Field of Science

Not dead yet: When do we give up on an idea?

Guest post by Carina Baskett written in response to Angela Moles and Jeff Ollerton's post on Dynamic Ecology: Is the notion that species interactions are stronger and more specialized in the tropics a zombie idea?

Carina Baskett is a PhD candidate at Michigan State University in the Department of Plant Biology and the Ecology, Evolutionary Biology, and Behavior Program. She posts photos from her fieldwork and occasional articles about tropical natural history, among other things, at Wandering Nature.




ResearchBlogging.orgIf you’ve traveled to the tropics, you know the drill. Get your shots for typhoid and yellow fever, and your meds for malaria (try to avoid the one with psychotic side effects). Don’t drink the water, and avoid the lettuce.

This over-abundance of diseases and parasites in the tropics is not just because sanitation is lacking in developing countries. Both diversity and severity of human parasites are higher in the tropics (Cashdan 2001; Guernier, Hochberg et al. 2004).

Could the same be true for plant enemies? What about other biotic interactions, like predator-prey relationships, and plants and pollinators? And why?

The first person to suggest that biotic interactions are somehow different in the tropical and temperate regions was Alfred Russell Wallace. Not only did he independently conceive of natural selection around the same time as Darwin (during a malarial fever in Malaysia, speaking of tropical diseases!), he was also a great tropical naturalist.

In the book Tropical Nature in 1878, he said, “Equatorial lands must always have remained thronged with life; and have been unintermittingly subject to those complex influences of organism upon organism, which seem the main agents in developing the greatest variety of forms and filling up every vacant place in nature.”

The “biotic interactions hypothesis” to explain high tropical diversity* is a descendent of Wallace’s beautifully stated explanation, with contributions from Dobzhansky (1950), Fischer (1960), and Schemske (2009). At its core, skipping over tangents about coexistence and specialization, today’s conception has three testable parts:
  1. The relative contribution of biotic interactions to variation in relative fitness of organisms is greater at lower latitudes.
  2. Biotic selective agents drive faster divergence of allopatric populations than abiotic selective agents due to coevolution.
  3. Therefore, isolated populations speciate faster when the main selective agents are biotic.
For parts B and C, I’ll just tease you with some references that explore or show evidence for these hypotheses in very different ways: Farrell, Dussourd et al. 1991; Schemske 2009; Paterson, Vogwill et al. 2010; Jablonski, Belanger et al. 2013.

I’ll focus the rest of this on part A, which was recently labeled a “zombie:” false, dead, disproven. I’ll try and convince you that it’s nowhere near dead yet. I’m NOT trying to convince you that the hypothesis is true, because I think the answer is very much up in the air, but rather that it’s plausible and that we need more data.

First, the dissection. Part A is represented graphically in Figure 1 (Schemske 2009). Each arrow is the proportion of variation in fitness for the focal species caused by different selective agents: mutualists, antagonists, and the abiotic environment. A wider arrow is a greater proportion. A solid line shows a positive effect on fitness, while a dashed line is negative. (Note that the arrows go both ways for the biotic agents. They coevolve, while abiotic agents do not, which gets into parts B and C of the hypothesis.)

Here’s what this abstract figure would look like on the ground. This past winter here in Michigan was, to put it lightly, a doozy. Two years ago, it was so mild that I was told that my first Michigan winter didn’t even count. It’s not hard to imagine that even after lineages have evolved to tolerate freezing (which is a big deal—it kills cells!), there can still be a lot of variation in fitness depending on the weather.

Think of a plant that lives for a few years, flowering in the summer, producing fruit in the fall, and dying back over winter. Let’s assume that there’s a resource tradeoff between manufacturing antifreeze and producing fruits.** This past winter, plants that invested a lot in antifreeze would have had high relative fitness in the population, because they alone survived. Two years ago, that same strategy would have had low relative fitness, because plants that produced less antifreeze would have survived the winter too, but had higher fruit production. In this hypothetical situation, there is some variation in fitness due to herbivores and pollinators etc., but most of it is due to the wildly variable weather.

In contrast, imagine a similar plant in a tropical habitat, growing in full sun. It experiences temperature stress too. The sunshine is actually more intense in the tropics because it’s hitting the Earth straight on instead of at an angle, so its energy is concentrated in a smaller area. It’s HOT! But it’s hot almost every single day of the year, so all the plants in the population invest in tolerating the heat to the same degree. Temperature isn’t contributing much variation in fitness in this population.

Life here is more like the Hunger Games. Who can grow the fastest? Who can avoid death by enemy herbivores and diseases? Who can form the strongest alliances with pollinators and fruit dispersers? Competition, antagonism, and mutualism is what determines fitness here, not the weather.***

Now that I’ve painted a picture of what Figure 1 could hypothetically look like in the real world, how can we figure out whether or not it’s true?

Ideally, you would pick a focal species and do an observational or experimental path analysis (e.g., Schemske and Horvitz 1988) to determine the relative contributions of various selective agents at different latitudes. Make sure you have an army of assistants, because you’ll need massive sample sizes. Did I mention you’ll have to do it for many years? You won’t want to miss important events like unusually bad winters or pest outbreaks. By the way, even though this kind of study would probably be impossible in animals, it’s also nigh-impossible to find an abundant plant species whose native range encompasses tropical and temperate latitudes, avoiding really dry places and high altitude. (If you know of one, please let me know!!)

Needless to say, filling in Figure 1 with real data has not yet been done, and given our funding climate, it probably never will. But, there are other ways to approximately test the hypothesis (Schemske, Mittelbach et al. 2009).

What we CAN ask is, what is the “intensity” of the interaction today? What do today’s traits tell us about selection in the past? And what is the frequency of an interaction in the community?

To illustrate each question in terms of pollination, we can ask how much do tropical plants rely on self-pollination vs. outcrossing; do tropical plants invest more in pollinator attraction and reward; and, do tropical plant communities show a higher frequency of animal vs. wind pollination? Fill in the blanks with your favorite interaction.

To build a relatively complete approximation of Figure 1, we should be asking these questions in many systems, across many types of interactions, and at many spatial and phylogenetic scales. For example, asking these questions within widely-ranging species (Salazar and Marquis 2012) is quite different from asking them at the community level, with disparate habitats, community membership, and growth forms (Moles, Wallis et al. 2011). Both approaches are needed, because each has huge advantages and severe limitations.

The most comprehensive review of the available data is a 2009 Annual Reviews paper by Schemske et al. (see their Table 1). They noted that the data was insufficient for meta-analysis. Nevertheless, they found that most interactions show greater “importance” at lower latitudes; that is, the interaction is more intense currently, the traits show that it was more intense in the past, or it is more frequent. None of the interactions shows greater importance at higher latitudes.

For example, in the tropics, predation rates on birds’ nests are higher. Ant predation rates on insect bait are higher. Parasite pressure is higher. Palatability of marine worms, salt marsh plants, leaves, and butterfly larvae is lower. The frequency of animal pollination, animal seed dispersal, ant-plant mutualisms, endophytes, and cleaning symbioses is higher. The review also finds that herbivory rates are higher and plants are better defended at lower latitudes, but a recent meta-analysis on herbivory came to different conclusions (Moles, Bonser et al. 2011).

Although the results are necessarily qualitative and we can’t put a p-value on this statement yet, this review shows that looking across many types of interactions, many ways of quantifying their importance, and over many spatial and phylogenetic scales, the weight of the available evidence supports Figure 1.

But I would be the last person in the world to tell you that we’re done testing part A of the biotic interactions hypothesis. Much of the available data was not generated to explicitly address it, so there’s always something missing. For example, herbivory rates could be the same at different latitudes, but tropical plants may be better defended, indicating that greater herbivore pressure has selected for stronger defense. You need both pieces of the puzzle, preferably measured at the same time on close relatives, to be able to say whether herbivore pressure is greater in the tropics.

I’ve spent the last three years thinking about how we can fill in the missing gaps. There are so many ways to test these questions, so many interactions and species to choose from. Each approach is limited in some key way; otherwise, the end-all, be-all experiment would have already been done! One could easily spend a lifetime chipping away at this question from different angles, without even addressing the bigger picture of whether this has anything to do with the latitudinal diversity gradient. (I’m working on that too though!)

Therefore, I was dismayed when I woke up on Tuesday to a post on a widely-read ecology blog that claimed that the hypothesis that biotic interactions are stronger in the tropics is a “zombie idea.” Meaning that it’s dead, it’s been disproven, we can all go home now, and anyone who studies it is just wasting their time.

Whoa. Not enough data for a meta-analysis, but we’re done with this question? A recent review concluded that there is support for the hypothesis, but now it’s been totally debunked? Did I miss something here?

In fact, I haven’t missed anything. As with any scientific controversy worth its salt, there are contradictory reviews, there are people who are highly skeptical, there is massive confusion about what the hypothesis is and how to properly test it. That’s all fine and good. It’s exciting, even.

What is not fine and good, in my book, is to proclaim from the rooftops that we’re done with a question that we’ve barely begun to address. To claim that a handful of publications on latitudinal gradients in herbivory are the end-all, be-all, period end of story of decades of research. To claim that any one of us has the final authority on how to define, test, and interpret an area of science.

A debate about an idea can be constructive and fun. But both my scientific and journalistic selves cry fowl when a story is presented hyperbolically from one point of view. I believe that it’s irresponsible and polarizing to instigate a debate by claiming that the problem is solved and there is no debate.

I’m glad that people are talking about the topic, though I wish it had been inspired by less inflammatory language. I hope the conversation inspires us to clarify what our questions are and how we can test them. I hope also that you agree that we don’t need more catchy metaphors (zombies, old clothes, lemmings, sheep). We need more data and more conversation. Period. But not the end of the story.


*There are so many species in the tropics! There are over 22,000 tree species in the Amazon, compared to 620 in temperate North America (Currie and Paquin 1987; Fine and Ree 2006). This pattern of higher species diversity in the tropics is remarkably consistent across different types of organisms and through time and space. How can the same underlying processes of ecology and evolution produce such different outcomes? We don’t really know! Sure, there are ideas. In fact, Palmer (1994) lists 120 hypotheses to explain it! But given the massive scale of space and time, it’s really hard to test these hypotheses, so a definitive answer remains elusive. See Mittelbach, Schemske et al. (2007) for a great review.

**For any of this to matter for evolution, we are also assuming that allocation strategies are not very plastic; that they are heritable; and that there is genetic variation for these strategies in the population.

***Why am I focusing so much on temperature? Lots of studies show that climatic variables, especially temperature, are tightly correlated with global diversity patterns (e.g., Currie, Mittelbach et al. 2004). In my opinion, for a few reasons, the biotic interactions hypothesis is the only latitudinal diversity gradient hypothesis that provides a plausible mechanism by which temperature can affect diversity. But actually, the hypothesis is generalizable to any gradient in abiotic stress. Although it was proposed to address the LDG, it applies to other gradients in abiotic stressors that covary with species diversity: altitude, ocean depth, precipitation, etc (Schemske, Mittelbach et al. 2009). This is a practical strength because components of the biotic interactions hypothesis can be tested in other systems, which may be more tractable than latitude. More importantly, it is a theoretical strength because confirming this hypothesis could revolutionize our approach to studying the origins of diversity in many systems.

References:
Cashdan, E. (2001). "Ethnic diversity and its environmental determinants: Effects of climate, pathogens, and habitat diversity." American Anthropologist 103(4): 968-991.
Currie, D. J., G. G. Mittelbach, et al. (2004). "Predictions and tests of climate-based hypotheses of broad-scale variation in taxonomic richness." Ecology Letters 7(12): 1121-1134.
Currie, D. J. and V. Paquin (1987). "Large-scale biogeographical patterns of species richness of trees." Nature 329(6137): 326-327.
Dobzhansky, T. (1950). "Evolution in the tropics." American Scientist 38: 209-221.
Farrell, B. D., D. E. Dussourd, et al. (1991). "Escalation of plant defense: Do latex and resin canals spur plant diversification?" American Naturalist 138(4): 881-900.
Fearnside, P. M. (2005). "Deforestation in Brazilian Amazonia: History, rates, and consequences." Conservation Biology 19(3): 680-688.
Fine, P. V. A. and R. H. Ree (2006). "Evidence for a time-integrated species-area effect on the latitudinal gradient in tree diversity." American Naturalist 168(6): 796-804.
Fischer, A. G. (1960). "Latitudinal variation in organic diversity." Evolution 14: 64-81.
Guernier, V., M. E. Hochberg, et al. (2004). "Ecology drives the worldwide distribution of human diseases." Plos Biology 2(6): 740-746.
Jablonski, D., C. L. Belanger, et al. (2013). "Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient." Proceedings of the National Academy of Sciences of the United States of America 110(26): 10487-10494.
Mittelbach, G. G., D. W. Schemske, et al. (2007). "Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography." Ecology Letters 10(4): 315-331.
Moles, A. T., S. P. Bonser, et al. (2011). "Assessing the evidence for latitudinal gradients in plant defence and herbivory." Functional Ecology 25(2): 380-388.
Moles, A. T., I. R. Wallis, et al. (2011). "Putting plant resistance traits on the map: a test of the idea that plants are better defended at lower latitudes." New Phytologist 191(3): 777-788.
Palmer, M. W. (1994). "Variation in species richness: towards a unification of hypotheses." Folia Geobotanica & Phytotaxonomica 29(4): 511-530.
Paterson, S., T. Vogwill, et al. (2010). "Antagonistic coevolution accelerates molecular evolution." Nature 464(7286): 275-U154.
Salazar, D. and R. J. Marquis (2012). "Herbivore pressure increases toward the equator." Proceedings of the National Academy of Sciences of the United States of America 109(31): 12616-12620.
Schemske, D. W. (2009). Biotic interactions and speciation in the tropics. Speciation and Patterns of Diversity. R. K. Butlin, J. R. Bridle and D. Schluter. Cambridge, United Kingdom, Cambridge University Press: 219-239.
Schemske, D. W. and C. C. Horvitz (1988). "Plant-animal interactions and fruit production in a neotropical herb: a path analysis." Ecology 69(4): 1128-1137.
Schemske, D., Mittelbach, G., Cornell, H., Sobel, J., & Roy, K. (2009). Is There a Latitudinal Gradient in the Importance of Biotic Interactions? Annual Review of Ecology, Evolution, and Systematics, 40 (1): 245-269 DOI: 10.1146/annurev.ecolsys.39.110707.173430.

Nature Communications faux pas

This article in Nature Communications


has this figure showing the phylogenetic relationship between "contemporary human populations and Neanderthals":

Basically, the contemporary "out-of-Africa" individual is in a suit and a bowler hat, and the individual of "purely African ancestry" looks like a thug.

How does something like this get published in a prestigious journal nowadays?

Ignored

There is a website I am ignoring.

Sometimes the best action to take is to ignore. The organization and the man leading it want to influence society in a major way, and I disagree with their agenda. If I were to share with readers who they are, some people would go to their website, and they would get even more attention (and considering the huge amounts of traffic I get, it would be a lot*).

But I wanted to say that on this website they are talking about a certain event that was much covered in the media recently. I vehemently disagree with their views in general, and I think they are misrepresenting the event in question.

Their views are factually wrong, which I know based on a lot of evidence. I'd love to share this publicly, but again, more attention probably benefits said organization, and so I think the best solution is to ignore them.

Hereby ignored.

* Ha!


Tadpole plasticity triggered by dragonfly nymph predation (video)

Professor Rick Relyea from the University of Pittsburgh gave a fascinating seminar today: "Phenotypic Plasticity: Stress-Induced Changes in Behavior, Morphology, and Life History of Aquatic Organisms".

He showed this amazing and somewhat scary video of dragonfly nymphs and tadpoles.



Rick's lab website. Movie is downloaded from here.

Pragmatic definitions in biology

Biology is littered with concepts that biologists cannot always agree on how to define or where there are special cases where the common definition have to be amended. Species. Complexity. Modularity. Evolvability. Evolution. Genes. Community. Robustness. Open-ended evolution. Fitness. Life.

Take species. The current state of affairs is that there are many different definitions, and people can't always agree which one is best. Each one of us may have a favorite. (Mine is the Ecological Species Concept by Van Valen (1976) Ecological Species, Multispecies, and Oaks. Also, best title ever.) This often leads to more or less antagonistic attitudes among people, and can have negative effects on the review process.

As far as I'm concerned John Wilkins is the man to go to for species definitions. He lists 26 of them.

In this case, "species" is the concept, and curse Ernst Mayr for being first to call a proposed definition a "concept" (i.e., the Biological Species Concept - which should also really have been the Reproductive Species definition).

What I propose is the stop calling the proposed definitions "definitions", and instead call them "criteria".

That would make it

  • The Reproductive Species criterion
  • The Ecological Species criterion
  • The Phylogenetic Species criterion
  • The Taxonomic Species criterion
  • ... et cetera.

When determining if two groups of living organisms are different species, all you'd have to do is go down the list and check off those criteria that are met (easier said that done, I know). And then when talking about this, qualify the type of species by naming it according to the matching criteria. Your two closely related groups of organisms would then be ecological and phylogenetic species in the case brown bears and polar bears, and reproductive species in the case of horses and donkeys.

The reason I propose this is that this sort of pragmatic meta-definition has the potential to end unproductive arguments and replace them with clarity - a clarity that emphatically depends on people qualifying the type of species/complexity/modularity or whatever else they are talking about.

Same thing for the other difficult-to-define concepts. Open-ended evolution is the idea that evolution just keeps going, and new forms and features (species, traits, genotypes, etc.) keep appearing. But for how long? Forever? That's longer than anything, so thats not very pragmatic, i.e. it is not a definition that can be applied, because we are too impatient to wait forever. Is natural evolution on Earth even open-ended? Would life on Earth ever reach a steady state after which evolution does not produce new things? Does co-evolution count if this produces new forms that have already existed in the past? Life on Earth is very much affected by the changing fitness landscapes when meteors arrive, volcanos erupt, and solar winds fry the planet, or whatever. Can we just create an evolving computational system in which huge disasters cause mass-extinctions at arbitrary intervals, and then say that the system exhibits open-ended evolution because it keeps evolving? How about these criteria:

  • System evolves in never-ending cycles (revolving open-ended evolution)
  • System reaches steady-state but is reset/interrupted by disasters (reboot open-ended evolution)
  • System continues to evolve new forms for as long as we could wait (temporal open-ended evolution)

The point is to move research forward, rather than letting it be mired in argument, and I think that can be done by simply being more explicit about what we mean when we say something.

Anybody feel like taking a crack at evolvability or life?

Origin of life video

I just did a reddit Science AMA today, and whenever you talk about evolution, invariably the question of the origin of life comes up. It's not my field, as I am not a chemist, but here is a great video explaining a model of how life could have formed spontaneously from chemical elements in the pre-biotic Earth. It is based on research from Jack Szostak's lab.



From now on I will be pointing to this whenever I'm asked how the first cells came about.

Evolutionary dynamics in holey fitness landscapes

ResearchBlogging.orgWhat do real fitness landscapes look like? Do they look more like the image on the left, a nearly-neutral holey fitness landscape, or the one on the right, a rugged fitness landscape with many distinct peaks?



Those are only in two dimensions, so the question is also if depicting anything in two dimensions conveys intuitions that are at all correct.

Holey fitness landscapes (Gavrilets and Gravner, 1997, Gavrilets 1997) are approximations of real fitness landscapes where all genotypes are assigned a fitness value of either zero or one. After normalizing fitnesses to be between zero and one, those that are lower than one are assigned a fitness of zero1. Because real fitness landscapes are of extremely high dimensionality2, and assuming that genotypes have fitnesses that are randomly distributed3, it follows that there exist a nearly-neutral network of genotypes connected by single mutations that has fitness (effectively) equal to one.

The proposition is then that this holey landscape model is a good approximation of real fitness landscapes. It hypothesizes that the evolutionary dynamics on real fitness landscapes is similar to that on holey landscapes, and that distinct peaks like in the image on the right do not really exist. And this is a testable prediction.

Take a look at these videos. They depict populations evolving in two-dimensional fitness landscapes at a very high mutation rate. (You can also download the videos from my research website.)


In all three cases the population size is 2304 (that's (3*16)2, in case you're wondering), mutation rate is 0.5, the grid is 200x200 pixels (i.e. genotypes), and mutations cause organisms to move to a neighboring pixel. Ten percent of the population is killed every computational update (which gives an approximate generation time of 10 updates), and those dead individuals are replaced by offspring from the survivors selected with a probability proportional to fitness (asexual reproduction). Top: neutral landscape where all genotypes have the same fitness. Middle: Half-holey landscape with square holes of 10% lower fitness (size of holes is 14x14 pixels). Bottom: Holey landscape where the genotypes in the holes have fitness zero.

The proposition is that the dynamics of the populations should be the same no matter how deep the holes are. The populations in the half-holey and in the holey landscapes should evolve in comparable ways if the holey landscape is a good approximation.

So what do you think?

What I think is that the evolving population in the top (neutral) and middle (half-holey) landscapes resemble each other, whereas they look nothing like the bottom (holey) landscape. In the half-holey landscape the population takes advantage of the holes all the time, meaning that many individuals who are in them reproduce, even though they have a clear fitness disadvantage. The lesson is that being disadvantaged is just okay, and populations can easily cross quite deep valleys in the fitness landscape. But obviously not when the valleys consist of genotype with zero fitness; evolution in holey landscapes is much impeded compared to rugged landscapes, which is why I think they are not a good approximation.

Caveats: These populations are evolving at a very high mutation rate. When I redid it with a much lower mutation rate (0.05), the neutral and half-holey landscapes stop resembling each other, and the half-holey and holey landscapes look more alike. However, evolution happens so slowly in this case that it is difficult to distinguish the dynamics, so the matter is unresolved so far (however, I have other evidence that lower and more realistic mutation rates do not change this conclusion - some preliminary data in Østman and Adami (2013)). A second caveat is that the whole holey landscape idea relies on the fitness landscape being multidimensional, and so how can I even allow myself to compare evolution of populations in half-holey and holey landscapes in just two dimensions? That is valid question: the intuitions we get from these animations may lead us to think we know something about evolution in multi-dimensional landscapes, while the original premise of Gavrilets' idea was that we exactly cannot. Unfortunately, while this is an empirical question - meaning that it could be tested - the holey landscape model posits that the neutral network appears at very high dimensionality. What this dimensionality is is unclear, so even if I were to evolve populations in 2,000 dimensions (which is not computationally feasible - the limit is a little over 30 binary loci), one could always claim that not even that many are enough. Sighs.


1 Genotypes with fitness greater than 1 divided by the population size, N, are effectively the same, because selection cannot "see" differences smaller than 1/N.
2 High dimensionality means a large number of genes (loci) or number of nucleotides.
3 We already know that this is not a very good assumption, as there are indications that fitness landscapes are non-randomly structured with high fitness genotypes clustered with other fit genotypes (Østman et al, 2010), but we don't know if it is enough to render the holey landscape model useless.

References
Gavrilets S, and Gravner J (1997). Percolation on the fitness hypercube and the evolution of reproductive isolation. Journal of theoretical biology, 184 (1), 51-64 PMID: 9039400

Gavrilets S (1997). Evolution and speciation on holey adaptive landscapes. Trends in ecology & evolution, 12 (8), 307-12 PMID: 21238086

Østman B and Adami C (2013). Predicting evolution and visualizing high-dimensional fitness landscapes, in Recent Advances in the Theory and Application of Fitness Landscapes" (A. Engelbrecht and H. Richter, eds.). Springer Series in Emergence, Complexity, and Computation DOI: 10.1007/978-3-642-41888-4_18

Why do you believe?

Important update April 22nd, 2014: I have been corrected on the usage of the phrases "believe in" and "believe that". In the first sentence below I wrote "believe in something", but what I really meant was "believe that something". Thus, saying "I believe in evolution" is wrong, because it is not a matter of faith. People often respond to this by saying "No, I don't believe in evolution. I accept that evolution is true based on the overwhelming evidence." I have objected to this on several occasions before, but now see the difference. I prefer to say "I don't believe in evolution, I believe that evolution is true (based on the evidence)".

If you say you believe in something, what is it that you mean by that? For example, if you say you believe you will find a hundred-dollar bill today, what is that belief built upon?

I posit that what you actually believe (as opposed to what you say you believe) is really based on probabilities. Perhaps not accurately so, but all future events are of course unknown, though some come very close to 100% certainty, and it is thus really the only way to predict anything with any kind of accuracy.

Trivial example: If you roll a die, you might say that you believe you will get a six. But if we assume this is a fair die, you must assess that the chance is about one in six, so your belief should really be that you do not get a six. In that case you really can't have a rational belief that any one side will come up, though you do of course know with almost 100% certainty (i.e., 100% probability) that one of the six numbers will come up (the die could land on an edge).

In science we make models. That is the essence of the scientific endeavor. A model is basically some explanation of something; hypotheses and theories at opposite ends of a spectrum of explanatory depth are models. So if you as a scientists say you cannot imagine how something would work, how something could have happened, etc., then you basically aren't doing your job. People who dismiss science as rigid and uncreative have not understood what it really entails. Coming up with explanations is among the most creative things people can do. If you're writing a work of fiction, it would surely be defeat if you cannot think of a way to make something click in the story. Same thing with science. If you observe something and you can't imagine how that could occur, then get to work!

Positing a hypothesis is emphatically not the same as "believing" it to be true. That I come up with one hypothesis to explain something doesn't mean that I think it is the most likely explanation, nor does it mean that I can't come up with anything else.

For example, why do I think John Travolta said Adele Dazim when referring to Idina Menzel at the Oscars?

Hyp1: He was high as a kite and just mixed up some slightly related names.

Hyp2: Someone played a joke on him and told him that was her name.

Hyp3: It was on purpose because he thinks that Adele Dazim is a prettier name for her.

Hyp4: He wanted to rock the establishment to secure a role in a new indie film.

Hyp5: He has an occasional speech impediment.

Hyp6: It's a special Scientology accent.


I can assign probabilities to each of these. It may not be accurate (they don't need to add to one, and can actually add to more than one since they overlap somewhat), but at least approximate values or perhaps just a relative ranking of them. Each of these hypotheses could be tested, and my personal belief doesn't really have much to do about anything. I don't yet have any evidence either way, and evidence is of course the only thing we can really base rational belief on, though oftentimes that evidence is reflected in theories about, say, human behavior, in which case I can say I find Hyp1 more likely than Hyp6, because I have seen evidence of only one of them happening before.

The answer is evidence. If you have none, they you have no reason to believe anything. Hypothesizing is not the same as believing, and can be done freely without repercussions. At least that is how things ought to be, everywhere and always.

Bill Nye totally won that debate

The debate tonight between Bill Nye and Ken Ham was won by Nye hands down. Hands up.

Take a look at this lovely slide:


That is a fantastic point. I have not seen it made before. The point is that if there were only 7,000 "kinds" on Noah's Arc, then with the conservative estimate of 16 million species today, then an average of 11 new species should have evolved (even in Ham's creationist model) every day. There should have, in Bill Nye's words, a daily newspaper column listing the new species. Yet nothing like that has ever been observed.

So that was one thing that made this whole debate really enjoyable or me.

Bill Nye did the right thing. In his opening 30 minutes he went right for the jugular of the creationism model. The question to debate was "Is creation a viable model of origins?", and Nye attacked that directly by making several points that shows that it is direct contradiction with science:

  • Antarctic ice-cores show that the first snow that fell and made the bottom layer of the ice is 680,000 years old.
  • There are trees  that are more than 9,000 years old.
  • Grand Canyon is many millions of years old.

These are all dated by different scientific methods, and directly contradict an Earth that would be only 6,000 years old.

Other points from the opening remarks:

  • If fossils all died during the flood, then similar species should not necessarily be found in the same sedimentary layers, but should be mixed.
  • If kangaroos walked from Mount Ararat to Australia (via a land-bridge for which there is no evidence), then there should be remains of dead kangaroos along the way, and yet there is not a trace.
  • The Arc as described in the Bible is simply too large to function when made of wood.
Ken Ham also said some things. The main point he made, which he made very many times, was that there is a difference between observational science and historical science. Historical science is not valid science, according to Ham, who said that if you weren't there, then you can never know. But since God was there, and because he wrote it down in the Bible, we can only know what happened by reading the Bible. This stance of course eliminates our ability to conduct criminal investigation, but no one would actually be that dumb. I have at least never heard of any creationist picketing crime scenes and courthouses when they obtain and allow historical evidence.

I predicted that Bill Nye would win this debate. What I meant was in the long term. What matters is inviting young people and children to explore science, and showing them that there is another model than creationism that in fact most people in the world find more credible. That was the goal, also as stated by Bill Nye.

However, I also think that Nye won in the short term. He clearly came away looking way better than Ken Ham, having presented his case with a confidence that I think most viewers noticed. He made great points that hopefully will make young creationists think twice and make them go look at the science for themselves (thank goodness for the internet) before they become hardened creationists heavily invested in creationism.

The fear of some people, like Richard Dawkins and Jerry Coyne, was/is that debating at all lends credibility to the creationists: "Well now, if Bill Nye takes Ken Ham seriously enough to publicly debate him, then maybe there really is something to creationism", or "That Bill Nye shows up in the first place confirms my belief that Ham's creationism model is correct". I just really, really don't think this is the case anywhere. I'd love some data on this, and to change my mind the data should show that this effect is greater than the effect of getting children interested in (real) science.

I think Nye did an excellent job, thank you very much.


Why Bill Nye will win this debate

In just two days Bill Nye and Ken Ham are having a public debate in Kentucky over evolution vs. creationism. The question to be debated is “Is creation a viable model of origins?”



Update: Sign up for free live streaming of the debate.

The meta-debate is whether it was clever or not of Bill Nye to accept the invitation to debate in the first place. Many people believe that Ken Ham has already won just because Bill Nye has agreed to debate. Debates are not the way science is done, and obviously both parties are going to stand their intellectual ground and not move an inch. What scientists seem to fear the most is that accepting to debate science with creationists lends them credence, that creationists looks like they are being taken seriously, and as a consequence that their theory, creationism, in the eyes of the public is afforded credibility.

Jerry Coyne, for example:

He thinks there are better ways for Bill Nye the Science Guy to make use of all the good will he's earned from his science TV shows. 
"I'd tell him, 'Keep going around giving talks about evolution. Write about it. Give lectures.' People love that," Coyne said. "He's greatly beloved by a large number of Americans. But don't get into a one-on-one with a creationist. If you show up for a debate like that, you lose."
"Poeple?" What people? Yes, people who watch science programs on the TV in the first place. But many of the creationists don't let their children watch them at all! With a debate like this, it is possible that Bill Nye can reach some of those, and sow a few seeds of enlightenment, so to speak.

I don't think there is anything to worry about for one simple reason: the facts are on our side. Evolution really is true, science really does work, and prayer really, really doesn't. Therefore, the more this debate is made public, the more children and high schoolers are made aware of the opposing sides, the more people will understand and believe in evolution (i.e., accept the evidence) in the future.


All Bill Nye has to do is calmly (or not calmly) explain why evolution is true and why creationism is not, and sit back and let Ken Ham make a fool of himself. Ham can go ahead and sound as eloquent and wise as he wants - the bottom line is that his view of the world is the wrong one, and there is nothing he can do to stop the coming generations from learning that, save for stalling it by affecting the school boards across the country that determines what is taught in school.


I predict that whatever commentators will say in the days following the debate on February 4th about who won and why, the real test will be determined years ahead when we see that, indeed, more and more young people flee from creationism and realize that science is the only reliable way to learn about the natural world, and that creationism can teach us nothing about it. That will be the real victory, and Bill Nye will have been part of it.


Besides, it's going to be a good old laugh, and you know it!

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Got a new question on the reddit AMA

from NorrisChuck via /r/IAmA/ sent  ago
Who is more evolved? White man or a Black man?

Sewall Wright's last paper

ResearchBlogging.org Sewall Wright lived to be 98. Two months before he died he published a paper in The American Naturalist titled Surfaces of Selective Value Revisited (Wright, 1988).

Wright was interested in adaptive evolution, and he originated the concept of fitness landscapes to qualitatively describe differences in fitness without using mathematics. He first called them adaptive landscapes, but also used surfaces of selective value.


Today we mostly call them fitness landscapes, though they were initially termed adaptive landscapes. 



As you can see from this figure that I made using data from Google Scholar, in most papers nowadays people refer to them as 'fitness landscapes' (red line) vs. 'adaptive landscapes'. I obtained this data by searching for either term in Google Scholar by year.

Evidently, the idea of fitness landscapes is catching on, to say the least. A Google Scholar search I just did returned well over 2,000 articles that used one of the terms in 2013. The reason for the wide usage is that the concept is very powerful and intuitive. Once the structure of the fitness landscape is known to some extent, we can understand evolutionary dynamics, i.e., how populations evolve can be predicted. I have written about that before (Smooth and rugged fitness landscapes, Can we predict evolution?, Crossing valleys in fitness landscapes), and have recently put up a number of movies that visualize the process.


I view fitness landscapes as being an explanatory framework similar to that of phylogenetic trees. These familiar trees are how we visualize the evolutionary past, and in the same way thinking about evolution forward in time I suggest is best done with fitness landscapes.

Basically, a fitness landscape is just something that describes fitness as a function of either the phenotype (the traits) or the genotype (the genes) of an organism (few people seem to have much use of the type of fitness landscapes where fitness is a function of allele frequencies, so I'll ignore it here, as I generally do). The problem is then how to visualize this map, and when there are only two dimensions, for example when there are only two traits (when we are ignoring all other traits), then the fitness landscape can be depicted as a two-dimensional surface where the height is fitness and depends on the two trait-values. You can see examples of populations evolving on such landscapes in the movies I referred to above.

Sewall Wright drew the first fitness landscape like this. It is originally from his 1932 paper, but was reused in the 1988 paper.



Unfortunately, this kind of map has since come under attack for being simplistic, misleading, and wrong. The main criticism is that real fitness landscapes are multi-dimensional, with many different traits (or many different loci/genes/nucleotides, in the case of a genotype-fitness landscape) making it impossible to visualize the whole thing in its entirety on a piece paper in a book. Thus, fitness landscapes has gotten flak for boiling the truth down to two dimensions, which then misleads the reader into thinking they can get an intuitive feeling for evolution when they really do not.

One such serious criticism was raised by Sergey Gavrilets who (long after Wright's death) gave a mathematical argument that multi-dimensional landscape will have neutral ridges (paths with no change in fitness) between any pair of genotypes, and population can therefore always evolve by neutral evolution, and crossing valleys in the fitness landscape is therefore not necessary (Gavrilet and Gravner, 1997). Valley-crossing is a famous problem in evolutionary biology, but it has been shown that populations can cross valleys routinely (Weissman et al., 2009; Østman et al., 2012), but never mind that for now. So, something profound supposedly happens when the dimensionality goes from two to very large that changes the structure of the landscape so fundamentally that the intuitions that we get from looking at two-dimensional maps do not transfer to higher dimensions.

Wright's last paper was, I have heard, supposed to address the shortcomings of the fitness landscape "metaphor" (not sure if that word was used back then, but it was later used by Kaplan and by Pigliucci who both denounces fitness landscapes following Gavrilets). However, finally coming to the point of what I wanted to say, I have now read that 1988 paper, and as far as I can see, Wright does nothing to discourage the use of fitness landscapes. The first five pages out of eight is spent describing fitness landscapes. In addition to his figure 2 above, he also reuses figures 3 and 4, the latter of which you can see here describing how a population can move through a rugged (i.e., multi-peaked) fitness landscape, including figure 4F, where the population moves from the original, sub-optimal peak in the upper left to the higher peak in the lower right via Wright's own proposed process of Shifting Balance (which involves genetically drift in geographically separated subpopulations and migration between them).



Wright then says this on the sixth page:
I became some-what dissatisfied with the substitution of a two-dimensional surface of selective values for the true pattern, which is multidimensional both among and within loci. I decided that this pattern should be explicitly assumed to underlie the two-dimensional one of the diagram and that its origin should be at whatever peak was under consideration. The contours should be considered as merely symbolic of the complex pattern to a greater extent that before. However, I did not arrive at any changes that should be made in the diagrams as presented.
This seems to me not to recant anything about the utility of fitness landscapes (aka surface of selective values), apart from admitting that two-dimensional landscapes are symbolic of the multi-dimensional nature of them.

At the end of the day, the possibility that there is something fundamentally different between fitness landscapes of low and high dimensions remain an empirical question. Fortunately, two-dimensional diagrams are not the only way the structure of fitness landscapes can be explored (see, e.g., Østman et al., 2010), and, thankfully, experimentalists are getting better and better at measuring large biological fitness landscapes. If it turns our that increasing the number of dimensions retains the multi-peaked picture as depicted above, then I rest my case. Except of course that it is always possible to argue that going from 2 to 20 to 2,000 dimensions is still not enough.

References

Gavrilets S and Gravner J (1997). Percolation on the fitness hypercube and the evolution of reproductive isolation. Journal of theoretical biology, 184 (1), 51-64 PMID: 9039400

Weissman DB, Desai MM, Fisher DS, Feldman MW (2009). The rate at which asexual populations cross fitness valleys. Theoretical population biology, 75 (4), 286-300 PMID: 19285994

Wright S (1988). Surfaces of Selective Value Revisited The American Naturalist, 131(1), pp. 115-123, DOI: 10.1086/284777

Wright S (1931). Evolution in Mendelian populations Genetics (16), pp. 97–159 

Wright S (1982). The shifting balance theory and macroevolution. Annual review of genetics, 16, 1-19 PMID: 6760797

Østman B, Hintze A, and Adami C (2010). Critical properties of complex fitness landscapes Proc. 12th Intern. Conf. on Artificial Life, H. Fellerman et al., eds. (MIT Press, 2010), pp. 126-132 arXiv: 1006.2908v1 

Østman B, Hintze A, and Adami C (2012). Impact of epistasis and pleiotropy on evolutionary adaptation. Proceedings. Biological sciences / The Royal Society, 279 (1727), 247-56 PMID: 21697174