Anthony’s Science Blog

Field trip to the Alps

Went on a great field trip today to the Alps where the Lasaunne crew does a lot of their research. Here are some pictures.

We first visited a botanical garden with alpine plants from all over the world. This is Gentiana farreri.

More cow bell! According to one of our Swiss companions, the Swiss countryfolk actually compete for the most enormous cow bell.

The cows create terracing on the alpine hillsides which then affects snow distribution.

Stuff white people like: fondue in an alpine hut in the Swiss Alps.

The chamois, Rupicapra rupicapra.

Marko, Andrew, Bill, Antoine, Anthony, Hope, Ann, Christophe, Loic, Julietta, Pascal, Ken, Bruno, Bill

And just to keep it real, a giant hilarious Swiss chicken.

I am deeply grateful to our Swiss hosts for an awesome trip.

Combining process-based and spatially explicit statistical modeling

Yesterday, my fellow graduate students and I gave talks about some of our investigations of various ecosystem functions on Niwot Ridge. I talked about nitrogen cycling and others talked about microbes, plant physiology, and hydrology. Just as was planned by the conference organizers, I think our graduate work provided a nice contrast to the type of spatial modeling of plant distributions that the group in Lausanne has been using. Hopefully my nitrogen obsession didn’t bore the participants too horribly.

On Niwot Ridge, a lot of the research has focused on understanding ecological processes such as biogeochemical cycles and the biotic interactions of plants, which at this workshop we have been calling a “process-based” approach. In contrast, the group in Lausanne has been using a statistical modeling approach where they measure species distribution in the field and then attempt to back out the conditions under which they occur in order to make predictions about other places or times. This might be called a “statistical modeling” approach.

During discussions this week, we have talked about how these two approaches complement each other and how they might be combined in order to make better projections of species distributions and ecosystem processes. I might add predictions of ecosystem services, similar to what’s being done at the Natural Capital Project.

The advantage of using the process-based approach that has been the paradigm on Niwot Ridge is that mechanistic knowledge improves our power to make predictions. The disadvantage is that in order to focus on these mechanisms, we typically have to ignore spatial heterogeneity, which reduces our predictive power. In contrast, the spatial statistical modeling does a good job of incorporating differences over large areas, but does not have the mechanistic basis of the process-based models.

We have been discussing how to combine these approaches, and it’s a brain twister. But, basically, the idea put forth by Chris Randin, the organizer of the workshop, is that we can use process-based models (like CENTURY) to create spatially explicit layers that can be used in statistical modeling. This type of approach has not, to our knowledge, been used for ecosystem modeling before.

For example, we might use a soil biogeochemical model to predict nutrient availability across the landscape and then use the nutrient availability in a statistical model that predicts plant distribution. Nutrient availability would add a whole new dimension–and presumably more predictive power–that is not available in the usual statistical models that only use topoclimatic information. Basically, it would improve our estimate of the plant’s niche space by including an essential niche axis: nutrients. Conversely, once we have the model results, the areas of poor fit may then inform which ecosystem processes need further investigation. I’ve also been trying to implement this approach in my relatively small study area on Niwot Ridge to predict N cycling rates.

We’ve been chatting all day about how to rig all of this up in some kind of group-authored theory paper. There’s always the danger that too many cooks are spoiling the broth! But it’s definitely been an enlightening discussion. And once the writing actually begins, there will be just one lead author, Chris, who is a pretty smart and organized guy. I’m optimistic.

I’m psyched about tomorrow, when we will head to see some field sites in the Swiss Alps. It should be sweet and I’ll post some pictures.

Mountain Ecology workshop in Lasaunne, Switzerland

This week I am attending a small workshop in Lausanne Switzerland (on beautiful Lake Geneva, above) to meet with the some fellow researchers who study mountain ecosystems in the Alps. I am here with several of my colleagues from the Niwot Ridge LTER site.

Our goal is to share different research ideas and approaches with our counterparts at the Université de Lasaunne. We may also write a collaborative manuscript on something like “predictive modeling in mountain environments” or “similarities and differences between the alpine ecosystems of the Rockies and the Alps.”

Yesterday I wandered around Lasusanne trying to stay awake. Lausanne is a beautiful lakeside city with neat old architecture and a very sophisticated and upscale sensibility. I am currently killing time until breakfast since I woke up at 2:00 a.m! Hopefully I will adjust to the time, but also find spare moments like this to blog more of our meeting.

Being a professor may not be as sweet as it used to be

On her 27th birthday, one of the graduate students in my department was told by her adviser that when he was 27, he got his first tenure-track job as an assistant professor at CU. She said, “Yeah, well, standards were lower back then.”

And in fact, it is the rarest of circumstances these days when a tenure-track position in a science department at a research-one university is handed out to a fresh off the boat 27-year old Ph.D. Nowadays there are one or more postdoctoral positions that are necessary for most candidates like myself who are interested in an academic position.

Being a professor is in many ways a totally sweet job, which is why it’s been my career goal for some time now. The tenure system affords unrivaled job security; the pay is more than adequate for the non-money-obsessed; the work is varied and interesting, including teaching, service, and research. Perhaps most appealing is the autonomy.

Earlier this year, there was an article in the New York Times about the declining prestige of traditionally prestigious professions such as law and medicine. I agree that the decline in prestige is real, but not necessarily for the same reasons that the author suggests. In the article, it is argued that changing social constructs of “success” are what has led to the decline in prestige. Specifically, the author cites the rise of entrepreneurship as the new standard for success.

That analysis may or may not be correct–there have always been successful business people to envy–but I also feel like the actual performance of these “prestigious” jobs is now more onerous than it used to be, which was discussed less in the article. People in these professions are expected to put in ridiculous amounts of time. This reduces prestige in two ways: first, as the amount of time increases, the job itself sucks more; and second, putting in ridiculous hours has, I think, become less socially acceptable. It’s pretty common these days to be accused of workaholism.

So this brings me back to being a professor. Because of increased competition for federal grants, the amount of time that it takes to be a successful science professor at a research institution has gone up. Combine that with lower pay and prestige during the years as a postdoc and the job is less appealing than when you could get a tenure-track job at age 27.

My hypothesis is that the institutions that employ these high-end professionals–universities, law firms, hospitals, etc.–are basically getting better at milking a talented and educated class of workers for all they’re worth. But there could well be other reasons driving this trend as well. I still think being a professor is a great job, but maybe just not as sweet as it used to be.

Ecology of the American West

I recently got back from the nineteenth annual Darrouzet-Nardi family vacation. We visited four national parks and one national monument during the trip: Great Sand Dunes, Mesa Verde, Hovenweep, Bryce, and Zion. Pictures are here!

During this great trip, I finally comprehended the awesomeness of the “Grand Staircase.” The Grand Staircase is the geologic progression of sedimentary rocks that is continuous throughout the Colorado Plateau region. The lowest step is at the bottom of the Grand Canyon and the highest step is on the plateaus around Bryce Canyon. Zion Canyon neatly fills in the middle of the staircase between the Grand Canyon and Bryce. Here’s a picture of the staircase courtesy of wikipedia:

With my 27 years of living in and learning about the landscapes, geology, geomorphology, pedology, hydrology, biology, zoology, evolution, botany, anthropology, sociology, archeology, and of course, ecology of the American West, I have been dreaming about creating and teaching the ultimate Ecology of the American West field course.

The Grand Staircase made it click because I realized that it would make a fantastic unit for the course. Add a unit on the amazing diversity of the Ecosystems of California, and then perhaps on the Rocky Mountains and the Great Basin. Throw in the Great Plains and you have a nicely divided transect of some of the most spectacular country on Earth, from the hundredth meridian to the Pacific Ocean.

Make it a five month course, all of it on the road, approximately one month per region. No boring textbooks: we’ll read Abbey, Stegner, Reisner, McPhee, and Leopold! We’ll even collect some data and do some real science while we’re at it. Anyway, just a thought. I mean, who would let me teach something that awesome? . . .

Soil nitrogen cycling field day on Niwot Ridge

If all goes well this week, a small army of field assistants and I will undertake what I believe to be the most comprehensive spatially explicit examination of soil nitrogen cycling rates in any ecosystem to date. We will simultaneously measure gross N mineralization, gross nitrification, and gross microbial N immobilization (thick arrows in the Niwot Ridge N cycle figure below) at 120 points across my alpine-subalpine study site on Niwot Ridge. This data set will help us to understand spatial variation in a key set of N cycling reactions and provide some insight on how this ecosystem is responding to anthropogenic nitrogen deposition.

The fastest and most important nitrogen cycling reactions in terrestrial ecosystems are the release of soil nitrogen from the large soil organic matter pool (catalyzed by microbial enzymes) and the subsequent assimilation of that nitrogen by the soil microbes (again, the thick arrows in the diagram). The constant cycling between the soil organic matter, the soil inorganic pool and the microbes is the underlying engine of terrestrial nitrogen cycling and occurs at rates that are on the order of 10 times higher than plant-soil exchange rates.

Variation in these rates with temperature, moisture, organic matter quality and other factors are essential in understanding how ecosystems processes nitrogen and how they will respond to the increased rates of available N stemming from human activities. While there have been many studies examining how different factors and conditions affect these processes, I know of only one small-scale study that has put these results in a landscape context to understand how the different parts of a landscape contribute to the overall ecosystem-level cycling of nitrogen. The data we will collect this week should help to fill this gap in our knowledge.

The measurement procedure we will be using is called the pool dilution method. At each sampling point, we will inject 6 ml of ¹⁵N-labeled solution into a patch of soil and then allow the microbes to process the nitrogen in that solution for four hours. After that four-hour incubation time, we will extract all of the inorganic nitrogen in the soil core and measure how much of the ¹⁵N has been processed. We will be able to tell how much processing has occured because the ¹⁵N-labeled soil inorganic pool will have been diluted by new nitrogen mineralized from the soil organic matter pool.

The field procedure is difficult to organize, but we’ve already done most of that and the implementation is actually pretty easy, so it should be a fun field day. Look forward to seeing some preliminary results posted here.

New book: Come on people, stop using p-values already

In the June 6 issue of Science, there is a review of a new book entitled The Cult of Statistical Significance: How the Standard Error Costs Us Jobs, Justice, and Lives. This book joins a long and loud chorus calling for the end of statistical hypothesis testing (frequently manifested as the reportage of p-values), a chorus of which I have been a member [this links to a long thread so do a search for my name]. The reviewer of the book, Theodore M. Porter, writes:

The authors do not claim much originality in recognizing [the use of statistical hypothesis tests] as an error; they list and discuss a distinguished roster of predecessors in statistics, philosophy, and the sciences who have called attention to it. And yet somehow the error persists, across a wide range of disciplines including some–such as pharmaceutical regulation, econometrics, and education studies–that feed directly into policy. The book was written to shake us out of our lazy habit of treating significance levels as an almost automatic criterion of scientific and practical worth.

This quote demonstrates some interesting points about the conflict between users and disparagers of statistical hypothesis tests. As Porter acknowledges, there isn’t any question about who is right: statistical hypothesis tests have been shown to be an epistemologically bankrupt approach to data analysis and people should stop using them. The book (which I won’t read because I can guess what it says) is undoubtedly correct on this point. But there is something else in the quote above. The use of the word “lazy” in the last sentence may be a subtle dig at the authors of the book for being preachy. Porter expands on this later in the review, and although he makes it clear that he agrees with the basic premise of the book, the overall review is decidedly mixed.

Porter is not the first book reviewer to skewer an author that writes on this subject. Here’s a review of another book called Statistics Without Math. The authors of the book are part of the chorus decrying statistical hypothesis tests, although their book includes many other subjects as well. The reviewer, William Baltosser writes:

I found myself agreeing with the authors on many points, disagreeing in other instances, or wanting them to get off their soapbox (e.g., types of statistics used “trivial,” “promote cultural identity,” a “cultural badge,” “display scientific culture”) in other instances.

The soapbox comment of course refers to the discussion in Statistics Without Math on the misuse of statistical hypothesis tests among a few other practices. I won’t argue that the authors of Statistics Without Math write with a cynical and preachy tone that may be counterproductive to their cause. However, it is ironic that the phrases Baltosser finds so offensive are in fact the best explanation for the perpetuation of statistical hypothesis testing.

Statistical hypothesis testing is so ingrained in some scientific circles that even though the technique is easily shown to be both silly and confusing, failure to use it can arouse suspicion. For example, in a paper where I reported effect sizes with estimates of uncertainty instead of statistical hypothesis tests, one reviewer wrote, “Overall, the authors do not show any statistical value besides confidence intervals and the reader is not confident whether the differences between [the treatments] are significant.” One way to deal with such a comment (thus allowing your paper to be published and your career to march forward) is to acquiesce and include p-values. Thus, the review process contributes to the perpetuation of statistical hypothesis testing. In this case, I used the mountain of literature invalidating the practice to handily rebut the criticism.

Unlike Porter, Baltosser does not acknowledge that the book authors are correct on the point of eliminating statistical hypothesis tests. The reason for this conspicuous absence in the review is suggested in the final paragraph: Baltosser reveals that he has for 15 years taught “biostatistics,” which is the name ususally given the offending course that is another key perpetuator of statistical hypothesis testing. It is easy to see how Baltosser might be offended by the implication that he is a perpetuator of intellectually fraudulent methods.

Like allowing gay marriage, people will eventually come around to realize that eliminating the use of p-values and statistical hypothesis tests is the right thing to do. But until then, the issue provides a fascinating window on how something as pseudo-rigorous as statistical hypothesis testing can linger in the scientific community.

And for those of us, myself included, that get a little too worked up about this, what should we do in the meantime to calm ourselves? That’s easy, just give people copies of the great statistician John Tukey’s take on the issue. He pretty much clears the whole thing up in the first three pages of his paper “A Philosophy of Multiple Comparisons.” His analysis is straightforward, logical, and instructive. And perhaps most importantly, his tone is reflective instead of preachy.

Nitrogen in the news

The Science paper I wrote about on May 16 created a mini press blitz. Here are some of the articles:

The Economist. Getting in The Economist is a big step for the nitrogen story, because The Economist has just the type of quantitative, policy-oriented audience that needs to be convinced of the problem.

Discovery Channel News

Science Daily

A.P.

Miller-McCune

The Telegraph

And in other blogs…

Grist Magazine

Wired Blogs

So, mostly sciency sources so far, but a few more high profile papers and discoveries could send nitrogen over the tipping point.

Biogeochemistry Reading Group: Roger Pielke Jr.

On March 6, 2007, Dr. Roger Pielke Jr. visited the Biogeochemistry Reading Group and talked to us about the interface between science and policy. Roger was a CU student as an undergraduate and is now a professor here. Back in the day, he worked at NCAR as a FORTRAN programmer and felt privileged to work with some of the preeminent scientists involved with the Montreal Protocol. After that, he went and worked for a lawmaker in Washington D.C. and observed that both scientists and policy makers wished that they understood each other better. We read a short opinion piece Roger wrote for Nature as well as a copy of some testimony that he gave in congress on the topic.

Roger made some provocative arguments about the role of science in society. First, he argued that taxpayers may eventually realize that they are not getting their money’s worth with public investment in science, causing the general public approval rating to fall, which could then potentially lead to a drop in public funding. Second, he argued, as he does in his book, that scientists should not demand extra influence in politics because of their status. Instead they should lay out the options for policy makers without advocating a particular cause. I don’t know if I agree with either of these arguments, but I like the large-scale thinking that he applies to the topics.

Although Roger discussed several interesting points about how high public research expenditures do not necessarily translate into societal benefit, I found a story he shared about the language of science policy particularly interesting. Before 1950, doing research for the sake of knowledge without concern for practical application was called “pure research.” Today, scientists call this “basic research,” which is what I learned in school. Why the change in terminology? Roger said that the term “basic research” may have become favored for its political convenience. Apparently, “basic research” means something different to policy makers than to scientists. To scientists, it’s the same as “pure research,” which appeals to scientists because they like to think their work is just inherently interesting and important. But to policy makers, basic research means the main basics of a field of interest, and this seems like something worth paying for. So, policy makers are not getting what they think they are getting.

Roger thinks that the approval rating for science will fall and that the political system (democracy) is set up so that if we do not show the societal benefits of our research, we will be out of a job eventually. He explained, “Science is one of the most favored and respected institutions in the country….[People think] We give money to science; we get iPods. That’s pretty cool.” In other words, the public understanding of science is currently oversimplified. Roger thinks that scientists should attempt to pre-emptively fix this problem. There has already been a move in this direction and I agree with Roger that it may grow stronger. After the cold war, interest in research that did not benefit society dropped. By 1998, NSF proposals changed to include a new requirement: the societal benefit section was added to NSF proposal criteria. Roger explained, “there’s really no such thing as basic research any more.” Roger thinks that this trend has been a good thing.

I agree that the trend has been a good thing, though I don’t think that it would be good to move too far toward eliminating any line of inquiry that does not have immediate practical application. There is a certain randomness to research in which just the doing of it is important because it allows for serendipitous discoveries.

We also talked quite a bit about the role for scientists in advocacy. Should scientists try to stay out of science or should they jump in and make recommendations? Roger says that as scientists, we should not demand more influence because of our status. He feels that the correct way to advocate is to organize through our institutions. He said not to make arguments like “the science dictates….” Roger says he does not think that organizations like the Office of Technology Assessment (OTA) will be reinstated, but that we need more of the culture of OTA where scientists lay out options that can then be picked through by policy makers. Roger thinks that we should integrate the science and policy to lead to better outcomes and that scientists have to resist the tendency in the policy world to reduce the options to a politically tractable number. So scientists should focus on finding outcomes. His book goes into this in a lot greater detail.

I like the laying out options idea, but I also don’t necessarily oppose scientists like Jim Hansen who are really vocal on the issues. I think scientists are just going to advocate like any citizen and some will and some won’t, but we can’t necessarily stop them.

Here’s a link to Roger’s book that he hopes will be a field guide for how scientists can become involved with policy. I took a look at it and while it is quite academic in tone, it had overall interesting ideas. His analysis of the controversy surrounding Bjorn Lomborg’s The Skeptical Environmentalist is quite good.

Finally, Roger said that he sees the politicization of the politicization of science is a disturbing trend. That’s a brain twister, but once you figure it out and listen to the candidates in the current election, I think he’s right that this is occurring.

Nitrogen: how important is it?

Today in the journal Science, a review article was published about human modification to the global nitrogen cycle. If you want to know about the environmental issues surrounding nitrogen and don’t mind a rigorous technical report, this is the best yet. You can read the abstract here and you can link to the full text if you have a subscription.

High-profile review papers in leading journals beg the question: exactly how important might the nitrogen issue become? Will it be the next inconvenient truth society has to grapple with? Although the global increase in reactive nitrogen is already acknowledged by some as an important environmental issue, it’s not clear whether nitrogen will ever rise to the fore the way climate change has. Will policy makers ever have to discuss their nitrogen policies as they now discuss their carbon policies? Right now, it doesn’t look like the shit (literally in the case of N-rich sewage) is about to hit the political fan. But like CFC’s in the 80’s and like climate change over the past decade, that could change as our quantitative knowledge of global N cycling improves and evidence emerges.

While there is public consciousness about climate change, invasive species, land cover change, and population growth, similar attention has not been paid to nitrogen although the effects on global ecology are arguably as dramatic. Click on this thumbnail (a figure from this paper) to see a graphic showing our species’ handiwork:

At issue is what has been termed by James Galloway, the most outspoken scientist on this issue, the nitrogen cascade. When reactive N (called Nr) is released into the environment, it can cause a cascade of environmental effects. A single molecule of N₂ oxidized in your car’s engine to become 2NO can pollute the air in your city, drift out of town and fertilize an invasive plant species while acidifying the soil, and then end up in a stream or river where it encourages algal growth and finally contributes to a dead zone in the ocean before it is denitrified and sent back to the atmosphere, perhaps as N₂O, a greenhouse gas. At the same time, nitrogen is important globally as fertilizer and a lot of people depend on it or need more of it to eat.

Scientists and a few other close observers are aware of the scope of the issue, but the general public is certainly not, and the educated public is only a little more aware. For example, take this recent article in The New York Times. It does a decent job reporting an increase in fertilizer demand, but it biffs when it talks about the environmental effects of nitrogen, mentioning only the water pollution and ignoring the other major parts of the cascade.

For whatever reason, and I can think of several, nitrogen has not yet gripped people the way climate change has. Perhaps because nitrogen-related issues are varied and complex, there is no main problem like rising global temperatures and sea levels to rally around. Perhaps it is just a smaller problem that doesn’t have room on the international stage. Perhaps the case to be made is still too murky and we need more information.

Whatever the reason for the lurking nature of this issue, I think that something more needs to be discovered for it move beyond the subject of wonky environmental policy discussions among experts. It doesn’t yet seem urgent enough for people to become mobilized. Although I can’t say the issue will continue to lurk or whether it will become more prominent, here are a couple scenarios that might turn attention to the nitrogen issue.

Right now, nitrogen is not included in global climate models. Why? Because spatially explicit global climate/carbon models that are coupled with nitrogen cycling models are too computationally intensive. We don’t have dedicated supercomputers that are fast enough. But climate scientists are trying to fund the next supercomputing facility for this type of analysis and more. If nitrogen turns out to be a key player in those models, we could find ourselves trying to reduce our nitrogen footprints as well as our carbon ones.

Another possibility that we should never discount is that someone could make some sort of black-swan-type scientific discovery that thrusts nitrogen to the forefront. Although this may not be the one, here’s an example of something unexpected that could be important. In Narragansett Bay in Rhode Island, researchers discovered that rising water temperatures, possibly due to climate change, have started to reduce the efficiency of microbes that scrub out nutrients and purify water flowing in from surrounding rivers:

If Narragansett is typical of other bays, they argue, it could be the harbinger of a new threat. Shifting the effect of anthropogenic nitrogen loading beyond the immediate coastal zone could destabilize ocean ecosystems by acidifying the waters, exacerbating harmful algal blooms, killing fish and shellfish, or perhaps even powering a vicious new cycle of global warming. The studies are currently hard to interpret and some say the system is poised to rebalance itself. But if they are wrong, global warming may do more to the oceans than make them rise.

The nitrogen issue is a lens with which to examine a lot of longstanding environmental issues like pollution, invasive species, and climate change. As recently as five years ago, it was difficult to imagine the public grasping this subtle approach. But now that the global carbon cycle has entered the public debate in a big way, we may be ready for nitrogen too. I recently saw a talk at a conference that ended with a slide that had a giant N on it. The speaker said that his message was that nitrogen is big. Time will tell if he’s right.