Complexity

Discussion in 'Health and medical' started by Chupacabra, Apr 14, 2004.

  1. Guy Hoelzer

    Guy Hoelzer Guest

    in article [email protected], Larry Moran at
    [email protected] wrote on 5/27/04 9:40 AM:

    > On Wed, 26 May 2004 23:12:56 +0000 (UTC), Tim Tyler
    > <[email protected]> wrote:
    >> Larry Moran <[email protected]> wrote or
    >> quoted:
    >
    > [snip]
    >
    >>> Hmmm ... I think I see your objection. You want a
    >>> precise definition of evolutionary change so you can
    >>> objectively analyze the mechanisms. I've been assuming
    >>> all along that changes are most easily quantified by
    >>> adding up mutations in DNA but you don't seem to accept
    >>> that particular measure.
    >>
    >> It's a great measure - but not the /only/ one - and as I
    >> mentioned in another post, it has some definite flaws as
    >> a metric of evolutionary change.
    >
    > What are the flaws ... other than the fact that it leads
    > to a conclusion you don't like?

    It seems to me that Tim and Larry are talking past each
    other. I think the cryptic difference underlying there
    differences have to do with the level of evolutionary
    interest. Tim is focusing on the evolution of populations of
    organisms in which DNA sequences are only tangentially
    relevant, while Larry is focusing on the evolution of
    populations of DNA sequences in which the organisms are only
    tangential vehicles (sensu Dawkins). If I may be so bold as
    to try to answer Larry's question on Tim's behalf, I would
    say that the nonlinearities involved in the
    genotype/phenotype map make DNA variation a generally poor
    marker of organismal evolution. In support of Larry's view,
    I would also argue that neutral genetic variation is
    generally useful for phylogenetic reconstruction; but then
    patterns of evolutionary path isolation lacks much of what
    is sought by those interested in processes of organismal
    evolution. The molecular phylogeny is often seen as a useful
    tool with which one can begin to map patterns of phenotypic
    change, but this is where the interesting questions can
    begin for those focused on organismal evolution.

    >> I am not my mind. I am not my body. I am not my DNA
    >> sequence ;-)
    >
    > What the heck does this mean? I sounds like new-age
    > doublespeak.

    I think it means that parsing the DNA sequences out of
    organisms fails to represent so much about the organism that
    it is doomed to incompleteness as a method for understanding
    organismal evolution.

    >>> It was obvious to me. If a new set of limbs is due to 74
    >>> different base substitutions in DNA then that's how you
    >>> measure it and compare it to, for example, 74 single
    >>> neutral base substitutions. I think you want to
    >>> substitute a subjective measure where a new set of limbs
    >>> has a much higher score because it's more significant to
    >>> your way of thinking. This is a new idea to me. Do you
    >>> have a clear quantitative way of calculating the score
    >>> of morphological changes or is this just a sleight-of-
    >>> hand way of trying to argue in favor of the supremacy of
    >>> natural selection?
    >>
    >> I hope not the latter ;-)
    >
    > Me too, but I'm not holding my breath. :)
    >
    >> Quanifying phenotypic change is difficult.
    >
    > That's probably why it isn't very useful. It's too
    > subjective and it ignores all the other kinds of
    > evolutionary change.

    DNA sequences may be objectively determined, but they too
    ignore all other kinds of evolutionary change at the
    organismal level (e.g., cultural evolution, epigenetic
    effects, developmental effects of sequence rearrangements
    that do not involve changes in nucleotide identities). Why
    doesn't your argument lead you to the conclusion that
    studying DNA sequences "isn't very useful" as a way to
    understand organismal evolution? [Note that I am not making
    this argument myself. I am just trying to explore the
    present argument.]

    >> However, the phenotypes of living organisms still form a
    >> tree where qualities very along the branches.
    >
    > You can group species by clades if you concentrate on
    > certain kinds of morphological change (shared derived
    > characters = synapomorphies). This requires you to pretty
    > much ignore most phenotypic change and it certainly isn't
    > quantitative. Besides, we have plenty of examples were it
    > led to an incorrect conclusion that was fixed by looking
    > at DNA/protein sequences. Even more important, it hardly
    > worked at all for bacteria and single-celled eukaryotes.

    All of this sounds like "hot air" to me. Plenty of molecular
    phylogenies have been in error, too. Does that mean they
    weren't quantitative or objective? I am sure you would agree
    that this should not cause us to give up on molecular
    systematics.

    >> Taxonomists don't *have* to look at an organisms' DNA
    >> sequence to begin to answer questions about which other
    >> organisms it is most closely related to.
    >
    > That's correct. It's quite possible to look at a subset of
    > all evolutionary change in order to work out some of the
    > history. This applies to morphological change as well as
    > to DNA/protein sequence change. Do you have a point?
    >
    >> As for general-purpose metrics - there are several of
    >> them. Length, lifespan, mass and number of cell types are
    >> all fairly useful means of quantifying evolutionary
    >> change.
    >
    > Now were getting a bit silly .....

    Silly? I can only attribute this comment to Larry's
    unvarying focus on the DNA level of evolution. These metrics
    of phenotypic dimensions would indeed seem besides the point
    to someone uninterested in organismal evolution. To anyone
    interested in the evolution of organismal form and function,
    these would seem like fundamental metrics in the study of
    evolution.

    >>> BTW, I'm not conceding that all morphological change is
    >>> due to natural selection. Do you have a quantifiable
    >>> measure of the amount of morphological change that's due
    >>> to natural selection?
    >>
    >> My impression is that this depends in a big way on the
    >> effective population size.
    >>
    >> In "small" populations, the founder effect is the
    >> main force.
    >>
    >> In "large" populations, the founder effect is of low
    >> relevance, and selective forces tend to dominate as
    >> causes of phenotypic change.
    >
    > Do you have a quantifiable measure of the amount of
    > morphological change that's due to natural selection?
    >
    >> This is *only* if you ignore neutral mutations, of
    >> course.
    >
    > What does this mean? I'm asking for a way to distinguish
    > between morphological change that's due to natural
    > selection and morphological change that's neutral. How can
    > you "ignore" neutral mutations when you can't even
    > identify them?

    I don't personally know of one. On the other hand, I think
    it is useful to begin moving beyond the notion of a
    drift/selection dichotomy, which should make a quantitative
    approach to evolutionary process at the whole organism level
    more tractable.

    >> *If* you use a metric that measures raw genome hamming
    >> distance, random noise is indeed the cause of most
    >> changes.
    >
    > "Random noise" is a loaded phrase that reveals a great
    > deal about your biases.
    >
    >> However, random noise is like radio static - interesting
    >> if you are wondering how far away the transmitter is -
    >> but if you are trying to listen to the radio program, it
    >> just gets in the way.
    >
    > I'm interested in molecular evolution and deep phylogeny.
    > Natural selection just gets in the way of such studies and
    > may even invalidate them. Natural selection is sort of
    > like radio static to me - I have to put up with it but I
    > try to ignore it whenever possible. However, in spite of
    > my personal interests I would never try and define natural
    > selection out of existence just because I'm not very
    > interested in it. That would not be scientific.

    Very well said.

    Regards,

    Guy
     


  2. [email protected] (Larry Moran) wrote in
    news:[email protected]:

    > On Tue, 25 May 2004 23:48:32 +0000 (UTC), William Morse
    > <[email protected]> wrote:

    (snip)

    >> I know there has been a previous discussion on the
    >> definition of evolution, and in many ways I can agree
    >> with the definition of any change in gene frequency as
    >> evolution, but I'm having difficulty resisting the
    >> temptation of playing devil's advocate.

    > No problem, playing devil's advocate can be a very
    > effective learning tool. Let's see if we can learn
    > something ....

    >> Now first I would like to clarify something. Bob's
    >> original agreement was that drift is unquestionably the
    >> main mechanism of change at the sequence level. I also
    >> agree with this. However change at the sequence level is
    >> not evolution by the generally accepted definition of
    >> evolution as change in "gene" frequency, at least not
    >> until the change in sequence affects the function of the
    >> "gene".

    > Evolution is the change in frequency of *alleles*, not
    > genes. Alleles are any differences in base sequence at a
    > particular position in the genome. This definition of
    > alleles has evolved from the original definition since
    > we've learned that lots of DNA isn't part of genes.

    A very wise man has said the following:

    "When biologists say that they have observed evolution they
    mean that they have detected a change in the frequency of
    _genes_ in a population." (emphasis added)

    The same wise man also suggested the following definition:

    "Evolution is a process that results in heritable changes in
    a population spread over many generations."

    (And just in case you get any ideas, if you start quoting
    things I have previously said back at me I'll come and stuff
    your hard drive full of peanut butter. Toronto ain't all
    that far from Syracuse :)

    Now you may call it quibbling, but in my book an SNP with no
    change in function does not qualify as an allele.It is not
    "a change". In my defense I quote the following definition
    for allele:

    "one of two alternate forms of a gene that can have the same
    locus on homologous chromosomes and are responsible for
    alternative traits;"

    Note the emphasis on traits. Again, a non-functional SNP
    doesn't qualify.

    >> Now as to actual changes in gene function, as far as I
    >> know there is still debate as to the relative importance
    >> of drift vs. selection in gene frequencies, so I would
    >> have to take issue with your characterization "by far",
    >> although you may well be correct about "majority".

    > If you want to redefine evolution so that it only refers
    > to changes in the functions of genes then that's a
    > possible way of restoring the supremacy of natural
    > selection. I think this is carrying devil's advocacy too
    > far but let's see where it takes us. Can you give me a
    > more precise definition of evolution that your devil would
    > like to defend? :)

    Now I can't define evolution only as changes in functions
    of genes unless I can define genes, and I don't really
    want to try to do that. Furthermore, a change in a
    regulatory sequence would certainly also qualify as
    evolution in my book. However I do not see a substitution
    of alanine for glycine in a region far from the active
    site of an enzyme as necessarily contributing anything to
    evolution. So let's try this:

    Evolution is a heritable, statistically significant
    change in a population of organisms that can be
    detected without using either DNA or protein
    sequence data.

    This sort of definition gets away from the problem of trying
    to define a gene and from assuming that "junk" DNA is
    actually junk. It has the advantage of including non-
    morphological changes, since I can presumably detect say a
    5% difference in Km for a dehydrogenase even if it doesn't
    affect morphology.

    Now under this definition, I am guessing that while the
    combination of neutral mutations and sampling error may
    still comprise the majority of evolutionary change, it will
    be a tight race with natural selection.

    >> But in either case:
    >>
    >> Since the extent of drift due to sampling error is
    >> dependent on effective population size, and since
    >> effective population size is dependent on the niche, and
    >> since selection pressure is also governed by the niche,
    >> it is clear to me that ecological niche development is
    >> the main mechanism of evolutionary change.

    > The overall rate and extent of evolution by random genetic
    > drift is independent of population size. Your devil seems
    > to be redefining random genetic drift as well as
    > evolution. Can you give me his new definition of random
    > genetic drift and the new population genetics equations
    > that support his statement?

    I had a rant about this subject recently, and it seems to
    be rearing its ugly head again. Are you including sampling
    error as part of drift, or defining drift as just neutral
    mutations? My statement on population size dependence only
    applies to sampling error - which is in fact exactly what
    I said ;-) The population genetics equation for this type
    of drift is:

    delta q = pq/2N

    (note that my reference for this is Wilson (1975), so I am
    risking putting foot in mouth, but that won't be anything
    new)(And also note that this is based on the definition of
    an allele to include SNP's :-( )

    Last time I checked my basic algebra textbooks this equation
    would indicate that drift is in fact inversely proportional
    to population size.

    > Niches are vastly overrated but they are popular among the
    > adaptionist crowd who believes that environmental change
    > drives evolution. Can your devil give me an estimate of
    > the total amount of evolution that is "driven" by niche
    > development as opposed to evolution that occurs in the
    > absence of any significant change in niches? Does your
    > devil believe that natural selection can only occur when
    > species move into a new niche?

    Apparently you are accusing adaptationists of being niche-
    pickers :)

    But I am going to put this back on you. Since in fact
    sampling error is dependent on population size, which is
    determined by the niche, all of this form of evolution is
    dependent on niches. It still may not be "driven" by niche
    development, since a stable niche that results in a small
    effective population size will still yield evolution due
    to sampling error drift. This was the original thrust of
    my statement - which was admittedly bait to get a comment
    from you - that even though drift is the proximate cause
    of the change in "effective allele" frequency, the
    ultimate cause is the niche that results in a low N. What
    I would ask you is, what is the total amount of sequence
    change that is due solely to neutral mutation, and of this
    change, what is the likelihood that a cumulative series of
    SNP's that are individually neutral will result in an
    effective change in a trait.

    I would like to spend more time on the subject of niches,
    but this is getting long and that subject might be better
    treated in a new thread.

    Yours,

    Bill Morse
     
  3. John Wilkins

    John Wilkins Guest

    Phil Roberts, Jr. <[email protected]> wrote:

    > John Wilkins wrote:
    > > Phil Roberts, Jr. <[email protected]> wrote:
    > >
    > >>
    > >>I agree with you about logic. One of the brightest among
    > >>us (Aristotle for instance) managed to cognize the order
    > >>in the manner in which we cognize order. But unlike my
    > >>read of you so far, I believe who ever this individual
    > >>was, he had intellectual acuities that went far beyond
    > >>rote learning and trial and error, the so-called
    > >>"darwinian" approach as you have deemed it, I believe.
    > >
    > >
    > > Well, all I can say is that there is no way I can
    > > conceive of for this to occur, apart from noetic rays or
    > > clairvoyance or divine revelation.
    > >
    >
    > Nah! It just presupposes that there's a little more to
    > reasoning than rote learning, that perceptiveness,
    > intuitiveness, brilliant insights that just pop up with
    > Aha! experiences are central to scientific progress, and
    > that most of this occurres at subconscious levels and
    > about which little is currently understood. But I think
    > Hume at least gave us a nudge forward in his recognition
    > of the centrality of the role of comparing. We'll just
    > have to agree to disagree on this. But your contention
    > that my claim that a central feature of reaoning is 'the
    > capacity to cognize abstruse similarity and difference'
    > requires invoking divine creation to explain its presence
    > is one hell of a stretch, if you don't mind my saying so.

    Then how do you account for that ability? In other words,
    where does the cognitive power come from? Why do brains work
    when they model their environment? I can't think of any
    other ways to ask that critical question...
    >
    > >
    > > I am not in this sense a Kantian (which is whence we get
    > > the pure and practical reason distinction, and the means
    > > and end contrast).
    > >
    >
    > Actually, the paradigm for the rationalty of ends is not
    > the categorical imperative but rather 'the equal weight'
    > criterion:

    I wasn't referring to the categorical imperative. ...
    >
    > Notice that this criterion entails two assumptions:
    >
    > 1. That rationality entails self-interest.
    > 2. That within the perimeter of self-interest,
    > rationality entails VALUATIVE OBJECTIVITY.
    >
    > I believe 1 is highly suspect, as exemplified in the
    > Parfit quote on self-interest I posted last time.

    You read widely, but I'd appreciate page numbers, so I can
    check the context of the discussions.

    Might I note that "self-interest" in our context merely
    requires the maximisation of the fitness of a particular
    allele? The interests of the constituted person are
    different. Genetic self-interest is not, so to speak,
    transitive all the way to social behavior, in large part
    because genes are not rigid determinants of behavior.

    <snip Luce and Rafffia>
    > >
    > > The rationality here is one of a course of action to be
    > > taken in a situation of agreed value and conflict of
    > > interest. But this is a very limited form of
    > > rationality.
    >
    > Its also a "theory" of rationality that is self-defeating
    > (e.g., see
    > p. 12 of Parfit's 'Reasons and Persons' and sanctions
    > rational irrationalty. So, although of practical value,
    > from an epistemic perspective such theories of
    > rationality are non-starters. There also lots of other
    > limitations, as Coleman points out, in addition to the
    > long standing acknowledged ones (Newcomb's problem,
    > prisoner's dillema, etc.). BTW, all these paradoxes and
    > contradictions can be circumvented if you simply assume
    > that 'being rational' is a matter of 'being objective',
    > not only cognitively, but valuatively as well. You also
    > arrive at the conslusion that the increased valuative
    > objectivity observable in man (increased intrinsic
    > valuing of non-related other juxtaposed with an
    > incrased volatility in self-value) constitutes evidence
    > that our species has become TOO RATIONAL (too valuative
    > objective) relative to the "ruthless selfishness"
    > predicted by our formal models. It doesn't explain the
    > anomality in our valuative profile, but it at least
    > offers us a new way of looking at the problem.

    I'm a bit lost here. How is one to be objective in
    valuation? Is there a gold standard? In biology, valuative
    assessments (by biologists about the organisms, not by the
    organisms themselves) are always relative to alternatives -
    strategies, genes, forms, traits, whatever - in the
    competitive population. There is nothing to be objective
    about a priori, only ever post hoc, although there are
    clearly objective physical facts; how they play out is
    generally unknown ahead of time.
    >
    > > This is why game theory is applicable to evolution - the
    > > "rational egoism" is specified in a very specific sense
    > > - of maximising the number of copies of a gene. But this
    > > does not transfer to social behaviors directly. Social
    > > action is not selfish because we can model genes as if
    > > they were selfish (something Dawkins notes quite
    > > explicitly in the Afterword to the 1989 edition of The
    > > Selfish Gene).
    >
    > But this gene selfishness should almost always translate
    > to plain old selfishness. The exceptions are "limited" and
    > "special". IOW, far from resolving the enigma of human
    > morality, as Wilson seemed to be implying in the last
    > chapter of Sociobiology, our fomral models have ONLY
    > SERVED TO DEEPEN THE MYSTERY.
    >
    > Your confusing co-operation with true concern for others.
    > The first can be explained, the second isn't so simple.

    The second is not entirely proven to exist :) I believe it
    is an illusion, myself. We have mechanisms (I hesitate to
    use the evpsych term "module") that enable us to imagine
    ourselves into the subjective states of others with some
    reliability; call it empathy. The reason we have this is not
    so that we can be saintly and care for all God's chillun,
    but because in having that we manage to maximise our fitness
    in our social environment.
    >
    > This is tricky stuff, but in general you should be able to
    > get lots of instrumental valueing of others out of
    > intellignece, but extremely limited intrinsic valuing of
    > others (immediate kin) out of natural selection, at least
    > to the extent that natural selection operates in the
    > manner in which it has been mathematically modeled. Humans
    > are wildly outside the parameters predicted by these
    > models by the way, which is precisely why Dawkins has
    > thrown up his hands and declared the need for a full
    > fledged addendum to the theory in order to accomodate the
    > benevolent selfishness found in man (e.g., concern for a
    > bird with a broken wing) and to a lesser extent, in
    > species phylogenetically proximal to man.

    I agree that the current models don't go all the way, but
    I think that has more to do with the problems of
    conceptualisation of what and how, than of the underlying
    logic. I think that we have genetic strategies in place
    for maximisation, not merely of parental investment, but
    of social investment. In short, we evolved a reciprocal
    altruistic strategy in order to ensure that we assist
    each other's progeny, so long as they are suitably
    related. The problem comes in when we try to apply that
    stratgy outside the EEA.
    >
    > >
    > > Genes can be considered *as if* they were selfish
    > > players in a game, and the end result of this selection
    > > can be apparently altruistic behavior on the part of the
    > > organisms, due to kin selection, and the fact that
    > > iterated Prisoner's Dilemmas (uncommunicative dilemmas
    > > where either one player loses out or both do less well
    > > than the optimum) will, if the initial population is
    > > suitably composed, evolve into equilibrium of "tit for
    > > tat" strategies.
    > >
    >
    > This is all pretty old stuff. Axelrod is the authority
    > most often cited that I'm aware of.

    Yep. Sorry for patronising you, but it's hard to know what
    people know over the internet.
    >
    > I agree with you that you can get lots of co-operation and
    > social contracts out of intelligence. And I agree that
    > most of this will be adaptive. But I disagree that that
    > automatically constitutes an explanation of the VALUATIVE
    > ANOMALIES in our species valuative profile (an inceased
    > intrinsic valuing of non-related others juxtaposed with an
    > increased volatility in self-value). That's an entirely
    > different subject altogether. And so far nothin you have
    > brought up even scratches the surface on the topic I
    > assumed we were discussing (valuative anomalies).

    OK. What anomalies, in detail? Are they anomalies from the
    environment of evolutionary adaptedness (EEA) or are they
    anomalies in modern society (agrarian and later), which is
    not at all what we adapted to when our strategies went to
    fixation for whatever reason?
    >
    > > In short, cooperation can evolve through the
    > > maximisation of genetic fitness. It won't always, but
    > > there is absolutely no justification for the direct
    > > transference of selfishness from the level of the gene
    > > to that of the individual or social group, contrary to
    > > Ghiselin's sarcastic and cynical comment, "scratch an
    > > altruist and watch a hypocrite bleed). It's all about
    > > keeping your levels straight when determining the
    > > interest bearers.
    > >
    >
    > Agreed. But when do we get to start talking about the
    > subject I am interested in, anomalies in our species
    > valuative profile.
    >
    > >>
    > > 9/11 poses nothing we didn't already know from a couple
    > > of millenia of documented fanaticism. It just hit
    > > America hard, that's all (from a theoretical
    > > perspective; it hit me hard as I had friends near
    > > there, and I had just been there a couple of months
    > > prior). There is no anomaly to deal with, but a well-
    > > known fact of cultural dynamics.
    > >
    >
    > True. But I'm not looking at 9/11 though my fellow human
    > being glasses, but rather through my natural scientist
    > glasses. There's one hell of a difference between what I
    > have come to expect from my fellow man and what I have a
    > right to expect from an organism designed by natural
    > selection. The latter is not a free ride, but comes
    > equipped with some fairly SEVERE CONSTRAINTS on what we
    > have a right to expect. If flying planes into buildings is
    > evidence to you of genes that have been endlessly honed to
    > maximnize reproductive success, maybe you ought to think
    > about going into a different occupation, John. :)

    Certainly I won't try to maximise *my* genes that way. But
    we want an explanation of the modules (damn! I used that
    term!) that, when placed into the modern situation, generate
    that behavior. I believe that what is adaptive is not the
    behavior, but the strategy that makes cultural "kin" take
    the place of genetic kin. Once upon a time (i.e., in the
    EEA) there would be no distinction between genetic
    relationship and cultural identity. It follows that if we
    evolved our defence of culture as a way of defending our
    genetic relatives, when the two were coterminous, the mere
    fact that modern social evolution has prised the two apart
    is irrelevant.
    >
    > What would an organism have to do before you finally got
    > around to considering its behavior anomalous? Or are you
    > suggesting we simply adopt nat selection as an
    > unfalisifiable dogma. Hey. If we're going to start a
    > religion here, I got dibs on being the Pope. :)

    Well, it is a truth by definition that what we see around
    must be able to remain around. But this is a slightly less
    truistic approach. I am making a claim that social
    structures are the result of particular strategies that once
    enabled us to maximise our genetic fitness, and which are
    still not so deleterious as to be the subject of massive
    selection against them. Few Muslims, for example, have blown
    themselves up in the Jihad, and their immediate kin are
    treated with respect. I think that this is a pretty
    nonanomalous case.
    --
    John S Wilkins PhD - www.wilkins.id.au a little emptier, a
    little spent as always by that quiver in the self,
    subjugated, yes, and obedient. -- Seamus Heaney
     
  4. Anon.

    Anon. Guest

    Larry Moran wrote:
    > On Tue, 25 May 2004 23:48:33 +0000 (UTC), Anon.
    > <[email protected]> wrote:
    >
    >>Larry Moran wrote:
    >>
    >>>On Sun, 23 May 2004 18:07:23 +0000 (UTC), A non.
    >>><[email protected]> wrote:
    >>
    >
    > [snip]
    >
    >
    >>>>I think I can still use my same question: Doesn't that
    >>>>depend on how you measure evolutionary change? It's not
    >>>>clear to me that we have to measure it at the sequence
    >>>>level.
    >>>
    >>>I didn't say you *have* to measure it at the sequence
    >>>level. I just said that when you take into account ALL
    >>>evolutionary change, including change at the sequence
    >>>level, then drift is the main mechanism.
    >>>
    >>
    >>To measure "all evolutionary change" you have to measure
    >>both phenotypic and genotypic change. How do you put these
    >>onto the same scale? You have to weight them somehow, and
    >>it's not clear to me that there is a unique way of doing
    >>this - it will depend on your ideas about the relative
    >>importance of the genotypic and phenotypic levels in
    >>evolution. You can, I think, get either selection, or
    >>drift, (or contingency?) as being the most important
    >>mechanism, depending on how you weight them.
    >
    >
    > Why not give it a try? We already have an effective and
    > quantitatvie way of measuring evolution by looking at
    > changes in DNA sequence. If you want to find a more
    > effective measure then let's see what you come up with.

    The first eigen value of the transition matrix for the
    changes in the phenotypic traits? You can define the process
    in either discrete or continuous time. You can even use a
    hierarchical model so that you can include discrete traits.

    It's not clear to me that simply looking at changes in DNA
    sequence is a good measure of evolution - how do you deal
    with polymorphism?

    Hmm, Actually, you can use the same sorts of models as I've
    suggested for phenotypic traits.

    So
    > far, all I've seen is some warm fuzzy feeling that
    > "phenotypic change" should get a higher score in order to
    > restore the supremacy of natural selection as a mechanism
    > of evolution. Can you turn that subjective feeling into a
    > scientific definition that we can examine?
    >
    That's a mis-representation - I'm not arguing that
    phenotypic change should get a highe score, but rather that
    there is no obvious single score, so whatever measure you
    use is subjective. Why remove phenotypic traits from
    evolution?

    > Let's take the evolution of humans and chimps as an
    > example. We already know that they differ by about 2% in
    > DNA sequence. How would you evaluate the "phenotypic
    > changes" along each lineage in order to arrive at some
    > quantitative measure of the amount of evolution in each
    > species from the time of the last common ancestor? How
    > much of that is due to natural selection?
    >
    That's actually something I'm starting to work on. Over
    short time scales, one can compare Fst and Qst (e.g.
    Palo et al. 2003 Molecular Ecology, 12: 1963-1978) but
    some more work needs to be done to find a more
    quantitaive formulation. I've started work with a
    colleague on the variation between species, but I'm not
    sure how that will pan out.

    Bob

    --
    Bob O'Hara

    Dept. of Mathematics and Statistics
    P.O. Box 4 (Yliopistonkatu 5) FIN-00014 University of
    Helsinki Finland Telephone: +358-9-191 23743 Mobile:
    +358 50 599 0540 Fax: +358-9-191 22 779 WWW:
    http://www.RNI.Helsinki.FI/~boh/ Journal of Negative
    Results - EEB: http://www.jnr-eeb.org
     
  5. Larry Moran

    Larry Moran Guest

    On Thu, 27 May 2004 16:40:40 +0000 (UTC),
    William Morse <[email protected]> wrote:
    > [email protected] (Larry Moran) wrote in
    > news:[email protected]:
    >
    >> On Tue, 25 May 2004 23:48:32 +0000 (UTC), William Morse
    >> <[email protected]> wrote:
    >
    > (snip)
    >
    >>> I know there has been a previous discussion on the
    >>> definition of evolution, and in many ways I can agree
    >>> with the definition of any change in gene frequency as
    >>> evolution, but I'm having difficulty resisting the
    >>> temptation of playing devil's advocate.
    >
    >> No problem, playing devil's advocate can be a very
    >> effective learning tool. Let's see if we can learn
    >> something ....
    >
    >>> Now first I would like to clarify something. Bob's
    >>> original agreement was that drift is unquestionably the
    >>> main mechanism of change at the sequence level. I also
    >>> agree with this. However change at the sequence level is
    >>> not evolution by the generally accepted definition of
    >>> evolution as change in "gene" frequency, at least not
    >>> until the change in sequence affects the function of the
    >>> "gene".
    >
    >> Evolution is the change in frequency of *alleles*, not
    >> genes. Alleles are any differences in base sequence at a
    >> particular position in the genome. This definition of
    >> alleles has evolved from the original definition since
    >> we've learned that lots of DNA isn't part of genes.
    >
    > A very wise man has said the following:
    >
    > "When biologists say that they have observed evolution
    > they mean that they have detected a change in the
    > frequency of _genes_ in a population." (emphasis added)

    This is the sort of thing a wise man might say to those who
    won't quibble about the defintion of a gene.

    > The same wise man also suggested the following definition:
    >
    > "Evolution is a process that results in heritable changes
    > in a population spread over many generations."

    This must have been a very wise man. By saying "heritable
    changes" you avoid semantic quibbles over the definition of
    an allele.

    > (And just in case you get any ideas, if you start quoting
    > things I have previously said back at me I'll come and
    > stuff your hard drive full of peanut butter. Toronto ain't
    > all that far from Syracuse :)

    Don't worry ... I haven't paid much attention to anything
    you've said in the past. :)

    > Now you may call it quibbling, but in my book an SNP with
    > no change in function does not qualify as an allele. It is
    > not "a change". In my defense I quote the following
    > definition for allele:
    >
    > "one of two alternate forms of a gene that can have the
    > same locus on homologous chromosomes and are responsible
    > for alternative traits;"
    >
    > Note the emphasis on traits. Again, a non-functional SNP
    > doesn't qualify.

    Let's no quibble. The minimal definition of evolution is a
    change in the heritable characteristics of a population over
    time. Changes in junk DNA count as evolution by this
    definition whether you want to call them alleles or not.
    They my not be very interesting changes to most people who
    aren't interested in genomes but that doesn't mean they
    don't exist.

    Would you prefer a definition where evolution is confined to
    changes in genes (alleles by your definition)? Do you
    realize what this would mean?

    >>> Now as to actual changes in gene function, as far as I
    >>> know there is still debate as to the relative importance
    >>> of drift vs. selection in gene frequencies, so I would
    >>> have to take issue with your characterization "by far",
    >>> although you may well be correct about "majority".
    >
    >> If you want to redefine evolution so that it only refers
    >> to changes in the functions of genes then that's a
    >> possible way of restoring the supremacy of natural
    >> selection. I think this is carrying devil's advocacy too
    >> far but let's see where it takes us. Can you give me a
    >> more precise definition of evolution that your devil
    >> would like to defend? :)
    >
    > Now I can't define evolution only as changes in functions
    > of genes unless I can define genes, and I don't really
    > want to try to do that. Furthermore, a change in a
    > regulatory sequence would certainly also qualify as
    > evolution in my book. However I do not see a substitution
    > of alanine for glycine in a region far from the active
    > site of an enzyme as necessarily contributing anything to
    > evolution. So let's try this:
    >
    > Evolution is a heritable, statistically significant
    > change in a population of organisms that can be
    > detected without using either DNA or protein
    > sequence data.

    I'm not going to argue with you over new definitions. If you
    can convince the scientific community to accept this then
    I'll bow to the consensus. Good luck.

    > This sort of definition gets away from the problem of
    > trying to define a gene and from assuming that "junk" DNA
    > is actually junk. It has the advantage of including non-
    > morphological changes, since I can presumably detect say a
    > 5% difference in Km for a dehydrogenase even if it doesn't
    > affect morphology.
    >
    > Now under this definition, I am guessing that while the
    > combination of neutral mutations and sampling error may
    > still comprise the majority of evolutionary change, it
    > will be a tight race with natural selection.

    Perhaps. Is that the main reason for re-defining evolution?

    >>> But in either case:
    >>>
    >>> Since the extent of drift due to sampling error is
    >>> dependent on effective population size, and since
    >>> effective population size is dependent on the niche, and
    >>> since selection pressure is also governed by the niche,
    >>> it is clear to me that ecological niche development is
    >>> the main mechanism of evolutionary change.
    >
    >> The overall rate and extent of evolution by random
    >> genetic drift is independent of population size. Your
    >> devil seems to be redefining random genetic drift as well
    >> as evolution. Can you give me his new definition of
    >> random genetic drift and the new population genetics
    >> equations that support his statement?
    >
    > I had a rant about this subject recently, and it seems to
    > be rearing its ugly head again. Are you including sampling
    > error as part of drift, or defining drift as just neutral
    > mutations? My statement on population size dependence only
    > applies to sampling error - which is in fact exactly what
    > I said ;-) The population genetics equation for this type
    > of drift is:
    >
    > delta q = pq/2N
    >
    > (note that my reference for this is Wilson (1975), so I am
    > risking putting foot in mouth, but that won't be anything
    > new)(And also note that this is based on the definition of
    > an allele to include SNP's :-( )
    >
    > Last time I checked my basic algebra textbooks this
    > equation would indicate that drift is in fact inversely
    > proportional to population size.

    This is true for a particular individual allele. If it
    occurs in a large population it will likely be eliminated.
    If it occurs in a small population it has a better chance of
    being fixed.

    However, when you look at the overall rate of evolution by
    random genetic drift you have to take into account two
    things: the probabilty of fixation, and the rate of
    mutation. There are more mutations in a large population and
    this exactly balances the decrease in the probabilty of
    fixation. Thus, the rate of fixation of new alleles in a
    diploid population is ....

    K = 2Nu (1/2N) = u

    where u (mu) is the rate of mutation. The overall rate of
    evolution by random genetic drift is independant of
    population size.

    >> Niches are vastly overrated but they are popular among
    >> the adaptionist crowd who believes that environmental
    >> change drives evolution. Can your devil give me an
    >> estimate of the total amount of evolution that is
    >> "driven" by niche development as opposed to evolution
    >> that occurs in the absence of any significant change in
    >> niches? Does your devil believe that natural selection
    >> can only occur when species move into a new niche?
    >
    > Apparently you are accusing adaptationists of being niche-
    > pickers :)

    I like that ... can I use it?

    > But I am going to put this back on you. Since in fact
    > sampling error is dependent on population size, which is
    > determined by the niche, all of this form of evolution is
    > dependent on niches.

    The rate of evolution by random genetic drift (sampling
    error) is independent of population size.

    Thanks for playing. There are no consolation prizes for niche-
    pickers. :)

    > It still may not be "driven" by niche development, since a
    > stable niche that results in a small effective population
    > size will still yield evolution due to sampling error
    > drift. This was the original thrust of my statement -
    > which was admittedly bait to get a comment from you - that
    > even though drift is the proximate cause of the change in
    > "effective allele" frequency, the ultimate cause is the
    > niche that results in a low N. What I would ask you is,
    > what is the total amount of sequence change that is due
    > solely to neutral mutation, and of this change, what is
    > the likelihood that a cumulative series of SNP's that are
    > individually neutral will result in an effective change in
    > a trait.
    >
    > I would like to spend more time on the subject of niches,
    > but this is getting long and that subject might be better
    > treated in a new thread.

    You mean we have to find a new niche?

    Larry Moran
     
  6. Larry Moran

    Larry Moran Guest

    On Thu, 27 May 2004 16:40:43 +0000 (UTC),
    Anon. <[email protected]> wrote:
    > Larry Moran wrote:
    >> On Tue, 25 May 2004 23:48:33 +0000 (UTC), Anon.
    >> <[email protected]> wrote:

    [snip]

    >> Why not give it a try? We already have an effective and
    >> quantitatvie way of measuring evolution by looking at
    >> changes in DNA sequence. If you want to find a more
    >> effective measure then let's see what you come up with.
    >
    > The first eigen value of the transition matrix for the
    > changes in the phenotypic traits? You can define the
    > process in either discrete or continuous time. You can
    > even use a hierarchical model so that you can include
    > discrete traits.

    Damn! I wish I thought of that. It's so sbvious.

    > It's not clear to me that simply looking at changes in DNA
    > sequence is a good measure of evolution - how do you deal
    > with polymorphism?

    Polymorphisms are evolution in progess. How do you deal
    with them?

    > Hmm, Actually, you can use the same sorts of models as
    > I've suggested for phenotypic traits.
    >
    > So
    >> far, all I've seen is some warm fuzzy feeling that
    >> "phenotypic change" should get a higher score in order to
    >> restore the supremacy of natural selection as a mechanism
    >> of evolution. Can you turn that subjective feeling into a
    >> scientific definition that we can examine?
    >>
    > That's a mis-representation - I'm not arguing that
    > phenotypic change should get a highe score, but rather
    > that there is no obvious single score, so whatever measure
    > you use is subjective. Why remove phenotypic traits from
    > evolution?

    Because nucleotide changes are mutations and because
    phenotypic traits are the result of, not the cause, of
    (some) mutation?

    >> Let's take the evolution of humans and chimps as an
    >> example. We already know that they differ by about 2% in
    >> DNA sequence. How would you evaluate the "phenotypic
    >> changes" along each lineage in order to arrive at some
    >> quantitative measure of the amount of evolution in each
    >> species from the time of the last common ancestor? How
    >> much of that is due to natural selection?
    >>
    > That's actually something I'm starting to work on. Over
    > short time scales, one can compare Fst and Qst (e.g. Palo
    > et al. 2003 Molecular Ecology, 12: 1963-1978) but some
    > more work needs to be done to find a more quantitaive
    > formulation. I've started work with a colleague on the
    > variation between species, but I'm not sure how that will
    > pan out.

    Let me know if you get anywhere and we'll see if the
    scientific community will agree to change the definitions.

    Larry Moran
     
  7. Anon.

    Anon. Guest

    John Edser wrote:
    >>>BOH:- The means of quantifying "all evolutionary change"
    >>>here is not clear. State the metric used - and the
    >>>question of whether genetic drift comes in at the #1
    >>>position will probably be clearer.
    >>
    >
    >
    >>LM:- I mean the sum all evolutionary changes of any sort
    >> by whatever definitions are used by a large number of
    >> scientists.
    >
    >
    >>JE:- Pardon me butting in but.. please state what would be
    >>EXCLUDED from such an _amazingly_ wide acceptance of what
    >>you insist can _scientifically_ constitute "evolution",
    >>i.e. please provide at least one example of a _non_
    >>evolutionary change within a biological system.
    >
    Any change that isn't heritable.

    >>LM:- Did you have something else in mind that would shift
    >> random genetic drift into second place?
    >
    >
    >>JE:- Darwinian natural selection, exactly as Darwin stated
    >>it but with his implicit assumptions made explicit.
    >
    >
    > BOH:- I think I should point out that John's definition of
    > fitness excludes the possibility of drift (because he
    > defines fitness in terms of the actual number of
    > offspring, rather than the expected value).
    >
    > JE:- Dr O'Hara has misrepresented my position. Drift is
    > _included_ as temporal variation (random variation over
    > time) within Darwinian selective events.

    John, what is your definition of fitness? I was specifically
    describing your definition of fitness, but in your reply you
    didn't make any mention of it, so it's not clear to me how
    I've misrepresented you.

    Bob

    --
    Bob O'Hara

    Dept. of Mathematics and Statistics
    P.O. Box 4 (Yliopistonkatu 5) FIN-00014 University of
    Helsinki Finland Telephone: +358-9-191 23743 Mobile:
    +358 50 599 0540 Fax: +358-9-191 22 779 WWW:
    http://www.RNI.Helsinki.FI/~boh/ Journal of Negative
    Results - EEB: http://www.jnr-eeb.org
     
  8. John Edser

    John Edser Guest

    > PR:- Your confusing co-operation with true concern for
    > others. The first can be explained, the second isn't
    > so simple.

    JW:- The second is not entirely proven to exist :) I
    believe it is an illusion, myself. We have mechanisms (I
    hesitate to use the evpsych term "module") that enable us to
    imagine ourselves into the subjective states of others with
    some reliability; call it empathy. The reason we have this
    is not so that we can be saintly and care for all God's
    chillun, but because in having that we manage to maximise
    our fitness in our social environment.

    JE:- I suggest that compassion as action (not the emotion of
    pity) is based on cognition. Here a person can hypothesise
    themselves into a situation that another
    is/may be, experiencing. I reason that this is the by
    product of an essential psychology required to evolve
    mutualised exchange using cognition. Trade is by far, the
    most significant human adaptation. Here, humans have to
    provide a testable picture of:
    1) others, their personal property and values.
    2) a testable comparative evaluation of what all sides have
    to offer for exchange.
    3) a real negotiated exchange that is mutually acceptable,
    without appropriation. Violence can produce a mutual loss
    in absolute terms for everyone concerned, even if a
    relative gain is secured by one respondee.

    Nature will not select a selectee that only secures a
    relative gain at a cost greater than a _mutualised_ gain for
    self. Helping mutualised respondee's does provide a gain to
    self because the gains are mutual. Such gains increase
    geometrically as the size of the mutualised group expands.
    If you do not end up with a group to mutualise within, or
    the size of your mutualised group is reduced because the
    individuals concerned fail to defend it, or you cannot
    quickly move to join another, the individual concerned will
    suffer enormous losses. As the gains to individuals
    increases via mutualised exchange (exponentially as the size
    of the group increases) the cost of defending the group that
    provides these gains also increases where the risk of death
    to an individual defending their group may be small, but
    real. A psychological group defence process could be
    selected for at the Darwinian individual level that in rare
    circumstances causes individuals to be irresistibly driven
    to sacrifice themselves to their trading group. Humans can
    commit suicide. This proves to me that emotion can over-ride
    reason even for survival. If the cognitive system attempts
    to stop such emotions it can be subverted by common beliefs,
    e.g. religious teachings of a better life after death. While
    this type of teaching remains non testable, all nature
    has to do is provide an emotion to convince believers
    that these types of beliefs are true.

    Mutual exchange is a difficult process. Building up respect
    within a group takes time. The maximum time available is one
    Darwinian time frame: the time required for one parent to
    complete a reproductive total of fertile forms within one
    population. One bad response can mean a group refuses an
    individual mutual exchange resulting in enormous losses for
    that individual. The opportunity cost of a failed mutualised
    gain is a large cost for any respondee to bear. Nature can
    only select for those that minimise this cost. The net
    effect is an "everybody wins", situation but not equally.
    This provides an unsolved problem.

    An unfortunate by product of trading cognition is the
    ability to compare gains. Envy and greed are both ethically,
    the opposite side of the same psychological adaptation. Any
    psychology that allows respondee's to exchange must also
    allow them to envy larger gains than their own. This
    produces greed that results in violence and a reduction in
    the total mutualised gains for all concerned. Nature cannot
    eliminate envy and greed without eliminating the cognition
    that allows trade in the first place, so we are stuck with
    it. Unless we can deal with this using cognition, the danger
    remains that greed may extinguish homo sapiens via insane
    acts or war. Ethically, violence used to defend individuals
    rights to trade must be separated from violence employed to
    remove it.

    > PR:- This is tricky stuff, but in general you should be
    > able to get lots of instrumental valueing of others out of
    > intellignece, but extremely limited intrinsic valuing of
    > others (immediate kin) out of natural selection, at least
    > to the extent that natural selection operates in the
    > manner in which it has been mathematically modeled.

    JE:- The models remain inadequate and are continually
    misused. Hamilton's model, which dominates Neo Darwinism in
    2004, cannot differentiate between organism fitness altruism
    (OFA) and organism fitness mutualism (OFM) because no
    Darwinian time frame exists within it. If the value cmax
    (maximum cost to the altruist) is appended to the model it
    can be proven that only OFM is operating within Hamilton's
    rule. The Neo Darwinians that post to sbe refuse to discuss
    it. They prefer to pretend that just an "instant now"
    relative comparison is all that is required to separate OFA
    from OFM when this relative measure was always insufficient.

    > PR:- Humans are wildly outside the parameters predicted by
    > these models by the way, which is precisely why Dawkins
    > has thrown up his hands and declared the need for a full
    > fledged addendum to the theory in order to accomodate the
    > benevolent selfishness found in man (e.g., concern for a
    > bird with a broken wing) and to a lesser extent, in
    > species phylogenetically proximal to man.

    JW:- I agree that the current models don't go all the way,
    but I think that has more to do with the problems of
    conceptualisation of what and how, than of the underlying
    logic. I think that we have genetic strategies in place
    for maximisation, not merely of parental investment, but
    of social investment. In short, we evolved a reciprocal
    altruistic strategy in order to ensure that we assist each
    other's progeny, so long as they are suitably related. The
    problem comes in when we try to apply that strategy
    outside the EEA.

    JE:- The so called "reciprocal altruistic strategy" is just
    a twisted version of OFM. Neo Darwinistic logic is so
    biased for OFA that the mutualisation that has been
    modelled are mostly mutual losses and not mutualised, total
    fitness gains.

    Regards,

    John Edser Independent Researcher (Posting from the Isle Of
    Sky, Scotland)

    PO Box 266 Church Pt NSW 2105 Australia

    [email protected]
     
  9. John Edser

    John Edser Guest

    >>>BOH:- The means of quantifying "all evolutionary change"
    >>>here is not clear. State the metric used - and the
    >>>question of whether genetic drift comes in at the #1
    >>>position will probably be clearer.

    >>LM:- I mean the sum all evolutionary changes of any sort
    >> by whatever definitions are used by a large number of
    >> scientists.

    >>JE:- Pardon me butting in but.. please state what would be
    >>EXCLUDED from such an _amazingly_ wide acceptance of what
    >>you insist can _scientifically_ constitute "evolution",
    >>i.e. please provide at least one example of a _non_
    >>evolutionary change within a biological system.

    BOH:- Any change that isn't heritable.

    JE:- The above becomes a self fulfilling prophecy when
    genetic epistasis is _defined_ as "inherited" but not
    "heritable" and thus, "selectable". Redefining genetic
    epistasis as additive just deletes all genetic epistasis,
    i.e. is only a gerrymander. The problem of heritable
    epistatic information has to be tackled in view of the fact
    that all genomic genes are epistatic to just _one_ fitness
    value: the Darwinian fitness total of each selectee which is
    a finite, _absolute_ value.

    >>LM:- Did you have something else in mind that would shift
    >> random genetic drift into second place?

    >>JE:- Darwinian natural selection, exactly as Darwin stated
    >>it but with his implicit assumptions made explicit.

    > BOH:- I think I should point out that John's definition of
    > fitness excludes the possibility of drift (because he
    > defines fitness in terms of the actual number of
    > offspring, rather than the expected value).

    > JE:- Dr O'Hara has misrepresented my position. Drift is
    > _included_ as temporal variation (random variation over
    > time) within Darwinian selective events.

    BOH:- John, what is your definition of fitness? I was
    specifically describing your definition of fitness, but in
    your reply you didn't make any mention of it, so it's not
    clear to me how I've misrepresented you.

    JE:- It is not how I define it but how Darwin would
    have defined it after his implicit assumptions were
    made explicit.

    I have posted what Darwinian fitness is (and the reverse
    engineering experiment needed to prove it) countless times,
    including, within this thread.

    _____________________________________________________
    Darwinian fitness is the _total_ number of _fertile_ forms
    reproduced by _one_ Darwinian selectee (one fertile form)
    within _one_ population.
    _____________________________________________________

    The reverse engineering experiment that proves the above is
    the case artificially holds the total number of fertile
    forms reproduced into one population by every Darwinian
    selectee within it, to remain equal for as long as is
    possible. The predicted result: all selection is halted
    within the experiment. Only Darwinian fitness equality can
    stop entirely, all selection within one population. No other
    altered defined fitness can halt entirely, natural
    selection. Thus Darwinian fitness provides an "on the face
    of it" view that is _alone_ required to cause evolution by
    natural selection. This means that multi level views of
    fitness can be validly deleted by Occam's Razor.

    Within this experiment random processes such as genetic
    drift, now work within a _controlled_ environment. The
    outcome is predicted to be the dissolution of all
    selectee's within the experimental population. This would
    prove that genetic drift, or any other random process,
    cannot cause evolution without selection. Of course,
    selection can cause evolution without genetic drift. Thus
    Dr Moran's case stands refuted.

    Neither Dr O'Hara, Dr Moran or anybody else here will even
    comment on the experimental confirmation that genetic drift
    can only validly constitute temporal variation and not
    evolution. If evolution is allowed to be redefined as
    dissolution then "anything goes" and no science of
    evolutionary theory now exists.

    Only Dr Hoelzer has commented on my proposed reverse
    engineering proof of what Darwinian fitness actually
    is. He only commented that he found it "interesting". It
    seems to me that Neo Darwinists are at a loss to
    know how to respond to the experimental proof of
    what Darwinian fitness actually is so they prefer to
    just ignore it. So much for Neo Darwinistic
    integrity and progress.

    Best Wishes,

    John Edser Independent Researcher

    PO Box 266 Church Pt NSW 2105 Australia

    [email protected]
     
  10. Peter F.

    Peter F. Guest

    "Anon." <[email protected]> wrote in message
    news:[email protected]...

    > John, what is your definition of fitness? I was
    > specifically describing your definition of fitness, but in
    > your reply you didn't make any mention of it, so it's not
    > clear to me how I've misrepresented you.

    Pardon my butting in but you ought to know, by now, that
    John's definition of fitness amounts to that an ancestral
    individual with 14 dead great-grand-offspring in its
    therewith extinct lineage, was twice as fit as another
    individual ancestor whose lineage went extinct with only 7
    dead great-grand-offspring. ;-)

    P
     
  11. Tim Tyler

    Tim Tyler Guest

    Larry Moran <[email protected]> wrote or quoted:
    > On Sat, 29 May 2004 23:42:11 +0000 (UTC), Tim Tyler
    > <[email protected]> wrote:
    > > Larry Moran <[email protected]> wrote or
    > > quoted:
    > >> Tim Tyler <[email protected]> wrote:
    > >> > Larry Moran <[email protected]> wrote
    > >> > or quoted:

    > >> >> I've been assuming all along that changes are most
    > >> >> easily quantified by adding up mutations in DNA but
    > >> >> you don't seem to accept that particular measure.
    > >> >
    > >> > It's a great measure - but not the /only/ one - and
    > >> > as I mentioned in another post, it has some definite
    > >> > flaws as a metric of evolutionary change.
    > >>
    > >> What are the flaws ... other than the fact that it
    > >> leads to a conclusion you don't like?
    > >
    > > The ones I mentioned in another post - namely a neutral
    > > mutation counts as the same quantity of evolutionary
    > > change as a mutation that causes speciation.
    > >
    > > This is contrary to common sense relating to the
    > > relative significance of such changes in evolution.
    >
    > That "significance" is subjective. You may think that some
    > heritable changes are more significant than others but
    > that perspective isn't shared by all scientists.

    IMO, most scientists would agree that speciation is more
    biologically significant that a genetic change that seems to
    produce no effect.

    > What I'm looking for is some objective measure of
    > heritable change that counts as evolution. So far, the
    > only one that seems to work is to count every mutation
    > even if it doesn't cause a phenotypic change that attracts
    > your attention.

    I was just giving an example where it didn't "work" very
    well - since it quantified a dramatic change which was
    likely to have many consequences as equal to one that was
    barely detectable - and was likely to have few consequences.

    > If you want to limit evolution to just a subset of all
    > heritable changes then please come up with an objective
    > way of defining this subset.

    Well, that's not my aim - but for example, instead of using:

    * Shortest program to transform between the genomes in
    question;

    ...you could use:

    * Shortest program which takes the first organism's genome
    and produces a genome which produces an organism which is
    functionally-indistinguishable from the second organism;

    The definition of "functionally-indistinguishable" would
    need to be given.

    For example, "functionally-indistinguishable" might be
    defined as producing the same expected fitnesses in 100
    environments taken from the species' natural range.

    Such a definition would de-emphasise *some* sorts of neutral
    mutation (those that really do have next-to-no effect).

    However other sorts of neutral mutation would still be
    counted as being significant (those that increase fitness in
    some environments but decrease it in other ones, and are
    only neutral on average).

    > >> > I am not my mind. I am not my body. I am not my DNA
    > >> > sequence ;-)
    > >>
    > >> What the heck does this mean? I sounds like new-age
    > >> doublespeak.
    > >
    > > The smiley was intended to indicate that this was
    > > a joke.
    > >
    > > However there was a hint of seriousness: evolution is
    > > about more than just DNA sequences. Attempt to measure
    > > it *only* in terms of DNA and much of its richness will
    > > be omitted.
    >
    > I don't disagree. Sometimes we don't know the underlying
    > mutations so we measure evolution by examining phenotypic
    > changes that are presumably due to mutations. If we knew
    > what mutations caused the phenotype then we could just
    > look at the DNA directly to follow their evolution within
    > the population. What I don't understand is why you want to
    > eliminate some kinds of mutations from even being
    > considered as valid characteristics for biological
    > evolution.

    As I wrote (above) of your preferred metric:

    ``It's a great measure - but not the /only/ one [...]''

    ...so I can hardly be said to be wanting to eliminate some
    kinds of mutations from even being considered as valid
    characteristics for biological evolution.

    Consider neutral mutations to have the same significance as
    other types if you so choose - but don't think that that's
    the *only* valid way of measuring the rate of evolution.
    --
    __________
    |im |yler http://timtyler.org/ [email protected] Remove
    lock to reply.
     
  12. Larry Moran

    Larry Moran Guest

    On Sat, 29 May 2004 23:42:11 +0000 (UTC),
    Tim Tyler <[email protected]> wrote:
    > Larry Moran <[email protected]> wrote
    > or quoted:
    >> Tim Tyler <[email protected]> wrote:
    >> > Larry Moran <[email protected]> wrote or
    >> > quoted:
    >
    > [snip]
    >
    >> >> Hmmm ... I think I see your objection. You want a
    >> >> precise definition of evolutionary change so you can
    >> >> objectively analyze the mechanisms. I've been assuming
    >> >> all along that changes are most easily quantified by
    >> >> adding up mutations in DNA but you don't seem to
    >> >> accept that particular measure.
    >> >
    >> > It's a great measure - but not the /only/ one - and as
    >> > I mentioned in another post, it has some definite flaws
    >> > as a metric of evolutionary change.
    >>
    >> What are the flaws ... other than the fact that it leads
    >> to a conclusion you don't like?
    >
    > The ones I mentioned in another post - namely a neutral
    > mutation counts as the same quantity of evolutionary
    > change as a mutation that causes speciation.
    >
    > This is contrary to common sense relating to the relative
    > significance of such changes in evolution.

    That "significance" is subjective. You may think that some
    heritable changes are more significant than others but that
    perspective isn't shared by all scientists. What I'm looking
    for is some objective measure of heritable change that
    counts as evolution. So far, the only one that seems to work
    is to count every mutation even if it doesn't cause a
    phenotypic change that attracts your attention.

    If you want to limit evolution to just a subset of all
    heritable changes then please come up with an objective way
    of defining this subset.

    >> > I am not my mind. I am not my body. I am not my DNA
    >> > sequence ;-)
    >>
    >> What the heck does this mean? I sounds like new-age
    >> doublespeak.
    >
    > The smiley was intended to indicate that this was a joke.
    >
    > However there was a hint of seriousness: evolution is
    > about more than just DNA sequences. Attempt to measure it
    > *only* in terms of DNA and much of its richness will be
    > omitted.

    I don't disagree. Sometimes we don't know the underlying
    mutations so we measure evolution by examining phenotypic
    changes that are presumably due to mutations. If we knew
    what mutations caused the phenotype then we could just look
    at the DNA directly to follow their evolution within the
    population. What I don't understand is why you want to
    eliminate some kinds of mutations from even being considered
    as valid characteristics for biological evolution.

    Larry Moran
     
  13. Larry Moran

    Larry Moran Guest

    On Sat, 29 May 2004 23:42:07 +0000 (UTC),
    Guy Hoelzer <[email protected]> wrote:
    > in article [email protected], Larry
    > Moran at [email protected] wrote on
    > 5/27/04 9:40 AM:
    >
    >> On Wed, 26 May 2004 23:12:56 +0000 (UTC), Tim Tyler
    >> <[email protected]> wrote:
    >>> Larry Moran <[email protected]> wrote or
    >>> quoted:
    >>
    >> [snip]
    >>
    >>>> Hmmm ... I think I see your objection. You want a
    >>>> precise definition of evolutionary change so you can
    >>>> objectively analyze the mechanisms. I've been assuming
    >>>> all along that changes are most easily quantified by
    >>>> adding up mutations in DNA but you don't seem to accept
    >>>> that particular measure.
    >>>
    >>> It's a great measure - but not the /only/ one - and as I
    >>> mentioned in another post, it has some definite flaws as
    >>> a metric of evolutionary change.
    >>
    >> What are the flaws ... other than the fact that it leads
    >> to a conclusion you don't like?
    >
    > It seems to me that Tim and Larry are talking past each
    > other. I think the cryptic difference underlying there
    > differences have to do with the level of evolutionary
    > interest. Tim is focusing on the evolution of populations
    > of organisms in which DNA sequences are only tangentially
    > relevant, while Larry is focusing on the evolution of
    > populations of DNA sequences in which the organisms are
    > only tangential vehicles (sensu Dawkins).

    No that's not an accurate description of my point of
    view. We began this thread when I said that most of
    evolution takes place by random genetic drift. We then
    drifted off into a debate about what I meant by "most" of
    evolution. I said that it included the fixation of every
    kind of mutation.

    Others have argued than we should eliminate the kinds of
    mutations that don't interest them and focus exclusively on
    mutations that cause phenotypic change. I don't have a
    problem with people having different interests but I object
    when they try to claim that the fixation of certain types of
    mutation isn't even evolution.

    BTW, I'm a strong opponent of Dawkins so please don't label
    me as one of his supporters. I oppose his adaptionist stance
    and I oppose his gene centric point of view - especially
    when it carries over into behavior.

    > If I may be so bold as to try to answer Larry's question
    > on Tim's behalf, I would say that the nonlinearities
    > involved in the genotype/phenotype map make DNA variation
    > a generally poor marker of organismal evolution. In
    > support of Larry's view, I would also argue that neutral
    > genetic variation is generally useful for phylogenetic
    > reconstruction; but then patterns of evolutionary path
    > isolation lacks much of what is sought by those interested
    > in processes of organismal evolution. The molecular
    > phylogeny is often seen as a useful tool with which one
    > can begin to map patterns of phenotypic change, but this
    > is where the interesting questions can begin for those
    > focused on organismal evolution.

    This isn't the point. The point is whether the fixation of a
    mutations that aren't due to natural selection is really
    evolution. What do you think?

    [snip]

    >> That's probably why it isn't very useful. It's too
    >> subjective and it ignores all the other kinds of
    >> evolutionary change.
    >
    > DNA sequences may be objectively determined, but they too
    > ignore all other kinds of evolutionary change at the
    > organismal level (e.g., cultural evolution, epigenetic
    > effects, developmental effects of sequence rearrangements
    > that do not involve changes in nucleotide identities).

    I'm not sure if "cultural evolution" counts as biological
    evolution in the sense we're discussing. All of the other
    things seem to qualify as biological evolution since they
    involve heritable changes or mutations of one sort or
    another. I hope you didn't get the impression that I was
    restricting the definition of evolution to nucleotide
    substitutions?

    > Why doesn't your argument lead you to the conclusion that
    > studying DNA sequences "isn't very useful" as a way to
    > understand organismal evolution?

    Because that's not the point. The point under discussion is
    what definition of evolution we should use. I claim that the
    most objective definition is a change in the frequency of
    heritable characteristics in a population where heritable
    characteristics are caused by any kind of mutation. Others
    would like to define evolution in a way that eliminates some
    kinds of heritable change but keeps others. We're exploring
    the possibilities but so far I haven't seen any good
    definition that allows us to distinguish between the
    mutations that count and those that don't. Do you have
    something in mind?

    [snip]

    >>> However, the phenotypes of living organisms still form a
    >>> tree where qualities very along the branches.
    >>
    >> You can group species by clades if you concentrate on
    >> certain kinds of morphological change (shared derived
    >> characters = synapomorphies). This requires you to pretty
    >> much ignore most phenotypic change and it certainly isn't
    >> quantitative. Besides, we have plenty of examples were it
    >> led to an incorrect conclusion that was fixed by looking
    >> at DNA/protein sequences. Even more important, it hardly
    >> worked at all for bacteria and single-celled eukaryotes.
    >
    > All of this sounds like "hot air" to me. Plenty of
    > molecular phylogenies have been in error, too. Does that
    > mean they weren't quantitative or objective? I am sure you
    > would agree that this should not cause us to give up on
    > molecular systematics.

    No, I'm not saying any such thing. I'm trying to find out
    how you define those mutations that will count as evolution
    and eliminate those that don't. So far, I've only seen some
    vague references to "phenotypic changes" and I'm trying to
    find out whether there's an objective definition of these
    kind of mutations. This doesn't have anything to do with
    what sorts of things are of interest to certain biologists.

    I'm also trying to find out why someone would want to limit
    evolution to obvious phenotypic changes. That's why I
    pointed out that this seems to be a perspective that is
    biased towards the evolution of certain organisms to the
    exclusion of others.

    >>> Taxonomists don't *have* to look at an organisms' DNA
    >>> sequence to begin to answer questions about which other
    >>> organisms it is most closely related to.
    >>
    >> That's correct. It's quite possible to look at a subset
    >> of all evolutionary change in order to work out some of
    >> the history. This applies to morphological change as well
    >> as to DNA/protein sequence change. Do you have a point?
    >>
    >>> As for general-purpose metrics - there are several of
    >>> them. Length, lifespan, mass and number of cell types
    >>> are all fairly useful means of quantifying evolutionary
    >>> change.
    >>
    >> Now were getting a bit silly .....
    >
    > Silly? I can only attribute this comment to Larry's
    > unvarying focus on the DNA level of evolution. These
    > metrics of phenotypic dimensions would indeed seem besides
    > the point to someone uninterested in organismal evolution.
    > To anyone interested in the evolution of organismal form
    > and function, these would seem like fundamental metrics in
    > the study of evolution.

    If the "metrics" are caused by an underlying mutation then
    it qualifies as evolution by my definition because it's a
    heritable change. If they're not due to a mutation, such as
    extended lifetime because of increased food supplies, then
    it's not biological evolution. We distinguish these
    possibilities by asking whether there's an underlying
    genetic change (mutation) that's responsible for the
    phenotype. If there is then we can just as easily use the
    actual genetic change as our measure instead of the gross
    phenotypic effect.

    Of course there will be examples of phenotypic change that
    are only *assumed* to have an underlying genetic cause. This
    is a reasonable assumption in most cases. But let's not
    forget that this assumption has to be made in order for the
    "metric" to really qualify as biological evolution. That's
    all I meant when I said we're getting a bit silly.

    If we're looking for a rigorous definition of evolution then
    just listing all kinds of phenotypic change that may, or may
    not, be due to mutation doesn't seem to be helpful.

    Larry Moran
     
  14. Guy Hoelzer

    Guy Hoelzer Guest

    Hi Larry,

    in article [email protected], Larry Moran at
    [email protected] wrote on 5/31/04 10:25 AM:

    > On Sat, 29 May 2004 23:42:07 +0000 (UTC), Guy Hoelzer
    > <[email protected]> wrote:
    >> in article c95[email protected], Larry
    >> Moran at [email protected] wrote on
    >> 5/27/04 9:40 AM:
    >>
    >>> On Wed, 26 May 2004 23:12:56 +0000 (UTC), Tim Tyler
    >>> <[email protected]> wrote:
    >>>> Larry Moran <[email protected]> wrote or
    >>>> quoted:
    >>>
    >>> [snip]
    >>>
    >>>>> Hmmm ... I think I see your objection. You want a
    >>>>> precise definition of evolutionary change so you can
    >>>>> objectively analyze the mechanisms. I've been assuming
    >>>>> all along that changes are most easily quantified by
    >>>>> adding up mutations in DNA but you don't seem to
    >>>>> accept that particular measure.
    >>>>
    >>>> It's a great measure - but not the /only/ one - and as
    >>>> I mentioned in another post, it has some definite flaws
    >>>> as a metric of evolutionary change.
    >>>
    >>> What are the flaws ... other than the fact that it leads
    >>> to a conclusion you don't like?
    >>
    >> It seems to me that Tim and Larry are talking past each
    >> other. I think the cryptic difference underlying there
    >> differences have to do with the level of evolutionary
    >> interest. Tim is focusing on the evolution of populations
    >> of organisms in which DNA sequences are only tangentially
    >> relevant, while Larry is focusing on the evolution of
    >> populations of DNA sequences in which the organisms are
    >> only tangential vehicles (sensu Dawkins).
    >
    > No that's not an accurate description of my point of view.
    > We began this thread when I said that most of evolution
    > takes place by random genetic drift. We then drifted off
    > into a debate about what I meant by "most" of evolution. I
    > said that it included the fixation of every kind of
    > mutation.
    >
    > Others have argued than we should eliminate the kinds of
    > mutations that don't interest them and focus exclusively
    > on mutations that cause phenotypic change. I don't have a
    > problem with people having different interests but I
    > object when they try to claim that the fixation of certain
    > types of mutation isn't even evolution.

    Thanks for filling me in. I was away at a Complexity
    conference (note the subject of this thread) for much of the
    discussion.

    > BTW, I'm a strong opponent of Dawkins so please don't
    > label me as one of his supporters. I oppose his
    > adaptionist stance and I oppose his gene centric point of
    > view - especially when it carries over into behavior.

    I'm sorry for the inadvertent insult. I think you and I are
    in the same camp on this issue.

    >> If I may be so bold as to try to answer Larry's question
    >> on Tim's behalf, I would say that the nonlinearities
    >> involved in the genotype/phenotype map make DNA variation
    >> a generally poor marker of organismal evolution. In
    >> support of Larry's view, I would also argue that neutral
    >> genetic variation is generally useful for phylogenetic
    >> reconstruction; but then patterns of evolutionary path
    >> isolation lacks much of what is sought by those
    >> interested in processes of organismal evolution. The
    >> molecular phylogeny is often seen as a useful tool with
    >> which one can begin to map patterns of phenotypic change,
    >> but this is where the interesting questions can begin for
    >> those focused on organismal evolution.
    >
    > This isn't the point. The point is whether the fixation of
    > a mutations that aren't due to natural selection is really
    > evolution. What do you think?

    I think that the fixation of any mutation by any means
    (e.g., drift) is undeniably an example of genome evolution.

    >>> That's probably why it isn't very useful. It's too
    >>> subjective and it ignores all the other kinds of
    >>> evolutionary change.
    >>
    >> DNA sequences may be objectively determined, but they too
    >> ignore all other kinds of evolutionary change at the
    >> organismal level (e.g., cultural evolution, epigenetic
    >> effects, developmental effects of sequence rearrangements
    >> that do not involve changes in nucleotide identities).
    >
    > I'm not sure if "cultural evolution" counts as biological
    > evolution in the sense we're discussing. All of the other
    > things seem to qualify as biological evolution since they
    > involve heritable changes or mutations of one sort or
    > another. I hope you didn't get the impression that I was
    > restricting the definition of evolution to nucleotide
    > substitutions?
    >
    >> Why doesn't your argument lead you to the conclusion that
    >> studying DNA sequences "isn't very useful" as a way to
    >> understand organismal evolution?
    >
    > Because that's not the point. The point under discussion
    > is what definition of evolution we should use. I claim
    > that the most objective definition is a change in the
    > frequency of heritable characteristics in a population
    > where heritable characteristics are caused by any kind of
    > mutation. Others would like to define evolution in a way
    > that eliminates some kinds of heritable change but keeps
    > others. We're exploring the possibilities but so far I
    > haven't seen any good definition that allows us to
    > distinguish between the mutations that count and those
    > that don't. Do you have something in mind?

    Your definition is very close to mine: evolution is the
    change in heritable information contained in a population. I
    use the term "mutation" broady to mean the creation of a
    heritable change, whether it be a genetic mutation or not.

    >>>> However, the phenotypes of living organisms still form
    >>>> a tree where qualities very along the branches.
    >>>
    >>> You can group species by clades if you concentrate on
    >>> certain kinds of morphological change (shared derived
    >>> characters = synapomorphies). This requires you to
    >>> pretty much ignore most phenotypic change and it
    >>> certainly isn't quantitative. Besides, we have plenty of
    >>> examples were it led to an incorrect conclusion that was
    >>> fixed by looking at DNA/protein sequences. Even more
    >>> important, it hardly worked at all for bacteria and single-
    >>> celled eukaryotes.
    >>
    >> All of this sounds like "hot air" to me. Plenty of
    >> molecular phylogenies have been in error, too. Does that
    >> mean they weren't quantitative or objective? I am sure
    >> you would agree that this should not cause us to give up
    >> on molecular systematics.
    >
    > No, I'm not saying any such thing. I'm trying to find out
    > how you define those mutations that will count as
    > evolution and eliminate those that don't. So far, I've
    > only seen some vague references to "phenotypic changes"
    > and I'm trying to find out whether there's an objective
    > definition of these kind of mutations. This doesn't have
    > anything to do with what sorts of things are of interest
    > to certain biologists.
    >
    > I'm also trying to find out why someone would want to
    > limit evolution to obvious phenotypic changes. That's why
    > I pointed out that this seems to be a perspective that is
    > biased towards the evolution of certain organisms to the
    > exclusion of others.

    I appreciate your concerns, but I don't think that is useful
    in this context to pit the quality of morphological data
    against the quality of molecular data, and I still think
    that it does have something to do with what sorts of things
    are of interest to certain biologists. I find your views to
    represent an excellent paradigm for the study of genome
    evolution, but how can you address questions like the
    dissociation between gradual DNA evolution in taxa
    exhibiting a punctuated equilibrium pattern of morphological
    evolution? Why (or how?) have "living fossils" failed to
    evolve much morphologically while they have continued their
    pace of DNA evolution? Why (or how?) have huge changes in
    morphology occurred in the face of very little change in DNA
    sequences? IMHO, these are interesting questions about
    biological evolution that cannot be answered satisfactorily
    by revealing molecular mechanisms of the genotype/phenotype
    map, or by limiting the study of evolution to molecular data
    (even if it is of better quality).

    >>>> Taxonomists don't *have* to look at an organisms' DNA
    >>>> sequence to begin to answer questions about which other
    >>>> organisms it is most closely related to.
    >>>
    >>> That's correct. It's quite possible to look at a subset
    >>> of all evolutionary change in order to work out some of
    >>> the history. This applies to morphological change as
    >>> well as to DNA/protein sequence change. Do you have a
    >>> point?
    >>>
    >>>> As for general-purpose metrics - there are several of
    >>>> them. Length, lifespan, mass and number of cell types
    >>>> are all fairly useful means of quantifying evolutionary
    >>>> change.
    >>>
    >>> Now were getting a bit silly .....
    >>
    >> Silly? I can only attribute this comment to Larry's
    >> unvarying focus on the DNA level of evolution. These
    >> metrics of phenotypic dimensions would indeed seem
    >> besides the point to someone uninterested in organismal
    >> evolution. To anyone interested in the evolution of
    >> organismal form and function, these would seem like
    >> fundamental metrics in the study of evolution.
    >
    > If the "metrics" are caused by an underlying mutation then
    > it qualifies as evolution by my definition because it's a
    > heritable change. If they're not due to a mutation, such
    > as extended lifetime because of increased food supplies,
    > then it's not biological evolution. We distinguish these
    > possibilities by asking whether there's an underlying
    > genetic change (mutation) that's responsible for the
    > phenotype. If there is then we can just as easily use the
    > actual genetic change as our measure instead of the gross
    > phenotypic effect.

    Of course, it is helpful to know when you can attribute a
    heritable change in the phenotype to a particular genetic
    mutation, but that seems to me like too narrow a view of
    "mutation". Heritability is determined using quantitative
    genetics, which explicitly acknowledges other (non-genetic)
    modes of inheritance. Why would you choose to eliminate
    those other modes as sources of heritable variation among
    individuals that could contribute to evolution of the
    population?

    > Of course there will be examples of phenotypic change that
    > are only *assumed* to have an underlying genetic cause.
    > This is a reasonable assumption in most cases. But let's
    > not forget that this assumption has to be made in order
    > for the "metric" to really qualify as biological
    > evolution. That's all I meant when I said we're getting a
    > bit silly.
    >
    > If we're looking for a rigorous definition of evolution
    > then just listing all kinds of phenotypic change that may,
    > or may not, be due to mutation doesn't seem to be helpful.

    But why should we choose to assume that the only mode of
    "mutation" leading to heritable changes in information is
    the genetic mode? I don't think that anyone would argue that
    genetics is not a very important mode of inheritance, but
    defining evolution by restricting its meaning to any
    particular mode of inheritance seems misleading to me. Even
    if we limit our discussion to genetics, how would your
    metric of evolution reflect changes in genomic architecture
    that are not reflected in DNA sequence variation? Couldn't
    changes in genomic architecture alone have important,
    heritable effects on organismal phenotypes?

    Regards,

    Guy Hoelzer
     
  15. Peter F.

    Peter F. Guest

    "Larry Moran" <[email protected]> wrote in message
    news:[email protected]...
    > On Thu, 20 May 2004 02:13:22 +0000 (UTC), Phil Roberts,
    > Jr. <[email protected]> wrote:
    > > Larry Moran wrote:
    > >> On Wed, 19 May 2004 05:33:01 +0000 (UTC), Phil Roberts,
    > >> Jr. <[email protected]> wrote:
    > >>
    <snip>
    > What's the problem? Intelligence may have been selected
    > (adaptive) but not all of the many consequences of that
    > intelligence (behavior) are necessarily adaptations by
    > themselves. The overall benefit of being intelligent may
    > have been a selective advantage but that doesn't mean that
    > every single act of an intellignet human has to be an
    > adaptation.

    What nearly everyone (not only people around here) fall
    short of getting an 'agnostic grip' (if there is such a
    thing :) on, is that an important ingredient of the mix of
    adaptive benefits bestowed on us by our extra capacity for
    convoluted and occassionally clever cognitive activity - is
    that it is a means of simultaneously harnessing and hiding
    ("hiding" - i.e. remaining selectively unconscious and,
    primarily, not self-defeatingly distressed by) naturally
    inevitable SHITS, come CURSES (-type memories).

    We have been phylogenetically painted into an 'AEVASIVE
    corner' -- from where most people (including so called
    intelligent ones) can't even begin to understand the
    'insidiously inbuilt dEPTh of irony' of this aspect of What
    Is going on.

    P
     
  16. [email protected] (Larry Moran) wrote in
    news:[email protected]:

    > On Thu, 27 May 2004 16:40:40 +0000 (UTC), William Morse
    > <[email protected]> wrote:
    >> [email protected] (Larry Moran) wrote in
    >> news:[email protected]:
    >>
    >>> On Tue, 25 May 2004 23:48:32 +0000 (UTC), William Morse
    >>> <[email protected]> wrote:
    >>
    >> (snip)

    >> The same wise man also suggested the following
    >> definition:

    >> "Evolution is a process that results in heritable changes
    >> in a population spread over many generations."

    > This must have been a very wise man. By saying "heritable
    > changes" you avoid semantic quibbles over the definition
    > of an allele.

    >> (And just in case you get any ideas, if you start quoting
    >> things I have previously said back at me I'll come and
    >> stuff your hard drive full of peanut butter. Toronto
    >> ain't all that far from Syracuse :)

    > Don't worry ... I haven't paid much attention to anything
    > you've said in the past. :)

    Touche!

    > Let's no quibble. The minimal definition of evolution is a
    > change in the heritable characteristics of a population
    > over time. Changes in junk DNA count as evolution by this
    > definition whether you want to call them alleles or not.
    > They my not be very interesting changes to most people who
    > aren't interested in genomes but that doesn't mean they
    > don't exist.
    >
    > Would you prefer a definition where evolution is confined
    > to changes in genes (alleles by your definition)? Do you
    > realize what this would mean?

    See my comments below.

    >> Now I can't define evolution only as changes in functions
    >> of genes unless I can define genes, and I don't really
    >> want to try to do that. Furthermore, a change in a
    >> regulatory sequence would certainly also qualify as
    >> evolution in my book. However I do not see a substitution
    >> of alanine for glycine in a region far from the active
    >> site of an enzyme as necessarily contributing anything to
    >> evolution. So let's try this:
    >>
    >> Evolution is a heritable, statistically
    >> significant change in a population of organisms
    >> that can be detected without using either DNA or
    >> protein sequence data.

    > I'm not going to argue with you over new definitions. If
    > you can convince the scientific community to accept this
    > then I'll bow to the consensus. Good luck.

    In order to convince the community I have to start
    somewhere, and this newsgroup is it. But actually I think
    that your definition - "heritable change" - is the same as
    my definition. Let's imagine a world in which the only
    change is in "junk" DNA, with no other change that "can be
    detected without using either DNA or protein sequence data".
    So I have a world in which fossil robins look exactly like
    modern day robins. There are no australopithecines, because
    humans show no discernible change in morphology no matter
    how far back you go in the fossil record. The dinosaurs may
    have existed and been wiped out, but they did not give rise
    to modern birds, because _there is no change other than in
    sequences_. There are lots of changes in DNA sequences, but
    no changes that can be seen by any other method.
    Morphologies are identical, resistance to disease is
    identical, blood types are identical.

    Now along come two scientists - let's call them Morwin and
    Wallant - with a new theory of evolution, which they explain
    on the basis of changes in sequences of "DNA" which randomly
    occur through "neutral drift" but which create absolutely no
    other change which anyone can measure by any other
    technique. Scientists solemnly note that independent
    research supports this theory - but go on to say that the
    result is interesting but of no theoretical value. The
    population as a whole quite rightly ignores the new theory
    and goes on to other pursuits, because this "evolution"
    _does not change anything_.

    (snip)

    >> I had a rant about this subject recently, and it seems to
    >> be rearing its ugly head again. Are you including
    >> sampling error as part of drift, or defining drift as
    >> just neutral mutations? My statement on population size
    >> dependence only applies to sampling error - which is in
    >> fact exactly what I said ;-) The population genetics
    >> equation for this type of drift is:

    >> delta q = pq/2N

    > This is true for a particular individual allele. If it
    > occurs in a large population it will likely be eliminated.
    > If it occurs in a small population it has a better chance
    > of being fixed.

    > However, when you look at the overall rate of evolution by
    > random genetic drift you have to take into account two
    > things: the probabilty of fixation, and the rate of
    > mutation. There are more mutations in a large population
    > and this exactly balances the decrease in the probabilty
    > of fixation. Thus, the rate of fixation of new alleles in
    > a diploid population is ....

    > K = 2Nu (1/2N) = u

    > where u (mu) is the rate of mutation. The overall rate of
    > evolution by random genetic drift is independant of
    > population size.

    No, this is only true for neutral mutations, and truly
    neutral mutations do not cause evolution, at least until
    enough of them accumulate so that they are no longer neutral
    - unless you still maintain that a change that doesn't
    change anything is a change. Deleterious mutations will
    rapidly be eliminated in large populations, and severely
    deleterious mutations will rapidly be eliminated in all
    populations. A dominant lethal mutation has exactly zero
    chance of being fixed. Advantageous mutations will rapidly
    (in evolutionary terms) be fixed, at least if they survive
    sampling error while still at low frequency.

    >> Apparently you are accusing adaptationists of being niche-
    >> pickers :)
    >
    > I like that ... can I use it?

    Since you did not object to being called a drifter, how
    can I refuse?

    >> But I am going to put this back on you. Since in fact
    >> sampling error is dependent on population size, which is
    >> determined by the niche, all of this form of evolution is
    >> dependent on niches.
    >
    > The rate of evolution by random genetic drift (sampling
    > error) is independent of population size.

    No, only the rate of _neutral change_ in DNA is independent
    of population size. The rate of _evolution_ (non-neutral
    change) by sampling error (if we are calling that drift) is
    dependent on population size.

    > Thanks for playing. There are no consolation prizes for
    > niche-pickers.
    > :)

    You are right - there are only first prizes :)

    >> I would like to spend more time on the subject of niches,
    >> but this is getting long and that subject might be better
    >> treated in a new thread.

    > You mean we have to find a new niche?

    No, we're talking about a whole new trophic level here.

    Yours,

    Bill Morse
     
  17. Anon.

    Anon. Guest

    Larry Moran wrote:
    > On Thu, 27 May 2004 16:40:43 +0000 (UTC), Anon.
    > <[email protected]> wrote:
    >
    >>Larry Moran wrote:
    >>
    >>>On Tue, 25 May 2004 23:48:33 +0000 (UTC), Anon.
    >>><[email protected]> wrote:
    >>
    >
    > [snip]
    >
    >
    >>>Why not give it a try? We already have an effective and
    >>>quantitatvie way of measuring evolution by looking at
    >>>changes in DNA sequence. If you want to find a more
    >>>effective measure then let's see what you come up with.
    >>
    >>The first eigen value of the transition matrix for the
    >>changes in the phenotypic traits? You can define the
    >>process in either discrete or continuous time. You can
    >>even use a hierarchical model so that you can include
    >>discrete traits.
    >
    >
    > Damn! I wish I thought of that. It's so sbvious.
    >
    :) I think that's why I'm exiled in a maths and stats
    :department.

    >
    >>It's not clear to me that simply looking at changes in DNA
    >>sequence is a good measure of evolution - how do you deal
    >>with polymorphism?
    >
    >
    > Polymorphisms are evolution in progess. How do you deal
    > with them?
    >
    One can actually use the same method as I've already
    described: the transistion matrix will be for transitions
    within a population (i.e. showing how the allele
    frequencies change).

    >
    >>Hmm, Actually, you can use the same sorts of models as
    >>I've suggested for phenotypic traits.
    >>
    >>So
    >>
    >>>far, all I've seen is some warm fuzzy feeling that
    >>>"phenotypic change" should get a higher score in order to
    >>>restore the supremacy of natural selection as a mechanism
    >>>of evolution. Can you turn that subjective feeling into a
    >>>scientific definition that we can examine?
    >>>
    >>
    >>That's a mis-representation - I'm not arguing that
    >>phenotypic change should get a highe score, but rather
    >>that there is no obvious single score, so whatever measure
    >>you use is subjective. Why remove phenotypic traits from
    >>evolution?
    >
    >
    > Because nucleotide changes are mutations and because
    > phenotypic traits are the result of, not the cause, of
    > (some) mutation?
    >
    As others are arguing with you, we might consider changes in
    phenotype to be a more important part of evolution, unless
    one adopts a militant gene's eye view. The magnitude of
    effects of point mutations on a phenotpye can vary widely,
    and I think this should be acknowledged.

    Bob

    --
    Bob O'Hara

    Dept. of Mathematics and Statistics
    P.O. Box 4 (Yliopistonkatu 5) FIN-00014 University of
    Helsinki Finland Telephone: +358-9-191 23743 Mobile:
    +358 50 599 0540 Fax: +358-9-191 22 779 WWW:
    http://www.RNI.Helsinki.FI/~boh/ Journal of Negative
    Results - EEB: http://www.jnr-eeb.org
     
  18. Anon.

    Anon. Guest

    John Edser wrote:
    >>>>BOH:- The means of quantifying "all evolutionary change"
    >>>>here is not clear. State the metric used - and the
    >>>>question of whether genetic drift comes in at the #1
    >>>>position will probably be clearer.
    >>>
    >
    >>>LM:- I mean the sum all evolutionary changes of any sort
    >>> by whatever definitions are used by a large number of
    >>> scientists.
    >>
    >
    >
    >>>JE:- Pardon me butting in but.. please state what would
    >>>be EXCLUDED from such an _amazingly_ wide acceptance of
    >>>what you insist can _scientifically_ constitute
    >>>"evolution", i.e. please provide at least one example of
    >>>a _non_ evolutionary change within a biological system.
    >>
    >
    > BOH:- Any change that isn't heritable.
    >
    > JE:- The above becomes a self fulfilling prophecy when
    > genetic epistasis is _defined_ as "inherited" but not
    > "heritable" and thus, "selectable".

    Huh? From the OED definition of heritable: Naturally
    transmissible or transmitted from parent to offspring;
    hereditary.

    You're mixing up being heritable with the qunatitative
    genetic concept of "heritability" (=the proportion of
    variance in a trait due to additive genetic variation). They
    are not the same thing.

    >>>LM:- Did you have something else in mind that would shift
    >>> random genetic drift into second place?
    >>
    >
    >>>JE:- Darwinian natural selection, exactly as Darwin
    >>>stated it but with his implicit assumptions made
    >>>explicit.
    >>
    >
    >
    >>BOH:- I think I should point out that John's definition of
    >>fitness excludes the possibility of drift (because he
    >>defines fitness in terms of the actual number of
    >>offspring, rather than the expected value).
    >
    >
    >
    >>JE:- Dr O'Hara has misrepresented my position. Drift is
    >>_included_ as temporal variation (random variation over
    >>time) within Darwinian selective events.
    >
    >
    > BOH:- John, what is your definition of fitness? I was
    > specifically describing your definition of fitness, but in
    > your reply you didn't make any mention of it, so it's not
    > clear to me how I've misrepresented you.
    >
    > JE:- It is not how I define it but how Darwin would have
    > defined it after his implicit assumptions were made
    > explicit.
    >
    > I have posted what Darwinian fitness is (and the reverse
    > engineering experiment needed to prove it) countless
    > times, including, within this thread.
    >
    > _____________________________________________________
    > Darwinian fitness is the _total_ number of _fertile_ forms
    > reproduced by _one_ Darwinian selectee (one fertile form)
    > within _one_ population.
    > _____________________________________________________
    >
    OK, so my point is that drift is the difference between
    observed and [mathematical] expectation of the change in
    allele frequency (the expectation coming from a model of
    selection, using the conventioal definition of fitness): the
    total number of fertile offspring is the sum of the expected
    number, and the drift effect. Your definition conflates the
    effects of selection and drift, by defining fitness in terms
    of the obseved number. Any random variation in the number of
    offspring that we would ascribe to drift you would include
    in the fitness measure, and hence would ascribe to
    selection.

    Bob

    --
    Bob O'Hara

    Dept. of Mathematics and Statistics
    P.O. Box 4 (Yliopistonkatu 5) FIN-00014 University of
    Helsinki Finland Telephone: +358-9-191 23743 Mobile:
    +358 50 599 0540 Fax: +358-9-191 22 779 WWW:
    http://www.RNI.Helsinki.FI/~boh/ Journal of Negative
    Results - EEB: http://www.jnr-eeb.org
     
  19. Friend

    Friend Guest

    John Edser wrote:
    >
    >
    >> JE:- Darwinian natural selection, exactly as Darwin
    >> stated it but with his implicit assumptions made
    >> explicit.
    >
    > BOH:- I think I should point out that John's definition of
    > fitness excludes the possibility of drift (because he
    > defines fitness in terms of the actual number of
    > offspring, rather than the expected value).
    >

    Is the expected value of any conceivable use?

    > JE:- Dr O'Hara has misrepresented my position. Drift is
    > _included_ as temporal variation (random variation over
    > time) within Darwinian selective events. Mutation is
    > included as random variation within genetic space.
    > Darwinian evolution by natural selection has, from its
    > inception, required variation that is assumed to be
    > random. Only _non_ random forms of variation can validly
    > compete against Darwinian selection for evolutionary
    > causation. Sampling error is not one of them.
    >
    > Isn't it just obvious that an "expected value" is just an
    > approximation of "the actual number of offspring" which I
    > stress (yet again) is the TOTAL (requiring a time frame to
    > complete) of only FERTILE forms reproduced into ONE
    > population by EACH Darwinian selectee (one fertile form)?
    >
    > Please note that Dr O'Hara, refused to address the problem
    > that I addressed in detail: setting up a _controlled_
    > experiment to test if random patterns can _alone_, cause
    > "evolution".
    >

    I think only with genetic engineering is it possible to even
    approach random patterns. And then it is very imperfect
    practically. Very difficult.

    >
    >
    > AGAIN: Please state what would be EXCLUDED from such an
    > _amazingly_ wide acceptance of what Dr Moran insists can
    > _scientifically_ constitute "evolution", i.e. would Dr
    > Moran please provide at least one example of a _non_
    > evolutionary change within a biological system.
    >
    > PLEASE COMMENT ON THE BELOW:-
    > 1) Drift defined as evolution is not testable because any
    > random pattern can validly be assumed to be caused by
    > either a random or non random process.
    >

    > 2) It is only possible to halt all selection within a
    > natural population by forcing the _total_ number of
    > _fertile_ forms reproduced by each Darwinian selectee
    > in one population to remain equal. Does Dr Moran agree
    > or disagree? Only by controlling selection can random
    > genetic drift patterns even be observed acting _alone_.

    If then...

    > Does Dr Moran dispute the fact that to just observe the
    > effect of random patterns on their own, selection must be
    > controlled? Does Dr Moran understand/teach the need for
    > controlled experiments to his students? The predicted net
    > result of drift without selection within a controlled
    > experiment is the dissolution of every Darwinian selectee
    > within that population. Does Dr Moran disagree with this
    > prediction? If Dr Moran agrees with the prediction, how
    > can he maintain that genetic dissolution that inevitably
    > leads to a _lowering_ of Darwinian fitness for every
    > selectee constitute "evolution"?
    >

    I think it is much worse than this; my understanding may be
    too narrow but too much has happened (eg. crossover) before
    the individual is subject to very much selection to regard
    it as 'just' random. So even with selection the prognosis
    may not be so good.

    > Genetic drift without selection cannot cause evolution
    > even it can cause gene freq changes in a deme. Selection
    > can cause evolution without genetic drift but genetic
    > drift cannot cause evolution without selection. Random
    > genetic drift is just temporal variation; nothing more
    > and nothing less. Evolution at the gene centric level can
    > only be validly defined as any non random gene freq.
    > change in a deme.
    >
    >

    Is selection on the random change exactly *that* non
    random change?

    Beginner
     
  20. John Edser

    John Edser Guest

    >>>JE:- Pardon me butting in but.. please state what would
    >>>be EXCLUDED from such an _amazingly_ wide acceptance of
    >>>what you insist can _scientifically_ constitute
    >>>"evolution", i.e. please provide at least one example of
    >>>a _non_ evolutionary change within a biological system.

    > BOH:- Any change that isn't heritable.

    > JE:- The above becomes a self fulfilling prophecy when
    > genetic epistasis is _defined_ as "inherited" but not
    > "heritable" and thus, "selectable".

    BOH:- Huh? From the OED definition of heritable: Naturally
    transmissible or transmitted from parent to offspring;
    hereditary. You're mixing up being heritable with the
    qunatitative genetic concept of "heritability" (=the
    proportion of variance in a trait due to additive genetic
    variation). They are not the same thing.

    JE:- "Heritability" and "heritable" mean the same thing: a
    selectable trait. You used the word "heritable" and not the
    word "heritability" as in: "Any change that isn't
    heritable".

    If you suggest that an example of a non evolutionary change
    is _any_ non heritable change then my example of epistasis
    constitutes a valid example of a defined non heritable
    change because it is _not_ "the proportion of variance in a
    trait due to additive genetic variation, it only refers to
    NON additive variation. You are the Neo Darwinist
    professional. Please explain the difference between
    "heritable", "heritability" and "inherited" so that it makes
    _logical_ sense to rational people.

    To help clarify things could you please supply an actual,
    specific. biological case of a non heritable and thus non
    selectable, trait.

    >>>LM:- Did you have something else in mind that would shift
    >>> random genetic drift into second place?

    >>>JE:- Darwinian natural selection, exactly as Darwin
    >>>stated it but with his implicit assumptions made
    >>>explicit.

    >>BOH:- I think I should point out that John's definition of
    >>fitness excludes the possibility of drift (because he
    >>defines fitness in terms of the actual number of
    >>offspring, rather than the expected value).

    >>JE:- Dr O'Hara has misrepresented my position. Drift is
    >>_included_ as temporal variation (random variation over
    >>time) within Darwinian selective events.

    > BOH:- John, what is your definition of fitness? I was
    > specifically describing your definition of fitness, but in
    > your reply you didn't make any mention of it, so it's not
    > clear to me how I've misrepresented you.

    > JE:- It is not how I define it but how Darwin would have
    > defined it after his implicit assumptions were made
    > explicit. I have posted what Darwinian fitness is (and the
    > reverse engineering experiment needed to prove it)
    > countless times, including, within this thread.
    > _____________________________________________________
    > Darwinian fitness is the _total_ number of _fertile_ forms
    > reproduced by _one_ Darwinian selectee (one fertile form)
    > within _one_ population.
    > _____________________________________________________

    BOH:- OK, so my point is that drift is the difference
    between observed and [mathematical] expectation of the
    change in allele frequency (the expectation coming from
    a model of selection, using the conventional definition
    of fitness):

    JE:- The "the conventional definition of fitness" is only
    relative at just ONE single point in time but the Darwinian
    definition is an absolute total over a defined TIME FRAME:
    the time required for one parent to complete one Darwinian
    total, within one population, i.e., the time required to
    raise to fertile adulthood all the immatures that a parent
    reproduced. Because the Darwinian fitness measure
    constitutes a finite total it exists unchanged over all of
    evolutionary history so you could reconstruct all selective
    events, just given this history. A lineage is composed of
    set of parental Darwinian totals where each total remains
    absolutely independent of every other within one population.
    Totals within one population can be mathematically combined
    but when they are, e.g. to form a composite fitness, the
    Darwinian level of selection is _always_ selected _firstly_.
    Additive fitnesses are ALWAYS sequential, i.e. NEVER
    simultaneous. Jim McGinn's model of an infinite number of
    simultaneous levels of selection that he incorrectly
    concludes has no selective focus is just the absurd result
    that you must end up producing when you delete all absolute
    measures of fitness within evolutionary theory. What is
    selected FIRSTLY within SEQUENTIAL levels of selection
    drastically alters what any composite selective effect can
    have. Only the first additive (independent) level of
    selection remains significant because only it can determine
    the direction of selective change. If a 2nd or subsequent
    additive level of selection selects against the first
    testable additive level that exists within nature, then
    Darwinian totals become absolutely reduced and the
    population heads for extinction. Subsequent additive levels
    of selection must go with and not against, the first
    additive level that exists within nature. Multi level
    theorists refuse to admit that such a SIMPLE logic is
    actually operating within evolutionary theory so they just
    bury their heads in the sands of indifference and pretend
    that ONLY a relative fitness comparison at any instant in
    time is all that is required to measure any natural
    selective event. In turn, this has allowed "any gene freq.
    in a deme" to constitute a so called "objective" measure of
    evolution within gene centric Neo Darwinism which cannot
    differentiate between a random and non random process. The
    error is enormous.

    BOH:- the total number of fertile offspring is the sum of
    the expected number, and the drift effect.

    JE:- Because any absolute measure of fitness has to, since
    it must also include all variation within one evolutionary
    change. Please note that a relative measure of fitness is
    not sufficient simply because you cannot differentiate
    between organism fitness altruism (OFA) and organism fitness
    mutualism (OFM) using just one relative comparative measure.

    While it is possible to separately measure the variation
    caused by random patterns from variation caused by non
    random patterns, it is not possible to say that a random
    variation pattern must have been caused by just, a random
    process. Drift theorists refuse to admit that this is the
    case and has always been the case throughout the history of
    science. This is why science throws out random patterns as
    inconclusive.

    BOH:- Your definition conflates the effects of selection and
    drift, by defining fitness in terms of the obseved number.
    Any random variation in the number of offspring that we
    would ascribe to drift you would include in the fitness
    measure, and hence would ascribe to selection.

    JE:- Yes, because Darwinian selection is the only testable
    theory of evolutionary change that we have, even today.
    Suggesting that just a random pattern can constitute a valid
    pattern of evolution without requiring any non random
    process remains, absurd. Why do you refuse to comment on the
    experimental test that I proposed, that demonstrated (what
    everybody already knows): selection can cause evolution
    without random sampling error (genetic drift) but random
    sampling error cannot cause evolution without selection,
    only the dissipation of Darwinian selectees? To
    _experimentally_ test if a random pattern like sampling
    error can cause an evolutionary change on its own, selection
    must be controlled. Such a requirement is just basic
    science. Why does Dr Moran et al refuse to submit their view
    to a controlled experimental test? Why is basic science
    being denied in this case?

    Regards,

    John Edser Independent Researcher

    PO Box 266 Church Pt NSW 2105 Australia

    [email protected]
     
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