Thursday, July 26, 2012

Nature photos for you(se)



Over the last 20 years, I have taken many nature photos – usually of cool critters in cool places. I had posted a few on my website but never had the time to keep it up to date. Nonetheless, people would see them and want to see more. Then I would have to dig through all of my files to find other ones I thought they might be interested in. Each time I did this, I would tell myself that I really should put them up all on line so that anyone could peruse them all. 


Well push came to shove and I have now posted 2,300+ of my best nature photos on http://www.flickr.com/photos/83007471@N04/collections/


I have organized them into two “collections” – one of cool places and one of cool critters. The latter is a subset of the former – having excluded non-critter photos. All of them were uploaded in the original size and can be downloaded in that original size or smaller versions thereof.


The photos are free for non-profit use and reasonably priced if used for profit. Just contact me for permission in either case.



Happy browsing.


ps. Let me know if you spot any errors - I am sure many lurk

Friday, July 20, 2012

Standards for evolutionary inference: some happy place between Baba Brinkman and Dick Lewontin.


Last week I was at the Evolution 2012 meeting in Ottawa. A joint meeting of five evolution and ecology societies, it was the largest collection of evolutionary biologists (plus some ecologists) ever assembled in a single place. It was an incredibly dynamic and exciting meeting with tons of opportunity for discussion and argument lubricated with appropriate – if expensive – beverages. Two presentations in particular, keynote addresses of a sort, stimulated a series of arguments that led to the reflections contained in this post.

UBC biologist Rosie Redfield gave a public outreach talk that detailed the debacle surrounding a paper published in Science where a bunch of NASA scientists claimed to have found bacteria that could construct their DNA backbone with arsenate rather than phosphorous. If true, this would have incredible implications for our understanding of life on earth and beyond. Rosie had read this paper and written in her research blog (http://rrresearch.fieldofscience.com/) about how horrible it was – stated simply, the work was far from providing the standard of evidence necessary for the inferences it was attempting to make. Rosie quickly became a scientific icon of the blogosphere for her withering criticisms of the paper. Rosie then redid the studies with the proper standards and showed that the original result didn’t hold – all organisms do in the end probably use phosphorus. Rosie’s paper was also published in Science – and it appeared online precisely in the middle of her talk, which was not a coincidence.  It has been said that “negative reviews often give a frisson of pleasure the reader” (Houle 1998 - Evolution) and so do negative talks to the listener – at least to many of them.

The other “keynote” I want to mention was the performance by Baba Brinkman of his “Rap Guide to Evolution.” I had known of, and greatly appreciated, this work of science/art/poetry/music for a few years but this was the first time I had seen it in person. In addition to giving great performances of some of the work I already knew of, he had some new – and equally hilarious and insightful – stuff (Don’t Sleep with Mean People was a highlight). Everyone should hear and see Baba’s work: http://www.bababrinkman.com/. Coincidentally, I happened to run into Baba during one of the mixers and also at bars on two other nights, which formed the second inspiration for this blog about standards of evidence.

Baba dropping an evolutionary rap anthem.
Baba’s work summarizes in entertaining and generally correct form many of the basic underpinnings – and also unique nuances – of evolutionary biology. He also strays into evolutionary psychology. Although prefacing his dialog with a disclaimer that much of the field might well be bunk, he is clearly a fan – even if only because of how it makes one think about human behavior.  His favorite example is the correlation among human communities between mortality rates and teen pregnancy rates (and other things). He explains in a rapid rap flow the hypothesis of Daly and Wilson (1988) about how it makes evolutionary sense to reproduce early if your mate is likely to die soon. In short, teen pregnancy might be an adaptive reproductive strategy (or tactic) in response to high-risk situations. The graph relating mortality rates (x-axis) to teen pregnancy (y-axis) is extremely strong; indeed, it would be the envy of most empirical evolutionary biologists working on any organism. But (to continue the point of my previous post on Faith’s Conjecture: http://ecoevoevoeco.blogspot.ca/2012/07/faiths-conjecture.html) how can we be sure this is a causal relationship. Perhaps high teen pregnancy rates (x-axis) lead to fathers adopting riskier and more aggressive strategies that increase mortality rates (y-axis). Or maybe both phenomena are independently driven by some external factor. What standard of evidence would be necessary to make this conclusion with surety?

In my conversation with Baba, he argued that work on humans should be held to the same standard of evidence as work on other organisms. With other organisms, however, we would perform experiments. We would alter mortality rates and see if it changed the age of reproduction. Indeed just such experiments have been done: when guppies are introduced from high-mortality environments to low-mortality environments they evolve delayed reproduction (and vice versa). But we can’t do this sort of controlled experiment with humans, of course. So we clearly can’t hold work on humans to the same standard of evidence – but we should push as far as possible. Or should we?

In 1999, I was in the audience for a symposium called “Darwinian Evolution Across Disciplines” held at Dartmouth College. A collection of speakers from a variety of disciplines (religious studies, anthropology, medicine, etc.) spoke about how evolutionary thinking had influenced their disciplines. (The representative real evolutionary biologist, Dick Lewontin, spoke about cosmic evolution – go figure.) At the end of the symposium, all of the speakers lined up their chairs at the front of the room and the audience was allowed to ask questions. My question started with the preface that evolutionary biologists were heavily criticized (by Dick) for telling “just so stories” to explain the adaptive significance of trait variation. (That is, inferences weren’t based on an appropriate standard of evidence.) I then noted out loud that it seemed like most of these other disciplines were still in the “just so” phase, and I asked what the prospects were for transitioning into the rigorous hypothesis testing now employed in evolutionary biology. A few speakers gave some comments and then one of them turned to Dick, who had not yet spoken, and asked something like “What do you think Dick?” After pausing for effect, he turned to face all of the other speakers and said something like “I don’t think that any of you know how evolutionary biology works.” And then he went on to disparage their fields for a few minutes before turning to me and saying that he still felt evolutionary biology was in the “just so” phase. Then he walked out. Frisson! (A video exists of Dick chastise us [although I can’t seem to access it right now]: http://www.dartmouth.edu/~dead99/Disc/Disc.htm. )

The lesson I think we should take from all this arguing and frissing is that we should push evolutionary psychologists to base their inference on the highest possible standard of evidence THAT IS APPROPRIATE FOR WHAT IS POSSIBLE. That is, we simply can’t perform evolutionary experiments on humans. We need to find some happy point between Baba Brinkman and Dick Lewontin – probably a lot closer to the former than the latter.

And, of course, we should strive for exactly the same thing in evolutionary biology in general: the highest possible standard of evidence. But striving is different from achieving, and so it is reasonable to ask should we also HOLD evolutionary biologists to those standards – by, for example, blocking the publication of studies that don’t perform manipulative experiments in nature or that don’t use the latest genetic methodologies? I don’t think so. First, incredible inequities exist in the manipulability and genetic resources for different taxa. We simply can’t expect people who work on mosquitofish and walkingsticks to deploy the same genetic tools as people who work on flies or mice or stickleback or humans. And we can’t expect people who work on elephants or hippos or albatrosses or humans to perform the manipulative evolutionary experiments typical of flies and mice and bacteria. This doesn’t mean that we should all work on those “ideal” model systems – we really do need to study the full pageantry of life. The solution then must be to hold work on a given taxon to the highest possible standards for that taxon – standards must be scaled to taxa.

Or is that really the case? Can we really expect everyone who works stickleback to fully sequence all the individuals in their study populations? Can we really expect everyone who works on guppies to perform manipulative evolutionary experiments? Clearly not, as the resources and opportunities to do so are out of reach of most people working even on these groups. Thus, we can’t apply a particular standard of evidence to all papers from a given taxonomic group – even in Science and Nature! Otherwise, we are always chasing the latest technology or the most money or the biggest collaborations – and we are saying, in essence, that work published just a few years earlier would not be worth publishing in the same form today. This is nonsense. The major advances in evolutionary biology were ideas – and ideas are what stand the test of time (V!). So I would encourage all of us, whether acting as authors or reviewers or editors or bloggers or rappers to strive for the highest possible standards of evidence in our own work while also judging the work of others according to what is reasonable and possible for them – and to what extent their ideas are interesting and stimulating. (Just think how much less exciting the last year would have been without those NASA scientists.) We need to find some happy place between Baba Brinkman and Dick Lewontin.

Baba, Mr. Simmonds, and Hendry lab graduates Xavier (far left) and Erika (far right)

Tuesday, July 3, 2012

Faith's Conjecture

Allen’s Rule. Rensch’s Rule. Cope’s Law. Bergmann’s Rule. Cheverud’s Conjecture. Who wouldn’t want one? Hendry’s Rule? Hendry’s Law? Hendry’s Paradox? Faith’s Conjecture? That’s right, Faith’s Conjecture!


Just recently, I spent a week in Bonito, Brazil, for the annual meeting of the bioGENESIS core project for DIVERSITAS. Over dinner, we strayed into rules, laws, paradoxes, and conjectures: which one we wanted to have and what it would be. Dan Faith decided that he wanted a Conjecture – and proceeded to suggest one. He proposed that any fairy tale or fable could be inverted so that its message would change in an interesting and informative way. Take, for example, the tortoise and the hare. Maybe the tortoise had heard the classic fable and so assumed he would win, thus losing owing to arrogance or inattentiveness. Or maybe the hare had heard it and so realized he would lose if he didn’t run steadily. Tortoise loses – hare wins – lesson changes: those who don’t pay attention to history are bound to repeat it. Having succeeded here, we tried a few other fairy tales and fables on the Conjecture and I have to confess it was a bit of a force to make it work. Time to give up on Faith's Conjecture.


A few days later, however, I got to thinking about it a bit more and realized that perhaps Faith’s Conjecture really was valid – but in a different context: ecology and evolution. I hereby restate Faith’s Conjecture as: any correlation from which a causal relationship might be inferred (the thing on the x axis influences the thing on the y axis) can be inverted (the things on the x and y are switched) to lead to a new causal inference. Here are some examples.

Gene flow is often assumed to constrain adaptive divergence. Thus, one would expect that populations experiencing higher levels of gene flow would show lower adaptive divergence. So one goes out in nature, samples a bunch of independent population pairs, and tests whether pairs that are more divergent in adaptive traits (y axis) are also those showing lower gene flow (x axis). If such a correlation is present, one infers that gene flow constrains adaptive divergence. However, it is also true that adaptive divergence might constrain gene flow. This is the hypothesis of ecological speciation, where increasing adaptive divergence causes greater ecologically-based reproductive barriers, which decrease gene flow. So one goes out in nature, samples a bunch of independent population pairs, and tests whether pairs that are more divergent in adaptive traits (now the x axis) are also those that show lower gene flow (now the y axis). If the correlation is present, one infers that adaptive divergence reduces gene flow: ecological speciation! Thus, the exact same correlation can be inverted for two different inferences. Remarkably this example is real: many studies have plotted gene flow on the x axis and adaptive divergence on the y axis and made the first inference while many other studies have plotted adaptive divergence on the y axis and gene flow on the x axis and made the second inference. Faith’s Conjecture in the machine!
A perennial topic in biodiversity science is the idea that increasing biodiversity (e.g., number of species) increases ecosystem productivity. This makes sense because, among several reasons, more species will presumably use a more diverse set of resources and thereby increase the overall productivity of the system. So one goes out in nature, samples a bunch of plots, and shows that plots with higher biodiversity have higher productivity: hypothesis validated - we need to save more biodiversity because it will increase productivity, a key ecosystem service. But, at the same time, it has long been known that increased productivity can increase biodiversity – at least up to a point. After all, higher productivity allows more total individuals in an ecosystem which increases both the width and depth of, and thus the number of species in, the food web. So one goes out in nature … you get the idea.

Many other examples exist – and, importantly, every one of these has been inferred in correlational studies. Smaller species' ranges should obviously lead to less genetic diversity, since smaller population sizes and adaptation to a narrow range of conditions should lead to the depletion of genetic diversity. Yet on the flip side, less genetic diversity should constrain evolutionary potential and thus lead to smaller species ranges. Increased diet diversity within a population leads to increased trophic trait diversity owing to disruptive selection, but increased trophic trait diversity leads to increased diet diversity because individuals with different traits can feed on different foods. Etc. Etc. Ad infinitum.
So, Faith’s Conjecture is upheld. Perhaps it is even a law or a rule but, for my money, I would rather have a conjecture too. It just sounds cooler- and easier! I should point out that Faith’s Conjecture cannot be directly tested simply through logic of the above sort. Instead, one needs to experimentally manipulate each of the axes to see if it really does causally effect the other axis and, interestingly, this has been done – and confirmed – in the above examples. In addition, Faith’s Conjecture does not necessarily apply to situations where one of the axes is not a biological variable. For example, increasing geographical distance decreases gene flow but increasing gene flow does not decrease geographical distance.

I propose the Faith’s Conjecture is commonly – perhaps universally – true, and I challenge the reader to provide putative instances where it succeeds or fails. In the latter case, I intend to either prove that cause and effect really are reversible in the proffered example or that the example does not apply. In short, I hope to redefine Faith’s Conjecture as necessary so that it conveniently excludes examples that do not abide. After all, the next best thing to having one's own conjecture is to be the person to name the conjecture.

Some cool things I conjectured in Brazil.


Monday, July 2, 2012

Carnival of Evolution #49

  Carnival of Evolution #49 is up at Mousetrap.  Our post this month is Andrew's tale of National Geographic, David Attenborough, Darwin's finches, and the Galapagos; if you haven't read it yet, check it out.  It's an interesting glimpse into how these amazing nature documentaries get made – and how much luck is involved in their making.

  Lots of other cool stuff in the Carnival too!  I've been enjoying wrapping my brain around all the controversy surrounding group selection and kin selection, and there are several posts on that; but a dozen or two other posts, too.

  It being the Mousetrap, they chose an animal trap theme for this month.  Well, it's hard to fit these themes sometimes, but here's Andrew catching fish (probably guppies):


  See you next month!