Mutationism is back

[PhDP]

...well it's not really back. Mutationist hypotheses have been present in the last 50 years. But as most evolutionary biologists were debating about the relevance of the neutral theory, nobody really cared about "mutationists". It's changing, in the last couple of years several strong articles were written about it, especially by Masatoshi Nei;

 

Nei, M. (2007) The new mutation theory of phenotypic evolution. Proc. Natl. Acad. Sci. USA, 104:12235-12242.

 

Nei, M. (2007) Historical perspectives of the above PNAS paper (informal comments).

 

Nei, M. (2005) Selectionism and neutralism in molecular evolution. Mol. Biol. Evol. 22:2318-2342.

 

Another great article was published by Arlin Stoltzfus, but it cannot be accessed by everyone;

 

Stoltzfus, A. 2006. Mutationism and the Dual Causation of Evolutionary Change. Evolution and Development 8: 304-317.

 

Many aspect of neomutationism are controversial and they will probably generate many studies. The Selectionist-Neutralist debate isn't over yet, I think it's fair to say the Mutationist-Selectionist-Neutralist debate will not be solved easily.

 

However there's at least one important (and noncontroversial) point advanced by mutationists; both for historical and mathematical reasons, mutations were often treated as the source of variations, and nothing more. We should get rid of this bias, as we know mutations can impose a direction to evolution (the case of the GC content is a key example). The simple notion; "mutation (variation) + selection = evolution", is simply not accurate in most cases.

[Paralith]

We should get rid of this bias, as we know mutations can impose a direction to evolution (emphasis mine - paralith) (the case of the GC content is a key example).

 

Am I just out of it, or is this not really anything that earth-shattering? It's called historical constraint, and it's something that I learned about in my first class on evolution. There are traits or suites of traits that evolve in such a way that they can't really be "undone," so any further adaptations or changes have to be done within the constraints of those traits. Animals evolved with one head, so at this point in the evolutionary tree it's pretty much assumed they can't evolve to have two. I think calling it "mutations imposing a direction to evolution" is just calling a rose by another name, as it were. I also think it's not necessary to decide which one is more important, mutation or selection. Doesn't evolution require both? Variation and differential selection of that variation?

[foodchain]

...well it's not really back. Mutationist hypotheses have been present in the last 50 years. But as most evolutionary biologists were debating about the relevance of the neutral theory, nobody really cared about "mutationists". It's changing, in the last couple of years several strong articles were written about it, especially by Masatoshi Nei;

 

Those were some very interesting papers to read. I don’t personally understand why there is such a debate on the topic past maybe what is more paramount in regards to time in relation to evolution I guess. The point I think that might be missing is simply comparing aquatic to terrestrial ecosystems. In the case of directed evolution I think it would be somewhat difficult to separate the environment from other factors as to what organisms exist and why. The ocean or aquatic environment obviously has its own environment with different variables then you would fine on land, such as in a forest or a desert environment. That being said I think its easy to see the profound impact such has had on the evolution of life in these ecologies. I think that such studies of gene networks and the impact they hold along with mutation and development for example could easily be studied in cross comparison of aquatic to non aquatic life, and subsequently possibly amphibians, or those that are inbetween somewhat.

 

In one of the papers the remark is made about count of genes responsible for certain function, such as smell, and its higher count in species more prone to use such. I guess a fine question to ask in that is overall if the mutation that lead to such a reliance on smell for survival is merely a product of those genes going in that direction and staying alive or if its a product of the environment more or less making having that a selective advantage. I only think more and more studies of life in those perspectives could answer the question, being natural selection in a sense does not shape but more or less only guarantees survival to what can survive. I though however again see that direction hard pressed to explain really the differences between aquatic and non aquatic life in regards to natural selection. I however also did not see other existing ideas incorporated into a data, such as the concept of the red queen for example, or optimality theory, or simply put why some biological structures in time become non functional vestigial structures, as with whales or blind moles for example, which I think hurts the progress a bit. Simply put those "ideas" if you will also come from what this is, or life in general.

 

If per chance I may have missed the mark and its primarily on mutation to a point only providing really mutation to X other points, I still do not see how that can properly explain life as powerful as natural selection can. Again I think a subtle and easily missed point in much of this is really the time span of evolution. In example I think it would be practically impossible to realistically gauge mutation in evolution over say 5 million years, and on that note of mutation did not have to work via natural selection, one would expect to see I guess for lack of better words aquatic grizzly bears that happen to be grizzly bears or whatever really, or life that has no adaptive value.

[PhDP]

Paralith,

 

I think you should read the articles; it's not about historical constraints. I'm not a mutationist, but...;

 

Doesn't evolution require both? Variation and differential selection of that variation?

 

...that's exactly the problem. That's not evolution; it's just an unrealistic view of evolution. The evolution of X can generally be explained by one of the three major type of evolutionary hypotheses;

 

(1) Mutations (variation) + Stochastic processes + Selection

(2) Mutations (variation) + Stochastic processes

(3) Mutations (variation + direction) + other mechanisms

 

(1) was discovered by Fisher et al. during the synthesis. The importance (and perhaps, prevalence) of (2) was discovered in the 60s. Mutationists argue that (3) is also a very strong force.

 

The point made by several scientists working on these hypotheses (mostly theoretical population geneticist and molecular biologists) is that, even thought (1) is not as dominant as we once thought, very few scientists outside the field even consider the other hypotheses, either because it's much easier to consider only selection or because they just can't understand (2) (which requires good maths) or (3) (which requires a good understanding of genetics). The point made by Nei and Stoltzfus is simply that (3) is important, perhaps the most important force in evolution. You're wrong to reduce mutations to "variations". You can't explain the evolution of the GC content unless you accept that some mutational bias imposes a direction to evolution.

 

I still do not see how that can properly explain life as powerful as natural selection can.

 

I don't think life is explained by natural selection. Natural selection is the best explanation we have for adaptations, but the vast majorities of variations are nonadaptatives. I don’t personally understand why there is such a debate on the topic Well, probably because it's the most important debate going on in evolutionary biology right now. If we want to improve the predictive power of evolutionary biology, we need to know what mechanisms shape life, how they are affected by the environment, and how strong they are compared to the other mechanism.

[pioneer]

The environment is important for determining which mutations will have any value for selective advantage and evolution. An easy experiment to prove this, is to switch a couple of eco-systems. We will move a sub artic eco-system to the Amazon and vice versa. Neither eco-system will be equiped to deal with those new environments, because each environment set constraints for determining which mutations had selective value.

 

Inspite of that, if we look at the basic features, of both sets of plants and animals, there are certain features that still both have in common. All the animals will have one head and two eyes. All the plants have roots and leaves. Both have creatures that fly. The single heart is common to all the animals, etc., These are not environmentally based. They appear to be a logical DNA extrapolation not based on mutations. In other words, the DNA defines a type of molecular potential, which lines genes into a default schema. This basic schema is what mutates within an environment.

 

For example, a two headed animal could have many selective advantages. While one head eats, the other can be on guard, allowing it to escape. The two-headed animal would be better in a fight. It has two sets of teeth and can attack its opponent from two angles at the same time. Although this is a monstrosity, protypes do occur in nature, which shows the genetics can sort of simulate it. Yet, DNA defaulted to one head inspite of random mutations and the possible selective advantage of this strange animal.

 

One may argue that maybe the two heads led to conflicting reactions. One wants to go left and the other right. But selective advantage would cause the two-headed animals that coordinates the best, to get stronger. This suggests, the DNA, by its molecular nature, will produce certain default life structures. When animals ended up with four legs, this was a DNA default. Two legs and two arms was also a default setting.

 

One way to look at it is to use a chemistry analogy. Diamond is a form of carbon that has a tetrahedral structure. This is a default pattern based on the chemical orbtal structure of C, at very particular conditions. If the conditions are not proper for diamond, another default is graphite. If the conditions are not correct for this, then we get carbon soot, etc., If we look at the DNA, as a molecule, lower lifeforms have more variety, i.e., soot, char, charcoal, etc. As it advances we get some graphite and then some diamond. DNA will not form structures like salt crystals, i.e.. two headed animal, because it configurational potential defines defaults.

[CDarwin]

Phil: I'm afraid I'm not quite literate enough to delve understandably into those articles. Are we talking about "mutation pressure" here, where a number of mutations will on their own drive "progressive" evolution? I suppose that would take only with neutral mutations? Enough neutral mutations accumulate so that the organism is mostly defined by them?

 

But selection acts on whole individuals, not just individual traits or genes. Wouldn't a single mutation of selective value or detriment mess the whole "neutral" thing up, because some "neutral" traits would end up getting preferred over others because of the selective value of some of the organisms other traits? It seems like mutation pressure's role in evolution should be reduced because of that.

 

I realize that's a lot of reasoning based on a whole lot of supposition and half-understanding.

[lucaspa]

...well it's not really back. Mutationist hypotheses have been present in the last 50 years.

 

You need to define "mutationist hypotheses"

 

From the Abstract: "However, once the mutations are incorporated

into the genome, they may generate developmental constraints that will affect the future direction of phenotypic evolution.

It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance."

 

Actually, if Nei had looked in the literature, he would have found that it is natural selection that puts on the constraints, not development! Look at the bold. When a trait is under 2 or more separate stabilizing (natural) selection, it is "fixed". It is natural selection that is doing the constraining.

 

EVOLUTION:

G Wagner, Complexity matters. Science, 279, Number 5354 Issue of 20 February 1998, pp. 1158 - 1159

 

Are organisms like liquid droplets, infinitely malleable by the changing forces of evolution, or do they contain a "frozen core"--the Bauplan, or body design, which remains little changed under the varying adaptive pressures a lineage encounters during its history? Until quite recently, these questions have divided evolutionary biologists (as well as philosophers) into two almost nonoverlapping camps. On the one hand are the so-called reductionists, largely recruited from the ranks of population genetics and associated disciplines, who are strongly committed to the adaptationist program of evolutionary biology. This group tends toward a world view in which there are no limits to an organism's variability and its ability to evolve. On the other hand are those biologists who primarily study whole organisms or complex phenotypic traits of organisms. This second group emphasizes the need to understand the constraints on evolutionary change that arise as a consequence of the intrinsic functional and developmental complexity of organisms. On page 1210 of this issue, Waxman and Peck (1) present a new mathematical result that reconciles most of the differences between these two camps. Population genetic equations predict, so they show, that parts of the phenotype effectively "crystallize" as the complexity of systems increase. But what is the problem to which this result is the solution?

 

The intellectual history of the problem goes back to the synthesis of Darwinian evolutionary theory and Mendelian genetics forged by the fathers of modern evolutionary theory, R. A. Fisher, S. Wright, and T. Dobzhansky. Through the marriage of genetics and Darwinism, it became clear that the process of evolution can be understood, or at least described, as changes in gene frequencies over time (2). New genes arise by mutation and are either lost (most likely) or they replace their parental genes, by selection or genetic drift. This, it turns out, is the most elementary level on which evolution can be explained. Consequently, a lot of effort was and continues to be invested in research directed at understanding these elementary processes. This remarkably successful research program has been pursued with the implicit assertion that evolution of real and complex organisms is just more of the same, and that no qualitatively new phenomena emerge as a result of increasing complexity (3). In this view, complexity is fundamentally irrelevant to an understanding of evolution. A corollary of this line of thinking is that all aspects and characters of the organism are variable and constantly changing (although at different rates), and the concept of a "Bauplan" (the body organization characteristic of a larger group of organisms) is an illusion (4).

 

A well-informed minority of organismal biologists, however, never were convinced of this radical view. Theirs is a more pluralistic view: yes, they agree, many characters are highly variable and their differences among species and populations can be understood as adaptations. But at some stages of evolution certain characters effectively "click in" and remain fixed in the descendent group of species (5-7). For instance, the chorda dorsalis (the embryonic precursor of our vertebral column) is absent in invertebrates, variably present in the relatives of vertebrates (ascidians and related groups) and absolutely fixed in vertebrates. The first who most clearly saw a connection between this pattern and increasing complexity was Rupert Riedl in the 1970s (6). He postulated that with increasing complexity some characters become more important because more and more new characters are functionally or developmentally predicated on them. Once such characters have accumulated many "responsibilities," mutational change will be detrimental and thus these characters become evolutionarily fixed. This increasing burden leads to fixation of characters. The problem with this view, however, was that it did not connect well with the then current population genetic theory.

 

Standard population genetic theory supports a liquid genome metaphor. In the balance between mutation and selection, each population settles into a state in which the most fit genotype is always surrounded by a sizable swarm of mutant genotypes buzzing around the best genotype (8), so much so that the concept of wild-type becomes meaningless. Variation is the name of the game. Only the amount of variation depends, in a continuous manner, on the relative strength of stabilizing selection, genetic drift, and mutation. Well, not exactly, according to the report by Waxman and Peck (1), which shows that there is a complexity limit beyond which genes can freeze into a fixed state and where the swarm of genetic variation suddenly disappears like fog in the sun. In the Waxman-Peck model, the complexity limit is reached once the genes affect more than two characters that are under simultaneous stabilizing selection.

To be precise, this freezing phenomenon has been described before (9), but it was seen as an arcane result of mathematical population genetics of uncertain significance and familiar to only a very few specialists. The significance of the present report is that Waxman and Peck have shown that this obscure property of mutation-selection equations has a connection to a generic property of organisms: complexity. Each gene has many effects and functions, each character is functionally connected to multiple others. Since this is the case, the freezing of genetic and phenotypic states is a necessary outcome, just as many organismal biologists have suspected for more than a century."

 

 

However there's at least one important (and noncontroversial) point advanced by mutationists; both for historical and mathematical reasons, mutations were often treated as the source of variations, and nothing more. We should get rid of this bias, as we know mutations can impose a direction to evolution (the case of the GC content is a key example). The simple notion; "mutation (variation) + selection = evolution", is simply not accurate in most cases.

 

It is accurate. GC content can't impose a "direction" to evolution because it is not the GC content that is important: it is the trait. Genes are not the unit of selection; the individual is. So, GC content does not dispose to one set of traits vs another, does it?

[foodchain]

I don't think life is explained by natural selection. Natural selection is the best explanation we have for adaptations, but the vast majorities of variations are nonadaptatives. I don’t personally understand why there is such a debate on the topic Well, probably because it's the most important debate going on in evolutionary biology right now. If we want to improve the predictive power of evolutionary biology, we need to know what mechanisms shape life, how they are affected by the environment, and how strong they are compared to the other mechanism.

 

I think I get where you are going but to simply subtract natural selection from evolution I think would basically shed light on its application really.

 

There is a vast amount of biodiversity alive now and also into the past. A simple example would be microbes in the soil underneath the nuclear site at Hanford Washington. They live in nuclear waste basically, and have adaptations that allow them to do that, without such, well I think it speaks for itself. The idea though is that through mutation or variation they were able to make it, but the fitness of such is relational to the environment. You can find this with just about any specie in any environment. Its not perfect of course, and of course life does go extinct, which again is relational to the environment, such as the existence of the immune system.

[PhDP]

Lucaspa,

 

If you're going, again, to misinterpret everything I say; don't bother replying, I'll do the same. I never said the GC content was imposing a direction, I was talking about mutational directionality and how the GC content was a key example. This explanation is 50 years old; it's hardly a new discovery and I used this example specifically because it's noncontroversial. If you had read his article before saying he should have "looked in the literature", you would have known. How ironic.

 

You need to define "mutationist hypotheses".

 

Mutationist hypotheses; Emphasis on the mutational input

Selectionist hypotheses; Emphasis on positive/balancing selection

Neutralist hypotheses; Emphasis on drift

 

I'm sure you can find longer and more accurate definition in most books on molecular evolution (books by Wen-Hsiung Li are generally very good). Obviously, all hypotheses are true in some circumstances; the question is; which one is more prevalent.

 

Foodchain,

 

I don't want to subtract natural selection; I want evolutionary biologists to have a realistic view of the impact of natural selection on evolution.

[foodchain]

Foodchain,

I don't want to subtract natural selection; I want evolutionary biologists to have a realistic view of the impact of natural selection on evolution.

 

Right, but I think natural selection is that. Even if you have a mechanism in biology that supports in some robust manner in defining evolution, say DNA for instance, where can you subtract natural selection from the equation?

 

I might be getting confused but evolution by natural selection is more or less a giant umbrella term for anything big and small. Simply because in reality its what can survive to reproduce that makes it for instance. Regardless or not if a predator cant hunt to any success it will die out. To deep sea vents. The organisms occupying such are allowed to simply because they evolved via natural selection to be able to, this is found in comparisons within biodiversity and ecology. So this has to then work all the way down to a cellular molecular level. Else I don’t see how variation in genomes comes to mean all that much.

 

I think another issue is the idea of natural perfection so to speak. IN many cases I don’t know how you rate any trait natural selection could work on from a scale of doing the best it could physically do, to being just enough to satisfy survival. I also do not understand how you can pick apart down to very discrete units with perfect separation from the rest of the organism and thusly ecology. I think such problems are the paramount issues today in regards to study in molecular biology really, at least in medical concerns. Which of course diversity via evolution in an intraspecies domain boggles down medical advance. why are some people allergic to something and not others? Which of course that question to can be environmental more so then intrinsic as gene function naturally without any environment, which of course does not exist in nature.

[dabs]

Foodchain, the issue with mutationism is not what happens if we try to "subtract natural selection from the equation" of evolution, but what happens if we control for, or account for, effects of differential reproduction (fitness differences) and then ask "what is left?". Is there anything else, any pattern or phenomenology, that is explained, not by selection, but by differential effects of mutation and development?

 

By analogy, we could ask (in the context of the nature-nurture debate), what happens if we subtract out the effects of genetic variance on some human behavior, e.g., violence? Is there anything left to explain?

 

It is crucial to understand that, by asking this question, we are not saying that genetics can be removed from the mechanism that generates humans and their behavior. However, we *are* assuming that we have experimental and mathematical tools to separate out genetic effects from other effects when we are accounting for patterns of behavior. Indeed, these tools exist. One relevant tool in this case is the study of identical twins raised apart-- same genetics, different environment (same "nature", different "nurture")-- but its not strictly necessary to do it this way.

 

And of course, the answer is that yes, when we subtract out the effect of genetic variation, we still have much to explain about behavior. There are environmental components to behavior.

 

Obviously both mutation and selection are necessary in any account of the mechanism of evolution. The historical position of mutationists is not a position of neutralism, of denying selection. The position of mutationists is that both steps influence the outcome of evolution in important ways.

 

By contrast, the neo-Darwinian position is analogous to genetic determinism, i.e., denying the relevance of one factor. The neo-Darwinians say that, although mutation is necessary for evolution to occur, the nature of mutation does not have any influence on *how* evolution occurs, what direction it takes, etc. Instead, the neo-Darwinian view is that "selection is the ultimate source of explanation in biology".

 

Of course if you re-define "natural selection" in a broad and fuzzy way so that it ends up meaning "whatever happens in evolution", then of course "natural selection" swallows up everything, including directional effects of mutation biases.

[foodchain]

Of course if you re-define "natural selection" in a broad and fuzzy way so that it ends up meaning "whatever happens in evolution", then of course "natural selection" swallows up everything, including directional effects of mutation biases.

 

Its nice that it has a bias, I can see life has an ATP bias sense endosymbiosis. The relevance to me is what persists is what can make it in the natural world. I mean can coevolution be impacted by LGT? Sure it could be a possible mechanism, but its relevance in time is simply a product of natural selection at any giving temporal moment. DNA on its own has a huge bias, so does iron. I can appreciate the attempt to reduce the complexity of natural selection into the physical mechanisms that are currently operating in such biologically speaking, like DNA, but the overall decision of what lingers and what does not in time is natural selection. Its a pretty moot discussion really. As in if a mutation is fatal, its fatal, if its not, its not, but what or how is this decided and again is any aspect of a biological entity free from environmental constraints. Natural selection is not the end all, but for sake of safety I really look for anything biologically speaking, such as a mathematical model for instance to satisfy what is known and for lack of better words empirically epic.

[dabs]

Foodchain, your sentences are nearly incomprehensible, so its hard to tell what you are saying. It might help to run your draft message through a grammar-checker.

 

In any case, it is simply wrong to suggest that natural selection determines what happens in evolution, which is how I interpret your claim that "the overall decision of what lingers and what does not in time is natural selection." Natural selection only "decides" between alternatives, but the alternatives must emerge first by mutation and development. Since the mutation rates are not all the same, this dependence on mutation can impose a bias on evolution.

 

To explain how this works, let me repeat a metaphor that Stoltzfus used at a scientific meeting last summer. To understand what he calls "dual causation", he asked the audience to imagine a climbing robot, placed on a rugged mountain. The climber operates by a two-stage proposal-and-acceptance algorithm. In the first stage, the climber reaches out with a foot or hand to find a hold. This might happen multiple times before the second "acceptance" step, when the climber commits to the hold and moves his body.

 

If the "acceptance" step is biased so that the climber is more likely to commit to a hand-hold that is higher (relative to one that is lower), then the climber will climb. That's like the effect of natural selection. It biases evolution to go up in fitness. But what if there is also a bias in the proposal step? What if the climber's left arm is more active and tries out more hand-holds? Then obviously, the climber is going to climb to the left.

 

One can't insist that the acceptance step (i.e., the analog of natural selection) determines the outcome, because obviously it doesn't determine the leftward bias. The leftward direction is caused by the bias in the proposal step, and the upward bias is caused by the bias in the acceptance step. The key to dual causation is that both biases can happen at the same time (up and to the left), and they have separable causes.

[foodchain]

Foodchain, your sentences are nearly incomprehensible, so its hard to tell what you are saying. It might help to run your draft message through a grammar-checker.

 

In any case, it is simply wrong to suggest that natural selection determines what happens in evolution, which is how I interpret your claim that "the overall decision of what lingers and what does not in time is natural selection." Natural selection only "decides" between alternatives, but the alternatives must emerge first by mutation and development. Since the mutation rates are not all the same, this dependence on mutation can impose a bias on evolution.

 

To explain how this works, let me repeat a metaphor that Stoltzfus used at a scientific meeting last summer. To understand what he calls "dual causation", he asked the audience to imagine a climbing robot, placed on a rugged mountain. The climber operates by a two-stage proposal-and-acceptance algorithm. In the first stage, the climber reaches out with a foot or hand to find a hold. This might happen multiple times before the second "acceptance" step, when the climber commits to the hold and moves his body.

 

If the "acceptance" step is biased so that the climber is more likely to commit to a hand-hold that is higher (relative to one that is lower), then the climber will climb. That's like the effect of natural selection. It biases evolution to go up in fitness. But what if there is also a bias in the proposal step? What if the climber's left arm is more active and tries out more hand-holds? Then obviously, the climber is going to climb to the left.

 

One can't insist that the acceptance step (i.e., the analog of natural selection) determines the outcome, because obviously it doesn't determine the leftward bias. The leftward direction is caused by the bias in the proposal step, and the upward bias is caused by the bias in the acceptance step. The key to dual causation is that both biases can happen at the same time (up and to the left), and they have separable causes.

 

 

Why is biochemistry nearly universal? Why do we have a immune system, vision, hearing. To say its all a mutation bias is an empty stance. Mutation is bias in that its random, what does that randomness work through to produce an organism, if you say something other then natural selection I don’t think we really need to debate any farther.

[dabs]

Why is biochemistry nearly universal? Why do we have a immune system, vision, hearing. To say its all a mutation bias is an empty stance. Mutation is bias in that its random, what does that randomness work through to produce an organism, if you say something other then natural selection I don’t think we really need to debate any farther.

 

I didn't say "its all a mutation bias", you did. I said "dual causation". The "dual" in this phrase refers to the concept of "two", and the "causation" part refers to causation. The two kinds of causes are biases in the introduction of variants that did not exist previously (mutation bias), and biases in the reproduction of variants once they exist (selection). Got it?

[vampares]

Right, but I think natural selection is that. Even if you have a mechanism in biology that supports in some robust manner in defining evolution, say DNA for instance, where can you subtract natural selection from the equation?

 

Can I say "artificial selection"? That the penis and vagina are what maintains the gene pool in the absence of natural selection?

 

There are many species who's traits show evidence of no other determining factors. For instance there are a million different types of tweetie bird, most of whom are about same. The niche factor hardly applies to tweetie birds, especially with so many kinds. What separates them is their own exclusive mating selection. As they become species they are able to diverge from the archetypal tweetie and become specialized.

 

Of course if you re-define "natural selection" in a broad and fuzzy way so that it ends up meaning "whatever happens in evolution", then of course "natural selection" swallows up everything, including directional effects of mutation biases.

 

The first article began with "survival traits that lead to minor imperfections". If a population is sequestered and selectively (or by unavoidable mating circumstances) mutates towards a vulnerability -- that vulnerability will be positively negated when it rejoins with the unmutated population. If there isn't one (maybe to evolved), well there you go. But there aren't a whole lot of examples of this. There just aren't that many hoops to jump through and I think this is the point the article is getting at: it all been done before. If you lose the ability, then it won't be done again.

 

Mutationst hypotheses; Emphasis on the mutational input

Selectionist hypotheses; Emphasis on positive/balancing selection

Neutralist hypotheses; Emphasis on drift

 

None of whom deny any of the others. Biologist have gone to great lengths to show through studies such as embryology, biomechanics, physiology, etc. why we have only one head. It is clear that having hooves rather than hands poses fewer issues than something like two heads. It can also be shown that going from flippers to hands is not such an amazing leap. In fact it can be show statistically and mathematically that this could have occurred "mutationally" by accident as a "new" event giving rise to a series of bones that are five fingers, hands on wrists.

 

It is unlikely such a mutation was drawn up in more discriminating higher order organisms whose lives are more complicated. So how many organisms do you see hobbling around? There are a few, but by in large animals are maintained in such away as not to become vulnerable. It should not come as a suprise that there aren't more hamhocked beasts in this world.