Mapping fitness: landscapes, topographic maps, and Seattle

A topographical fitness map is smplistic. Creationists look at ti and ask how evolutionary travels between the peaks when it must travel downward between them.

If we represent such a map more realistically in dozens or even hundreds of dimensions, there are no such things as "peaks" and "valleys." (Ask a mathematician.) For more than just a few dimensions, there is always a way to move upward in at least one dimension.

Secondly, the fitness landscape changes in time. It is not only possible but likely that what is now a peak will become a slope that leads upward toward a new peak, even in a few dimensions.

Representing a fitness landscape as a static 2-dimensional map is deceiving.

While agreeing with Olorin, I'll point out that at least two times that I'm aware of, experiments show that a mutation that reduces fitness ultimately led to a variation that was waaay more efficient than the original.

So, within that simplistic frame, a deleterious mutation can actually be useful, if it's required to 'traverse' to a higher peak on the fitness landscape.

My understanding of fitness landscapes is that in real life they change all the time -- finch beak length changing year-by-year as droughts or rains come in is a good example -- and also the process of adapting to the fitness landscape changes the landscape itself (e.g. foxes getting more efficient at hunting rabbits changes the population dynamics). I predict that this will be a fertile area of research for some time!

Thanks for the references. I found the first one particularly interesting.

It's great to know that creationists are finally getting around to doing real science and rigorously testing their, ... what? Wait ... never mind.

Oh well, at least I'm sure they will read these papers with interest and ... what? Wait, ... never mind again.

Olorin is right that the landscape metaphor can be misleading when misused (intentionally or not), but wrong to suggest that it is inherently deceiving. Olorin should read the Carneiro & Hartl paper, especially the last paragraph. Heck, everyone should read that last paragraph (or, better, the whole paper) before wading into discussions of adaptive landscapes. Suffice it to say that Olorin's comments are accurate, but as criticisms of the metaphor or of the topic at hand, they are simplistic.

As a slightly off-topic comment, I love how the Carneiro and Hartl paper puts the lie to Dembksi's interminable invocation of evolution as random search in his recent stuff with Marks.

The (deliberate) misunderstanding of a fitness landscape, it appears to me, led Dembski to believe there was a Target (tm) out there that organisms strived to find. Foolishness, but he wrote a book trying to prove that Fool's Gold point. Of course, there is no target.

Furthermore, the landscape is dynamic, changing every moment. To me it's more akin to an equilibrium where quantities that shift on one end of the equation affect products on the other, achieving balance. Simplistic in the biological sense, I realize, but in concept I think the same. Thus a local maximum or minimum might be OK, as opposed to one that is "better", but OK is good enough for today and hopefully there's a tomorrow.

Great post Steve and am glad you are doing a fine job illustrating for most of the PT readership what is meant by an adaptive landscape. In the past I have used the topographic map analogy myself (appropriate since I have a background in geology), but I have rarely seen it presented in as lucid a manner as you have done.

DS said: Thanks for the references. I found the first one particularly interesting. It's great to know that creationists are finally getting around to doing real science and rigorously testing their, ... what? Wait ... never mind. Oh well, at least I'm sure they will read these papers with interest and ... what? Wait, ... never mind again.

The Hartl paper gives the reference for Wright's biography. I highly recommend it. It fits perfectly well with other fascinating science biographies from the early 20th century.

All this fitness landscape stuff has the same problem as the fictional supply and demand curves in economics. You have to understand that fitness is a vector quantity, not a scalar. So, in reality, fitness maps do not exist. They are a scalar approximation to a vector valued function, and a very high-dimensional vector at that.

The truly amazing thing is that these fictions, so far from any reality, have any usefulness at all. But they are definitely fictions, so if one obtains any questionable results at all, one would be wise to abandon these results immediately in favor of facts.

Renee Jones said: All this fitness landscape stuff has the same problem as the fictional supply and demand curves in economics. You have to understand that fitness is a vector quantity, not a scalar. So, in reality, fitness maps do not exist. They are a scalar approximation to a vector valued function, and a very high-dimensional vector at that. The truly amazing thing is that these fictions, so far from any reality, have any usefulness at all. But they are definitely fictions, so if one obtains any questionable results at all, one would be wise to abandon these results immediately in favor of facts.

Mike and Renee, I suspect that Carneiro and Hartl had objections like yours in mind when they wrapped up their paper. They could have added something about the difference between "metaphor" and "fiction" but they might have thought that should be obvious.

Steve, The question of the shape of evolutionary trajectories does not need to wait on our technical skill in biology to be investigated well. Genetic algorithms are evolution, just as much wet biology. Experiments with GA show these trajectories quite well, across all kinds of landscapes, including noisy, deceptive, and time-varying landscapes.

I've always thought the analogy works better as a seascape than as a landscape. In fact, David Merrell published book a book on the concept in 1994: "The Adaptive Seascape"

Dave Wisker said: I've always thought the analogy works better as a seascape than as a landscape. In fact, David Merrell published book a book on the concept in 1994: "The Adaptive Seascape"

You have to understand that fitness is a vector quantity, not a scalar.

If we represent such a map more realistically in dozens or even hundreds of dimensions, there are no such things as “peaks” and “valleys.” (Ask a mathematician.) For more than just a few dimensions, there is always a way to move upward in at least one dimension.

I'm seeing some statements I disagree with:

1. Steve Matheson, each point on the Wright diagram is not necessarily a different genotype, or even a different allele. The diagram is vague, but usually adaptive surfaces are plotted against gene frequencies, so we have gene frequencies at two loci in a 2-dimensional diagram.

2. I agree with Bjorn Østman contra Renee Jones that fitness is (in all usual models) a scalar number.

3. Also I agree with Østman that Olorin is not justified in saying that there is always a way uphill if one is in high dimensions. Just ask a biologist.

A story somewhat off these points: around 1980 I sent Sewall Wright a preprint of a paper defending one of his models against some criticism. He sent back a reprint of the 1932 International Congress of Genetics paper (the one containing the figure in this posting). I was astonished and was sure I must have received one of the last few precious reprints. Later I heard of a student getting another one, and I got suspicious. I asked Will Provine. He said Wright proudly had that paper reprinted many times, and when Wright died will said there was a large stack of them remaining.

Of course all these models are oversimplifications, but they do help us to understand the messy reality.

Oops, apologies to “Bjorn” who is really Bjørn.

Creationists look at ti and ask how evolutionary travels between the peaks when it must travel downward between them.

Bjørn Østman said:

You have to understand that fitness is a vector quantity, not a scalar.

Right.... fitness is not a number, but a vector. That makes a lot of sense in... what way, exactly? But seriously, fitness is indeed a scalar that describes a single measure of reproductive fitness.

If we represent such a map more realistically in dozens or even hundreds of dimensions, there are no such things as “peaks” and “valleys.” (Ask a mathematician.) For more than just a few dimensions, there is always a way to move upward in at least one dimension.

What?! Utter BS. Whether a landscape contains peaks and valleys is not a function of the dimensionality, but of the amount of interaction between the dimensions (epistasis). Unless there is no epistasis whatsoever, the landscape will be epistatic, and there will be local and suboptimal peaks. As for fitness landscapes being metaphors... of course they are. They are models of reality, just like any other component of any other theory is. Forgive me for pointing to two of my own papers on the subject: Impact of Epistasis and Pleiotropy on Evolutionary Adaptation Critical properties of complex fitness landscapes

These networks undergo a percolation phase transition as a function of minimum peak height, which indicates that evolutionary trajectories that take no more than two mutations to shift from peak to peak can span the entire genetic space. These networks have implications for evolution in rugged landscapes, allowing adaptation to proceed after a local fitness peak has been ascended.

Mike Elzinga said: What Renee Jones and I were thinking is that the fitness of an organism can be described by a set of specific values that describe the current state of the organism. And yes, the organism sits in a local quasi-stable point in that multidimensional space just long enough to acquire a description as a specific organism (or state).

But each of the components of the vector pointing to that state is influenced by many factors, including what is going on with other components (hence, my comment about the vectors not being a linearly independent set or not being able to span the space as the dimensionality increases with increasing complexity).

Percolation is another term used in physics. While one can picture specific examples of water seeping into sand and forming more and more dendritic pathways as it goes, more generally, it refers to a set of branching pathways conecting one state of a system to another.

Bjørn Østman said:

Mike Elzinga said: What Renee Jones and I were thinking is that the fitness of an organism can be described by a set of specific values that describe the current state of the organism.

Hmm. What if I told you that temperature is really a vector, because the state of the system is determined by the interaction of many components? Makes about as little sense.

Bjørn Østman said: If you really want to build bridges, please explain what you mean by "just long enough to acquire a description as a specific organism."

Hmm. What if I told you that temperature is really a vector, because the state of the system is determined by the interaction of many components? Makes about as little sense.

We did indeed borrow the concept from physics, of course. If you’re interested, here’s a paper about the similarity between evolutionary dynamics and thermodynamics: The application of statistical physics to evolutionary biology.

Agree. Fitness is a scalar which is a function of all the variables that indicate the state of the organism.

Bjørn Østman said: We did indeed borrow the concept from physics, of course. If you're interested, here's a paper about the similarity between evolutionary dynamics and thermodynamics: The application of statistical physics to evolutionary biology.

Mike Elzinga said:

Agree. Fitness is a scalar which is a function of all the variables that indicate the state of the organism.

Yes, it could be described as the magnitude of a resultant vector. This is the same kind of usage found in quantum mechanics in which the magnitude of a vector has a physical meaning, but the components of that vector are subject to underlying physical states that change the length of the resultant through time under the action of some kind of Hamiltonian.

Joe Felsenstein said: Look, suppose you wrote a big description of the state of an automobile. Is the speed of the car the length of that vector? Of course not.

Mike Elzinga said: Fitness perhaps corresponds to a concept of a physical system that gives it a higher probability of settling-in to changes in potential. There are various terms from physics and engineering, such as pliability, compliance, conductance, etc. that reflect the fact that a system can easily reach an adjacent state from its current state.

Joe Felsenstein said: But there may be no easy correspondence between the molecular energy calculations and the fitness. One individual might be of higher fitness because it was smaller than the other, and that might be just because there were more small food items around than larger ones. I don't think that will be easy to predict from the molecular energy potentials. Of course, it is never a bad idea to try to connect these concepts.

Mike Elzinga said: But the idea of meta-stable states goes back to potential wells in a more general sense. If one observes any tendency of a system to remain in a somewhat stable configuration (meaning that it has a tendency to persist for a “significant” period of time), then we tend to see it as a system nestled in a local minimum that is a phenomenological manifestation of all the “forces” returning the system to this current configuration. Now forces in physics are derivatives (negative gradients) of potentials relative to spatial location. But one can speak of “generalized forces” that are the gradients of some other parameter of the system. These generalized forces and the parameters from which they are derived are usually called “conjugate pairs.” Usually these find their way back to the more fundamental forces - i.e., they are not metaphorical - but most often it becomes easier and more instructive to speak of the more complex system in those terms. So I would expect that further development of the concepts of evolution could benefit from finding such conjugate pairs. Since these are physical/chemical systems immersed in a temperature bath, I would suspect such pairs could be found once such systems are seen in a different perspective. If such pairs are found and tend to be fairly robust descriptions of living systems in general, then perhaps they could be linked to physics and chemistry more clearly. There are many examples of these kinds of processes occurring in physics (superconductivity comes to mind most immediately).

Joe Felsenstein said: Well, maybe. Two frogs sit by a pond. One does nothing as insects fly by. The other is more reactive, when it sees an insect flying by, it flicks out its tongue and eats it. The former is more stable. The latter is better-fed.

Steve Matheson, each point on the Wright diagram is not necessarily a different genotype, or even a different allele. The diagram is vague, but usually adaptive surfaces are plotted against gene frequencies, so we have gene frequencies at two loci in a 2-dimensional diagram.

Steve Matheson said: Joe Felsenstein, aka "The Resident Expert," wrote:

Steve Matheson, each point on the Wright diagram is not necessarily a different genotype, or even a different allele. The diagram is vague, but usually adaptive surfaces are plotted against gene frequencies, so we have gene frequencies at two loci in a 2-dimensional diagram.

Thanks for the clarification, Joe. I know that landscape diagrams like Wright's often depict population-level walks (speaking colloquially here), so that points on the landscape represent allele/gene frequencies in populations. I was hoping the general term "variants" and my deliberate focus on general applications of landscape metaphors would communicate the flexibility of the tool, especially since the work I will discuss does involve fitness/function of specific and individually identifiable identifiable variants. In any case, I'm glad you're peer-reviewing our work here; if nothing else it exhibits the kind of intellectual accountability we demand of creationist think tanks.

Steve Matheson said: In any case, I'm glad you're peer-reviewing our work here; if nothing else it exhibits the kind of intellectual accountability we demand of creationist think tanks.

With the complex systems in biology, one has to know much more, keep track of many more interrelationships, and discern patterns that are far more subtle than those found in chemistry and physics.

Joe isn’t just “The Resident Expert”. When I was in graduate school, I read papers authored (or co-authored) by him on molecular systematics. We are fortunate to have someone of his stature - based on his work in evolutionary genetics and molecular systematics - willing to devote time to online commentary here at Panda’s Thumb.

Steve Matheson said: John Kwok writes:

Joe isn’t just “The Resident Expert”. When I was in graduate school, I read papers authored (or co-authored) by him on molecular systematics. We are fortunate to have someone of his stature - based on his work in evolutionary genetics and molecular systematics - willing to devote time to online commentary here at Panda’s Thumb.

Well, that's precisely what I meant. I hope no one else thought that my dubbing him "The Resident Expert" was in any way sarcastic. You're right that we're lucky to have him hanging with us.

Thanks, folks, flattery will get you everywhere.

Let me clarify a little about adaptive topographies. Actually, as Steve Matheson implies, they do vary somewhat in their meaning. Here are three versions:

1. Mean fitness plotted as a function of gene frequency, usually one axis per locus.

2. Mean fitness plotted as a function of mean phenotype, where there is one character per axis, with the character varying because of variation at many loci, and implicitly the variances of the characters not changing as their population means change.

3. In some of Sewall Wright's mid-1930s papers, he makes a sort of lattice, with a vertical dimension that is fitness, and the points individual genotypes. Not explicitly an adaptive surface but close.

It's a good teaching metaphor, but you have to watch out. The first one ignores linkage disequilibrium, implicitly. The second doesn't convey whether the characters covary within the population, though they might. The third is not really continuous in space, and the population does not necessarily climb it.

I have a (quite probably) dumb question.

How does one determine the “closeness” of two genotypes or phenotypes independently of fitness? In other words, if fitness comes far down a chain of events after a change in genotype, how would one know without knowing fitness where to place a genotype – or even a phenotype, for that matter – on a horizontal axis?

I can see taking a genotype that is known to have a high fitness as the location of a fitness peak, but how does one know where to place other genotypes on such a landscape without knowing their fitness ahead of time?

Or is the point to use fitness to map the closeness of genotypes or phenotypes?

Mike Elzinga said: How does one determine the “closeness” of two genotypes or phenotypes independently of fitness? In other words, if fitness comes far down a chain of events after a change in genotype, how would one know without knowing fitness where to place a genotype – or even a phenotype, for that matter – on a horizontal axis? I can see taking a genotype that is known to have a high fitness as the location of a fitness peak, but how does one know where to place other genotypes on such a landscape without knowing their fitness ahead of time? Or is the point to use fitness to map the closeness of genotypes or phenotypes?

Whether the dimensions of a "landscape" are genotypes or allele frequencies is profoundly important and signals deep and unresolved issues in evolutionary thinking. If the dimensions are allele frequencies, then movement on the "landscape" poses no problems and makes perfect sense: it is movement of a population by changes in its allelic frequencies. In a population of size N, the smallest shift is 1 part in N. If N is large, these are infinitesimal shifts. A shift in any direction can be accomplished simply by changing the numbers of individuals with each type of allele. It is also evident that any of the population-genetic "forces" (selection, drift, mutation, migration) in principle, could cause any conceivable shift.

In other words, the metaphor is coherent and relevant with respect to a particular way of looking at change and the "forces" that cause it.

Bringing in the idea of new mutations, and discrete "genotype" dimensions, confuses things in a way that the metaphor simply cannot survive. It was designed for a different way of thinking about evolution that has gone down the memory hole.

What was that way of thinking? In a paper in 1996, Patrick Philips wrote about "phase 0" of the shifting balance process. He called it "phase 0" because it represents a prior stage that Wright had not included. Phase 0 consists of waiting for a new mutation. Wright did not include this phase because, in his view, it was not important to understand the dynamics of evolution.

The architects of the Modern Synthesis simply did not think of evolution as a process of the random occurrence of a new mutation, followed by its acceptance or rejection (by selection and drift in combination). This would have made them "mutationists" like TH Morgan. Morgan's view was reasonable, but the architects of the Modern Synthesis deliberately rejected it as contrary to their Darwinian beliefs. They believed each species has a "gene pool" that automagically provides abundant infinitesimal variation, so that "selection" never has to "wait for a new mutation". On this basis, they redefined "evolution" to mean "shifting gene frequencies", the way it is defined implicitly by Wright's metaphor. I have provided extensive documentary evidence of this theory in Stoltzfus, 2006 (Evol & Dev paper).

Mutationism re-entered evolutionary thinking with studies on molecular evolution. Evolutionary theory has not come to grips with its implications. This is a case in point.

Arlin

(correction) smallest shift is 1 part in N for haploids, or 1 part in 2N for diploids. Please pardon my prokaryotic bias.

arlin

Arlin said: Whether the dimensions of a "landscape" are genotypes or allele frequencies is profoundly important and signals deep and unresolved issues in evolutionary thinking. Arlin

Arlin Stolzfus said: Whether the dimensions of a "landscape" are genotypes or allele frequencies is profoundly important and signals deep and unresolved issues in evolutionary thinking. ... Bringing in the idea of new mutations, and discrete "genotype" dimensions, confuses things in a way that the metaphor simply cannot survive. It was designed for a different way of thinking about evolution that has gone down the memory hole.

Arlin also said: What was that way of thinking? In a paper in 1996, Patrick Philips wrote about "phase 0" of the shifting balance process. He called it "phase 0" because it represents a prior stage that Wright had not included. Phase 0 consists of waiting for a new mutation. Wright did not include this phase because, in his view, it was not important to understand the dynamics of evolution. ... Mutationism re-entered evolutionary thinking with studies on molecular evolution. Evolutionary theory has not come to grips with its implications. This is a case in point.

I agree that this is a good synopsis of some key issues.

Another issue, relevant to the "landscape" discussion, has to do with "forces". According to the textbooks, evolutionary theory is a theory of population-genetic "forces", and (according to philosophers, at least) this is what makes modern evolutionary theory so rigorous.

This conception of forces depends on the idea of a common currency of causation. In physics, the common currency is the capacity to displace a particle in space over time. Various forces can do this. This puts them all on the same playing field. Even though each force is distinct, their instantaneous effects on a particle can be combined and separated. We can compare them directly and quantitatively-- which one is stronger or weaker in a given case, how each force affects a trajectory.

The "forces" conception in the Modern Synthesis is similar, but the common currency is the capacity to shift an allele frequency. Evolution is "shifting gene frequencies", so anything that can "shift frequencies" is an "evolutionary force". This is what puts all the "forces" in the same role and allows questions about comparing and combining forces.

The rub is that mutation is the only process that can shift an allele frequency from 0 to 1/N (1/2N for diploids). This was not a problem in the Modern Synthesis, because new mutations weren't important-- in the MS, "evolution" is defined as "shifting gene frequencies" in the "gene pool", which supplies abundant variation in all directions. The common playing field for the forces of "evolution" is the domain of frequencies between 1/N and 1, like in the original Wrightian landscape.

Once one recognizes the importance of new mutations in evolution, this "forces" conception becomes inadequate.

Arlin

Arlin said: Another issue, relevant to the "landscape" discussion, has to do with "forces". According to the textbooks, evolutionary theory is a theory of population-genetic "forces", and (according to philosophers, at least) this is what makes modern evolutionary theory so rigorous. Arlin

I think this is partly the reason ID/creationists like to attack biology more than physics. In physics it is much easier to shoot them down.

If physics directly conflicted with the foundation of their faith, they’d be jumping up and down

Henry J said:

If physics directly conflicted with the foundation of their faith, they’d be jumping up and down

radiometric dating?

Flint said: And as you're aware, they often say things about biology that are so obviously wrong that even the simplest non-biologist can see it. Doesn't deter them a bit. Faith provides one model, facts provide another - and the faith model is the only one against which any claim is compared.

biology is intrinsically a more complex field filled with empirical observations and relationships that have not found their way back to solid mathematical theories as is the case with physics.

Arlin --

Perhaps this is exactly what you have been saying about the adaptive topographies, but it strikes me that the one that connects genotypes has a natural role in a mutationist approach. If we assume (for the sake of simplicity) that fitnesses of heterozygotes are somewhere in between those of the corresponding homozygotes, and we consider only the homozygotes (and hence only the haplotypes, in effect) we can have a diagram that has fully homozygous genotypes, connected whenever a single locus changes from homozygosity for one allele to homozygosity for another.

Thus we would connect AABBccDD with AAbbccDD but not directly with aaBBccdd, which would be two steps away. Each time a population makes a substitution (such as, here, of b for B) it would make one move in that graph. The vertical dimension would be fitness and that would show whether each move climbed uphill. That seems to be a natural structure for a mutationist approach.

Joe--

In general, yes. If we have a discretized "space" like "sequence space" or "genotype space", we may as well think of it as a graph in which nodes are possible states of the evolving system, and edges are evolutionary changes.

My earlier point-- and I suspect we have moved beyond this already-- is that this breaks the "landscape" metaphor. The mojo of the "moving on a landscape" metaphor depends on the fact that space is continuous and homogeneous, so that a movement of distance d is possible for any value of d, and a movement of d from point (x,y) is (in some sense) equivalent to that from (x',y'). When I take a walk, I can take a small step or a big step, and I will go just as far regardless of the direction I choose. This remains true (in a sense) on a Wrightian landscape of allele frequencies (its all a matter of adding and removing some numbers of individuals with certain genotypes), but not on a landscape of genotypes.

In any case, getting back to Joe's model, evolution will trace a path through the graph, based on events of evolutionary change that move the system from one node to another. I don't agree that its very helpful to say that changes via a double mutation are impossible-- they simply occur at a lower rate. But that's a separate issue.

Whether or not this is a mutationist view depends on how we treat the rates or probabilities of movements between nodes. I've never seen anyone try to work this out for a neo-Darwinian view, where "selection" and "chance" determine outcomes, within what is allowed by "constraints".

But for a (simplified) mutationist view, we could just render these probabilities based on a mutation-fixation process with a rate of the form u * N * Prob_fixation. I've used this conception before in simulations of adaptation. Its also the basis for the "mutational landscape" model used in the parallel evolution study by Rokyta, et al, hailed by Bull & Otto (http://www.nature.com/ng/journal/v37/n4/full/ng0405-342.html) as "the first empirical test of an evolutionary theory".

Arlin

As has been pointed out elsewhere on PT, I don't think that the complexity of biology or geology wrt physics is the main difficulty that makes them amenable to attack. Rather, it is time. You can "do" physics in a high school science lab. You can see the changes to physical systems in "real time" (ie, "human time"). You can't "do" biology or geology in "real time". You can sample the current state of a small point in the system, but you can't "see" the changes in the system over geologic time. More than the complexity, that seems to be a more fundamental psychological barrier to comprehension.

Please forgive the naive question. I'm no expert in either physics or biology, and didn't do well in statistics. But this is the first I've heard of a "mutationist", as a concept distinct from the Modern Synthesis (MS).

If I understand what you're saying, the MS describes selection "pressures" that operate on an existing (perhaps fixed?) set of variations within a population, whereas a Mutationist would want to include in that description the change over time of the set of available mutations within the population. Is that (very roughly) the distinction being described?

(BTW, I much prefer such discussions where I'm just barely able to keep up, to those typical troll-lead PT "discussions". There's only a small, finite amount that one can learn from a one-dimensional point of view. :-) Thanks.)

Its not a naive question. The distinction of fixtation-of-new-mutations vs. shifting gene frequencies is a good start. The architects of the MS said very clearly that evolution works in the latter way and not in the former, even though they could not possibly have known that for certain.

But ultimately its more complex than that. Indeed, why would the architects of the MS advocate a position they could not prove? The answer is that they were committed Darwinians. The MS represents a set of discretionary Darwinian doctrines-- discretionary in the sense of not being required by the facts. In my analysis of original sources (your mileage may vary), the doctrines that distinguish mutationism from the MS relate to discontinuity, creativity, direction, and initiative. For instance, the mutationists said that evolutionary change was *initiated* by a new mutation, where the MS architects said that it was *initiated* by a change in environment that brings on selection of available variation at many loci. This idea of initiative affects one's views on whether the dynamics of evolution are determined externally or (at least partly) internally.

What some might find more contentious (assuming that anyone is paying attention) is my argument that these doctrines remain deeply entrenched in evolutionary thinking, in ways that experts have not yet learned to recognize, and in ways that we need to change in order to move ahead.

For instance, "forces" are an example. The results from the work by Rokyta, et al that I cited above reveal an excess of parallel evolution that is readily understandable as an effect of a mutational bias in the origin of new alleles. But this same effect cannot be understood in terms of classic "forces".

You won't find any knowledgeable evolutionary geneticist who would dismiss the study by Rokyta, et al.

But at the same time, there has been no deep thought about how this study challenges prevailing concepts. What we tend to get in response to such results are IMHO very silly and unsatisfactory invocations of "contingency" or "chance". Several authors absurdly refer to the underlying mutationist models as models of "Darwinian" adaptation.

So, in spite of cutting-edge research published in a top journal that-- if anyone bothered to think it through-- would undercut the "forces" view, you are still going to be taught the "forces" view in your next evolutionary genetics class. You will learn to talk about selection as though it were the creative principle in evolution, because the language for talking about mutation as a creative principle has not been invented.

In a nutshell, this is the current situation: superficially, the evolution community accepts mutationist models of adaptation while referring to them as "Darwinian". But this has had no impact on evolutionary theory, because evolutionist have been lulled by the belief that the MS somehow covers everything. I honestly do not know the extent to which evolutionists truly are devoted to Darwinian doctrines. I know some who aren't devoted to these doctrines, but that continue to use a language of causation designed for a view that they do not accept. All of which is holding us back (IMHO).

sorry for writing such a long post.

Arlin

Arlin, I appreciate your response. I'm not a biologist, but it seems your description hinges on the definition of "evolutionary change".

Mutations happen. Some more, some less. Some have a "noticeable" effect on the organism, some don't. If a mutation has no noticeable effect on the organism, has there been an "evolutionary change"? I imagine that some mutations are reversible, such as most point-mutations. If such a mutation happens, and is later "reversed" or even "corrected", have two "evolutionary changes" occurred?

As for "selection", my limited understanding is that "selection" is based on environmental factors, typically external to the organism. "Selection" can only select from a set of alleles; the set of alleles that exist at the time the "selection" is made. This is, of course, a simplification, as the "selection" process happens over time in a population, and (through mutation) the set of alleles also varies over time in that population, possibly (even likely) in response to the "selection" process itself. I imagine squeezing on a liquid filled balloon (the simpler model), but where the elasticity of the balloon and the malleability of its contents can vary over time, possibly even in response to being squeezed (the more complex, time-varying model), something like non-Newtonian fluids.

Is that sort of what you're getting at wrt fixation-of-new-mutations vs. shifting gene frequencies? From what little I understand, it seems that the "fixation" of new mutations is a specific "path" (if you will) or set of "paths" within a larger space of gene frequencies that are shifting over time. For "evolutionary change" to occur, a mutation has to become stable within the flow of shifting gene frequencies. In terms of transient changes, the mutation at least has to remain stable long enough to have some influence on the flow of gene frequencies. (One transient change enabling another, etc)

How does one view preclude the other? Or rather, how does one view obscure important considerations that the other does not?

Thanks for your help and patience.

Scott F said: it seems your description hinges on the definition of "evolutionary change".

How does one view preclude the other? Or rather, how does one view obscure important considerations that the other does not?

Arlin,
I'll give your paper a try. Thanks.