Field of Science

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.

video


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.)

video
video
video

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?

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 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 the 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.