Monday, May 11, 2015

Biological Rules: breaking them because I'm a rebel, or, a rant on why Bergmann's "Rule" makes me twitch

I love rules. That is to say, I hate them, which is why I love to break them.

There are a slew of biological "rules" that people such as myself love to hate. I put rules in parentheses because, in reality, a lot of these patterns we observe in nature have so many exceptions that I am reluctant to use that word. But for the sake of argument and typing, I'll go ahead and use it here.

My favorite among these is something called Bergmann's Rule. The rule originally stated that species within a genera tend to exhibit an inverse relationship between body size and climatic temperature. Said anther way, big things are found in cold places, small things are found in hot places.

But first. Why do we care? I'll tell you. It turns out that body size places physical constraints on a lot of ecological and physiological properties of organisms. Since I study mammals, that's what we'll focus on here. Gestation time, body size predicts that. Digestive tract length. Home range size. Metabolism. Trophic interactions. All related to body size. Body size can also be estimated from fossil material, allowing us to go back in time and interpolate all sorts of cool stuff about animals we can't observe, which is something I like to do. SO. Asking what controls or influences body size is one of those "big questions" in biology. Which brings us to Bergmann's Rule.

Okay. We're comparing species within a genera across a temperature gradient. Easy.


This rule has problems from the get go, before we can even start critically analyzing it. It turns out that most studies examining Bergmann's Rule use latitude as a proxy for temperature. I'm not really sure why. Maybe it's because taking a thermometer outside is unreasonably difficult. Maybe it's because we don't really know what we mean by "temperature". Is it average annual temperature, minimum seasonal temperature, something else? Latitude is correlated with a bunch of these temperature variables, so maybe we're good? Close enough? Okay, again for the sake of argument, sure. Moving on.

It turns out, however, that most studies have taken the original concept of comparing species within a genus and instead compare populations of individuals within the range of a species. So before I've even started my critical analysis of this so called rule, all the data and studies that have been used to address it in the past fail to conform to the central tenets of the rule.

It's no small wonder, then, that every paper published on this dammed "rule" over the last few decades has come up with a different answer as to "how many things conform to Bergmann's Rule?" 30-50% of mammals? Unless you are an animal that burrows. Oh, and if you're a carnivore it's not such a great rule either.

This is problematic for a graduate student such as myself trying to understand "basic ecology". One of the things we strive for in science is consensus. The inability to reproduce what someone else has done because "we don't know how to define the problem" or because an analysis "lacks the statistical power to reject the null hypothesis" is, for lack of a better word, dumb.

Furthermore, why? Let's say, again for the sake of argument, that most mammals do follow the rule. Okay. What does that mean? This is perhaps my biggest problem with these rules: they have very little explanatory power. We spend all this time arguing over whether or not things follow a rule, and we don't even have a good reason for WHY it would happen in the first place. All sorts of things have been proposed: thermoregulation, productivity, competition. But, I have little faith in these explanation given that we 1. can't agree on what we're testing and 2. we can't come to a consensus on what we're observing.

Also, it happens that often the answer in biology ends up being "it depends, and it's a little of all of the above."

Not very satisfying.

Monday, April 13, 2015

And before you know it, a year has gone by

I've neglected my blog. It turns out, graduate school takes up a lot of time. Add on top of that, life. Also, all the links to photos seem to be broken... I'll get to fixing that some time in the next year. Ha.

Quick update: yes I'm still working on my PhD at UNM. No, I'm not almost done, I have about a year to go, putting me at about a 6 year duration. This is still somewhat flexible depending on what I want to do with regards to finishing or doing a predoctoral fellowship.

Major events: I'm presenting a talk at the annual meeting for the American Society of Mammalogists, during the plenary session. It comes with money and honors and all that good stuff. It's kind of a big deal.

The past year, while pretty awful regarding emotions and my personal life, has been really good to me professionally. I have a couple publications that should be coming out in the next 6 months or so (assuming other people stop dragging their feet) in high impact journals. I'll post links to the abstracts once they are available.

Right now what's on my plate is getting my ASM talk put together. The challenge is getting all the technical details in there while still making it accessible and interesting, and limited to about 15 minutes long. This is hard because the talk is pretty heavy on modeling and computering, and I'm talking about paleo stuff at a meeting dominated by people who work with still living animals. But they gave me an award, so I must be doing something right.

I will be giving a similar version of said talk at the annual Vert paleo meeting in Dallas. Which brings me to this lovely gem I came across while procrastinating on Facebook.

That's all for now. Yes, I'm alive. And I'm going to make an effort to post once a week on this thing. And those posts will be more coherent and thoughtful than this.


Next time: Bergmann's Rule, what is it, and is it a thing, and if it is a thing what does it mean?

Wednesday, April 9, 2014

Megafauna and Ecosystem Function Conference in Oxford: My spring break and my first solo international travel, Part 1

It's been ages since I've updated my blog. There's a lot to catch up on, but today I'm just going to fill people in on my trip to St. John's College in Oxford a couple weeks ago for my first international conference. Mostly, this will be pictures for my mom to gawk at.

The meeting was a gathering of people who study large animals, mostly mammals, and the extinctions that happened at the end of the last ice age and beyond. In case you were unaware, there was an extinction across the globe that killed most large animals. In North America, something like 33 genera of mammals went extinct, most weighing over 50-kg. This no doubt had effects on ecosystems and surviving biological communities. The point of the conference was to discuss all these things, including the potential for reintroducing large animals back into environments (very controversial). I gave a talk on the impacts of the extinction on surviving carnivores in North America.

If you want to get an idea of what was going on with the talks, you can go on Twitter and search #oxmegafauna, the official hashtag for the meeting. There's also a website from the conference For several reasons, my talk is not on the website. Primarily, all my work is unpublished, so I don't really want it out there too much, yet.

The first leg of my trip began in London, where I did some sight seeing before I took the train to the actual conference.

Big Ben, London, UK
Double Decker Bus, London, UK
The River Thames, London, UK
The Big Eye and Lights, London, UK
Camden Lock for some quick shopping, London, UK
I found Heisenberg in Camden! Do you see him? Tip of the hat to the 505
Extinct Giant Ground Sloth claws, skin, and poop! Natural History Museum, London, UK
Sloth Skeleton, London, UK
Me and the sloth
Paying homage to Charles Darwin
The great hall at the Natural History Museum, London, UK
Paying homage to Mary Anning, one of the most important people in paleontology. This is a Plesiosaur, an extinct marine reptile. London, UK
Another extinct sloth!
The Natural History Museum of London is a beautiful building

Friday, December 20, 2013

It's been a rough semester

Rather than spend an entire post complaining, again, about the difficulties I've been having at school I'll just give a quick update.

Yeah, I'm still pursuing my degree. I started out this past semester with some pretty lofty goals: submit one of my master's chapters to a journal, finish my first analysis of my first dissertation project, submit my dissertation proposal to the department. What ended up happening was that I started reanalyzing my master's data and coming up with new ways to deal with it. Then I go caught up with teaching and grading. Then I got caught up with trying to get the dissertation project going and I haven't touched the master's work for months. In short, everything has been started, but nothing is done.

The one thing I did mange to do in the past week was submit an abstract to a conference where I will be presenting my Chapter 1 work. That conference isn't until March, which seems like a lot of time but it isn't. The past 4 months have taught me that everything I want to do is going to take at least twice as long as I plan. So, having said that, here is the game plan for the next semester:

Over winter break, write a first draft for a departmental grant, and get the modern museum data for my chapter 1 project.
First two weeks of school, grant done for the department.
End of January, have a first analysis completely done of the chapter 1 data.
End of February, finished analysis of chapter 1.

This list can't be changed, which means anything else without hard deadlines will have to be flexible. It's amazing how little things here and there can chip away at what seems like limitless time. I'm supposed to be the teaching assistant for a different course than I normally teach, which will likely have significantly less grading than has been expected of me before. My adviser is also the instructor, so we'll see what her expectations are.

I think I have to make something perfectly clear to everyone, including myself. I am in graduate school primarily to graduate, and everything else in my graduate school life that doesn't move me in the direction of graduating is not my primary concern at this point. I need money to survive, and teaching is a means to an end. Things that cause me stress and make me miserable don't need to be a part of my life, either. I need food, shelter, exercise, a social life that balances out my work, and to graduate. That's it.

It's been a very rough semester.

Saturday, July 27, 2013

The "Uncle Rico"s of Graduate School: I Don't Care Where You Went to College

In the movie "Napoleon Dynamite" there is a particularly pathetic character: Napoleon's uncle, Rico. He's kind of a sad dude for a variety of reasons, but what really sticks out in my mind is that he is a full grown adult that bases his entire self worth on the accomplishments and dreams he had decades earlier, in high school. He's sad because on the exterior he seems very confident, but you know that deep down he is barely hanging onto his sanity and security of self. 

After having been in graduate school for a number of years I find it very surprising when I run into an "Uncle Rico". The people who act like anyone gives a damn where they managed to get into college when they were in high school. The kind of people who at the drop of a hat will brag about where they went, how prestigious, exclusive, etc. etc. barf barf etc. it was. Maybe that was impressive then, but it isn't now.

Don't get me wrong. I went to a decent college, and I'm proud of what I feel culminated in an excellent education. My education was a means to an end. I consider my undergrad a piece of trivia of my life, and it only comes up if it is relevant to conversation or if someone explicitly asks, for the following reasons...

Where you went to school has little to no bearing on your quality as a graduate student/researcher/whatever
Where I went for undergrad was a reflection of where I was as a person at age 17. I don't know about anyone else, but I wasn't a fully developed human being when I was 17, when I barely squeaked my way into a university. I was NOT a good student in high school, not good enough to go to the schools I wanted to. I wasn't even a fully developed human being when I LEFT college. 

If you've found yourself in graduate school and are still bragging about something you did a decade ago, open your myopic little eyes and take a look at the people around you. Chances are they come from all different walks of life and found their way to the present on their own unique path. You probably have people around you that went to an ivy league, or a small private college, or a public university. You might even find someone who got a later start, worked, and maybe even went to community college for a while. My point, and the good news, is that these are all equally valid ways of navigating academic life. If graduate school has taught me anything it's that there is no "right" way.

Very Few People Care
By the time you're in graduate school, your undergrad is almost nearly irrelevant. The only people that care are as follows:

Your parents or immediate family
-- Its ok if other people brag about your past accomplishments, but doing it yourself is sad (see Uncle Rico).
Other alumni if you bump into them
-- Bro-like hand slapping and "We Are!"s when I bump into a former school mate are guilty pleasures. Then I calm myself and return to reality.
Those annoying bastards that call looking for money from your alma mater
-- Please. Stop. Calling. Me. When I finally manage to make piles of cash to donate, I'll call you.
Your CV/Resume
-- Not really a person, but you get the idea. Older and lesser accomplishments are inappropriate on this document, anyway, even if your basic education information stays on it. That's not my rule, that's common knowledge.

If someone asks where you went to school, it's just polite small talk. And unless you're talking to an old friend that you haven't seen in YEARS, you would be better served to talk about more recent things.

No one likes a bragger
Nuff said, and it's a transparent facade.

Wednesday, July 10, 2013

The Cost of Research

I've been kind of in the research doldrums. Right before I went to CT I got a lot of bad news regarding research funding. This isn't uncommon, most research proposals, even good ones, don't get funded right away. I'm not going to starve to death or anything like that, I have a TA stipend to live off of for the next two years. The issue is finding money to pay for the research that will ultimately get me my degree. There's costs with travel, lab samples, overhead costs for the university... it kind of goes on and on.

While I've been working to find research money for 3 out of the four projects I want to do, I have been working on a project that doesn't require any money what-so-ever. It's a computer modeling project that uses databases, which are free. I also have access to geographic information systems software at school, which is also something I don't have to pay for. I'm thinking this project is going to take about a year to finalize.

Once the fall semester starts again, I'll get back into grant writing mode, try again with some other agencies, and cross my fingers that the funding gods decide to grace me with some good luck. In the mean time I've been seeking out alternative ways to jump start my research. A friend recently tried out a website for personal donations to fund some field research to look for thought-to-be-extinct Costa Rican frogs. As of today he's made about $200 of his $1200 goal, so it's a start. I decided to try making one for myself. I'm hoping I can get enough to travel to a few museums to get some preliminary data. Here's hoping!

And if this doesn't work, perhaps some bake sales will bring in some much needed revenue...

Saturday, May 25, 2013

Post Written Exams

Hello friends, I'll be recounting the last couple of months from the comfort of my mother's couch in CT.

Don't worry. I didn't drop out of graduate school, I'm just taking a short holiday now that the semester is officially over.

I guess the big event since my last entry would be my comprehensive exams, which was quite the adventure. Part of what made it so "exciting" was that I made the decision to have an extra person on my committee, even though by guidelines it wasn't necessary. I only needed 3 people, but I opted for 4. Personally, it felt necessary. Comps are viewed by many as a hoop that needs to be navigated to get on with the PhD process, and that just seems pointless to me. They were going to make me do this anyway, so I decided to get as much out of it as possible and poke the brains of as many smart people as I could. Now that it's all over, I feel like I have a much wider base of knowledge, and that I set a precedent for what my expectations are for myself and the people I work with.

Originally I was scheduled to have the big day on April 25th. Then, my committee had some scheduling issues and the date was in limbo before we landed on May 2nd as the only available day everyone could get together for a 3 hour block of time. I was really upset about the change. It was the lowest part of of the ordeal for me, especially since this news came during my second set of written questions. I was livid that they were putting my through that stress during a time where I should have been concentrating only on my exam response. Eventually, however, I accepted it as just another inevitable thing and got over it. Part of the issue was having a larger committee than usual.

In the end I passed, with distinction. Phew. It actually wasn't so bad in retrospect. The hardest thing was not really knowing what they were going to test me on. I had people from three disciplines who were going to be testing me, which leaves a lot of fair game. In the end I taught myself population and community ecology, and read as many papers as I could find that were relevant to my research. I had made a short talk to give at the beginning, but we ended up spending two hours going through each slide, and they completely directed the conversation.

I learned some important things during the process, unrelated to my actually dissertation.
1. If not given guidelines on the length to a written response to a question I will produce 12 pages, on average, not including references.
2. Faculty are far less intimidating if you treat them like colleagues.
3. Scheduling meetings that include more than 3 people is a lot like herding cats.
4. When you are the focus of a discussion, be in control.
5. Nothing is so important that you should make yourself psychologically or physically ill over it.

I've actually been aware of that last point for a while, seeing as how I've been doing the whole grad school thing for many years now. During my exam preparation, I didn't isolate myself or go into seclusion. I decided from the beginning that I was allowed to have a life. That's my attitude toward grad school and life in general, and it kept me sane during comps. I didn't give up weekly hang-outs with my friends, game nights, etc. Studying and planning my PhD research became my job for a couple months, and I treated it different from the rest of my life. No job is worth being miserable over.

I came out of comps as a well defined PhD candidate. I'm sure my research will change, given  unforeseen hurdles or funding issues, but I have direction at this point and can get this ball rolling finally.