Tuesday, May 1, 2007

Independent Project done

I finished up my independent project over the weekend. I ended up going back to my original idea - using Mantel tests to test for niche complementarity in understory flycatchers at La Selva. The data was collected primarily by my advisor, Tom Sherry, in the 1970s with some recent observations collected in 2000 and 2003. The data included habitats, foraging heights, diet (order/family of arthropods consumed, as determined from gut contents), and prey size (again from gut contents) of 15 species. The hypothesis was that birds that were similar in one niche dimension - e.g., habitat - would differ in another niche dimension - e.g., diet - or, at the least, not be similar in more than one.

I took the compiled data, imported it into R, and calculated dissimilarity values for all pairs of species (e.g., 1 vs 2, 1 vs 3, 2 vs 3, and so on...) for each niche parameter. These values were then compiled into matrices, which were then run through Mantel tests. Mantel tests allow you to test for correlations between two matrices - essentially they're like Pearson's correlation coefficients on steroids. Each pair of matrices (diet and habitat, diet and prey size, etc.) was tested for correlations.

As it turned out, there was no correlation between either food-related parameter (diet or prey size) and any other parameter. Oddly enough, though, I found a significant and positive correlation between habitat and foraging height. That is, species that overlap in habitat also overlap in foraging height, and conversely species that occupy different habitats have different foraging heights. Rather counterintuitive, contrasting with both theory and our hypotheses. However, this was a preliminary study, and we're in the process of collecting additional data and obtaining some old data that is currently in another lab, so perhaps this will help. It is true that the gut content sample size is very low - but LSU has an extensive collection, so perhaps we can improve power by boosting the sample size (now there's an idea - but for later).

Thursday, April 19, 2007

Framing Science

There's a heated debate going on in the science education corner of the blogosphere this week over how best to convey scientific knowledge to non-scientists. Matthew Nisbet (a communications prof) and Chris Mooney (a science writer and author of two excellent books on the intersection between science, politics and the media) wrote an article for this week's Science entitled "Science and Society: Framing Science" (you can access the article here ).

They start out with a good point: despite the near-universal acceptance of the existence of phenomena such as global warming and evolution amongst scientists, most Americans - even many college-educated Americans - doubt the veracity of these reports, with viewpoints strongly associated with individual politics. They cite polls showing that while 75% of Democrats agree that global warming is attributable to human activities, only 23% of Republicans accept what is - according to the latest IPCC report - widely considered to be nearly as close to "fact" as is possible to say in science (~97% odds). Similarly, only 27% of Republicans and 42% of Democrats or Independents believe in evolution according to a 2005 Harris poll (I've heard as low as 23% belief across the board in other studies - the lowest level of all developed nations), and a full 45% (!!!) believe that humanity was created by God less than 10,000 years ago (last numbers from this webpage). I read recently (sorry, can't find the citation) that the average American has approximately an 8th-grade level of scientific knowledge (if that). There's no doubt that scientists need to find better and more effective ways to communicate scientific knowledge to the general public, both in school and to adults via the media.

However, there's a hearty debate over how best to go about this. Although in actuality the debate is quite complex, it seems to boil down to this: do we teach science and the scientific method in all it's intricate (though - to many people - boring) details, or do we find a way to "re-frame" science in a way to make it more accessible to non-scientists. Nesbitt and Mooney argue for the latter, going so far as to say: "In short, as unnatural as it might feel, in many cases, scientists should strategically avoid emphasizing the technical details of science when trying to defend it". They stress that rather than emphasizing data - and actually educating people about the scientific method, processes, etc. - we should find ways to "package" information in ways that are "relevant" to people's lives (i.e., speak to the pocketbook).

In the other corner, you have scientists such as P.Z. Myers - a highly-renowned evolutionary scientist and blogger at Pharyngula, and - gasp! - an atheist. He argues, in essence, that we should not "dumb down" science, nor should we have to find a way to repackage and make excuses for evolutionary theory so as not to offend biblical literalists.

Think scientists are just dull, mellow, soft-spoken people locked up in their labs? You should see the jabs going around the blogosphere right now!

Anyway, as for me - well, I'm still waffling. The idealist in me says that we need to improve science education right from the beginning - back in elementary and junior high school. Teach kids the "hows" and the "whys" and find a way to keep it interesting. I don't think we should just toss out the "meat" of science to come up with fluff that will fit within the 30-second soundbite format of modern news. I believe we need to increase scientific knowledge as a whole, so that people can understand the difference between a "theory" and a "hypothesis", can understand why scientists are so reluctant to say something is "absolutely true", and can understand the method behind the results. This is supported by some recent studies (e.g., this paper, which found that in the US - unlike in other developed nations - level of scientific knowledge was the primary factor influencing variation in attitudes towards science.

But yet, I'm aware that many (most?) non-scientists just tune-out discussion of what they consider "boring" details - in this fast-paced information world, they just want the bottom-line. And I think there's a place for the Bill Nye's and the Mythbusters, who make science fun and thus more accessible. We certainly need to improve our skills at writing and speaking to the lay public. But I would caution against going for the soundbite, and softening down your results, at the expense of further diminishing public understanding of science. There has to be a happy medium in there somewhere...

Thursday, April 12, 2007

Stilla's Sense of Snow

...ok, so it wasn't snow exactly, but as I'm sure you all noticed it was bloody cold last weekend! I woke up Sunday morning - on the Florida coast near Pensacola, mind you - to find ice on the windshield and sleet collected on the cycad plants. Ice - in Florida - in April!!! I tried to find historical weather data for Pensacola to see if I could calculate the probability of temperatures <40 in the first week of April, but couldn't find any free data. I imagine the probability's pretty low, though.

I'm slowly poring through the Bayesian papers and book. It's quite complicated - both theoretically and practically - but we've had a local Bayesian expert, Chuck Bell, speaking to our Phylogenetics class, which has been helpful. He uses Bayesian stats in a different manner (specifically for phylogenetic tree selection, which uses somewhat different techniques and software programs than ecological analysis), but his lectures have been a huge help in understanding the theory behind the techniques (and learning how to read all that Greek code - ok, Latin, but it looks like Greek to me!).

Tuesday, April 3, 2007

On objectivity

I just read a great quote by Stephen Jay Gould - one of my favorite recent (though recently deceased and greatly missed) evolutionary scientists. I practically grew up reading his work - he published monthly columns in Natural History magazine (back when it used to publish semi-technical pieces), and I always admired his abilities for insight, self-reflection, making connections between evolutionary concepts and popular culture references, and in turn explaining complicated theories in terms many laymen could relate to.

Anyway, here's the quote: "The most erroneous stories are those we think we know best - and therefore never scrutinize or question." This was a frequent theme of Gould's (see, e.g., his well-known and oft-cited "Spandrels of San Marcos" paper), and also a frequent topic of interest to me (e.g., discussed in this blog post from earlier this year: Ch. 2, Gotelli and Ellison)

The scientific method is dependent, among other things, upon objectivity, and scientists tend to pride themselves on their ability to approach a system or a question with no pre-conceived notions or biases. But yet, we're all human, and as such we naturally tend to make assumptions, prefer evidence which supports our conclusions, and fail to question that which we "know" to be true, despite our best efforts to the contrary. I'm not saying that all scientists are biased - not by any means! - just that -we have to continually work to question our presumptions.

This is an especially relevant topic at this point in my career, as I'm delving deeper and deeper into one obscure corner of the literature, and at this point in time, as I'm reviewing proposals by other scientists at similar points in their careers. I catch myself viewing general ecological questions through the filter of my particular study system and organism, while failing to consider alternate viewpoints - often just because they never crossed my mind! In reviewing proposals and published papers, I find other scientists doing the same thing - looking only at the influences of one particular set of forces, or one particular group of organisms, while not taking into consideration other forces that could be equally, or of greater, importance. To give an example, imagine that you want to study plant-herbivore interactions. I as a bird person tend to focus on the roles avian predators have on controlling insects while failing to recognize the roles of parasitoids, while a recent frog paper I read built exclusions that did not exclude birds, but then failed to recognize their likely role in altering insect abundances.

So, I'm going to copy that quote (and save it in yet another Notepad file somewhere on my Desktop, Megan!) in an attempt to remind myself to question my assumptions and filters...

Thursday, March 29, 2007

This and that...

I'm finally back, after a several-week blogging hiatus. The last few weeks have been incredibly hectic, between working out the final details of my experimental design, writing 3 proposals, and generally preparing for my field season which will begin May 7 (getting permits, equipment, etc etc). Oh yeah, then I took a few days off to go to Big Bend NP in Texas - a much-needed break in an incredibly beautiful spot!!!

I'm beginning the process of learning Bayesian analysis techniques. I contacted Jackie Mohan, a candidate for the EBIO dept's Global Change position, regarding good intro texts, and she made several recommendations. Several of the papers she recommended were helpful and provided a good introduction, especially "Alternatives to statistical hypothesis testing in ecology: A guide to self teaching" by Hobbs and Hilborn (Ecological Applications 16(1): 5-19; 2006).

I also purchased several Bayesian Analysis textbooks (thank goodness for cheap used textbook websites - how did I ever manage to get through undergrad without the internet?!?) and am starting to work through them. Interestingly, we've been discussing Bayesian techniques quite a bit in my Phylogenetics class as well, and we even have an "expert" in the use of likelihood and Bayesian techniques for phylogenetic studies speaking to our class next week.

Tuesday, March 6, 2007

Losing Ground

If you haven't already read the 3-part series "Losing Ground" featured in the Times-Picayune, do so now! There is an excellent interactive graphic as well, explaining the issues clearly and concisely for those who have little time for extensive, non-scholarly reading (e.g., students).

The bottom line is, wetlands have been and are currently being lost at a rate far more rapid than most people had realized. Those maps of Louisiana's coastline that we're all familiar with, showing miles of intricately webbed marshes protecting New Orleans from storm surge? Turns out those are based on 1930s data, and the modern-day picture is disturbingly worse.

Think we still have a long time - maybe 30-50 years, beyond most of our lifespans - to solve the problem? Think again - turns out we have 10 years to restore wetlands before they're too far gone to repair.

Think solving the problem is too expensive? Well, yes, $45 billion is a big number, but here are a few points to consider to put this number into perspective:
> $45 billion = 5-8 months in Iraq at recent (pre-surge) spending rates of ~$6-9 billion/MONTH (source: http://usgovinfo.about.com/library/weekly/aairaqwarcost.htm)
> Louisiana is critical to the nation's oil and gas industry infrastructure, with 19 active refineries (15% of total refining capacity in the country), thousands of miles of pipelines, and the closest access to the huge offshore oil-drilling industry (source: http://www.lmoga.com/industryoverview.html). Whatever your opinion may be re: our dependence on oil, currently the nation's economy is inextricably linked to petroleum prices.
> Estuaries are critical to the seafood industry. Louisiana is the largest producer of crawfish in the world, and also exports huge quantities of oysters, catfish, and other seafood nationally and globally (source: http://en.wikipedia.org/wiki/Louisiana)
> The Mississippi River is an important shipping channel and New Orleans is a crucial access point and port, with ~80 million tons/year passing through (source: http://www.yearontheriver.com/stories/rvr_nav.php)
> This isn't even getting into all the qualitative, difficult-to-quantify reasons why New Orleans and southern Louisiana are crucial to the United States - culturally, musically, et al. - nor does it touch on the fact that we are the United States of America, and we as a country didn't shirk at spending huge sums to rebuild Manhattan post-9/11, San Francisco post-Loma Prieta (or post-1906), Chicago post-fire, etc.

OK, stepping off the soapbox - what does this have to do with biostats or science in general? Well, the need for "proper" science, for thorough studies and full understanding of all potential impacts of action has hindered our actions to this date, and brought us to the point we are at today. While it's true that as scientists we need to be cautious and objective and understand impacts of potential conservation and restoration measures, when do the dangers of inaction or postponement of action outweigh the need for urgent action? How many pilot studies need to be done before we accept the data and act on it? I'm torn, because as a scientist I say we need to fully understand the processes before acting, but as an environmentalist and concerned citizen I say that we need to do something about this, and fast. And I'm concerned that science and the lengthy process of conducting studies and writing reports is all too commonly abused by politicians who benefit from retaining the status quo (see this book for an excellent summary of this abuse, particularly as perfected by the current administration)...while meanwhile opportunities are slipping out of our hands. See this quote in the first TP article for just one example:

"In a convoluted process, restoration projects proposed by a local sponsor must undergo a series of studies of their economic and ecological benefits and detriments. Congress must approve the studies, which can take three to five years. Then, in a separate process, the corps must seek money in its annual budget to conduct them."

In all, it can take over 10 years for any - even small - restoration action to occur, by the time all studies and bureaucratic processes have been completed. We don't have 10 years...

So, where do we draw the line? When - if ever - should the slow, cautious steps prescribed by the scientific method be overruled by the need for urgent action? Who should make the decisions regarding when or how - scientists (ecologists, engineers, wetland biologists?)? Politicians? Committees?

Friday, March 2, 2007

Independent Project

After speaking with Mike Guill re: Bayesian stats earlier this week, I've decided to change my independent project. I'm really interested in learning more about Bayesian analysis - I like the philosophical concepts behind the techniques (directly testing the hypothesis rather than the data, using prior information to come to a conclusion). I'm curious to see for myself how the analysis works (I can't really fully understand a technique like this until I've done it myself), and just how influential informative priors are on the outcomes. So, rather than analyze Tom's dataset of niche breadths for competitive exclusion, I'm going to revisit an old dataset of mine comparing arthropod abundance and defenses and avian insectivore foraging success in two Costa Rican forests.

This data was collected to test one component of an avian life-history theory which my lab has been working on. Birds - like many other organisms - have a distinct latitudinal gradient in demographic rates (most notably clutch size, but also survival et al.) wherein tropical birds have "slow" life-histories (low reproduction, high survival, low metabolic rates) and temperate birds have "fast" life-histories (high reproduction, low survival, high metabolic rates). Hypotheses have been proposed to explain this since the early 1900s, but none fully explain the observed patterns.

We suspect that food limitation is at the root of this gradient. Specifically, we cite references showing that tropical insectivorous birds face strong food limitation - contrary to popular belief - due to the low seasonality (lack of a seasonal "flush" of resources), low population densities of arthropods, and strong predator pressure (due to many species of insectivorous birds feeding on arthropod prey) leading to development of strong anti-predator defenses (physical, chemical, and behavioral) by arthropods. These forces should be strongest in so-called "perhumid" moist tropical rainforests with limited seasonality, moderate in dry-seasonal tropical forests, and weakest in temperate areas.

I sought to test this by comparing arthropod population densities and defenses in a moist tropical forest (La Selva, go figure) and a dry-seasonal forest (Palo Verde), both in Costa Rica. I also observed insectivorous birds and recorded various measures of foraging success & movement rates. I originally analyzed this data using univariate parametric and non-parametric statistics (t-tests, ANOVA, Chi-square, Kolmogorov-Smirnov) and also ran it through a multivariate MANOVA, but found few significant results.

I'm very curious to see if Bayesian analysis will produce similar results. I also have several references upon which I based my hypotheses from which I can draw data for prior distributions, and I want to test the influence of several different informative and non-informative priors.