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Fisher’s Fundamental Theorem of Natural Selection: the death sentence for Darwinism

Consider the following claims:

Darwinism requires that the Fundamental Theorem [of Natural Selection] does not apply most of the time.

Walter ReMine
Biotic Message

and

a relative lack of natural selection may be the prerequisite for major evolutionary advance

Mae Wan Ho
Beyond neo-Darwinism

and

Concerning this theory [Darwinian evolution], I believe that we might question (or at least note) the following:
….
(10) The internal contradiction in its major theoretical cornerstone — Fisher’s fundamental theorem

Stanley Salthe
Analysis and critique of the concept of Natural Selection

and

many genomic features could not have emerged without a near-complete disengagement of the power of natural selection

Michael Lynch
opening, The Origins of Genome Architecture

Distinguished evolutionary biologist Michael Lynch recently published a much anticipated book, The Origins of Genome Architecture. Curiously, in this magnificent 494-page book, only an obligatory mention of the name of Charles Darwin was made. Darwin was mentioned passingly on 3 pages in the chapter entitled “GenomFart”.

It was also in this book Lynch demonstrated his great irritation with the advocates of Natural Selection (like Richard Dawkins). So great was his irritation that he gave the hard core Darwinists the ultimate insult, he likened them to ID proponents!

the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer

Michael Lynch
The Origins of Genome Architecture, p 368

Why the disdain for Natural Selection? It follows beautifully from Fisher’s Fundamental Theorem of Natural Selection.

Lynch is one of the world’s foremost experts in population genetics. Population genetics is the sort of anomalous discipline in biology that has a rich tradition of mathematics, and one that commands both respect and disdain. Lynch himself points this out, “It is well known that most biologists abhor all things mathematical…”

What sort of things do population geneticists do? They mathematically describe the evolution of populations. They quantify the amount of natural selection going on in a population. If natural selection is like the notion of force in physics, then it only makes sense to attempt to quantify how much or how little of this “force” must be in operation.

A central figure creating the ability to quantify and measure the amount of selection acting in a population is R.A. Fisher. Fisher was a first rate mathematician, and his work is celebrated in ID circles as it led to the formalization of the Explanatory Filter and other means of complexity analysis.

But in addition to the groundwork Fisher provided for design detection, he has provided much ammunition for ID proponents in the field of population genetics. Make no mistake, Fisher is a Darwinist, hailed by Stephen Gould as a “patron saint”, so the irony is that he continues to be an unwitting hero for the ID hypothesis.

If his Fundamental Theorem of Natural Selection gave population geneticists the tools to measure the amount of natural selection in a population, what would happen if these sophisticated techniques demonstrated Natural Selection had to be next to non-existent for evolution to advance? Answer: Darwin’s theory would be formally disproved! And in fact that is the case, and it is only quietly acknowledged in the literature (as hinted by the quotations above).

How can we measure natural selection? Without going into the deep details, we conventionally assert selection exists if there has been a reduction in diversity in a population. For example, let’s say we have a population of fruit flies and apply a pesticide to the population such that only 1 in 1000 fruit flies survives. The diversity of the population is severely reduced, and we can assert the pesticide applies a very strong selection force on the population.

It’s actually a bit clumsy to use the fundamental theorem of natural selection to describe the strength of natural selection and the reduction of diversity. With some degree of gyration one can probably do it using Fisher’s Fundamental theorem. But the bottom line, according to Fisher’s fundamental theorem, as “fitness” increases, diversity must decrease! [I'll save the technicalities in the notes below and comment section.]

As an aside, Fisher’s theorem was controversial and misunderstood until the Creationist George R. Price reformulated it. The new version of Fisher’s Fundamental Theorem by creationist George Price can be found at Wiki here.

The Wiki biography comments:

[Price] thus clarified Fisher’s fundamental theorem of natural selection, which had caused some controversy and misunderstanding. He believed that this equation had been a gift from God, a miracle after a religious experience.

And given that Fisher’s theorem essentially destroys any hope of Darwinism being true, I would have to agree with George Price, that Fisher’s Theorem and Price’s reformulation was a gift from God. After Price’s renounced Darwinism and became a creationist, he managed to publish his ideas in the prestigious scientific journal Nature in the article, and The Journal of Theoretical Biology. It is noteworthy he published in the prestigious journal Science on Science and the Supernatural.

In Death of Altruist we read:

Price made his final revisions to “The Logic of Animal Conflict” the following February. In a cover letter, he explained to Maynard Smith that he had made a few changes to accommodate his newfound belief in creationism. “I think I found wordings that you won’t object to, and that won’t shock Nature’s readers by making them suspect what I believe,”

Ah the irony of it all!

But let me return to the issue of Fisher’s Fundamental Theorem, and particularly Lynch and Salthe’s observations. Recall Lynch wrote:

the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer

I highlighted the word “diversity” for a reason. How does fitness improve according to Fisher’s Fundamental Theorem or Price’s Equation? Answer: by reducing diversity.

If we presume that all life descended from a single species and diversified, how can we logically argue that diversification happens through a process of removing diversification! Some may invoke things like allopatric (geographic) speciation or sympatric speciation where mutant forms are isolated somehow from the parent population, but is this not essentially a means of protecting new species from the culling effects of natural selection? It’s surprising the illogic of Darwinian claims has not been readily apparent!

Consider for example the problems of evolving a 3-chambered heart to a 4-chambered heart. The IDEACenter website has a wonderful treatment of the problem. See: The Vertebrate Animal Heart: Unevolvable, whether Primitive or Complex.

If we have species with 3-chambered hearts, how can species with 4-chambered hearts evolve? Let’s say a creature with a 3-chambered heart gives birth to a creature with a 4-chambered heart. This of course would be a saltational miracle in light of the fact a LOT of associated plumbing and developmental pathways have to be in place to make this possible. If the plumbing is hooked up in the wrong way, death results, no reproduction, no evolution.

But even granting this miracle set of mutations can happen, what role can selection possibly play? It has to allow both changes to exist simultaneously. If selection for the 4-chambered heart overtakes the population, then the 3-chambered hearts are eliminated (which is definitely not the case since reptilian 3-chambered hearts still exist). If selection for the 3-chambered heart takes place, then 4-chambered hearts are eliminated (which is clearly not the case since mammalian 4-chambered hearts exist).

Of course, one will argue that the two kinds of heart architectures might fall in separate niche’s (either geographically or via other means) and thus we prevent competition between the 3-chambered and 4-chambered heart. But competition is at the heart of natural selection. Thus I’ve demonstrated that in order for natural selection work, we have to prevent natural selection from working!

One of course would object and say that such saltations from 3 to 4 chambers violates Darwinian gradualism. Fair enough, but one is still confronted with the same problem. Let’s say one part of the population has pre-cursors to 4-chambered hearts and the other part of the population does not. For the 4 chambered heart to evolve, selection pressure has to be non-existent on the pre-cursors, exactly in the spirit of what Mae Wan Ho asserted: “a relative lack of natural selection may be the prerequisite for major evolutionary advance”. And if one thinks of it, this is actually a more forceful statement of the problem posed by irreducible complexity. But I save development of that brainstorm for another day…:-)

This contradiction between Fisher’s Fundamental Theorem and Darwinism has not been lost upon those I quoted above, and it has not been lost on those who research molecular evolution. In the 1960′s and 70′s, a problem emerged in trying to reconcile the existence protein polymorphisms (another word for “diversity”) and the “fact” of natural selection. Heated debates ensued, but the molecular quants like Jukes, King, and Kimura prevailed in putting forward the idea of non-Darwinian evolution for molecular evolution. See: Non-Darwinian Evolution and Neutral Theory of Molecular Evolution.

This fine tradition of “non-Darwinian” evolution has been quietly handed down and slowly extended to other domains of evolution, not just molecular. Lynch’s latest book is rich with Kimura’s math, and if one wishes to see the ID perspective on population genetics and Kimura’s math, I highly recommend Genetic Entropy by renowned Cornell geneticist John Sanford or Biotic Message by Walter ReMine.

And I close with this thought. Fisher’s Fundamental Theorem and its logical consequences cannot be properly taught in the School District of Dover Pennsylvania since Judge Jones ruled it unconstitutional to critically study the ideas of Charles Darwin. I’m grateful that the internet still provides a means for spreading the truth.

NOTES:

1. Walter ReMine has a wonderful exposition of Fisher’s fundamental theorem in his book Biotic Message. He explains Fisher’s Theorem by likening genotypes to bank accounts. Consider you have a portfolio of 2 bank accounts, one account starts with 10,000 earning 10% interest and the other starts with 10,000 at 5%.

The composite starting value of the portfolio is $20,000 with an instantaneous mean interest rate of 7.5% [ 7.5% = (10% + 5%) / 2].

However the mean interest rate of the portfolio will not be 7.5% forever, but will eventually move asymptotically toward 10% over time. The portfolio will thus become over-weighted and less diversified toward the more “fit” account bearing 10%. Fisher-Price describes the evolution toward an over-weighted portfolio.

How are interest rates related to the notion of selective fitness? This follows from Fisher’s Malthusian notion of fitness as is readily seen in this Wiki treatment Fitness

Wabs = N_after/N_before

Wabs = absolute fitness
N_after = number of individuals or money after selection
N_before = number of individuals before

For example, using the money analogy with an interest rate of 10% we can say a generational cycle is 1 year. Let

N_after = $11,000
N_before = $10,000

Wabs = 1.1 or a 10% increase

It can be see from the theorem it is a bit clumsy to actually apply it in terms of trying to analyze something like heart evolution, but I believe it is still correct, and I hope it suffices to at least get the discussion of these issues going.

2. I provided my take on Massimo Pigliucci’s review of Michael Lynch’s book in Michael Lynch: Darwinism is a caricature of evolutionary biology

3. To the formalists out there, I concede that reduction of diversity is formally only necessary, but not sufficient condition to assert the existence of selection since it is possible survival might be owing only to luck and not “fitness” as Raup pointed out in his book Bad Genes or Bad Luck! But Lewontin essentially pointed out (in Santa Fe Winter 2003) enforcement of this formalism would effectively discredit the concept of fitness and natural selection altogether! Kimura also shows the problem of distinguishing the effect of random walks from the effects of selection. Good luck often trumps good genes!!!!

4. A thriller movie actually W delta Z came out this year with Price’s equation as a central theme.

5. NAS member Masatoshi Nei is extending Kimura’s ideas to domains outside of molecular evolution. See: Prominent NAS member trashes neo-Darwinism

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75 Responses to Fisher’s Fundamental Theorem of Natural Selection: the death sentence for Darwinism

  1. Without going into the deep details, we conventionally assert selection exists if there has been a reduction in diversity in a population.

    As a population geneticist who works on quantitative genetics, I can confidently assert that this is rubbish. Firstly, a reduction in diversity can occur due to drift or bottlenecks. Hence, an observation of a reduction in diversity does not equate to an observation of selection. Secondly, selection can also act to increase diversity, for example if selection is disruptive.

    Sal, before declaring that Fisher’s Fundamental Theorem destroys Darwinism, I suggest you find out what it actually says.

    Yes, directional selection will usually have the effect of reducing additive genetic variance, but there are other forces which increase it (e.g. mutation, migration).

  2. Firstly, a reduction in diversity can occur due to drift or bottlenecks. Hence, an observation of a reduction in diversity does not equate to an observation of selection.

    See my note #3 Bob. You’re wrong to claim that I didn’t acocunt for that possibility.

  3. Thanks Sal for a great and thought provoking post!

    I have some questions that I am willing to ask, but first I must state that I am no biologist nor do I have much knowledge of biology (I am actually planning to study more biology in depth after finishing college, hopefully I will have time for this), and I believe in ID more-or-less on intuitive bases rather than in-depth scientific consideration of the matter.

    That said, I was thinking about your post and I am not sure if I got your point. I cannot see why the neccessary lack of natural selection in the begining of speciation invalidates the role played by it later on.
    I thought of an example (not a really good one!) of a car that is moving through a path full of falling rocks. The car (and therefore its engine) has to turn off for a while to let the rock fall then moves until there is another rock, and so on.
    Can we say that because the car engine had to stop many times through the walk that it actually played no role in moving the car through?

  4. IDist,

    Seleciton probably has some role, but when we actually quantify the numbers, we have to conclude it was weak, and if it was weak it cannot be the major explanation for the features of life.

    The point however, is that I was trying to demonstrate the fundamental incoherency of trying to explain diversity through mechanisms of natural selection. The two are fundamentally contradiction.

    Let’s say selection accounts for 1% of how biology is shaped. What accounts for the other 99%? Lynch and Kimura goes into beautiful math as to where selection is almost indistinguishable from a random walk, and thus casts doubts on the role of natural selection in the majority of cases in the first place.

    For molecular evolution, there is strong belief that the majority of molecular evolution had to happen in the absence of selection. This is primarily known as neutral theory. However, how does neutral theory account for irreducible complexity. Neutral theory is thus fatally flawed as well…

  5. Secondly, selection can also act to increase diversity, for example if selection is disruptive.

    I thank you for this comment and I encourage the readers to ponder it.

    However disruptive selection is evidenced by the reduction in diversity of the genotypes in the center of the distribution, so it’s still a reduction of diversity in genotypes.

    I look forward to your futher comments as you are indeed a professional population geneticist.

  6. Sal –

    @2: OK, but, as I have pointed out, it is not even necessary.

    @5: There will be a reduction in the frequency of genotypes after selection, but then there will be mating and recombination, which (unless there is assortative mating) will regenerate these genotypes.

    Do you actually know what And Fisher’s Fundamental Theorem’s states? It certainly does not say that diversity is reduced.

  7. Do you actually know what And Fisher’s Fundamental Theorem’s states? It certainly does not say that diversity is reduced.

    I believe I do.

    The mean fitness increases (i.e. like the mean interest rate increases in my example form 7.5% asymptotically to 10%) in relation to the genic variance in fitness.

    In the example above, the “genic” fitness variance is maximal at the initial condition of $20,000 portfolio value. It is clear as the fitness increases, there must be a corresponding drop in variance in genic fitnesses (in this case the weight of the portfolio).

    As the portfolio becomes more “fit”, having a near 10% interest rate, the corresponding variance in genic fitness is lower since the portfolio is now overweighted in the account bearing 10%. This also implies the increase in fitness (because of lower genic fitness variance), will be less and less — as I said, an asymptotic increase capped at a 10% interest rate. It is not hard to see that a Malthusian formulation of fitness is practically analogous to a diversified interest bearing portfolio.

    Thus the less fit have a smaller proportion in the composite population as time goes on. This is a reduction in diversity on a percentage basis.

    I welcome your comments if this if fundamentally incorrect.

    Yes, I’m aware of variations to my simplistic example, but I think it is materially correct.

  8. The mean fitness increases (i.e. like the mean interest rate increases in my example form 7.5% asymptotically to 10%) in relation to the genic variance in fitness.

    That would be marked incorrect, but not totally. Firstly, “in relation to” is vague. Are you a field biologist? Secondly, it’s not genic fitness that’s important, but additive genetic fitness.

    For the purpose of the discussions here you got one thing right. Nothing is said about a reduction in the variance or diversity. IOW the whole post is based on a total mis-understanding of the theorem.

  9. Let GR be the average growth rate.

    Rate of increase of GR = Variance of growth rates

    Suppose there are N groups, each with its own Malthusian growth rate. let p_i be the fraction of the total group that is in group i. Let m_i represent the growth rate of group i. Then GR is the growth rate averaged over m_i and the distribution of p_i. The mean is the sum of m_i p_i as i goes from 1 to N.

    Variance is sum of [p_i (m_i^2-GR)] as i goes from 1 to N.

    Recall, the growth rate of each group is correlated to Fisher’s Malthusian notion of fitness.

    In the above interest rate case, the mean is .075 the variance is
    0.000625. Thus the average Malthusian growth rate is .075 and the rate of increase in that growth rate will be 0.000625. At the end of one year the average growth rate will be .075 + 0.000625.

    Is that calculation materially incorrect?

    Unless the individual groups have identical absolute growth values, I don’t see that there wil be any thing but a reduction in the variance of the growth rates. Is that correct, Bob. And if they all have identical fitness values, it’s hard to argue natural selection will work at all!

  10. As to his initial statement:

    “Secondly, selection can also act to increase diversity, for example if selection is disruptive.”

    Bob O’H adds this clarification:

    “There will be a reduction in the frequency of genotypes after selection, but then there will be mating and recombination, which (unless there is assortative mating) will regenerate these genotypes.”

    ————

    Thus we can see that the first statement was indeed an inaccurate description of the particular process in mind.

    Notice that recombination is not a selective event. It may indeed result in diversity, but it did not result from natural selection. If what Bob is saying is that selection (by eliminating some genotype) makes way for others, then that is probably true as far as it goes (and indeed, may be so obvious as to avoid the need for significant discussion). However, selection does not itself produce the new “others.”

    I think this is an example of ascribing powers to selection that properly should be ascribed to other events (in this case recombination).

    Regardless of the nuances of Fisher’s theorem, are we actually suggesting that selection is not, by definition, a culling process? Any way you cut it, it seems difficult to sustain the idea that selection produces anything. That is certainly not how Darwin used the term, and it is not the typical understanding today.

  11. Note to the reader, the interest rate calculation I made was in a 1 year discrete one shot iteration, not continuous compounding over infinitesimally small (as in less than pico seconds), hence you’ll find the final interest rate I provided above is slightly off.

    If one uses a daily compounded formula, the result is more accurate where the initial effective annual interest rates are:

    5.1267% and 10.5156% for a starting mean of 7.8212% and a variance of .0726%. The end result after year in light of this refinement of daily compounding is 7.8212% + .0726% = 7.8938% which is better.

    Further refinement to nano-second compounding would probably yield better results.

    Let the reader understand, Bob accuses me of not fundamentally understanding the theorem. I’ve laid out the case in terms of an interest rate bearing portfolio. He can at least argue that I don’t understand Fisher’s theorem in terms of the math in this context.

    I welcome his analysis.

  12. [...] UD on fundamental theorem of NS the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer [...]

  13. Seems to me, since future conditions are unknown and may favor either this or that, the most fit species is the one that is most diversified. Any population culled for fitness to a particular set of circumstances (by natural selection or whatever) must therefore be less diverse and less fit to face a foreboding and indeterminate future.

    A portfolio maximized for short-term gains is not likely to be a portfolio suited to weather the vicissitudes of an unknown future economy.

    Is this this what you’re trying to say, Sal?

  14. Good analogy, Gerry.

    In theory, natural selection is always interested in what provides the greatest gain. However, given that natural selection only acts in the present (and only with one particular living organism at a time), it is more accurate to say that it is only interested in immediate gain. As you point out, this could well be very different from what is best in the long run (this is another example, really, of the foresight problem irreducible complexity attacks).

    Frankly, natural selection is only interested in culling the organisms that don’t make the grade today. Here. Right now. It has no foresight; creates nothing; produces nothing; generates nothing. It only culls.

    Thus, natural selection, by definition, can only eliminate, not create. Yet the irony is that people often confuse the issue and think that natural selection is somehow a driving force for creating new kinds of things.

    The concept of natural selection may have some (exceedingly limited, in my view) value in terms of describing the survival of the fittest, but has absolutely nothing to say about the arrival of the fittest.

    I think Sal’s post is interesting because it highlights that not only is natural selection unable to create anything, but also that natural selection — the culling force that it is — often needs to be suspended in order for any real creative work to take place. I’ll have to think about Sal’s point a bit more, but I think this is a very significant additional nuance.

  15. Greetings, Sal:

    Throughout this discussion, I think it is very important to keep in mind that Darwin’s algorithm (Daniel Dennett’s term) for natural selection has three prerequisites:

    1) variety (that is, substantive differences between phenotypes in populations);

    2) heredity (that is, vertical inheritance of phenotypic characters); and

    3) fecundity (that is, reproduction that can, but need not necessarily, exceed replacement).

    Given these prerequisites, the following outcome is virtually inevitable:

    4) unequal non-random survival and reproduction (i.e. proliferation of certain phenotypes relative to others).

    As I have pointed out repeatedly, the key to understanding evolution is to focus on the “engines of variation”; that is, those mechanisms (there are literally hundreds, perhaps thousands) by which new phenotypic characters are produced. These characters, produced by the various mechanisms that I list at my blog:
    (http://evolutionlist.blogspot......awman.html)

    provide the raw material upon which natural selection, sexual selection, genetic drift, meiotic drive, and all other sources of linkage disequilibrium operate.

    Fisher’s Fundamental Theorem, concisely stated, says that the rate of natural selection is a direct function of the amount of genetic variance in a population. That is, the greater the variation, the more raw material natural selection has to work on, and therefore the greater the degree of genetic change over time (note the emphasis on genetic change; as I have already pointed out in other threads, this is a serious limitation of Fisher’s approach, a limitation that also applies to the “modern evolutionary synthesis” as it existed in 1959).

    But, according to Fisher’s mathematical models, natural selection can only result in a decrease in overall genetic variance. This is because the effect of natural selection is to remove some variants while preserving others. The variants that are removed represent a decrease in genetic variance, hence Sal’s contention is essentially correct.

    While it is true that disruptive selection (also called “diversifying selection”) has the effect of producing two (or more) peaks in mean character states, rather than one (as in the case of both directional and stabilizing selection), it is not true that disruptive selection produces a net increase in genetic variation by itself. Only if the “engines of variation” produce the requisite new genetic material to allow for the shift in mean character state(s) will this happen.

    Ergo, it is not natural selection that “produces” new variation at all. On the contrary, natural selection merely channels the immense variety produced by the “engines of variation” into particular adaptive zones. Those zones exist, not because of selection, but because of the tremendous capacity for producing new variations that exist in the sources of variation that I have listed on my blog.

    So, in the interests of fair play, I hereby suggest to the ID supporters reading this post that opposing natural selection is a pointless exercise. Current evolutionary theory has already moved far beyond the limited theoretical models that formed the basis for the “modern evolutionary synthesis”. You are literally attacking a dead horse.

    Rather, the real focus of everyone’s attention should be on the “engines of variation”. That is, on those mechanisms by which variation in phenotypic characters is produced. If I were an ID supporter (I’m not, BTW, but I have good friends who are), I would strongly recommend investigating the dynamics of the various mechanisms by which phenotypic variation is produced (it is maintained, of course, by selection and drift, but that’s not the point).

    If the processes by which variation are produced can be shown convincingly to demonstrate foresight (i.e. that they produce characters that, when produced, are already necessarily adaptive), then ID may be a reasonable and useful component of any hypothesis for the origin and proliferation of adaptive characters in populations.

    If, however, the processes by which variation are produced can be shown convincingly to not demonstrate foresight (i.e. that they produce characters that, when produced, are not necessarily immediately adaptive, but become so following a change in environmental conditions), then ID is unnecessary as an hypothesis for the origin and proliferation of adaptive characters in populations.

    And please: in the interests of intellectual integrity, please do not quote parts of the foregoing analysis out of context. In particular, it would be grossly intellectually dishonest to characterize the foregoing as asserting only that “ID may be a reasonable and useful component of any hypothesis for the origin and proliferation of adaptive characters in populations”, without also including the second half of that assertion: that without a convincing demonstration that new variations are immediately adaptive, “ID is unnecessary as an hypothesis for the origin and proliferation of adaptive characters in populations.”

    Thank you for a very stimulating discussion!

  16. I think Sal’s post is interesting because it highlights that not only is natural selection unable to create anything, but also that natural selection — the culling force that it is — often needs to be suspended in order for any real creative work to take place.

    Right on!!

    And most problematic for Darwinism is whether it is even possible in principle to suspend natural selection in the first place!

    For example, to evolve a heart, the heart has to become non-critical to survival and thus not subject to strong selection. This would be like changing a tire on a moving truck (but far more difficult).

    Salthe echoes the idea here where diversity is be reduced in order for the population to be more reproductively successful. A corollary is that traits that have little variability (like a 3-chambered heart in amphibians) are the least likely to evolve.

    For example we have the highly “conserved” architecture of the 3-chambered heart in amphibians. By Darwinian accounts and physiological considerations alone, deviations from the 3-chambered architecture ought to be heavily selected against since deviations would be fatal.

    Changes in hearts are not like changes in Peppered Moth colors. A vein or artery in a different place is usually lethal. Likewise a malformed chamber or valve…

    Did evolution somehow permit the existence of non-functioning hearts in order to allow the evolution of 4-chambered hearts from 3-chambered hearts? Seems far-fetched.

    Here is Salthe’s take:

    (10) The internal contradiction in its major theoretical cornerstone — Fisher’s fundamental theorem

    Fisher’s theorem has it that population variance in fitness is exchanged over the generations for population fitness increase — that is, for adaptedness. A corollary would be that traits having been subjected to heavy selection pressures, because of their importance in the lives of the organisms, should be less variable than less important traits….note that when asked which traits are most likely to be able to evolve, evolutionary biologists, again citing Fisher’s theorem, will reply, “those that have more variability in fitness”. That is to say, traits that have been most important in the lives of
    organisms up to this moment will be least likely to be able to evolve further!

  17. A portfolio maximized for short-term gains is not likely to be a portfolio suited to weather the vicissitudes of an unknown future economy.

    Is this this what you’re trying to say, Sal?

    Not exactly, but what you said is also correct. If a population has no variability, it can be at risk of extinction. For example, if the most “fit” eat only one kind of food, and because of reproductive success, it overtakes the population, it will be at risk of extintion if that food source is eliminated.

    The highest returning portfolios can subject the investor to high risk of loss. Thus, even in human affairs we don’t necessarily overweight the most “fit” (i.e. highest past performance investment) for a portfolio.

    Salthe echoes this point in his own way:

    There are two major theoretical prongs in neoDarwinism: the Fisherian dynamical approach and
    the Wright-Dobzhansky kinetic approach. Neither delivers real long term evolution. In Fisher’s
    version, which does track over many generations, we begin with a population having a degree of
    variability in characters that could link to fitness. The environment changes, and, as a result of differential reproduction, some variants are discarded from the population while a few as a result increase in frequency of representation. This process, generation after generation, results in a net
    decrease in population variability in fitness as population fitness with respect to the altered
    environment improves (Ronald Fisher’s ‘fundamental theorem of natural selection’). …By the time the population has achieved an adaptive gene pool configuration (if it hasn’t gone extinct for lack of appropriate variability), it has lost variability to the extent that, if the environment should change again, extinction would be a likely result. The population has become overspecialized. In this model, evolution leads to the brink of extinction.

  18. Eric @ 10 – Strictly you’re correct, for this case. But we usually think over the full life cycle, i.e. from one developmental stage to the same one in the next generation. Otherwise it gets too complicated.

    Sal @ 9 –

    Unless the individual groups have identical absolute growth values, I don’t see that there wil be any thing but a reduction in the variance of the growth rates. Is that correct, Bob.

    No it isn’t. Think of two genotypes, with the fitter one being rarer.

    Sal @ 11 –

    Let the reader understand, Bob accuses me of not fundamentally understanding the theorem. I’ve laid out the case in terms of an interest rate bearing portfolio. He can at least argue that I don’t understand Fisher’s theorem in terms of the math in this context.

    You totallyu mis-represented FFT in your original post – put simply, it does not say that selection reduces diversity. Either you didn’t understand the theorem, or you did, and you were being dishonest. I’d rather go for the former theory: I’m an optimist and believe most people are honest. Now if you want to argue me out of that position…. :-)

    Incidentally, the statement that natural selection doesn’t create is hardly controversial. Declaring it defeats evolution is like declaring that it is impossible for a car to have been driven more than a few kilometers, because after that its petrol would have run out.

  19. No it isn’t. Think of two genotypes, with the fitter one being rarer.

    I meant eventually. For example

    Genotype A has intially 100 individuals and a malthusian fitness .05 (fitness stated as natural log of N_after/N_before)

    Genotype B initially has 200 individuals and a malthusian fitness .01

    The variance in composite fitness will increace temporarily and then decrease as the fitness asymptotically approaches .05.

    Will not the variance in fitness eventually shrink below the initial variance in fitness given sufficient time?

    The result is selection given sufficient time reduces diversity. Unless of course one argues selection abates, which supports the point selection must be disengaged to allow sustained diversity.

  20. I meant eventually. For example

    But FFT is only about what will happen over a short period of time. So this would be an irrelevant attempt to shift goalposts.

  21. One thing I like about posts like these is that it does something that, frankly, the public world needs more of – showing that even among non-IDists, there’s quite a lot of discussion about the mechanisms of evolution, just how much natural selection factors into the process, etc.

    Even as someone who leans more towards TE than ID, I love to read about these divisions, innovations, models, etc. It’s my view that ID will have reached a point of mainstream acceptance when it begins to provide predictive, design-based models of evolutionary development – how to promote the introduction and direction of traits in a given environment over a long period of time.

    It’s a tall order, but I still think the day will come.

  22. Good post and discussion, Sal, et al.

    Everyone, please note that Allen MacNeill has a fair and relevant comment at #15. Approval for this comment would have occurred after subsequent comments were posted and it ought not be lost to readers.

  23. Allen,

    Greetings. My sincere apologies for any delays in the appearance of your postings.

    I have little no control over these issues. Thank you for bearing with us.

    I encourage you to save your posts in MS word or something before you write.

    Thank you very much for offering your insights. Please know you are always welcome on my threads.

    regards,
    Salvador

  24. Bob OH wrote:

    But FFT is only about what will happen over a short period of time.

    Thus it is questionable how fundamental it really is because the deep questions are with respect to the long term.

    Walter ReMine points out:

    1. The theorem holds true only when growth rates are constant and unchanging.

    2. The process itself diminishes the ‘variance’ in growth rates, so the process (of increasing fitness) slows to a halt.

    The fundamental theorm has been mishandeled in the past even by the greats like Crow:

    If we take the theorem literally, the mean fitness of the population should increase indefinitely as long as there is additive variance for this trait. (Crow, Basic Concepts in Population, Quantitative, and Evolutionary Genetics, p85)

    Well sure, if mutants keep popping up in the population that are more reproductively successful than the existing population, growth rates will grow indefinitely till the species is practically an epidemic. Recall in the Fisher model, “fitness” = ability to make the most surviving babies.

    Reproductive success is not necessarily to be equated with more complex organisms. We know that some species like blind cave fish are more reproductively effective by becoming more simple….

    I do not think it can be demonstrated that natural selection naturally leads to the emergence of complexity. I cited the Fundamental Theorem to suggest that Natural Selection might actually have to be disengaged for evolution to move forward.

    It is telling someonne as respected as Michael Lynch would argue that for certain major features of biology.

    How can we statistically say how much or how little natural selection occurs. Kimura and others suggest a bean count — namely they state that X Percent of the genome was subject to selection.

    This bean count was based on the work of Haldane on the amount of population resources that would be needed to evolve each independent trait. The surprising conclusion was tha 99% or more of the genome could not be policed by natural selection. There are simply not enough population resources.

    It seems to me the main driving force of evolution (assuming one is not a creationist), would have to be mutation 99% of the time. Selection can only influence 1% of evolution. Sanford’s chapter on Interference Selection seemed quite convincing to me.

    If mutation is the principal architect for the emergence of integrated complexity, can it be fundamentally stochastic. I don’t think so…

    What do I mean by stochastic. We can describe the works of William Shakespeare stochastically — as in numbers of letters, mean, variance, etc. etc.

    But if we describe Shakespeare’s work stochastically, and thus create a stochastic mechanism defined in terms of mean, variance, and statistical moments, does anyone on the planet expect a stochastic mechanism to account for the linguistic features (a stealth word of specified complexity).

    For example, we could characterize Shakespeare in terms of mean, variance, and the nth statistical moment and build a random number generator that obeys this stochastic rule. No one expects the random number generator to create anything resembling his works. The output will be complex, but SPECIFICITY requirement (some thing as basic as semantic coherence) will not be in evidence [at least that's what ID proponents predict, it would be an interesting experiment :-) ]

    So I think Lynch, Nei, and the neutralists are correct in as much as they are critical of Natural Selection. It seems mutationism is coming back in vogue as Nei himself cites William Bateson favorably.

    Whether their theories and the ideas of the mutationists like are correct is another story and perhaps the subject of another thread….

  25. Sal – regardless of what we call Fisher’s theorem, it is what it is.

    As for ReMine, he’s wrong on point 1, it still holds if growth rates change, but the changing growth rates have to be accounted for. As I’ve already pointed out, FFT is a short-term theorem.

    Crow doesn’t mis-handle the theorem. If you read what you quoted, you’ll see that he puts qualifiers in there. Your comment after the quote is fully accounted for by the “as long as there is additive variance for this trait” qualification. I guess you’re too busy learning new skills to have remembered you Introductory Quotemining lessons. That qualification should have been changed to an ellipsis.

    You comparison of mutation and selection as forces in evolution is comparing apples and oranges. Mutation is a force that adds variation, and selection is one of the many forces that molds the variation. Both are important, but they’re important for different parts of the process.

  26. “as long as there is additive variance for this trait”

    One could of course increase variance in fitness by putting in underperformers, but that wouldn’t cause indefinite increase in fitness, except via creative redifinitions of what it means to be constantly improving.

    The analogy would be having a portfolio composed of a fixed-rate CD earning 5%. You deliberately add an underperforming security to the portfolio to increase the variance. At first the portfolio average 5% annual growth. Then you add large amounts of an underperformer (like pure cash bearing no interest) such that you average 1% instantaneous growth, but this adds the “magic” quantity known as variance in fitness.

    Fisher’s theorem predicts the portfolio will eventually return to 5% growth. In that sense you create opportunity for the fitness score to “improve” from 1% to 5% by decreasing the overall fitness in the first place. A setback is deliberatly introduced so one can say, “we’re improving most of the time”!

    After the portfolio starts performing at almost 5% again, you can then repeat the process and add underperformers to the portfolio and thus drive the instantaneous return back down to 1%. Fisher’s theorem says it will revert again toward 5% fitness, but not to infinity….

    Thus you can, through selective observation of this example argue that the fitness is always improving (except when you have a setback). In that respect Crow is absolutely correct.

    Crow echoes the sentiments of Findlay:

    Fisher’s (1930) fundamental theorem of natural selection states that the rate of change in the mean biological fitness of a population is equal to the additive genetic variance in fitness. Since variances are always positive, this implies the mean fitness never decreases, an elegant result which neatly captures the flavor of Darwin’s assertion that natural selection leads inevitably to the improvement of the species.

    Findlay
    “Fundamental Theorem of Natural Selection in Biocultural Populations,” Theoretical Population Biology, Vol 38, p 367-384

    But Findlay equivocates the notion of improvement to reproductive effectiveness. This is not necessarily true, at least with respect to the question of the evolution of complexity.

    Secondly, adding variance in fitness does not inevitably imply continued growth in mean fitness –unless one views the scenario I gave above as an example of continued growth in fitness…

    selection is one of the many forces that molds the variation.

    But selection seems quantifiably limited in what it can do.

    If we have a populaiton with 1000 individuals with 4 billion base pairs each, how much can natural selection possibly do in finite time?

    This is the classic channel capacity problem in communications engineering. Modems have finite bandwidth and so does natural selection.

    If one has 1000 individuals and each and each has 1000 unique advantageous traits, the preservation collectively of all these good traits from every individual cannot possibly be infused into the population. The culling process throws out the good with the bad. That is the problem of interference selection which Sanford argued quite well.

    It’s like trying to pump through a movie over the interenet and lots of frames have to be skipped because of limited bandwidth. It is analogous to the problem of how much music can fit on a CD. Given a finite number of population resources, there is a finite limit to the amount of change natural selection can influence.

    The problem is even more severe when you have limited population resources and large numbers of base pairs. The way out is to hope against hope that “junk DNA” is really junk, and that epigentic information is not as large as the info in the genome, as that could multiply the problem by several fold.

  27. Sal you don’t seem to be responding to what I write any more, so I’ll just point out that you’re also ignoring the possibility that a mutant increases fitness.

  28. Sal wrote (in #24):

    “…if mutants keep popping up in the population that are more reproductively successful than the existing population, growth rates will grow indefinitely till the species is practically an epidemic.”

    However, both sides in this debate agree that deleterious mutations greatly outnumber beneficial ones. Hence, only those relatively rare mutations that have a positive effect on reproductive success will increase in relative frequency in populations.

    “Reproductive success is not necessarily to be equated with more complex organisms. We know that some species like blind cave fish are more reproductively effective by becoming more simple”

    Indeed, as Stephen J. Gould often pointed out, assuming that selection necessarily results in increased complexity is a fallacy. This argument is analogous to his argument against “progress” in evolution. As a good friend of mine (who is also a herpetologist) likes to assert, “It’s all been downhill since the Mesozoic.”

    “I do not think it can be demonstrated that natural selection naturally leads to the emergence of complexity. I cited the Fundamental Theorem to suggest that Natural Selection might actually have to be disengaged for evolution to move forward.

    This is an absolutely crucial insight. Indeed, if Fisher’s Fundamental Theorem has any bearing on reality (and I believe it does), then really rapid variation in populations can only happen when selection is indeed relaxed. Under what conditions does this happen? There are two that I can think of:

    1) Domestication, in which breeders deliberately keep alive (and help with the reproduction of) individuals that would be less “fit” under natural conditions. Darwin pointed out repeated examples (among pigeons and other domesticated animals and plants) in which domestication resulted in dramatically increased variation, including variants that could not possibly survive under natural conditions (this is why variation is typically much less under natural conditions than under domestication).

    2) Adaptive radiation following mass (or at least multiple) extinctions. The removal from a biotic community of a relatively large number of closely adapted species frees the survivors to radiate into the “empty niches” vacated by the newly extinct species. This is because the survivors have much less competition. In other words, they are in the same position as domesticated organisms; increased relative fitness as the result of decreased selection against variants.

    “How can we statistically say how much or how little natural selection occurs. Kimura and others suggest a bean count — namely they state that X Percent of the genome was subject to selection.”

    Here, once again, we have a problem. This formulation of “fitness” is focused on the genome, rather than on differential survival and reproduction of individuals with particular phenotypes. This excessive focus on gene- and genome-level selection is precisely the problem with the “modern evolutionary synthesis” and is the reason that new theories of variation and selection (such as those described by Jablonka and Lamb (in Evolution in Four Dimensions) and Margulis and Sagan (in Acquiring Genomes) are currently on the cutting edge of evolutionary theory. That is, they focus on phenotypic changes at the level of individuals (and groups), rather than at genotypic changes at the level of genes (i.e. what Dawkins called “selfish genes”).

    “This bean count was based on the work of Haldane on the amount of population resources that would be needed to evolve each independent trait. The surprising conclusion was tha 99% or more of the genome could not be policed by natural selection. There are simply not enough population resources.”

    Which is precisely why the new focus on phenotypes has revolutionized evolutionary theory. This new focus is relatively immune to both Haldane’s dilemma and to Kimura and Ohta’s theories of neutral and nearly neutral molecular evolution. In other words, focusing on phenotypes recognizes what Waddington recognized almost a half century ago: that changes in genotypes are only weakly correlated with changes in phenotypes.

    “It seems to me the main driving force of evolution (assuming one is not a creationist), would have to be mutation 99% of the time. Selection can only influence 1% of evolution. Sanford’s chapter on Interference Selection seemed quite convincing to me.”

    I would agree with you if you changed the word “mutation” to “variation”. As I have repeatedly pointed out, the term “mutation” captures only a tiny fraction of the full range of variation produced by the “engines of variation” listed at my blog:

    http://evolutionlist.blogspot......awman.html

    The vast majority of these mechanisms of variation are not “mutations” in the classical genetic sense, but do indeed produce tremendous heritable variation between phenotypes in populations. Also, most of these mechanisms of variation are not “random” in the classical genetic sense, but rather are “canalized” (to use Waddington’s term in a different context). They are, in other words, “guided” into particular adaptive zones as the result of a combination of environmental determinism and historical contingency.

  29. Sal you don’t seem to be responding to what I write any more

    Which I thought was very gracious of Sal, given #25.

  30. so I’ll just point out that you’re also ignoring the possibility that a mutant increases fitness.

    I did not ignore it. I wrote in #24:

    Well sure, if mutants keep popping up in the population that are more reproductively successful than the existing population, growth rates will grow indefinitely

    I think you missed what I said earlier.

    In any case I value your particiapation since you are a professional population geneticist.

    I have been in contact with Walter ReMine, author of Biotic Message and he has helped me with the discussion on this thread and has been reading it. I hope he takes your comments into consideration.

    So please don’t think your insightful comments are falling on deaf ears.

  31. Allen

    I see you’ve got 47 different ways that heritable variation can occur.

    I’m rusty in my Ptolemaic astronomy but I seem to recall that’s how many epicycles were required to explain the earth at the center of the solar system before someone figured out the much simpler explanation that the sun was at the center. I think I can hear Sir Occam sharpening his razor even now.

  32. 32

    DaveScot (31):

    Evidently you think the principle of parsimony in scientific explanations is sound. I wish everyone here would agree to that.

    I think I can hear Sir Occam sharpening his razor even now.

    “Occam’s Razor” is a metaphor for the assumption, widely accepted by scientists, that simpler explanations are preferable to more complicated ones. Allen’s list of empirically observed sources of variation is not an explanation, and Occam’s Razor is not applicable.

  33. Allen– That is, they focus on phenotypic changes at the level of individuals (and groups), rather than at genotypic changes at the level of genes (i.e. what Dawkins called “selfish genes”).

    Can something have wings if it has not been coded for them in the genome?

  34. 34
    Thought Provoker

    I would like to emphasize Allen’s comment #15 where he said…

    “If I were an ID supporter…I would strongly recommend investigating the dynamics of the various mechanisms by which phenotypic variation is produced (it is maintained, of course, by selection and drift, but that’s not the point).

    If the processes by which variation are produced can be shown convincingly to demonstrate foresight (i.e. that they produce characters that, when produced, are already necessarily adaptive), then ID may be a reasonable and useful component of any hypothesis for the origin and proliferation of adaptive characters in populations.”

    While I am a critic of the ID Movement, I support the potential outside-the-box-thinking ID Science offers. Which is one of the reasons I put together my own ID Hypothesis (involves interconnected quantum effects).

    What clearly fell out of my effort was that supporting evidence would be of a nature similar to Front Loading and/or a demonstration foresight.

    Looking for demonstrations of foresight would seem to be a natural for people truly interested to promoting the scientific potential of ID.

  35. I would like to thank everybody who is participating in this discussion :).

    Allen_MacNeill

    In other words, focusing on phenotypes recognizes what Waddington recognized almost a half century ago: that changes in genotypes are only weakly correlated with changes in phenotypes.

    This is interesting, and makes me willing to ask this:
    if changes in genotypes are only weakly correlated with changes in phenotypes, how are phenotypes produced in the first place?
    This implies that there are other sources of information, sources that we do not know of, or at least do not understand to a satisfactory degree that produce the phenotype. If this is true it leads to another question, if we do not know how the organism is put together, how can we say anything about its origin and evolution?

  36. Sal @ 30 –

    so I’ll just point out that you’re also ignoring the possibility that a mutant increases fitness.

    I did not ignore it. I wrote in #24:
    I had missed that, but then you wrote this in post 26:

    “as long as there is additive variance for this trait”

    One could of course increase variance in fitness by putting in underperformers, but that wouldn’t cause indefinite increase in fitness, except via creative redifinitions of what it means to be constantly improving.
    Which appears to ignore it too.

  37. Aagh! There’s a blockquote missing: The “One could…” paragraph should be in blockquotes, and the final sentence is mine.

  38. “[Francis] Crick challenged me with the statement that nothing can be said about evolution until we understand how organisms are put together.” (Geneticist Gabriel Dover)

    Quote from: http://www.uncommondescent.com.....5B1%5D.pdf

    Looks like Francis Crick agrees with me :D.

    I hope that Prof. MacNeill will help me in this question.

  39. Indeed, if Fisher’s Fundamental Theorem has any bearing on reality (and I believe it does), then really rapid variation in populations can only happen when selection is indeed relaxed.

    No. A change in the environment can change the adaptive landscape, so that traits which were previously under only weak selection can become more strongly correlated with fitness, and hence change rapidly.

    Which is precisely why the new focus on phenotypes has revolutionized evolutionary theory. This new focus is relatively immune to both Haldane’s dilemma and to Kimura and Ohta’s theories of neutral and nearly neutral molecular evolution.

    I guess you haven’t heard Nunney talk about Haldane’s dilemma recently, have you? He showed that, in fact, you do get the same “problem”. He compared a model of phenotypic evolution in a changing environment (it might even have been one of Mike Lynch’s!) with his model of Haldane’s dilemma from the Extinction Thresholds meeting (it appeared in Annales Zoologici Fennici later. ReMine knows the reference. :-)), and found they were giving similar predictions.

    As for the neutral theory, we have to deal with that in evolutionary quantitative genetics as well (i.e. the area of evolutionary biology where FFT fits in, and which concentrates on phenotypic changes and their response to evolution). I’ve been having to deal with the neutral theory when looking at population divergence, because populations drift, and so too do their phenotypes.

  40. H’mm:

    For what it’s worth, lurker X again:

    __________________

    Salvador: “If we presume that all life descended from a single species and diversified, how can we logically argue that diversification happens through a process of removing diversification! Some may invoke things like allopatric (geographic) speciation or sympatric speciation where mutant forms are isolated somehow from the parent population, but is this not essentially a means of protecting new species from the culling effects of natural selection? It’s surprising the illogic of Darwinian claims has not been readily apparent!”

    X: But the illogic of Darwinian claims has been readily apparent — and all the way back to 1859! One of the chief criticisms of the original formulation of “Darwinism” is that “natural selection” destroys, but does not create, diversity; or, at best (i.e. with optimistic assumptions), relatively preserves some status quo.

    When Mendel’s work was “rediscovered” in 1900, the criticism of “Darwinism” again pointed out this problem. But Darwin’s Disciples, even to this day, as with the Master Himself, ignore telling criticisms … and then later “refute” them by pointing that they are old criticisms.

    And, more recently . . . [the matter, e.g on Chromosome 2] involves the recognition that ‘modern evolutionary theorists’ can’t naturalistically get the proto-human species (with the human-like 2n=46 karyotype) from the hypothetical-parent species (with the ape-like 2n=48 karyotype) — for there is no naturalistic “means of protecting [the] new [proto-]species from the culling effects of natural selection.”

    Salvador: “But competition is at the heart of natural selection. Thus I’ve demonstrated that in order for natural selection work, we have to prevent natural selection from working!”

    X: Exactly! This is why ‘modern evolutionary theory’ has *always* had to rely upon the Just-So Story. This is why ‘modern evolutionary theorists’ always place great stock in plausibility (i.e. if one first assumes ‘modern evolutionary theory,’ then of course the Just-So Stories become plausible!) This is why ‘modern evolutionary theorists’ so often try to denigrate criticism as mere “argument from incredulity,” as though that were an effective refutation of the criticism. (Because, of course, credulity is the preferred intellectual posture of all serious and critical thinkers!)
    __________________

    What do you think gentlefolks?

    GEM of TKI

  41. Thomas

    Well, I guess I’ll agree with you that Allen’s 47 ways by which heritable phenotypic modification can occur is not an explanation. It’s a laundry list. I’d make the list 48 items long by adding intelligent agency to the list of mechanisms and then with the addition of that start applying Occam’s Razor to the other 47, trimming away those which are made unnecessary by the mechanism of intelligent agency.

  42. Allen

    I agree that phenotype and genotype are only loosely correlated. Two years ago I made that point here myself in a series of articles describing recent experiments which “exploded” different bits of neo-darwinian assumptions. Phenotype and genotype linkage was one of those bits. Another bit was linkage of DNA sequence conservation to DNA sequence function.

    That said, just so you don’t think I’m gratuitously disagreeing with all you propose, I find your reference to “canaling” quite interesting. You propose that random changes aren’t necessarily random as they may be directed in certain useful directions by biological “canals” much as water is directed in useful directions by canals.

    What I find most interesting is that canals are artificial constructions. No matter how hard you try, Allen, you can’t escape making references to design in biology. This is what separates biology from every other natural science. Modern biology uses engineering terminology ubiquitously in its decriptions and explanations. No other natural science does that.

    Since ID is in large part an argument from analogy and analogic arguments are often useful in making predictions here’s an ID prediction for you. The canals you speak of, upon closer examination, will continue to exhibit the charateristics of designed structures. In other words the appearance of design won’t go away as more details are revealed – it won’t be found to be an “illusion” of design. Illusions tend to disappear when examined at higher resolution. Case in point, the “canals” of Mars. Under low resolution Mars had what appeared to be canals on its surface. Under higher resolution it was found that these were natural waterways easily explained by water, gravity, and erosion rather than artificial constructions serving some purposeful channeling of the water. If your biological canals are only illusory designs then upon closer examination the illusion should reasonably be expected to collapse. If intelligent design is true we can reasonably expect, by analogy to other intelligently designed structures, the illusion of design will not disappear.

  43. Allen

    P.S. I’m removing you from the moderation list with a caveat: if you’re commenting under an article I wrote keep your comments confined to the topic of the article.

  44. There is the central issue lacking here of “backwards extrapolation” in the proper understanding of the dichotomy between the two theories (ID/DE).

    Darwinian evolution does indeed extrapolate backwards. After all, what more can anyone do? History is inextricable from origins science. ID however always gets falsely criticized for “calculating probabilities backwards” as if it is illegal or something- but that is all that Darwinism ever does with its mechanisms- that is it makes speculative statements about history- after the fact- and ones that usually cant even be verified. Michael Behe says you cant have a mouse trap without all of its parts. They then take the liberty to “make up” a “highly improbable” and “totally backward speculative” explanation that barely even works and may not even work all — and so probably never even happened. Then, ID theorists say “wait a minute here, do you have any idea how unlikely that explanation of yours really is?” Then the DE’s scream (in the so called name of good science) “You cant calculate probabilities backwards!” Why not?

    The only goal of this, obviously, is to try and construct an illogical and rigged view of science (and history) that gives their theory not only a 100% monopoly on “all of history” but makes methodological materialism “the only possible explanation by default” a priori. Yet, all the while they know that their entire explanation is nothing but a backwards historical extrapolation based theory of the gaps itself, built off of an illogical and unjustified philosophical precommitment to the methadological materialistic scienfific and philosopgical platform. Obviously, hypocrisy is not a concern for their theory. They aren’t mad about calculating probability backwards because it’s actually somehow unsceintific. No, they’re mad because its just plain unfair.

    Obviously the probabilistic TRUTH about history is unfair and to be ignored because it doesn’t accord with their theory is nonsense. No one ever said that hisotry is fair. All theories are not equal.

    Despite their theory consisting of stories that “they make up” (and even after the fact), they still cant (should say won’t) allow people to calculate the likelihood of their stories and explanations being true. Why, because nothing they can even “fictionally invent” can justify and constitute rationality and reason. Yet it is to be accepted and held beyond mathematical reproach.

    The theory of neo-Darwinian evolution is therefore obviously irrational and unreasonable.

    Math has revealed itself as materialistic evolution’s great enemy and for good reason too, because math is logical and when correctly constructed useing good historical data- refuses the lie for a broken theory.

  45. “Well, I guess I’ll agree with you that Allen’s 47 ways by which heritable phenotypic modification can occur is not an explanation. It’s a laundry list. I’d make the list 48 items long by adding intelligent agency to the list of mechanisms and then with the addition of that start applying Occam’s Razor to the other 47, trimming away those which are made unnecessary by the mechanism of intelligent agency.” — DaveScot

    Exactly. And that’s what almost all ordinary people do, intuitively, and in a matter of seconds, with this whole issue. “Looky yonder, Jeb. D’ya think that there just a-happened, all by hisself?” “Uh, lemme chaw on that a bit Roy. Nope.” Only a truly edjikated man can so easily deny the obvious.

  46. “The only thing that interferes with my learning is my education.”

    -Einstein

  47. Dave,

    The idea of canaling is discussed over several pages in the Jablonka and Lamb book. Don’t ask me yet for good understanding of it. The book is interesting but often convoluted. The more convoluted the topic gets the more iffy the proposition. There are several good things in this book and not one challenges ID. It just expands what comes under what micro evolution can do.

    The link to Lamarck in the book is a little stretched but interesting. The people who wrote the book are Darwinist and anything they cannot explain they say was selected. It is their answer to everything unknown.

    One interesting example they use and it is a thought example is a world where all the creatures had identical DNA but completely different phenotypes. That is because cell types are not based on DNA but epigenetic factors such as methylation which determine which genes get expressed in the cell.

    The topic of genotype and phenotype matching or not matching or one changing without the other changing is discussed in several places.

  48. Allen_MacNeill (29): “Also, most of these mechanisms of variation are not ‘random’ in the classical genetic sense, but rather are ‘canalized’… They are, in other words, ‘guided’ into particular adaptive zones as the result of a combination of environmental determinism and historical contingency.

    Asa Gray, Professor of Natural History (Botany), Harvard University, in his review of Darwin’s The Origin of Species, 1860:

    [W]e should advise Mr. Darwin to assume in the philosophy of his hypothesis that variation has been led along certain beneficial lines. Streams flowing over a sloping plain by gravitation (here the counterpart of natural selection) may have worn their actual channels as they flowed; yet their particular courses may have been assigned; and where we see them forming definite and useful lines of irrigation, after a manner unaccountable on the laws of gravitation and dynamics, we should believe that the distribution was designed.

    To insist, therefore, that the new hypothesis of the derivative origin of the actual species is incompatible with final causes and design, is to take a position which we must consider philosophically untenable. We must also regard it as highly unwise and dangerous, in the present state and present prospects of physical and physiological science. We should expect the philosophical atheist or skeptic to take this ground; also, until better informed, the unlearned and unphilosophical believer; but we should think that the thoughtful theistic philosopher would take the other side. Not to do so seems to concede that only supernatural events can be shown to be designed, which no theist can admit — seems also to misconceive the scope and meaning of all ordinary arguments for design in Nature. This misconception is shared both by the reviewers and the reviewed. At least, Mr. Darwin uses expressions which imply that the natural forms which surround us, because they have a history or natural sequence, could have been only generally, but not particularly designed — a view at once superficial and contradictory; whereas his true line should be, that his hypothesis concerns the order and not the cause, the how and not the why of the phenomena, and so leaves the question of design just where it was before.

  49. 49

    scordova said (comment # 26 ) –

    The culling process throws out the good with the bad.

    Good point. Fruit flies, for example, are considered to be likely survivors of a nuclear war because of a high resistance to radiation. Does that make the fruit flies “fitter” than other organisms — including humans — that are less resistant to radiation?

    Also, natural selection does not necessarily consist of just culling. For example, a bird that is a mutation of a lizard can enter a new ecological niche, and other lizards are unaffected at least for the moment. That is natural selection, too.

    My favorite criticism of evolution is the Fundamental Theorem of Co-evolution of Total Co-dependence of Two Different Kinds of Organisms: In such co-evolution, unlike in evolutionary adaptation to widespread fixed physical features of the environment, e.g., water, land, and air, there may be nothing to adapt to because the corresponding co-dependent trait in the other organism is likely to be locally absent.

    First corollary: Where the corresponding co-dependent traits in both organisms are fatal in the absence of the corresponding co-dependent trait in the other organism, co-evolution by means of random mutations is virtually impossible.

    Second corollary: Even where the corresponding co-dependent traits are not fatal or harmful in the absence of the corresponding co-dependent trait in the other organism, the creation of only one of the pair of co-dependent traits confers no advantage in natural selection.

  50. Thom English is once again no longer with us.

  51. 51

    Huh? Any reason why? Just curious.

  52. 52

    Huh? Any reason why? Just curious.

    Yes, Dave. You even agreed with Thomas English at one point:

    Thomas

    Well, I guess I’ll agree with you that Allen’s 47 ways by which heritable phenotypic modification can occur is not an explanation.

    You should see the crap that I have to put up with on my own blog because of my no-censorship policy. At one point I had to enable comment moderation because some trolls insisted on posting gossip about my private affairs.

  53. DaveScot wrote (in #41):

    “…trimming away those which are made unnecessary by the mechanism of intelligent agency.”

    “Trimming them away” how? Virtually none of the mechanisms I’ve listed are theoretical constructs. On the contrary, almost all of them are empirically verified processes, which have the effect of producing phenotypic variation. Since variation is the core of what we are all trying to understand here, it would seem much more logical to me to examine each of the mechanisms in the list, to determine exactly what kinds of effects they have on phenotypic change over time, and if any of them show any indication of foresight (a very difficult thing to do, BTW).

    And the number 47 is already out of date. The list grows longer every day, as more research results are published. Also, most of the entries in the list are simply “headings”, encompassing dozens (and in some cases hundreds) of different, related mechanisms of phenotypic variation.

  54. I will be on travel for a couple days before I return to this wonderful discussion.

    I wish Dr. Thomas English the best in his partnership with Robert Mark’s Evolutionary Informatics Lab. For the record, I stay out of decisions regarding who and who does not participate, excepting for the fact I can on occasion delete posts on threads that I begin if I feel a troll is in evidence.

    I have not excercised this option in this discussion so far, and I welcome hearing criticism from Dr. Bob OH and Dr. Allen MacNeill. I leave the moderation decisions to those who have been kind enough to volunteer their time for the task, and to them I extend my thanks for a thankless job.

    Regarding Natural Selection, my main point is that it must be disengaged in some way for diversity to exist.

    I think it can be mathematically argued natural selection can influence a mere 2 bits per 300 generations according to Haldane’s Dilemma. This is far slower than the slowest modem on Earth! Morse code transmissions are more efficient in infusing information.

    When I say 2 bits per generation, I mean the net gain. Because of interference selection, natural selection will destroy large numbers of good traits in addition to bad with a net gain of 2 bits per 300 generations according Haldane’s work and supported by Kimura.

    THERFORE, on a percentage basis 99.99% of evolution must be driven by mutation and stochastic factors or better yet, imho, front loading. If anything, Natural Selection gets in the way of increasing complexity and diversity rather than assisting it.

    The kinds mutations that drove evoltution in the past are probably no longer in operation today. That was John Davison’s thesis. There are some of us that believe in special creation (the very thing Darwin argued against). I’m only positing that if there were common descent, it had to proceed in the absence of Natural Selection exactly as Mae Wan Ho asserted:

    a relative lack of natural selection may be the prerequisite for major evolutionary advance

    and Michael Lynch

    many genomic features could not have emerged without a near-complete disengagement of the power of natural selection

    I think some are reluctant to put hard figures, but I would venture less than 1% is in the ball park for the influence of selection as far as the evolution of complexity. We know when there are selective sweeps where 99% of the population is wiped out (as in a pesticide or sweeps resulting in antibiotic resistance), it’s hard to argue there is much of an net gain of information!!!

    If we are talking about the speed that an evolutionary algorithm can infuse information into a genome, it’s pretty dang SLOW! There are finite speed limits to how fast Natural Selection can modify a genome or epigenetic information.

    I believe, statistically speaking, most of the mutations that would have had to drive evolution, had to do so without the sheparding of natural selection. I think front loading is the best scenario if one is a mutationist. I personally hold out hope for the special creation model, but this model so far is hard pressed to be demonstrated from scientific first principles, thus I’m left only arguing a few negative cases against prevailing views.

    From a scientific vantage point, I can only argue to the extent that David Berlinski is arguing, namely, in terms of what appears will not work for sure…and so far I think we can rule out Natural Selection as a major force for the evolution of complexity. Natural Selection seems to be more a destroyer than creator of complexity and diversity.

  55. “Canalization” as Waddington frist proposed it, and as Jablonka and Lamb have described it in their new book, doesn’t refer to “canals”. Rather, it refers to the idea that, as development proceeds, it develops a kind of “momentum” in which traits that were originally set in motion by genetic programs become modified and stabilized as the resjult of interactions with the environment. The metaphor that Waddington was using was “channelization” – the idea that, when water first runs over a surface (say at the top of a hill), it can flow almost anywhere. However, as it flows (and as more and more water follows it), it scours out channels that “canalize” where subsequent water flows can move.

    If this sounds like natural selection, that’s no accident. What Waddington was arguing for was a process like natural selection, but applied to the process of development, in which the genetic program of an organism is modified by interactions with the environment to produce the phenotype of the organism. Waddington was trying to explain why some genetic changes do not produce significant effects on phenotype. He proposed that the genome “gets the ball rolling”, but that most of the actual phenotype is the result of the “ball” wobbling down a series of “epigenetic trajectories”, in which historical contingency plays an enormously important role.

    Once again, this whole view of development and its relationship to evolution is almost completely outside the bounds of the “modern evolutionary synthesis” (aka “neo-darwinism”). It is, however, supported by massive and increasing amounts of empirical data, and represents the cutting edge of evolutionary theory today.

    Admittedly, we have a long way to go. We are only just beginning to understand how development is regulated, and the part that the environment plays in it. As we learn more about it, our models of how development and evolution are related inevitably change, to accommodate new research results.

    Again, I would urge ID supporters to recognize that there is nothing intrinsic to evolutionary theory that would necessarily rule out design in nature. Indeed, as I have argued in several venues, nature is packed with design; that’s what a genome is – a design for an organism. So the question really is, where does the information in the genome come from, and how much does it contribute to the actual phenotypes of organisms? How much of the “design” of an organism is provided by its environment? And can any of this be shown to be foresighted? All good questions, and all answerable by empirical research. However, absent empirical support, none of them can be answered by theoretical speculation alone.

  56. Allen, he is saying that from an informational perspective the principals that can be eventually said to govern species development with replace the chaotic physical ones that you listed once we understand their limits as well. You are talking about physical processes but ID is about the informational principals that complex specified information not only requires but can be reduced to via Intelligent Design explanation.

    This is obviously well in the future but Jonathan Wells thinks not too far in the near distant future. That is why Dave phrased his comment

    …and then…start trimming away…

    We have a lot of work to do but materialisms utter inadequacy as an explanatory template for origins requires it.

  57. As to the assertion that “common sense” can immediately answer questions about these topics, “common sense” tells me that the desk I am writing at is made of completely solid material, not mostly empty space, and that the light streaming down on it from my desk lamp should move faster with the rotation of the Earth than against it. That light also seems to have the characteristics of a wave-like process, as it clearly shows interference patterns at edges (I can see them pretty well, especially if I take off my glasses). And, “common sense” tells me that it should be possible to determine simultaneously both the momentum and position of a moving object, including an electron. After all, that’s how you catch a baseball, right? It’s just “common sense”.

    But we all know what happened to those “common sense” ideas…

  58. Sal:

    Have an enjoyable and safe trip!

    A clarification: I appreciate that you always address me as “Dr. MacNeill”, but the fact is that I do not have a PhD nor any other doctoral degree. I earned a bachelor’s degree in biology and a masters degree in science education, both from Cornell, but have been on (unofficial) leave from the PhD program here for nigh on thirty years.

    I am what is known in academic circles as “ABD”; I was hired over thirty years ago at Cornell without having finished a dissertation, and have never taken the time to do so. I would like to at some point; maybe after I retire?

    The lack of a PhD has not prevented me from teaching either introductory biology nor evolution at Cornell, where I have been nominated for and/or awarded several honors for my teaching, including the Clark Award for Outstanding Teaching at Cornell University.

    Nor has it prevented me from doing my own research. As a Senior Lecturer at Cornell, I am a full member of the faculty, but unlike my colleagues in tenure tracks, I can research quite literally anything I want, so long as I am willing to pay for it myself ;-)

    When I reflect on my lack of a doctoral degree, I consider the fact that neither did Charles Darwin nor Thomas Henry Huxley. Indeed, Darwin’s only academic degree was a bachelor’s degree in Anglican theology, and Huxley never finished his bachelor’s, joining the Royal Navy instead.

    Ergo, I conclude (perhaps a tad self-servingly) that one’s contributions to intellectual progress need not necessarily by tied to a string of letters following one’s name.

  59. Allen_MacNeill,

    “Once again, this whole view of development and its relationship to evolution is almost completely outside the bounds of the “modern evolutionary synthesis” (aka “neo-darwinism”). It is, however, supported by massive and increasing amounts of empirical data, and represents the cutting edge of evolutionary theory today.”

    I have to ask. Are you aware that most people – and I mean ID-proponents, ID-opponents, from every religious and areligious stripe – are utterly, blissfully unaware of this? That the typical view of evolution amounts to ‘stuff kills other stuff and the stuff that lives reproduces and that’s how we got apes’? Kind of excessively reducing it there, but it’s not far from the truth.

    I mean, I’ve seen people sternly correct others about how evolution was just mutation and natural selection, period. This, from people who believe in evolution.

    Just wondering.

  60. A clarification: I appreciate that you always address me as “Dr. MacNeill”, but the fact is that I do not have a PhD nor any other doctoral degree.

    Egad! Does that mean that “Dick the Dawk” is smarter than you (per the Machine video)? ;)

  61. Haha, yeah, I suppose so (if having a PhD makes one “smarter than you”).
    –Allen

  62. nullasalus wrote (in #59):

    “I’ve seen people sternly correct others about how evolution was just mutation and natural selection, period. This, from people who believe in evolution.”

    As have I. That was one of my motivations in posting my blog on the 47 mechanisms for producing phenotypic variation. I remember my evolution professor at Cornell railing about precisely the same problem, and about the grossly mistaken notion that natural selection is the principle creative process in evolution.

    Nothing could be further from the truth, of course. Natural selection produces absolutely nothing. It is an outcome, and is most emphatically not a “creative force.” The “creation” of new variation is what the “engines of variation” (the 47 different mechanisms) do, not natural selection.

    The whole point to natural selection is that it preserves those variations that have the effect of allowing those individuals who have them to survive and reproduce more often than other individuals who have different variations. This is why Darwin preferred the term “natural preservation” to “natural selection”, as the latter sounded too active, as well as too “intentional.” However, he waited too long to try to change the terminology. By the time he expressed this opinion (in a letter to Charles Lyell; see http://www.darwinproject.ac.uk.....-2931.html), “natural selection” had become entrenched in the vocabulary of evolutionary theory.

    On the other hand, natural selection is the explanation for why complex adaptations can evolve in surprisingly brief periods of time (e.g. 10,000 generations). Selection limits the possible range of variations in each generation to those that are closest to the forms that are already most adaptive.

  63. Allen_MacNeill (55): “So the question really is, where does the information in the genome come from, and how much does it contribute to the actual phenotypes of organisms? How much of the “design” of an organism is provided by its environment? And can any of this be shown to be foresighted?”

    Your posts are delightfully informative, as always. And these are good questions. However, there is a logical error in the following.

    (15): “If, however, the processes by which variation are produced can be shown convincingly to not demonstrate foresight (i.e. that they produce characters that, when produced, are not necessarily immediately adaptive, but become so following a change in environmental conditions), then ID is unnecessary as an hypothesis for the origin and proliferation of adaptive characters in populations.”

    This is assuming that all the new information comes from the engines of variation, with complexity only coming in the bottom-up fashion of being always preceded by a simpler ancestor. That might be so, but it also might not be so.

    You mentioned a friend’s thought that “It’s all been downhill since the Mesozoic.” What if there is more “downhill” to evolution than even your friend supposed?

    You acknowledged “Admittedly, we have a long way to go. We are only just beginning to understand how development is regulated, and the part that the environment plays in it. As we learn more about it, our models of how development and evolution are related inevitably change, to accommodate new research results.”

    This leaves open the possibility of instances front-loaded development where it truly is “downhill” with the crest of a hill as a starting point. Notice that in such a scenario, it is not necessary for the engines of variation to demonstrate any “foresight” in the sense of reliably yielded immediately adapted variation. Nevertheless, the conclusion that “ID is an unnecessary hypothesis” in this scenario is false. One valid hypothesis is that the role of ID was at the point of front-loading the organism with the information, control mechanisms, and/or potential regarding development that makes the diverse variations we see possible.

    In short, even though it may take no special intelligent intervention to roll downhill, employing variations that are not foresighful, that does not allow us to conclude that intelligent agency had no role, as you suggested. Rather, intelligence may be essential to getting to and starting from the top of a hill.

    I agree this cannot be decided by speculation. Just wanted to point out that your list of possibilities was too short, with an important omission.

  64. Allen_MacNeill,

    In (15) (I know, this is late) you wrote a couple of paragraphs which I am still trying to decipher. In the interest of not quoting you out of context, as you warned about, (or at least trying), I will quote them in full (I see one of them was quoted by ericB in (63)).

    If the processes by which variation are produced can be shown convincingly to demonstrate foresight (i.e. that they produce characters that, when produced, are already necessarily adaptive), then ID may be a reasonable and useful component of any hypothesis for the origin and proliferation of adaptive characters in populations.

    If, however, the processes by which variation are produced can be shown convincingly to not demonstrate foresight (i.e. that they produce characters that, when produced, are not necessarily immediately adaptive, but become so following a change in environmental conditions), then ID is unnecessary as an hypothesis for the origin and proliferation of adaptive characters in populations.

    The above apppears to be making two assumptions (among others). First, that we can study, in a given organism, the processes by which variation are produced, and that these can be identified with the processes whereby the organism itself was originally produced. The second is that if traits are somehow produced that are not adaptive at present, but become adaptive in a changed environment, this is somehow less indicative of foresight than the production of traits that are immediately adaptive.

    Now perhaps I have misunderstood you, and If so I would appreciate correction. If not, the second point seems weak, and the first counterfactual.

    Preadaptation seems to me to require more foresight than plain old ordinary adaptation. Adaptation can immediately be preserved and enhanced by natural selection, but preadaptation requires the preservation of traits that are not presently advantageous, and may even be presently deleterious, for some future advantage, and this foresight would seem to be a hallmark of intelligence. One could argue that if the adaptations are complex and specified enough, either one could be evidence of intelligence. But the reversal makes no sense to me. Putting a spare tire and a jack in a car takes at least as much intelligence as putting the original four tires on.

    But that seems a minor quibble compared to the question that can be raised about the first assumption. What this seems to be saying is that the 47 (and counting) sources of phenotypic variation in a given organism necessarily account for all the variation needed to create it, or to modify it from some previous organism. I’m not sure that this is accurate. An example might illustrate the problem.

    As you probably know, extensive attempts to take natural variations and artificially select them for the effect of a blue rose have uniformly resulted in failure. However, recently because of some careful gene insertions and manipulations, scientists have been able to produce a rose that can reasonably be described as blue, and that has no known counterpart in nature.

    Now supposing that we are alien scientists exploring the earth after a disastrous epidemic has wiped out humankind, and enough time has passed so that the products of civilization (including records of what happened to make the roses blue) have disappeared, but the varieties of roses live on. Could we apply those 47+ kinds of phenotypic variation to the roses now (then) existing and explain how the rose became blue? Would we not be tempted to call it “lateral gene transfer” (meaning undirected lateral gene transfer)? And would we not be dead wrong? How could we possibly arrive at the correct answer to the origin of blue roses without allowing for the possibility of intelligent design?

    Furthermore, imagine an island where blue roses were planted and survived because there were few natural enemies. We might observe the roses exhibiting many variants, and identify experimentally confirmable sources of variation until we were blue in the face, and still not be able to identify the correct reason why these roses differed from the vast majority of those on the mainland.

    Part of the problem would seem to stem (ahem) from the assumption that all causes that have ever operated are now operating roughly equally to how they operated in the past. For intelligent agents, that may not be a valid assumption. Intelligent agents may very well create episodically, and they are not required to create when we want them to so that we can see how it is done.

    I don’t see how your proposed way of determining whether ID is involved in present-day biology is either sensitive or specific. Perhaps you can clarify.

  65. Gentleman,

    This is wonderful discussion. I was en-route 16 hours yesterday, and it is good to be on my laptop again for a few minutes.

    I see that DaveScot has posted a link to the paper by Lewontin which I mentioned in my original posting. I thank him for finding the paper in the first place since I could not longer find it on the net.

    Lewontin’s paper was highly influential to Stanley Salthe and myself. It is technical, but wow, I learned so much from it. Lewontin was Gould’s colleague and also (along with Gould) a mentor to creationist Kurt Wise. When I asked Wise about Lewontin last year at Baraminology 2007, Wise spoke glowingly of Lewontin. It is easy to see why, when reading this paper…

    Salthe considered this paper fatal to Darwinian evolution becuase it showed the difficulty of defining fitness.

    Scroll to page 19:
    http://tinyurl.com/4sjthv

    To simplify:

    In Physics the notion of force is measured in Newtons or Pounds. We can measure mass by the amount of pounds of force a gravitational field creates on object. The typical measuring device is a scale. I can even compare apples and oranges using a scale. :-)

    In math, if objects A and B and C have real values, we can say:

    if A > B, and B > C, then A > C

    ( to put hard numbers, for example, consider A = 10, B =8, C = 5)

    This is the Transitive Property of Inequality. In this manner we have a means of even comparing apples and oranges. :-)

    We can objectively say, one object has more mass than another. We cannot say the same about biological organisms with respect to fitness.

    Lewontin demonstrated the difficulty of making such objective statements in defining fitness. For example, in sports competition we can’t make the following statement with certainty.

    If team A beat team B, and if team B beat team C, then team A will beat team C.

    Lewontin shows this difficulty with respect to the competition among varities, along with some very distressing situations where the defintion fitness varies radically with context. Thus Lewontin showed the difficulty in showing that fitness is anything more than a restatement of known statistics, and not a very good restatement at that.

    If fitness cannot obey the transitive properties of inequality (which is so fundamental to properties in physics and chemistry, or practically any other scientific discipline except Darwinian evolution), trying to use this concept to make statements about the evolution of complexity become essentially incoherent.

    We can compare apples and oranges in terms of their weight. Can we do so in terms of fitness? That’s the problem.

    At best we can say the statistics may be evolve in a way analogous to a Darwinian model, or it may not. If things can evolve in a manner that is non-Darwinian, then the question is how much evolution is Darwinian, how much is non-Darwinian. I have suggested based on the channel capacity problem and Haldane’s dilemma, that even if fitness could be defined (which as Lewontin showed is a hopless quest in general), only about 2 bits ber 300 generation could be attributable to Darwinian evoltuion. That correlates to less than .1% of the human genome. The rest of the evolutionary story, 99.9% is non-Darwinian. That figure is already roughly accepted for molecular evolution (Kimura and friends). The question then is why shouldn’t that figure apply to just about everything else (which is Nei’s thesis).

    I have suggested that Fisher’s theorem implies that selection actually has to be substantially relaxed to account for diversification, which will permit the evolution of complexity. The euphamism used by some to say this is “time-varying fitness landscapes”.

    So, on many accounts, independent of ID, I don’t think the overwhelming majority of evolution can be Darwinian. Lynch’s irritation is so great, he practicallly faults Dawkins and Dennent (as well as ID folks) for making evolution a caricature by ascribing so much power to selection.

    There are other naturalistic models for evolution that are non-Darwinian:

    1. Brain Goodmans evolution via cooperation (rather than competition)

    2. Saltationism, mutationism

    3. neutral theory

    Of course I have my ideas. My personal challenge is that it is hard to frame the answer in terms of direct empirical science. If God were readily apparent, I’d have an easier time arguing for special creation. ID on the other hand is at the doorstep of empirical science, but it is unfortunately still only and inference, it is not a direct empirical observation in the sense of observing mass or other physical quantities. The task is complicated because information and complexity (including specified complexity) is not a physical quantity.

  66. Allen wrote:

    The lack of a PhD has not prevented me from teaching either introductory biology nor evolution at Cornell, where I have been nominated for and/or awarded several honors for my teaching, including the Clark Award for Outstanding Teaching at Cornell University.

    And this relfects well on Cornell letting the best teachers teach independent of the letters after their name. The IDEA club there spoke highly of you and it is easy to see why. I think I would have very much enjoyed taking the classes you taught.

    And from my perspective, your Evolution and Design class at Cornell where the Bill Dembski and Michael Behe’s works were studied critically was the best course of its kind anywhere.

  67. scordova, (65)

    I did what you suggested and scrolled to what was labeled page 19 of

    http://tinyurl.com/4sjthv

    and was unable to see how page 19 or the immediately surrounding pages demonstrated the difficulty of defining fitness. Could you please check the reference here and/or explain how the printed material makes your point.

    Thanks

  68. Dr. Giem,

    My apologies for a bit of confusion. Lewontin’s essay begins on page 19, but his section on fitness begins on page 23.

    On page 24:

    The difficulties of the concept of fitness are, unfortunately, much deeper than the problem of frequency
    and density dependence. The problem is that it is not entirely clear what fitness is.

    In Fisher’s formulation fitness is growth rate. Thus bacteria are more fit than humans. Lewontin points out that these sort of notions are in conflict with Darwin’s notion of some sort of inherent biological property of what is “good”.

    Darwin’s sense of fit has been completely bypassed.

    For example, in sheer numbers, the mammalian eye would be less fit than the insect type eye(s). This is problematic for explaining the evolution of the mammalian eye in terms of fitness scores. This problem I think is pervasive….How can we explaing eukaryotes if prokaryotes are more “fit”?

    Lewontin wasn’t the easiest read, but each time I have re-read it I gain something more.

    If a type increases in a population then it is, by definition, more fit. But this suffers from two difficulties.
    First, it does not distinguish random changes in frequencies in finite populations from changes that are a consequence of different biological properties.
    Finally, it destroys any use of differential fitness as an
    explanation of change. It simply affirms that types
    change in frequency.
    But we already knew that.

  69. “It simply affirms that types
    change in frequency.”

    What causes these frequency changes?

  70. scordova, (68)

    I found out what I was doing wrong. The article you cite is found between pages 16 and 17, if you look at the bottom of the pages. My browser doesn’t give me precise PDF pages; instead I have to scroll down using the pages listed on the PDF. That of course threw me off.

    It is quite a delightful article.

  71. What causes these frequency changes?

    Jerry,

    I recommend the examples in the article itself.

    Frequency change can be due to:

    1. Random Drift
    2. Bad luck
    3. Intitial density of population
    4. Mix of population

    Problematic is defining “fit” in the most general sense as we define mass or force or temperature in physics or even moles in chemistry. If one cannot do this, one has to question the difficulty of putting selectionist theories on par with the other sciences. I think the neutralist theories are at least framed in a way that puts them on a more sound footing scientifically (I say that as one who actually rejects mainstream neutral theory).

    With respect to anti-biotic and pesticide resistance. The way we are able to argue for the presence of selection is repeated trials. If for example, one trait is observed in 100 petri dishes where anti-biotic resistence occurs and no resistance occurs in 100 petri dishes where the trait is absent, we can say a selectionist metaphor is applicable. In the absence of such repeated trials, how is it possible even in principle to argue selection was the cause or not. The only way I know how is to argue “not” through issues with population resources, as Kimura did using Haldane’s dilemma.

    However form Fisher’s fundamental theorem alone, it’s kind of hard to argue eukaryotic evolution from prokaryotes since, in terms of Matlthusian reproductive fitness, prokaryotes seem more “fit”.

    One might argue the exitence of allopatric (geographic) or sympatric niches to enable selection to work in selected isolated domains, but this seems like a special pleading. In such case, Goodman’s cooperative (versus competition) model would seem more accurate. i.e. a species develops ability to digest a different food source, thus it becomes sympatrically isolated without competing with the parent. The populations then live cooperatively together. This would accord well with symbotic and ecosystem evolution. I think Goodman is closer to the truth, but I say that as someone who personally disagrees with Goodman.

    PS
    by the way, I keep forgetting to list “self-organization” as a naturalistic theory. I consider that the main competitor to ID theories. I think Pigluicci of late is quite enamored with self-organization. So is Denton….

  72. Especially problematic is the phrase “random with respect to fitness”. If fitness cannot be defined in general (except for special cases like antibiotic resistance), then how can we even say “random with respect to fitness”?

    Sanford argues the difficulty with this becuase empirically speaking mutations on the whole do not seem random with respect to fitness. For example environmentally induced mutations (like radiation) seem to be statistically correlated against reproductive success, thus it is not random.

    On the other hand we have adapative mutation which seem positively correlated to fitness. Ok, for another naturalistic theory, consider the work of James Shapiro (who seems privately favorable to Behe).

    See Who are the Multiple Designers? James Shapiro offers some compelling answers

    Bacteria as natural genetic engineers….

    This remarkable series of observations requires us to revise basic ideas about biological information processing and recognize that even the smallest cells are sentient beings.

    Thus there are observed non-Darwinian modes of evoltution, an I would argue they constitute 99% of the evolutionary modes present today and in the past.

    I do believe in ID and even the more extreme hypothesis of special creation. The fundamental theorem of calculus was widely accepted as true even 300 years before it was proven. I think the case for special creation (if true) or ID might be in a similar boat. It may seem reasonable to many, but from a theoretical and empirical standpoint the proofs are not quite mature. Seeing these hypotheses put on a more solid foundation is my personal area of interest. Time will tell if ID proponents and their creationist cousins will be successful in these endeavors.

  73. I read the Lewontin article. It is a fascination article and I am glad it was recommended. It celebrates fitness as an important variable in evolution, not discounts it.

    In the examples on pages 24-26 it does not discount fitness but essentially says we do not know how to measure it. (Fitness may not be a single gene oriented concept by a gene network concept.) The examples used illustrate that varying environments and ecologies affect reproduction rates and measures the reproduction rates by variant. What can not be determined is what variables/networks determine the reproduction rates. It does not seem to be a random effect so it is variable related. So as the density of the population varies by the different species in the ecology, the reproduction rates vary by variant. What they cannot do is isolate the characteristics/networks within the species that are responsible for the varying reproduction rates when the various external variables are manipulated.

    The article highlights micro evolution and why macro evolution may be impossible because the variation within the gene pool does not have the variation necessary to do anything really complex. It also defines novelty as trivial and only as changes not seen before. It is not what we usually mean by novelty.

    I highly recommend that everyone read it and see if they come to the same conclusions that I did, which are different from Sal’s conclusions.

  74. 74

    scordova: How can we measure natural selection? Without going into the deep details, we conventionally assert selection exists if there has been a reduction in diversity in a population.

    So, according to the logic in the OP, how can Darwinian evolution produce diversity if by definition, natural selection decreases it?

    Maybe this should be a question on “Are you smarter than a fifth grader?”

    The most elementary formulation of evolution that I think anyone is familiar with always characterizes mutation and the like as the engine for producing variants, and natural selection as a culling factor. So what brilliant insight has been conveyed in the OP, or what oversight has been unveiled?

    The word mutation is only mentioned once in the entire piece:

    “But even granting this miracle set of mutations can happen, what role can selection possibly play?”

    This is merely a passing comment in a discussion regarding the evolution of a four chambered heart, and it is that discussion I want to focus on now. The central insight of the author is that if a four-chambered heart appeared, and was superior and thus replaced through natural selection the three-chambered heart, it would be a reduction in diversity, as there would only be one type of heart (4-chambered) whereas previously there were two types.

    But the logic of this utterly eludes me. From my perspective, a four-chambered heart is more diverse than a three chambered heart. It is certainly more complex, and I think ‘complex’ and ‘diverse’ or near synonyms.

    From my perspective as a software engineer, an increase in fitness always entails an increase in complexity. (We’ll get to Occam’s razor in a minute.) Let’s throw a very instructive cliche into the mix here: “The devil is in the details.” Your original understanding of a problem is nearly always incomplete, so your original solution may be very neat and tidy and elegant. But as you start testing it in real world situations, you start encountering exception after exception after exception, and you have to go back and modify your original solution continuously to account for all these exceptions. This is not merely a result of bad planning – you can imagine consumer’s giving feedback, “but I want this feature or that feature”, or maybe modifications are driven by a need to keep up with competitors or new technologies. So despite Gould’s claim that evolution does not necessarily entail an increase in complexity, I would strongly disagree with that. (Do society, technology, laws, etc. get more or less complex over time?) In spite of all this it is certainly and obviously true that if you can ever take some big chunk of your software, and say, “Wait a minute, I could replace this 200 lines of code with 10.” Then by all means do it. This is apparently the brilliant insight of Occam. So complexity in an artifact is often an indication of a lack of planning and foresight.

    By the end of this thread, Scordova is arguing that fitness is not even a meaningful concept:

    In math, if objects A and B and C have real values, we can say:
    if A > B, and B > C, then A > C
    ( to put hard numbers, for example, consider A = 10, B =8, C = 5)
    This is the Transitive Property of Inequality. In this manner we have a means of even comparing apples and oranges.
    We can objectively say, one object has more mass than another. We cannot say the same about biological organisms with respect to fitness.
    Lewontin demonstrated the difficulty of making such objective statements in defining fitness. For example, in sports competition we can’t make the following statement with certainty.
    If team A beat team B, and if team B beat team C, then team A will beat team C.
    Lewontin shows this difficulty with respect to the competition among varieties, along with some very distressing situations where the definition fitness varies radically with context. Thus Lewontin showed the difficulty in showing that fitness is anything more than a restatement of known statistics, and not a very good restatement at that.
    If fitness cannot obey the transitive properties of inequality (which is so fundamental to properties in physics and chemistry, or practically any other scientific discipline except Darwinian evolution), trying to use this concept to make statements about the evolution of complexity become essentially incoherent.

    So is scordova or Lewontin claiming that the concept of fitness among football teams is meaningless because the transitive property does not hold there (e.g. If team A beat team B, and if team B beat team C, then team A will beat team C. )

    Certainly I don’t think Lewontin believes this (or other thoughts scordova credits to him) as I think the football analogy is scordova’s. But let’s examine the analogy for a minute.

    If team A beat team B, and if team B beat team C, then it most certainly increases the probability that team A will beat team C (if that’s all you know about the teams).

    If through tradition Michigan has Cincinnati on their schedule every year, and beats them nearly every year and Cincinnati plays East Toledo State every year and beats them nearly every year, then certainly it is highly probable that if Michigan played East Toledo State, Michigan would beat them. Maybe some think these observations are too simplistic for this forum or thread, but apparently they elude scordova.

    But to continue with the sports analogy, Highly successful programs end up with teams from around the league snatching up all their assistant coaches and thus the strategies, schemes and plans of successful teams are disseminated around the league and persist for decades, long after these schemes are effective (e.g. “The West Coast Offense”). However The fact that fitness is certainly a meaningful concept in football does not imply that there is not also random genetic drift. You can have some obscure conference that for no apparent reason gets hot one year send a few teams to bowls, and then immediately descends back into obscurity. (Perhaps there’s a better analogy for genetic drift specifically, however.)

    Here was the transitivity problem in Lewontin’s words:

    In experiments involving competition of several genotypes taken two at a time, Dobhzansky (1948) showed lack of transitivity in fitness. That is, genotype A is more fit than genotype B in an experiment involving only these two genotypes, and B is more fit than C in two-way competition, but in three way competition C beats A.

    But does this imply that fitness is a vacuous concept (Or does Lewontin think that – I don’t think so.)

    In basketball, height is a huge advantage. In a one-on-one competition, even more so. But with five players on each side, throw an extremely quick but very short guard into the mix, and suddenly his height is not a factor. Does this make meaningless the concept of tallness or fitness? Hardly.

    (And for the record, in response to a remark made by someone recently in another thread, I am one of those people that still believes the story of Noah’s ark is literally true.)

  75. [...] Fisher’s analysis of the effect of gambler’s ruin essentially trashes his own theorem, Fisher’s Fundamental Theorem of Natural Selection. Fisher’s Malthusian notions of “fitness” in his fundamental theorem do not [...]

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