End of semester

I walk by one of the older buildings on campus most mornings, shown above. With the semester over and campus less busy, I've enjoyed the calmness and the extra time to read papers and work on ideas. (For reference, I'm not in my lab on Christmas Eve, just posting from home.)

Last night, I had dinner at Passage to India, which I think still qualifies as something new and therefore exciting in Laramie. In the past couple years, I've lived in larger college towns (Fort Collins and Corvallis), but Passage to India might be the best Indian restaurant in any of them. (Their naan is certainly the best.) Even if it isn't that new, it still qualifies as exciting.

So after living in Laramie for a semester, my expectations of the town have been exceeded. It's prettier than I thought, and the dining options are quite decent. I'm looking forward to checking out the skiing in the coming year.

Losing forests via carbon trade?

A fantastic opinion piece was published yesterday in the New York Times on the threat of the current carbon trade/offset mentality to forest ecosystems (linked below).  A good summary:

'Contrary to what you might hear from energy companies and environmentally conscious celebrities, offsets don’t magically make carbon emissions disappear. Worse, relying on them to stem global warming may devastate our vital forest ecosystems.'

I encourage you to read the entire article.  It is well written and makes some excellent points.  I really hope more people take note of this issue.

One of my close friends is working with the Costa Rican government to create and link their country's "carbon economy" with others in Latin America and around the world. While Costa Rica has historically conserved their tourist-targeted ecosystems, they are ignoring this potential offsets/conservation dichotomy as they progress toward their goal of carbon neutrality (as a country) within the next decade or so. But they do support farmers who plant and harvest single or mixed species plantations as a means of selling carbon credits to polluters. And I imagine it will be even worse in countries that cannot afford to be as conservation friendly.

I just emailed my friend this article. And I am very interested to see what his response will be....

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READING: Heinrich (2009) Clear-Cutting the Truth About Trees. The New York Times.
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Skiing and sea ice

Skiing can be a big part of life in Laramie. If you already enjoy skiing, there are lots of opportunities; if you don't ski, it is a great place to start. There is excellent cross-country skiing (classic, skate, ski-jouring) at the Happy Jack ski trails, about 15 minutes from town. The trails are groomed by a local club and the skiing is free, although a National Forest parking permit is required. Terrain varies from flat meadows to steep wooded hills, and even on busy days you generally have the trail to yourself (http://mbna.pbworks.com/).

The local ski resort, Snowy Range (http://www.snowyrangeski.com/) has been open for almost three weeks (36" of base snow already!). It is small in comparison to most western mountain resorts, but it is less than an hour from Laramie and the season pass ($150) is much cheaper than bigger resorts. Steamboat Springs, CO, is also two hours away (http://steamboat.com/).

Lastly, there is plenty of backcountry skiing within an hour to several hours of driving. I was surprised by how easy it was to connect with other folks to get out. I began telemarking last winter, and I quickly found out that my neighbor and several acquaintances regularly went into the backcountry and they were happy to let me tag along. In early January I am taking an avalanche-safety course so I can try and get out a bit more.

Classes finished last week, and after lots of hours I completed all of my make-up work for biochemistry. I am now focused on optimizing assays for the muscle samples I collected from polar bears in the field. Our project technician has extensive experience with some of the assays from her previous work on hibernating ground squirrels, and I am looking forward to learning from her as we figure out techniques for these samples. I am also returning to my project proposal. Because our funding began immediately after I accepted this PhD position, I began field work on the basis of the grant application rather than my own proposal. As I return to my proposal I am reading some of the latest articles regarding sea ice loss in the Arctic and related topics.

READING

Despite climate change and ice loss in the Arctic, ice extent in the Antarctic has actually been increasing. J. Zhang proposed this is due to a decrease in Antarctic ice melting that overwhelms a decrease in ice formation. J. Turner and others proposed this is due to alterations of ozone, and that there is a chance the changes in Antarctic ice extent are potentially still within a natural range of variability.

Zhang J. 2007. Increasing Antarctic sea ice under warming atmospheric and oceanic conditions. Journal of Climate 20:2515-2529.

Turner J, et al. 2009. Non-annular atmospheric circulation change induced by stratospheric ozone depletion and its role in the recent increase of Antarctic sea ice extent. Geophysical Research Letters 36:L08502 (5 pages).

If you give an octopus a coconut shell...

I turned in my updated proposal to my advisor today, finished up my Christmas shopping in downtown Laramie, and will head out soon for a lab dinner at my advisor's house.  Bob (my advisor) is a fantastic cook and a master brewer, and the extended lab family (labmates + our better halves) is a great group, so I really look forward to these occasional get-togethers.

Another cool story came across my science news today: "Octopus carries around coconut shells as suits of armour" (video of the coconut-shell-armour-in-action is embedded below).



Don't let anyone tell you that inverts aren't amazing!

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READING: Rinella (2008) American buffalo: In search of a lost icon.
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New in Laramie = Exciting

Friends often ask me how I would define Laramie, and I guess I would have to go with Small College Town.  I think population estimates are <30,000 (and that total must include some off-campus students).  The small town environment isn't for everyone, but I happen to love it.  And Laramie does have the benefits of a being a "college town" even if it is on the smaller side.

Options for eating out or going out for drinks are decent given the size of Laramie, but the idea of a new restaurant or bar is pretty exciting after you've been frequenting the same few places for several years.  Some recent additions have included a Thai restaurant and an Indian restaurant (both serve good food and are very loved by those in Laramie looking for options beyond the standard steakhouse or chain restaurant).

That brings me to this week's shiny new thing: Front Street Tavern, a bar affiliated with Sweet Melissa's (fantastic locally owned veggie & vegan restaurant that rivals what you find in big cities - but with lower prices).

Eager to check out the newest addition to downtown Laramie, I met up with several friends for drinks at Front Street last night.  Front Street Tavern is in a beautiful space downtown and the atmosphere is great: minimal decor, beautiful wood bar, classic brick walls, good music, and (my favorite) NO televisions!  They are still working out seating and getting beers on tap, but they have a decent selection of bottled beer and wine.

Overall: It's exactly what I've been looking for while making do with other bars that often feel too sporty or too flashy. And I'm glad I don't have to "settle" anymore.

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READING: Sinsabaugh et al. (2009) Ecoenzymatic stoichiometry of microbial organic nutrient acquisition in soil and sediment. Nature.

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Cookies

I'm taking a break from my final project to grab dinner and plan the rest of the week. Some grad students are getting together for a cookie exchange/holiday party on Friday night and I am really tempted to make some of these:

Think anyone would actually eat petri dish cookies? I totally would.

And now I'm wondering what other dorky science themed cookies I can come up with in my "spare time" before Friday....

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READING: Lasslop et al. (2009) Separation of net ecosystem exchange into assimilation and respiration using a light response curve approach: critical issues and global evaluation. Global Change Biology.

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Nice, if not magical

I enjoyed reading a recent op-ed about colleges touting themselves as being similar to Hogwarts, the wizard school in Harry Potter. While none of the grad schools I visited thought to do that, and I don't suggest any grad school should, I enjoyed spending a bit of down time during finals week considering how Hogwartsian Wyoming could claim to be.

Faculty I haven't encountered any Snapes yet, nor do they wear robes or extravagant hats. Solidly muggle.

Grounds Actually, mildly Hogwartsian. Currently, the evergreens and stone buildings are white from a recent snow, making a nice comparison to all the winter scenes from any HP movie. A pair of owls hang out on campus as well. Slightly magical.

Feasting Between PiE and my home department, there's actually a fair amount of food accompanying talks and speakers. The department holiday party last weekend had plenty of tasty stuff, although that's because the faculty and grad students can apparently cook well. However, there's nothing inherently magical about that, and we tend to consume it in rooms that do not qualify as great halls. Solidly muggle.

Creatures A nice variety of species are represented, from plants to polar bears, although all are actually real. No Sasquatch research. Solidly muggle.

Housing No castles in Laramie. But my apartment seems to have insulating capabilities verging on alchemy - at times, it's 50 degrees above outside temperature without turning on the heat. A touch magical.

Superficially, then, there's not a great deal here to market as Hogwartsian. But as the high school student writing the op-ed agreed, that's not really why you choose a school.

How does science work?

A computer hacker recently stole hundreds of internal emails and documents from the Climate Research Unit (CRU) at East Anglia University in England, and made them publicly available online (NY Times story: http://www.nytimes.com/2009/11/21/science/earth/21climate.html). The emails reveal portions of discussions on analysis and presentation of data related to climate change, and some believe they are evidence of conspiracy surrounding climate change. I am not going to address that – skepticism is a prerequisite for good science, and the theory and data behind climate change should and do stand on their own – but this event does raise interesting questions about science as whole.

There can be a public perception of scientists as “analysis machines”: give a scientist raw data and get back objective conclusions, regardless of the context. This does not reflect reality. There are many subjective elements to science. Simply the process of selecting topics to study is subjective. Framing a hypothesis is a highly creative act, requiring equal parts imagination and critical thought. Likewise, there is no concrete guide for selecting methodology, for resolving uncontrollable events during data collection (people gathering data forget to write down something, batteries fail in a data collection device, etc), for selecting analytical approaches, or for drawing inferences.

How then can science “work?” How can it provide any objective, important observations? The first course in PiE is 5100, “Ecology as a research discipline.” Last year it was co-taught by PiE faculty from botany and philosophy. We extensively discussed this question and related questions about the philosophies behind scientific processes and values. I really enjoyed the course – to me, it seems far too rare that scientists can take time to thoroughly examine their implicit assumptions about science as a whole.

Many very smart people have considered the question of how science can work, and a lifetime could be spent trying to answer the question. Here are just a couple thoughts from my personal perspective. I think asking a good question is important; the question needs to address a very specific gap in knowledge, where surrounding material is well understood. Preferably, the question should have multiple potential answers, each with a clear relationship to the data that will be gathered. And, very importantly, the different answers should clearly relate to each other (for example, are they mutually exclusive?). Also, speaking more broadly, transparency is critical. Scientific reports should include enough information so the subjective judgments described above (framing a hypothesis, selecting methodology, selecting analytical approaches, etc) can easily be understood by the reader.

READING

John Platt’s 1964 article “Strong inference” (Science, vol 146, pages 347-353) lays out an interesting possible framework for doing good science.

PS – On an unrelated note, we had the Zoology and Physiology holiday party last night. The local band “The Patti Fiasco” performed and they were great; we even got faculty on the dance floor. Great job by those who organized it.

Boundaries

It's end-of-semester crunch time, so I probably won't be rambling on here much for the next week or so. I have a final project due for my ecological systems modeling course that includes a manuscript and conference-style presentation. And I need to write a proposal for my final dissertation chapter topic to give to my advisor before I leave town for winter break. At this point I will just be thrilled to finish everything in time!

Before "signing off" for a bit I do want to share an article that was in my science news email this morning:

What is the meaning of 'one' plant or animal?

The paper promotes an interesting discussion of boundaries and what the definition of an organism should be based on levels of cooperation (link to actual paper is below).  We cover topics like this in the Ecology as a Research Discipline course at the start of our PhD studies - one of the two required courses for PiE students.

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READING: Queller et al. (2009) Beyond society: the evolution of organismality. Philosophical Transactions of The Royal Society B Biological Sciences.

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Shifting baselines

Taking a cue from the other bloggers, I thought I'd mention the most interesting science I've been reading lately. Or rather, the science I've been reading about, since the media coverage seems to have preceded the article's publication (thanks to Newswise's science coverage).

Essentially, it appears our baselines for evaluating species - in this case, fish - can be severely off-target depending on where we set the baseline. Karin Limburg and John Waldman compared shad populations from the late 1800s, where baselines usually begin, and the early 1800s. The baseline levels derived from catches in the late 1800s represented a population that had crashed from previous levels. There's a nice graph of this in Newswise's coverage. (The article appears in the December issue of BioScience.)

In other words, many of our restoration goals could be based on already diminished populations. Fascinating, if depressing.

Comic relief for TAs

I am a TA for General Biology (LIFE 1010) this semester.  This involves teaching two lab sections a week, holding office hours, and helping out with lecture exams and exam grading.  Being a TA is pretty time consuming, but I really enjoy my interactions with the undergraduate students here at Wyoming.  They come from a wide range of personal and academic backgrounds, but most are genuinely interested to learn more about how science relates to their own lives and interests.

We gave and graded the laboratory final exam last night.  Most students did well.  Some did not.  (Nothing out of the ordinary.)  But there are always a few students who provide comic relief during grading based on what they choose to write on the exam when they don't know the answer.

My personal favorite from last night's grading festivities:

[V_i of enzyme B = Chuck Norris / π]

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READING: Van Nes & Scheffer (2005) A strategy to improve the contribution of complex simulation models to ecological theory. Ecological Modelling.

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Taking advantage

I suppose I should follow up on yesterday's rant about "What to ignore?"  Although the narrow mindset of some scientists bothers me, I am actually taking advantage of some questions ignored by others.

The recent call to include inland waters (lakes, streams, rivers) in the global carbon (C) cycle (1) motivates a lot of my current research.  Why?  Because inland waters process at least half of the C they receive from terrestrial ecosystems (2; figure below) - C cycling models assume this C is stored in terrestrial ecosystems (even though it is respired, stored or transported by inland waters).

In other words, large-scale C models have ignored the role of inland waters.  If freshwater ecosystems are included in these models, they are merely "pipes" or transport vectors, not C processors.

One of the major questions now is how to include freshwater C cycling in predictive landscape-scale C cycling models.  My current research is focused on quantifying and modeling the drivers of C inputs, cycling and availability in freshwater ecosystems.

So...I suppose I should really be grateful for what has been ignored?

It certainly makes my own research more meaningful and exciting.

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READING: (1) Battin et al. (2009) The boundless carbon cycle. Nature Geoscience. 

(2) Cole et al. (2007) Plumbing the Global Carbon Cycle: Integrating Inland Waters into the Terrestrial Carbon Budget. Ecosystems.
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Cheers and Thanksgiving

How do you become a better scientist? I try to consider that question frequently in grad school. While I don't claim to have a definitive answer, I've found discussing the issue with fellow grad students and professors to be one of the more enjoyable ways to think about it.

Last night, I had a beer with a professor to talk about using my time in school to become a better scientist. It was a good time - nice beer (Altitude has some fine choices) and good conversation. One of the things I've appreciated most since coming here is the openness of the faculty and grad students - if you want to grab a cup of something (cold or hot) and talk about something more or less related to your interests, it's usually not hard.

And since John mentioned it, I thought I'd echo his thoughts - it's pretty easy to travel from Laramie. I spent Thanksgiving with family in Denver, then made a quick trip to Durango for the weekend. It was a bit of driving, certainly, but having spent my formative years within the Capital Beltway, I don't mind the distance as long as the roads are good and the scenery is pleasant.

What to ignore?

As I have refined my own interests for my PhD research and beyond, I realize that you cannot measure everything - something falls by the wayside and is ignored in every project.  In some ways, this is "good" for other scientists and also promotes collaborations...although the abandoned and unanswered questions are often the ones that were deemed "too difficult" to address by earlier projects.

My reason for rambling about this topic during my morning coffee intake is this: I am reading an article on modeling nitrogen (N) export from New England watersheds (1) for my Ecological Systems Modeling course.  Many scientists have tried to answer the following questions from a terrestrial, aquatic, and/or whole-watershed approach: why does N export vary over time?  What controls N export?  And why has there been an overall decline in N export in the past 40-50 years?

My frustration is this: the terrestrial modeling papers ignore the fact that any N is processed in streams - the vectors of N transport from the watershed.  Because of this, many terrestrial models fail to accurately predict watershed N export, especially in low export years.  Instead of considering that something might be happening in aquatic ecosystems, terrestrial modelers just try different types of models and ranges of parameters over and over again to try to make better predictions.

It turns out that at least 30% of the decline in N export can probably be explained by higher N processing in streams (streams aren't just pipes!).  The increase in N processing (and decrease in N export; figure below) was a function of higher woody debris inputs from an aging and disease-ridden forest as well as higher primary production (noted by an increase in algae and biotic uptake) in the streams flowing through these watersheds (2).

And looking back at the terrestrial modeling paper that ignores stream processing: their model output confidence intervals do not even overlap with the N export data in years of low export (figure below).  I understand that not all models can include everything (something has to be ignored), but they don't even mention that aquatic N processing could explain this problem with their watershed model.

As someone with more of an aquatic bias, I cannot understand why none of the terrestrial modelers thought to look at the non-forest part of the watershed.  But maybe that's because I have been forced to think "beyond the stream" as a result of my interest in aquatic ecosystem ecology.  Aquatic ecologists are often chastised by reviewers if they do not include "enough" non-aquatic citations in their publications. In contrast, terrestrial ecologists are not generally asked to cite aquatic papers (3). 

This frustration is sometimes carried over to my day-to-day life at Wyoming: there aren't many "aquatic" labs in the Zoology department and often labs do not think beyond specific study organisms or systems.

I think this frustration is one of the main reasons why I really appreciate the Program in Ecology for providing me with a group of colleagues who enjoy thinking about "the big picture" - often well beyond their own study systems or favorite organism - keeping me (somewhat) sane in a field dominated by terrestrial studies.

Okay, time to write my "real" response to this terrestrial modeling paper for class this afternoon.  I will try to be kind....

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READING: (1)Hong et al. (2005) Bayesian estimation of input parameters of a nitrogen cycle model applied to a forested reference watershed, Hubbard Brook Watershed Six. Water Resources Research.

(2)Bernhardt et al. (2005) Can't See the Forest for the Stream? In-stream Processing and Terrestrial Nitrogen Exports. BioScience.


(3)Menge et al. (2009) Terrestrial ecologists ignore aquatic literature: Asymmetry in citation breadth in ecological publications and implications for generality and progress in ecology. Journal of Experimental Marine Biology and Ecology.
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