Field of Science

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 landscapesCan 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 isolationJournal 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 macroevolutionAnnual 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 adaptationProceedings. Biological sciences / The Royal Society, 279 (1727), 247-56 PMID: 21697174


Two new books on evolution


Here are two new books on evolution. I wrote chapters for both :o

Predicting Evolution and Visualizing High-Dimensional Fitness Landscapes

Effects of Epistasis and Pleiotropy on Fitness Landscapes

You can download the chapters via those links at least for a while. After that they can always be downloaded from the arXiv.

Both chapters are about fitness landscapes. The first one explains that fitness landscapes is the third "parameter" that is needed to make predictions in evolution. The first two are the population size and the mutation rate. If all the known effects of mutations are known (which implies the fitness landscape), then it is possible to statistically say which direction an evolving population will go and where it will end up. Stochasticity is still important, but one can still make sensible predictions.

Admittedly, both population size and mutation rates can change over time, and so can (and does) the fitness landscape. But we have to start somewhere if we want evolutionary theory to make predictions about the future. Simplify the problem to one that can be solved, rather than including every factor that contributes to the real-world problem.

In the second chapter I argue that ruggedness of fitness landscapes (think of many hills and valleys, rather than a single peak to ascend) is created solely by epistatic interactions between mutations or genes or traits. No other mechanism creates ruggedness, and epistasis always creates ruggedness.

For more about fitness landscapes and epistasis, see
Smooth and rugged fitness landscapes
Can we predict evolution?
Epistasis in evolution
Crossing valleys in fitness landscapes

Life was not created

This brochure from The Watchtower was sent to me by a reddit user, who in turn received it from a friend who believes God chose this place for us and directed evolution. You can download it here.

Here are a few comments on the section that attempts to refute evolution.
Myth 1. Mutations provide the raw materials needed to create new species.
Mutant fruit flies, though malformed, are still fruit flies
This is a stupid semantic argument. Does calling them fruit flies make them the same species? Suppose I choose to call one of these differently looking organisms something else, like "Østman fly", then have we learned anything at all, or are we just playing a semantic game?

The Drosophila fruit flies (there are other fruit flies, btw), such as the famous Drosophila melanogaster, are species members of the genus Drosophila. Thus, if we observe speciation (which we have) within Drosophila, it would be most appropriate to classify that new species within the same genus, thereby still making it a fruit fly. For actual, observed speciation in Drosophila, see this article in the TalkOrigins Archive (e.g., 5.3.5 Sympatric Speciation in Drosophila melanogaster).

Are Great Danes and Chihuahuas the same species? They are still dogs, right? But no matter what we do, we can always just say "they are still dogs". The point is that in a relative short period of time (insanely short, actually), both flies and dogs have evolved enough variation to argue that we have observed speciation. Just imagine what could happen to them if the different variants or flies and dogs were separated and allowed to evolve independently for another 100,000 years or more. If 200 years of changes in dogs can produce such differently looking dogs, imagine what 500 times more of that could produce.

If you can't imagine, let me do it for you: Suppose you had been living in Australia all your life, and suppose no dogs had been seen there for as long as you had lived. Then one day you have the chance to sail to sea with some friends in on a large raft (this is clearly after our present civilization has collapsed), and after getting into a storm, you end up somewhere in Indonesia. There you find two different species of four-legged furry carnivores. One is about a foot in length with really long hair, and the other is tall enough to lick your face without standing on its hind legs. They eat different things, live apart from each other, and do not mate whenever they come into contact with each other. You have absolutely no reason to think that they are the same species, but just to be sure you forcefully mate them with each other, but this never amounts to anything, as they are just too different genetically to impregnate each other, just like humans and chimps. They are different species. However, what you don't know is that only about 115,000 years before they both descended from the same species of wolves.
Mutations can introduce changes in plants—such as this mutant with large flowers—but only within limits
How do they know that it can only produce changes within limits? That is an unverified claim that at most rests on the shallow observation that "plants are still plants". In fact, speciation has been observed numerous times in plants. The "only within limits" argument is pulled out of a creationist's hat. The reason why we observe that evolution only produces new species "within limits" is that the time we are here to observe these events is limited. We simply do not expect that a dog or a hibiscus evolves into something that we would never recognize as dog or hibiscus in our comparatively short lifespans. Mechanistically there is absolutely nothing to prevent organisms to evolve beyond their "kind", except in the minds of humans. The only border between microevolution and macroevolution is time, which is what we as humans do not have enough of.
    So, can mutations cause one species to evolve into a completely new kind of creature? The evidence answers no! Lönnig’s research has led him to the conclusion that “properly defined species have real boundaries that cannot be abolished or transgressed by accidental mutations.”
    Consider the implications of the above facts. If highly trained scientists are unable to produce new species by artificially inducing and selecting favorable mutations, is it likely that an unintelligent process would do a better job? If research shows that mutations cannot transform an original species into an entirely new one, then how, exactly, was macroevolution supposed to have taken place?
Lönnig is saying this without any evidence whatsoever - contrary to evidence, actually. The reason why he is saying it simply that creationists do not want evolution to work because it contradicts the Biblical account of creation. The real lesson to take from the quote above is that the unintelligent processes are actually better at producing new species than humans. Neglecting those processes is not learning, but ignorance.
Myth 2. Natural selection led to the creation of new species.
Indeed, Darwin’s finches are not becoming “anything new.” They are still finches.
And you are still using the same fallacious semantic argument. The point is that natural selection can drive organisms in different directions, and with sustained environmentally driven divergence they can become different species. So in the case of the finches, that selection pressure reversed back, but this again ignores that these processes can take a long time. However, they don't always. One group of a lizard in Crotia, Podarcis sicula, underwent amazing changes in just 30 generations on an isolated island, adapting to a new environment (i.e., different selective pressure). More examples of speciation.
Myth 3. The fossil record documents macroevolutionary changes.
To date, scientists worldwide have unearthed and cataloged some 200 million large fossils and billions of small fossils. Many researchers agree that this vast and detailed record shows that all the major groups of animals appeared suddenly and remained virtually unchanged, with many species disappearing as suddenly as they arrived.
Eeerh, no... Not very many researchers agree that the fossil record shows that all the major clades appeared suddenly. The Cambrian explosion took 70-80 million years! It may well be that species sometimes do change abruptly on geological time-scales, but the more fossils are analyzed, the clearer it becomes that evolution is a gradual process.
Many scientists refuse even to consider the possibility of an intelligent Designer because, as Lewontin writes, “we cannot allow a Divine Foot in the door.”
Lewontin can speak for himself. There are many scientists who can consider the possibility of a designer, myself included, but there is just no evidence for it. None. It is the difference between a conclusion from the evidence vs. a foregone conclusion that comes from a book that some people cannot allow being wrong.
In this regard, sociologist Rodney Stark is quoted in Scientific American as saying: “There’s been 200 years of marketing that if you want to be a scientific person you’ve got to keep your mind free of the fetters of religion.” He further notes that in research universities, “the religious people keep their mouths shut.”
No, the religious do not keep their mouthes shut. The religious do great science, but they do not mix science and religion, because religion has no say in the matter. Ask Kenneth Miller.
Really, belief in evolution is an act of “faith.”
Really, it isn't. Belief in evolution is based solely on the available evidence. Nothing more. Empty your mind of any preconceived notion about the natural world, and just look at the evidence, and the best minds have nearly unanimously come to the conclusion that life evolved. Life appeared and evolves by natural processes, and there is no need to hypothesize that any intelligent being ever interfered. Even scientists who are religious believe in evolution (of course). Just take a look at the Clergy Letter Project.

★  ★  ★ 

I know, I know, I know that the reason creationists can't allow themselves to accept evolution is that it directly contradicts what scripture teaches about our origins. But you cannot refute evolutionary theory if you do not understand it. You cannot refute evolutionary theory by quote-mining scientists. Evolutionary theory is one of the very best supported scientific theories - comparable to the theory of relativity - based on fossil evidence, field observations, laboratory experiments, computer experiments, and a thorough theoretical understanding. And the evidence keeps coming in with new scientific papers published every week. A person can either read scripture and believe it is the infallible word of God, or they can join the rest of the growing amount of people who understand that religion has no place in science.

Smooth and rugged fitness landscapes

ResearchBlogging.orgHere are a couple of maps of different landscapes I just made today. The top landscapes are "smooth" and the bottom ones is "rugged". Smooth means that if you start anywhere on the map, there is a route to the highest point on the map that only goes up. Rugged means that there are multiple peaks. The bottom right is more rugged than the bottom left. Update 11/15/13: the smooth landscape depicted on the top is not un-epistatic. There is epistasis (interaction between gene or mutations), as can be seen if you imagine moving from the bottom left corner to either neighboring corner: fitness doesn't change. However, if you start in the middle of one of the axes and move parallel to the side, then you will cross the hill: fitness does change. In other words, what value one trait is when the other is changed can result in different changes in fitness, which is exactly what epistatic interactions mean.

In evolutionary theory, a fitness landscape is a map where fitness is a function of either the genotype or the phenotype. The genotype is some description of the genetic make-up of an organism. This can be the DNA or a list of the mutations/alleles, and are discrete variables. The phenotype is the complete set of physical and biological features of the organism (e.g., weight, height, wing-span, hair color, number of limbs, blood-type, probability of courting a female, temperature tolerance, etc., etc.). A phenotype component can be either discrete (number of limbs) or continuous (weight). Both the genotype and the phenotype of real organisms are multidimensional, having very many different axes describing each component of the type.


Fitness - aka reproductive success - is then a function of the genotype or phenotype, and is represented by the height in the maps above. An evolving population will seek the highest point it can. In the smooth landscape it will not have trouble finding the highest point on the map (the global peak), because there is only the one. However, when the landscape is rugged, the population may initially ascend a peak that isn't very high, and it can potentially get stuck there. The problem in evolutionary dynamics is then how populations cross the fitness-valleys between peaks in order to ascend adjacent peaks that are higher. Several papers in recent years have addressed this problem (e.g., Weissman et al, 2009; Østman et al., 2012).

Here is the fitness graph of Aspergillus niger, a filamentous fungus. 


The data is taken from Franke et al. (2011). Here the data is fitness as a function of genotype. The data is displayed such that an arbitrary genotype is on the left at zero mutation (call it the wild-type), and every other genotype is displayed a distance away on the x-axis equal to the number of mutations away from the wild-type. Lines between genotypes indicate that the two genotypes differ by only one mutation. Peaks are genotypes whose neighbors (genotypes one mutation away) all have lower fitness, and are displayed in red.

The structure of fitness landscapes is informative about evolutionary dynamics, i.e., how populations behave as they evolve. Just a quick glance at the Aspergillus niger landscape make it apparent that a population could potentially get stuck on one of the lower peaks if it started out way over on the right of the landscape. Whether the population can cross the valleys to the global peak depends on both the population size and the mutation rate. The more mutations in the population (given by the mutation-supply rate, the product of population size and mutation rate), the higher the chance of crossing valleys. See Østman and Adami (2013) for more on how these three parameters enable prediction of evolutionary dynamics, or this post with some more details and a video: Can we predict evolution?

References:

Jasper Franke, Alexander Klözer, J. Arjan G. M. de Visser, Joachim Krug (2011). Evolutionary accessibility of mutational pathways PLoS Computational Biology 7 (8) e1002134 (2011) arXiv: 1103.2479v2

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.

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


Østman B, Adami C (2013). Predicting evolution and visualizing high-dimensional fitness landscapesTo appear in "Recent Advances in the Theory and Application of Fitness Landscapes" (A. Engelbrecht and H. Richter, eds.). Springer Series in Emergence, Complexity, and Computation, 2013.




Reddit AMA FAQ

I did a Reddit/r/IAmA AMA yesterday and got a huge amount of questions. Some of them were repeats, so I post them here with answers. I'm planning to do another AMA perhaps next month, so this can serve as a reference.

Update 11/12/13: Randy's interview about this AMA is featured on BEACON's blog.




Q. What came first the chicken or the egg?


A. The egg. All chicken start out as eggs, but eggs evolved long before birds. Lots of animals start life as hard shelled eggs, including of course dinosaurs and reptiles, which birds evolved from. So when the first chicken was born to non-chicken parents (though it is hard to say when that would be, even if we know every chicken ancestor) it came from an egg, just like its parents did. The egg is also the earliest developmental stage, so therefore comes first in that sense as well.


Q. Are you religious?


A. No. I am not religious and I have no faith. I am atheist with respect to any gods that I have heard of. I have been non-religious since I started to think about it as a child. My parents did not raise me with religious beliefs.


Q. Are humans still evolving?


A. We are not done evolving. We still evolve biologically, though there are some aspects of humans life that have been taken over by cultural evolution. Just to mention one prominent aspect: medicine has alleviated many selection pressures. For much of our history a large factor in how we evolved was diseases. Diseases is a very strong selection pressure for evolving resistance. We are now resistant to many diseases that previously killed us, and yet when new ones arise today, we can fight back with medicine. For example, we don't need to succumb to HIV/AIDS, such that only the few that by chance are lucky to be resistant will survive, while everyone else dies (which incidentally is an excellent example of how selection works). As a result in part of medicine (particularly improvements in hygiene), the human population is now as large as it is. However, most people who argue that humans have stopped evolving seem to not have understood 1) that the increase in our population size leads to an increase in genetic diversity, which is the fuel for evolution, and 2) that evolution takes time, and there will come a time (perhaps in hundreds of thousands of years, but I am not so optimistic) when things will change, and the environment will again favor some human subpopulation over others. You can read more about this from my colleague Madhusudan Katti in reply to the sad claim from David Attenborough's that humans are no longer evolving. http://www.thehindu.com/sci-tech/sorry-attenborough-humans-still-evolve-by-natural-selection/article5141928.ece


Q. What do you think of the Aquatic Ape theory?


A. The aquatic ape theory is not plausible. I do not think humans need to have been semi-aquatic for a while in order to look the way we do (little hair, bipedal, and I forget what else they claim is evidence of it). Tim White once in 2009 told me and Daniel Dennett (who at the time liked the theory) that if it was true, then certain isotopes should be detectable in our bones, which they are not. I don't know the details of this, but can say that it is not a theory that many evolutionary biologists take seriously.


Q. How do you deal with creationists?


A. I start by being as rational as possible, answering their questions and focusing on the biology rather than their religion (which I don't really care about). As long as they try to listen, and acknowledge that I probably know more about it than they do, then we can have a conversation. If and when they start lecturing me, then I quit, as I have no patience for that. I focus on explaining that there is overwhelming empirical evidence for evolution, and give example of what some of it is. I don't have the most patience with people who think one book is all you need to read to learn about the world, though.


Q. Why did you become an evolutionary biologist?


A. I was looking around for a programming job in Santa Barbara, and one professor, Todd Oakley, said that he needed one, but that I should become a graduate student instead. So I accepted. This was extremely lucky, as I had been interested in evolutionary biology for a few years before that. I had even purchased Douglas Futuyma's textbook Evolutionary Biology to read in my spare time.


Q. How much money do you make as a scientist?


A. Not enough. I am a postdoc, which is the job you take after you get your PhD and before you become a professor. Postdocs make between $35 and $55 per year (in the United States), typically between $40k and $50k. Professors make more, up to somewhere between one and two hundred thousand per year.


Q. Have we found the missing link?


A. It's called "transitional fossils", and we have found a plethora of those: http://en.wikipedia.org/wiki/List_of_transitional_fossils


Q. Any advice for an aspiring biologist?


A. Go to college. Read as much as you can muster. Read widely rather than deeply, at least in the first few years. Go to seminars even if you don't think that the talk is about something you are very interested in. You may still learn something, and you may find new interests. And don't be afraid of not understanding everything. No one does, even professors. Discuss everything with your peers. Enjoy it - it's going to be so much fun, intellectually and socially.


Q. Do you find it difficult to get funding for your research?


A. I am a postdoc, so at this stage in my career I don't have to worry too much about applying for funding myself. But yes, generally it is very difficult, as a lot of researchers compete for very little money. The situation is quite bad these years, and applying for grants is the thing I worry the most about for my future. I think the most important contribution from evolutionary biology is simply that it explains our origins, which I think is very important for our curious species. But evolution is also becoming more and more important in medicine and engineering, where evolution explains antibiotic and antiviral resistance , and allow engineers to build better cars, antennae, and other things.


Q. What authors would you recommend for a non-scientist interested in evolutionary biology?


A. Stephen J Gould (mostly his essays from the Natural History magazine, which have been collected in a number of books).

Richard Dawkins (The Selfish Gene, Th Extended Phenotype, Climbing Mount Improbable, and more).
Carl Zimmer (he writes a column for The New York Times, and is the best journalist writing about evolution, in my opinion - and many evolutionary biologists I know would agree. He also wrote a highly acclaimed textbook for undergrads: The Tangled Bank).
Neil Shubin (Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body).
Jerry Coyne (Why Evolution is True).
EO Wilson (Naturalist).
Donald Prothero (Evolution: What the Fossils Say and Why It Matters).

Q. If we found life on another planet similar to earth, do you think the animals would be recognizable? 

A. I think they would be similar to something here on Earth, which has an incredible variety of species.

Q. What is your favorite animal?


A. Cheetah. And corvids, because they are so intelligent and creative (which is largely the same thing). Prehistoric: Argentinosaurus. For evolution: A croatian lizard, Podarcis sicula. Read more about the lizard in this paper: Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource.


Q. What is the definition of a species?


A. The most common definition used for sexual species is the Biological Species Concept, coined by Ernst Mayr. It says that two populations are different species if they are reproductively isolated from each other. There are other definitions, but this is the most widely used one when we aren't talking about species that are mostly asexual, such as bacteria, in which case I prefer to use the Ecological Species Concept by Van Valen (1976), which states that a species is a group that occupies a distinct nice (i.e., a unique way of life): "A species is a lineage (or a closely related set of lineages) which occupies an adaptive zone minimally different from that of any other lineage in its range and which evolves separately from all lineages outside its range." The paper is titled Ecological Species, Multispecies, and Oaks. Best title ever.


When house cat and bobcat split from each other, reproductive isolation probably took a while to occur. So for some period of time and evolutionary biologist would have a hard time figuring out if and when they became different species, if they only use the BSC.


Q. Is there a gene for homosexuality?


A. There is no evidence of such a gene, and also only little evidence that homosexuality is heritable in a significant way (e.g., most homosexuals being born from heterosexuals, but see comment by uyedaj below). That doesn't mean that homosexuality is a choice, any more than heterosexuality is ("when did you choose to become heterosexual?"), but it is not likely tied to any specific gene. That said, we don't know what determines our sexuality.


Q. How come there are no other species as intelligent as we are?

A. Why would you expect other species as intelligent as we are? I have been thinking about this for a while, and one answer has to do with competition between species who share similar niches, which is conceivable when they are both intelligent humanoids. Neanderthals were probably pretty intelligent, more so than any other non-human animal (had slightly bigger brains than we do, though that doesn't imply higher intelligence).

Another answer may be that someone has to be the most intelligent. You could equally well ask why there are no animals as fast as the cheetah, or why no other animals has trunks as long as those of the African elephant. You would perhaps be somewhat amazed if there were two different species who were equally fast and faster than all others. That would be some coincidence, no?

Yet another reason could be that it may be really difficult to evolve to our level of intelligence. Perhaps it is short of a miracle that any species are as intelligent as we are. Maybe there is life on many other planets, but it is super rare that any of those species are more intelligent than a pig. I don't think that is a likely answer, but we don't know.