Chance and Selection

Darwin’s conforming of his theory to the old vera causa ideal shows that the theory of natural selection is probabilistic not because it introduces a probabilistic law or principle, but because it invokes a probabilistic cause, natural selection, definable as nonfortuitous differential reproduction of hereditary variants.

Chance features twice in this causal process. The generation of hereditary variants may be a matter of chance; but their subsequent populational fate is not; for their physical property differences are sources of causal bias giving them different chances of survival and reproduction. This distinguishes selection from any process of drift through fortuitous differential reproduction in the accumulation of random or indiscriminate errors of sampling. To confirm the theory of natural selection empirically is to confirm that this probabilistic causal process exists, is competent, and has been responsible for evolution. Such hypotheses are both falsifiable and verifiable, in principle, if not in practice.

Natural selection has been accepted and developed by biologists with very diverse attitudes toward chance and chances. But the theory and its acceptance have always involved probabilistic causal judgments that cannot be reduced to correlational ones. So, the theory has contributed to a probabilistic shift within the development of causal science, not to any probabilistic rebellion in favor of science without causes.

– M.J.S. Hodge
– Natural Selection as a Causal, Empirical, and Probabilistic Theory
– The Probablistic Revolution: Volume 2
– p. 233

Thoughts?

130 Replies to “Chance and Selection”

  1. J-Mac
    Ignored
    says:

    What Joe is worried about, that if there is a strong element of randomness in natural selection, then the process loses it ascribed creative power. The finding of novelty in structures and functions in the vast space of non-function without direction natural selection is unlikely to hit the functional target….

  2. Mung Mung
    Ignored
    says:

    dazz is focused on survival and and leaving more offspring. Genes for intelligence come in a distant second to the survival and reproduction imperative.

  3. Neil Rickert
    Ignored
    says:

    Moved a couple of comments to guano.

    Please try to avoid the insults.

  4. Mung Mung
    Ignored
    says:

    The Genetical Theory of Natural Selection
    Chapter 4
    page 73
    The chance of survival of an individual gene

    …the probablities…these contingencies…the chance…the chance…the total chance…an independent probability…the chance…the probabilities…it is probable…independent chance of success…the chance…the chances… the probability…the chance of survival…a chance of about 1 in 50…

    dazzplosion!

  5. J-Mac
    Ignored
    says:

    Joe Felsenstein: Do you think that, in population genetics, an allele that has lower fitness is certain not to increase?

    So what if it does? It can still be easily lost in the natural population…

  6. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    So what I get from all this is that phoodoo, Mung and J-Mac

    1. … do want to establish that selection is a stochastic process so they can take that to mean that it will be ineffective in changing gene frequency in the direction that would increase fitness (or increase function, if we have a model of how phenotypes affect fitness),

    2. … often get confused about whether we are talking about the net effect of selection and genetic drift, or whether we are talking about selection. If I acknowledge that the net effect of the two processes is stochastic, they take that as an admission that the selection part is stochastic.

    3. … have not a clue as to how much effect selection has in the presence of genetic drift. (Hint: it depends on population size; this is covered in some of the texts they are cutting and pasting from.)

  7. Allan Miller
    Ignored
    says:

    Mung,

    But because I don’t want dazz to think that we’re complete IDiots, if an allele does get fixed in spite of it’s lower fitness, we can always blame that on drift and thus save our theory from falsification. How convenient.

    You want people to agree that selection is a stochastic process, but when the inevitable consequences of it being a stochastic process are conceded – that sometimes the ‘fittest’ alleles are not the ones that prevail – you get all snippy.

  8. Allan Miller
    Ignored
    says:

    Creationists and probability is quite a thing to behold. If ‘random’ effects can cause a certain result in smaller samples, that result apparently remains equally likely as one increases sample size, or number of trials. If ‘fitter’ alleles can be lost, they will always be lost, no matter how many trials are performed, and no matter their current frequency. The Law of Large Numbers passes them by.

  9. J-Mac
    Ignored
    says:

    Joe Felsenstein:
    So what I get from all this is that phoodoo, Mung and J-Mac

    1. … do want to establish that selection is a stochastic process so they can take that to mean that it will be ineffective in changing gene frequency in the direction that would increase fitness (or increase function, if we have a model of how phenotypes affect fitness),

    2.… often get confused about whether we are talking about the net effect of selection and genetic drift, or whether we are talking about selection.If I acknowledge that the net effect of the two processes is stochastic, they take that as an admission that the selection part is stochastic.

    3. … have not a clue as to how much effect selection has in the presence of genetic drift.(Hint: it depends on population size; this is covered in some of the texts they are cutting and pasting from.)

    So, Joe has read the papers he claims we have been pasting from and missed the essence; the most important points?
    Or has he deliberately omitted them?

    Why doesn’t he say YES or NO whether there is an inescapable, strong element of randomness in natural selection; that the great number of progeny are eliminated by random processes rather than worrying how this fact is going to be used?

  10. phoodoo
    Ignored
    says:

    Joe Felsenstein,

    How do we distinguish drift from beneficial?

  11. newton
    Ignored
    says:

    phoodoo:
    Joe Felsenstein,

    How do we distinguish drift from beneficial?

    One starts with a “d”, the other a “b”

  12. J-Mac
    Ignored
    says:

    1. “Despite the impossibility to produce a strictly deterministic model for natural selection in the face of myriad varying parameters, there have been several attempts to quantitatively assess this problem. Fisher, perhaps the most important forerunner of the neo-Darwinian theory, has calculated (1930) that new alleles with even 1% selective advantage (i.e., more than is usually expected by neo-Darwinian theorists), will routinely be lost in natural populations. According to these calculations the likelihood of loosing a new allele with 1% advantage or no advantage is more than 90% in the next 31 generations (Fisher, 1930/1958; Dobzhansky, 1951; Schmidt, 1985; see also ReMine, 1993; Futuyma, 1998; Maynard Smith, 1998). Considering genetic drift, i.e. random fluctuations of gene frequencies in populations, Griffith and colleagues state in agreement with these authors (1999, p. 564):

    Even a new mutation that is slightly favorable will usually be lost in the first few generations after it appears in the population, a victim of genetic drift. If a new mutation has a selective advantage of S in the heterozygote in which it appears, then the chance is only 2S that the mutation will ever succeed in taking over the population. So a mutation that is 1 percent better in fitness than the standard allele in the population will be lost 98 percent of the time by genetic drift.”

  13. phoodoo
    Ignored
    says:

    J-Mac: So a mutation that is 1 percent better in fitness than the standard allele in the population will be lost 98 percent of the time by genetic drift.”

    I think what this is saying is that most of the time the alleles that are fittest, aren’t the fittest, until sometimes when they become the fittest.

  14. J-Mac
    Ignored
    says:

    2.
    “Nevertheless, it appears that if such a mutation occurred at a constant rate in a large population, it would have a fair chance to become established after an average occurrence of about 50 times. However, such estimates are made on exceedingly imperfect assumptions biased in favor of the modern synthesis. Note that the basis of these calculations are dominant mutant alleles with 1% fitness increase in the heterozygous state. In the plant kingdom, however, more than 98% of all the mutations are recessive and more than 99.99% of the dominant (as well as homozygous recessive) mutants in the plant and animal kingdoms are lowering fitness. Modifications, juvenile stages, and the endlessly varying environmental parameters are not (and hardly can be) taken into account, nor is the objection of the French biologists quoted above addressed. Dobzhansky’s “death and destruction of a majority of the individuals” occurs mainly before sexual maturity – as can be seen, for instance, each spring when billions of tree-seedlings appear, of which only an extremely low minority will ever become adult or full-grown trees: obviously the environment is far more relevant than a 1% genetic advantage.

    Most importantly, the calculations are invalid for small populations where most of the evolutionary novelties are said to have arisen according to the neo-Darwinian theory of evolution and punctuated equilibrium alike (Gould & Eldredge, 1993; Mayr, 1976/1997, 1998; Stanley, 1999). In a small population the rate of advantageous mutations is extremely low (if they appear at all; aeons of time are needed to obtain the average 50 identical advantageous dominant mutations for one success) and genetic drift is almost totally substituting natural selection. Also, it is not possible in nature to raise mutation rates indefinitely since error catastrophe occurs when the mutation rate is too high, thereby terminating the existence of the population.

    Neutral, slightly deleterious and moderately favorable alleles all have nearly equal chances to spread in diploid populations – as the neutral theory of population genetics has definitely shown (Kimura, 1983; ReMine, 1993; see already Fisher, 1958). The neutral theory “contends that at the molecular level the majority of evolutionary changes and much of the variability within species are caused neither by positive selection of advantageous alleles nor by balancing selection, but by random genetic drift of mutant alleles that are selectively neutral or nearly so” (Li, 1997, p. 55). Hence, the net result of larger numbers of gene mutations can mean overall degeneration of a species instead of ‘upward‘ evolution. Moreover, the costs of the many substitutions necessary for neo-Darwinian evolution to function successfully in large populations can quickly surpass the adaptive possibilities of a species (see the discussions of Haldane’s Dilemma by Dobzhansky et al., 1977; and especially ReMine, 1993.)”

  15. newton
    Ignored
    says:

    phoodoo: I think what this is saying is that most of the time the alleles that are fittest, aren’t the fittest, until sometimes when they become the fittes

    Like when say a comet slams into the earth and changes the rules of the game.

  16. J-Mac
    Ignored
    says:

    phoodoo: I think what this is saying is that most of the time the alleles that are fittest, aren’t the fittest, until sometimes when they become the fittest.

    Even if the alleles are beneficial with 1% selective advantage or no advantage (as per population genetics, they are lost 98% of the times by genetic drift… (see my next comment).

  17. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    J-Mac: Even if the alleles are beneficial with 1% selective advantage or no advantage (as per population genetics, they are lost 98% of the times by genetic drift… (see my next comment).

    This is true when they start out as one copy in a large population of (say) 1,000,000 individuals, with a selection coefficient of 0.01.

    Now we need to compare that to what would happen if the allele were instead selectively neutral. Then the probability of fixation is the same as the initial gene frequency of the allele, which is 1 part in 2,000,000 or 0.0000005.

    40,000-fold less. In this case natural selection is very effective.

  18. J-Mac
    Ignored
    says:

    Joe Felsenstein: This is true when they start out as one copy in a large population of (say) 1,000,000 individuals, with a selection coefficient of 0.01.

    Now we need to compare that to what would happen if the allele were instead selectively neutral.Then the probability of fixation is the same as the initial gene frequency of the allele, which is 1 part in 2,000,000 or0.0000005.

    40,000-fold less.In this case natural selection is very effective.

    So, what you are claiming is the size of the population is important or natural selection is ineffective?

    Did you read my quote # 2?

  19. Mung Mung
    Ignored
    says:

    phoodoo: How do we distinguish drift from beneficial?

    The rate of fixation.

  20. Mung Mung
    Ignored
    says:

    Joe Felsenstein: Now we need to compare that to what would happen if the allele were instead selectively neutral. Then the probability of fixation is the same as the initial gene frequency of the allele…

    So without selection it is probabilistic, but with selection it is not probabilistic?

    Because, presumably, there is then (with selection) no longer any probability of fixation.

  21. dazz dazz
    Ignored
    says:

    J-Mac: So, what you are claiming is the size of the population is important or natural selection is ineffective?

    Even I know that. FFS, do you realise you’re talking with a fucking living legend in Joe Felsenstein?

  22. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Mung: So without selection it is probabilistic, but with selection it is not probabilistic?

    Because, presumably, there is then (with selection) no longer any probability of fixation.

    Wow, I really must have been totally unclear. If the “it” in these cases is selection, then, no that “it” is not probabilistic in these cases. In all cases there is also genetic drift. When that is present, the overall process, the result of natural selection and genetic drift, is probabilistic. When the overall process is “it”, then “it” is probabilistic in both cases.

    But the natural selection part is not probabilistic.

  23. phoodoo
    Ignored
    says:

    Joe Felsenstein,

    Joe, how do you know if something is genetic drift or natural selection?

  24. J-Mac
    Ignored
    says:

    dazz: Even I know that. FFS, do you realise you’re talking with a fucking living legend in Joe Felsenstein?

    Are you sure that the living legend, Joe Felsenstein and possibly FFS – whoever that is, agree that natural selection is ineffective unless there is right size of the population?
    Take it away all four!

  25. J-Mac
    Ignored
    says:

    Joe Felsenstein: Wow, I really must have been totally unclear.If the “it” in these cases is selection, then, no that “it” is not probabilistic in these cases.In all cases there is also genetic drift.When that is present, the overall process, the result of natural selection and genetic drift, is probabilistic.When the overall process is “it”, then “it” is probabilistic in both cases.

    But the natural selection part is not probabilistic.

    How do you like that answer, Mung?
    A story like that has gotta be true…

  26. Allan Miller
    Ignored
    says:

    J-Mac,

    Are you sure that the living legend, Joe Felsenstein and possibly FFS – whoever that is, agree that natural selection is ineffective unless there is right size of the population?

    So do you think populations are always too small for natural selection to be effective?

  27. Flint
    Ignored
    says:

    J-Mac:

    Why doesn’t he say YES or NO whether there is an inescapable, strong element of randomness in natural selection; that the great number of progeny are eliminated by random processes rather than worrying how this fact is going to be used?

    Seems to me selection has NO random component. Selection is by definition the opposite of random. But you might be confusing selection with survival. Think of the Real World as an essentially random filter. If the majority of organisms entering that filter have been selected for some trait, the majority of organisms surviving that filter will ALSO have that trait.

  28. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    phoodoo: Joe, how do you know if something is genetic drift or natural selection?

    I have used here the analogy with particles in suspension in a liquid, acted upon by gravity and by Brownian Motion. Suppose that, after 10 seconds, one of them is observed to be somewhat closer to the bottom of the container. Do we try to figure out whether that “is” the result of Brownian Motion or of gravity? Is it a devastating rebuttal of physical theory if we can’t easily say which? If we say that it is the net result of both?

  29. J-Mac
    Ignored
    says:

    Joe Felsenstein: This is true when they start out as one copy in a large population of (say) 1,000,000 individuals, with a selection coefficient of 0.01.

    Now we need to compare that to what would happen if the allele were instead selectively neutral.Then the probability of fixation is the same as the initial gene frequency of the allele, which is 1 part in 2,000,000 or0.0000005.

    40,000-fold less.In this case natural selection is very effective.

    Off it goes the omnipotence of natural selection…

  30. J-Mac
    Ignored
    says:

    Flint: Seems to me selection has NO random component. Selection is by definition the opposite of random. But you might be confusing selection with survival. Think of the Real World as an essentially random filter. If the majority of organisms entering that filter have been selected for some trait, the majority of organisms surviving that filter will ALSO have that trait.

    Have your read all my comments? No. So read them…
    Out of necessity, there has to be a strong element of randomness in natural selection for the populations to remain numerically stable;

    “…A single individual of the fungus Lycoperdon bovista produces 7 x 10 ^11 spores; Sisymbrium sophia and Nicotiana tabacum, respectively, 730,000 and 360,000 seed; salmon, 28,000,000 eggs per season; and the American oyster up to 114,000,000 eggs in a single spawning….

    Then we have random genetic drift…
    Is it still random as Larry Moran insists it to be?

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