took a break year (and especially if you did not), I’d love to hear about your experiences!

  • Excitement on the horizon

    I’ll be starting a PhD with Nathan Kraft at the University of Maryland this fall! This announcement is obviously not timely — I’ll (pretty disingenuously) chalk that up to being without internet at home for the past 1.5 months. To answer the next question: no, I am not sure yet what my PhD will be all about. What I do know is that I am very excited by tropical forests, and by Nathan’s lab, and by the prospect of being near Washington DC, and I am eager to spend some time figuring out what research niche I’d like to carve out for myself in this fascinating field. Maybe I’ll make a little diagram to describe what my interests are some time soon.

    Right now, I am broadly interested in the evolutionary ecology of tropical forest trees — how has the community of trees been interacting in tropics? And how have these interactions determined the composition of the communities? I am also interacted by how trees interact with other organisms — especially the microbes that live all over and around the trees. I am really excited to see how this interest evolves as I learn more of the scientific literature and develop my own ideas.

    I will move to DC/Maryland in mid-August, but I also have an exciting summer between now and then! From mid-June to mid-July, I will be in Costa Rica for an OTS course in Tropical Plant Systematics. I’ve been bemoaning my lack of systematics skills and field identification abilities, so I’m really looking forward to filling those gaps in my education.

    Then, towards late-July, I will be traveling to Boise, Idaho for the Botany conference (and while you are at it, check out my abstract!), where I will present the research I conducted last summer during my REU at the NMNH. This is my very first big societal conference, and I’m super excited! I’ve been crawling through some of the abstracts on the website, and will probably start thinking about who I want to meet pretty soon.

    Here’s where the “Gaurav goes on incoherent rants” part of the post begins. I really need to get better at avoiding this, but c’est la vie

    On flying: input appreciated.

    Last weekend, my mom was talking about her impending trip to India, and was lameting that she couldn’t meet one of her nephews (i.e. my cousin), who was going to be away from home the whole time. I flippantly told my mom to go visit him where he’s staying (knowing full well that this was logistically totally unfeasible), but my dad reacted by saying something like “What, and just spend a bunch of carbon? Don’t fly, we can’t expect air travel to go down if you just keep flying.”

    Being the argumentative snot I am, I snapped back, saying something like “That’s easy for you to say — after you’ve spent the past 25 years of your life travelling around internationally!” We didn’t really have a conversation about it then, but later that evening, I brought it up again, and he emailed me a very thoughtful response:

    You asked me about flying – should one fly in the face of the fact that flying contributes to global warming?

    Easy for one to say either way depending on their personal history, preference and the fact that there is a significant cost externality that is not paid for by any one, but by all.

    So here is my more considered reply –

    You should avoid flying if you can. Ask the question can I not fly this time? Not merely replace this mode by another like road travel. But genuinely can I not go this time. Can I deal with my need to be there another way?

    Slowly, embed this consideration in every small thing we do – food that we eat (is it OK to insist on kothimbir (i.e. cilantro) in winter? or do we replace our veggie intake with pumpkin, potatoes and canned/ frozen veggies?), how we make and process trash. How we garden.

    if each one of us does his thing, we will be ok.
    And then do not hesitate to call our some one who you think is doing all wrong.

    Because while nominally, they are doing it their way with their money, they are not paying for costs that you are paying for…

    Obviously (and as usual), dad is spot on here. The price we pay as consumers doesn’t really reflect true costs at all*. We need to be conscious about the downstream impacts about our actions. But I am not sure how to go about making the cost-benefit analyses to come to a measured decision.

    Consider my decision to fly to Boise for Botany: Did I absolutely, positively need to go to this? Not at all. The research I am presenting here is something I am proud of, but I am not actively working on it right now. I don’t know anyone else who is going. I probably am not going to be a professional Botanist (though I certainly want that to be a part of what I do). I will have plenty of opportunities to go to conferences like this (and probably Botany itself) over the next few years. So no, I did not need to absolutely go.

    But is going to the conference a good thing for me, personally and career wise? Definitely! I will meet a lot of people I can build relationships with during my graduate school and subsequent career, and may potentially begin life-long friendships with future colleagues. If this wasn’t muddy enough, consider that I don’t have to pay for my attendance — the Smithsonian is paying for my airfare, and I got an Undergraduate travel award to cover on-site expenses. On top of that, I’ve registered to volunteer at the conference to work off my registration fee (and on top of that get some insight into the behind-the-scene work at events like this).

    So, is not going even an option here? Or would I just be silly to say not such a promising opportunity?

    I don’t know yet, and I’d love to hear what you have to say.



    *This is the topic of another discussion I’ve been having with Gautam. In the US, why don’t commodity prices ever actually fluctuate with changes in production costs? For example, we’ve been reading a lot about a Banana virus that is devastating crops, but I can still get a banana for 19 goddamn cents at Target, just the same as I did a year ago! When I was in India last year, Onion prices were stupid high because production costs had increased, so this is obviously not unheard of. I am no economist, but surely there’s a good answer to this. Suggested readings appreciated.

    On Dinosaur Intelligence

    Did dinosaurs really have an extra brain near their butts? No.

    Apparently, kids’ books and TV shows often make claims about the two-brainedness of dinosaurs. I’ve never heard about this before, but there’s a really good explanation here.

    Facts aside (that phrase is used far less often than it needs to be, by the way), here’s a wonderful poem on the intelligence of dinosaurs, written by Bert Leston Taylor:

    Behold the mighty dinosaur,
    Famous in prehistoric lore,
    Not only for his weight and length,
    But for his intellectual strength.
    You will observe by these remains
    The creature had two sets of brains,
    The one in his head, the usual place,
    The other at his spinal base.
    Thus he could reason a priori
    As well as a posteriori.
    No problem bothered him a bit,
    He made both head and tail of it.
    So wise he was
    So wise and solemn
    Each thought filled just a spinal column.
    If one brain found the pressure strong,
    It passed a few ideas along.
    It something slipped the forward mind
    ’Twas rescued by the one behind.
    And if in error he was caught
    He had a saving afterthought.
    As he thought twice before he spoke
    He had no judgment to revoke.
    For he could think without congestion
    Upon both sides of every question.
    O gaze upon this noble beast,
    Defunct ten million years at least

    “Thus he could reason a priori / As well as a posteriori.” Come on!

    I should credit that I came across this poem when reading Dawkins’ An Appetite for Wonder. A pleasant read; looking forward to part 2.

    What’s with these “dye mixing in water” pictures still representing science?

    A pretty cool thing happened earlier last week — here’s a summary from the Scholarly Publishing and Academic Resources Coalition (SPARC):

    Washington, DC – Progress toward making taxpayer-funded scientific research freely accessible in a digital environment was reached today with Congressional passage of the FY 2014 Omnibus Appropriations Bill.  The bill requires federal agencies under the Labor, Health and Human Services, and Education portion of the Omnibus bill with research budgets of $100 million or more to provide the public with online access to articles reporting on federally funded research no later than 12 months after publication in a peer-reviewed journal.

    This is of course a step in the right direction, on a path that extends much further than where we’ve gotten so far. I’m glad that there’s a lot of energy behind sticking to common sense and opening up science, but there’s a lot of really smart people talking about that and so I won’t even try.

    Instead, I’ll complain about the pictures we use to represent “science.”

    The Switch blog at WaPo wrote a piece about the bill that was passed, and if you click over there, you’ll be hit with a big picture of dyes mixing into water:

    Screen Shot 2014-01-19 at 8.06.24 AMI know it’s dye mixing in water, because I’ve done it before:

    IMG_0316

    I took this picture when I was asked to have a photo of me “doing science” during my internship at the NMNH. But hey, I was dumb, and had about 20 minutes to get a picture, and was confined to the lab. What’s a guy supposed to do. Since then, I’ve realized my mistake, and have made it a point to take a lot more photos when I’m in the field (or even when I’m sitting in front of a computer screen that has something cool going on!)

    So why the hell do reporters at major news organizations like WaPo still need to use these stupid pictures to represent “science”? Surely there’s more exciting things to show: physicists working at ginormous electromagnets, chemists building 3D models of headache-inducingly complicated molecules, conservation biologists using drones to monitor forests, ecologists dangling around the canopy of a forest,… A lot of scientists have brilliant pictures that they are happy to share with these reporters (#mammalwatching is a testament to this, as are @katefrogg’s wonderful amphibian pictures. There’s a lot lot more too!), to say nothing of the wonderful nature photographers who can be truly professional about this.

    Enough with dyes mixing in water!

    Beginning to get comfortable as a computer guy. Also, PLoS rocks.

    It’s a good week to start seriously using computers for science.

    (For non-bio-y friends: all this paragraph is saying is that I’ve more or less settled into my new role in doing science solely off of a computer, but that the transition has been pretty challenging). After nearly a month of writing perl scripts to to parse increasingly convoluted files and reading about high throughput sequence analysis software, I was given the reins to several transcriptome data sets on Monday. I spent Monday getting used to working on the Minnesota Supercomputing Institute’s servers and running FastQC on subsets of the data. Tuesday was going to be a big day: I planned to run FastQC on all of the files, begin looking through the output, and start pruning/filtering with the FastX toolkit. This is probably a light schedule for serious bioinformatics people, but it was enough for me to get worked up — I was pretty damn apprehensive Monday night!

    Luckily for me, I woke up on Tuesday morning to find a couple of highly relevant (and strangely comforting) papers in PLoS Biology:

    1. Best Practices for Scientific Computing (http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001745). Though I’m not really writing my own software (not for now, anyway), there’s a lot of great stuff in this article. It has been very challenging to live by Best Practice 4 (Don’t Repeat Yourself, or DRY). So far, I’ve been writing my perl & shell scripts locally, uploading it onto the MSI cluster, and running it there. If I run into any error, I’m never sure whether I should edit locally and reupload the script, or whether I should just edit it on the server and download the updated copy! Augh!

    2. A Field Guide to Genomics Research (http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001744). I don’t really know what kind of genomics researcher I will shape up to be (if any). For now, I guess “Servant” is the most appropriate, though Dr. Hirsch is a much better Master than the one portrayed in the paper.

    Then, today, I came across the preprint to “10 Simple Rules for the Care and Feeding of Scientific Data” on arXiv (http://arxiv.org/pdf/1401.2134v1.pdf). Now that I’ve seen how intense the datasets and associated scripts can be, I appreciate everything in this paper! I am becoming increasingly convinced that I should start using Git (or even just Figshare?) to manage the scripts I am writing. Luckily there’s a nice little tutorial to begin on that too!

    Though my more-or-less solo adventures into world of “supercomputing institutes” and processing hundreds files that contain 16000000 lines of text each have been kind of bewildering, these sorts of papers are helping a lot. There’s nobody in the lab (other than Dr. Hirsch, whose schedule as a new professor doesn’t offer much wiggle room) who I can turn to for help, so I really appreciate these general pieces of advice.

    Now if only I can figure out a good system to manage the 100s of shell scripts I have written over this week to run jobs on the MSI servers, I’ll feel even better! I have no idea if people’s “scripts” folder looks like mine did after half a day of data processing:

    Screen Shot 2014-01-10 at 11.10.28 AM

    And while I’m talking about PLoS love, I’ll also add that the work I am doing is follow-up work on the science published by my advisor in this PLoS One paper.

    Next time, I promise to write a less introspective, more interesting post 😉

    Mermaid-gate, and why it matters that we talk so much about what doesn’t matter

    Remember that time when the United States Government (via NOAA) had to issue an official statement about the non-existence of mermaids? If not, here it isI’m a little late to the Mermaid-gate game, but I’d like to bring it up here to write about two issues that have been bugging me for the past week.

    This whole “debate” was kicked off after Animal Planet aired two (probably) terrible shows to showcase “the Aquatic Ape Theory, which claims that humans had an aquatic stage in our evolutionary past.” There was, evidently, a very small disclaimer thrown in that none of what was portrayed in the show was supported by science, but very few people seem to have noticed it. Anyway, if you need some more back-story, you can choose among these articles.

    “Are mermaids real? No evidence of aquatic humanoids has ever been found.” — NOAA website

    I really liked Marine Biologist David Shiffman’s reaction in this tweet:

    The two parts of this tweet hit on the two issues that have been bothering me.

    First is the issue that most non-scientists evidently place “little faith” in what they hear directly from scientists. Peculiarly, people seem to be even more distrustful of the science they hear from journalists, but in this case, the Animal Plant mockumentary was evidently more convincing than facts. I guess that this might be because of the large number of reports along the lines of “those vitamins we promised were beneficial don’t actually do anything anymore, and we scientists have known this for a long time,” but I wonder what we can do to reverse this. I will do some small part by just chatting with people about how I see science being done, and by writing about it here.

    The second issue the tweet hits on is that a large number of people seem to be perfectly happy to engage in inane conversations like those about the existence of mermaids (or about whether Phil Robertson ought to have been kicked off of Duck Dynasty — sadly, I didn’t get a screenshot of the time when the top two trending topics in Minneapolis were “Duck Dynasty” and “Phil Robertson”), but those same people seem to be uninterested in engaging in conversations that matter.

    This is something I will write more on later, but I think that as a well educated youngun, it’s my responsibility to voice my thoughts in Conversations That Matter. Society has invested a lot in my education, and the least I can do to give back is be an engaged citizen. And it is really easy to be an engaged citizen now! Until recently, I thought, as I suspect many do, that I could do nothing to reach the ears of the Higher-Ups (HUs) and the Head-Honchos (HHs), but I’ve realized I couldn’t be further from the truth. Social media has made it really easy for bums like me to reach these HUs and HHs. There is nothing stopping me from tweeting at Minnesota Public Radio about a story I’d like to see covered. Or I could tweet at Dr. Kristofer Helgen about how awesome the discovery of a new carnivore is, and what I think about his discovery’s implications are for me personally and students of nature generally. Sure, the HUs and HHs might summarily dismiss my tweets, but I’ve lost nothing by trying. And I might stand to gain a lot.