Dawkins on Kimura

Discussion in 'Health and medical' started by Tim Tyler, Feb 22, 2004.

  1. Guy Hoelzer wrote:
    > in article [email protected], Jeffrey
    > Turner at [email protected] wrote on 4/7/04 9:38 AM:
    >>Guy Hoelzer wrote:
    >>>in article [email protected], Jeffrey
    >>>Turner at [email protected] wrote on 4/3/04 8:02 PM:
    >>>
    >>>
    >>>>>Life's Solution: Inevitable Humans in a Lonely Universe
    >>>>>http://www.amazon.com/exec/obidos/tg/detail/-
    >>>>>/0521827043/
    >>>>>
    >>>>>Morris argues from examples of biological convergence
    >>>>>that life is anything but accidental - but that its
    >>>>>tendency to repeatedly discover the same things over
    >>>>>and over again shows that the forms of living organisms
    >>>>>are _not_ accidental - or due to chance - but rather
    >>>>>are consequences of natural law.
    >>>>
    >>>>Bother! While striping arose twice in the evolutionary
    >>>>lineage of the three species of zebra, I find it
    >>>>laughable to hypothesize that there's some metaphysical
    >>>>preference for striped equines.
    >>>
    >>>I could not agree more strongly that allowing for ANY
    >>>involvement in metaphysics undermines the scientific
    >>>endeavor. However, you seem to have leaped for some
    >>>reason to equating metaphysics with natural law. I see
    >>>these as being entirely unrelated. Would you find it of
    >>>scientific interest to understand whether physics tends
    >>>to generate convergent patterns when similar species
    >>>encounter similar circumstances? Why would you find this
    >>>implausible?
    >>
    >>I don't. But the book cited - well, it takes a
    >>different view.
    >
    > [snip]
    >
    > Note that I never cited this book. You have confounded me
    > with another sbe poster. While I tend to agree with many
    > of Morris' conclusions, I frequently find the formulations
    > of his arguments unappealing.

    I didn't say you cited it. Tim Tyler cited it. You stepped
    in to defend it. I'm not sure how you separate the
    conclusions from the arguments. In order to understand how
    something happens you have to have the full story, not just
    "...and it comes out here."

    >>>>Natural law presupposes a natural lawgiver, something
    >>>>that's decidedly beyond the realm of science.
    >>>
    >>>Natural law does not presuppose a natural lawgiver.
    >>>Universalities at macroscopic scales can emerge from the
    >>>physics of small scale. I am not going to try to convince
    >>>you to join my point of view here, but I hope you open
    >>>your mind to the possibility of top-down causation as a
    >>>physical phenomenon. It is unfair and obstructionist to
    >>>paint this viewpoint with the rhetorical taint of
    >>>metaphysics as a way to shut down scientific discussion
    >>>of this topic.
    >>
    >>In doing science, one of the goals is to put into language
    >>our understanding of how the universe behaves. These human
    >>descriptions are often referred to as laws of nature,
    >>though nature itself isn't cognizant of any such things.
    >>Natural law states that these descriptions antedate human
    >>intelligence and we "discover" them.
    >
    > As someone who chooses not to use the concept of "natural
    > law", I think that you ought to keep your hands off of the
    > definition intended by others. I don't know of any
    > scientists who uses this term the way you want it defined,
    > although I appreciate that its original use was by
    > religious intellectuals as you pointed out in the bit I
    > snipped at the end of your post. I don't generally use the
    > term "natural law", but for me it evoke the concept that
    > there are universal rules governing the behavior of things
    > whether or not they have ever been articulated. We don't
    > so much "discover" natural laws, as attempt to articulate
    > them. We modify the way we articulate these laws as we
    > find data that call into question aspects of what we think
    > natural law works.

    Well if terms are going to mean what they evoke for you then
    who am I to argue about it.

    >>It is fundamentally a metaphysical construct.
    >
    > Then we mean something very different by this term. To me
    > it is fundamentally a question of physics. In fact, I
    > would say that there is no such thing as a metaphysical
    > construct of any kind. It seems to me that it would be
    > hard to be a scientist and believe in metaphysics at the
    > same time. Do you struggle with this apparent
    > incompatibility?

    No. It is quite difficult to think about two separate topics
    at the same time. If I am thinking hard about stamp
    collecting there's a good chance that I might burn my
    dinner. So I try to avoid being a philatelist and a cook at
    the same time. I don't actually think about metaphysics very
    often (it gives me headaches) but I find it useful when
    discussing a subject to use the terminology of that subject
    and not make up my own meanings for the words as I go along.

    >>If whales and fishes have similar external form it is
    >>because that form is advantageous to their existence, not
    >>because there is somehow an "inevitability" to that form.
    >
    > This does not sound like an open-minded, scientific
    > hypothesis. Why should I take your word that this is true?
    >
    >>Jellyfish have been around longer than either whales or
    >>herring and still have avoided the inevitable.
    >
    > Whose argument is supposed to suffer more from this
    > observation?

    Well, I suppose the implied argument was that there is a law
    of nature that says that all swimming creatures will end up
    with a tapered ellipsoidal body with fins and that a
    jellyfish obviously violates this "law." But I have no idea
    what you are intuiting so I will leave it alone.

    --Jeff

    --
    A man, a plan, a cat, a canal - Panama!

    Ho, ho, ho, hee, hee, hee and a couple of ha, ha, has;
    That's how we pass the day away, in the merry old land of
    Oz.
     


  2. Tim Tyler

    Tim Tyler Guest

    Jim Menegay <[email protected]> wrote or quoted:
    > Jeffrey Turner <[email protected]> wrote in message
    > news:<[email protected]>...

    > > Let's do a nice little experiment with random drift.
    > > Fill a box with marbles, half blue and half red. Proceed
    > > to shake the box. How long before the red marbles drift
    > > to one side of the box and blue marbles to the other?
    > > Now, again, explain why two halves of a population with
    > > a non-adaptive trait "differentiating" them would
    > > separate into two species.
    >
    > You appear to be giving an argument against sympatric
    > speciation. Congratulations! On this subject, at least,
    > you have joined the orthodoxy. Pretty much no one believes
    > that sympatric speciation is possible.

    Whoah there!

    Pretty much *everyone* thinks that sympatric speciation
    is possible.

    Genetic isolation can happen in ways that are not associated
    with geography - e.g. through differences in habitat,
    symbiotes or heredity.

    Plants can speciate just by changing ploidity.

    Geographic isolation is *not* required - and this is widely
    appreciated.
    --
    __________
    |im |yler http://timtyler.org/ [email protected] Remove
    lock to reply.
     
  3. Jim Menegay wrote:
    > Jeffrey Turner <[email protected]> wrote:
    >
    >>... Now, again, explain why two halves of a population
    >>with a non-adaptive trait "differentiating" them would
    >>separate into two species.
    >
    > In my other post, I tried to explain how drift might be
    > part of an explanation for speciation. After further
    > thought, I realize that "might" just ain't going to cut it
    > with you. We just don't know enough about what really
    > "causes" speciation. (Sure, in some sense a species is
    > "sucked apart" by the existence of two different niches
    > that it can adapt to and occupy, but how does this
    > causality work?)
    >
    > Here is the real reason why drift is important in the
    > study of speciation:
    >
    > By counting the number of base pair differences between
    > sibling species, and by understanding the details of how
    > rapidly those differences arose through drift, scientists
    > can estimate how far back in time the divergence occurred.
    > This estimate is an important input into any attempt to
    > explain the causality of a speciation.

    So it is important for archaeo-anthropologists to study the
    mechanisms of radioactive decay in great detail so that they
    can properly Carbon 14 date their finds? How can butchers
    properly sell a pound of meat if they don't study
    coefficients of elasticity and the their application to
    spring scales? Hell, does your biology department offer a
    course on auto mechanics because everyone knows that you
    will probably have to drive a vehicle to your observation
    site and it might break down along the way.

    --Jeff

    > Similarly, all other uses of comparative sequence data -
    > from the human out-of-Africa hypothesis, to Woese's three
    > domains, to the question of whether the first life was
    > hyperthermophilic, to the question of horizontal gene
    > transfer - all of these things depend on an understanding
    > of drift. In fact, you need to also understand all sorts
    > of technicalities, such as transversion vs transition,
    > codon preferences, Dayhoff matrices, and GC/AT. Drift is
    > not a trivial subject.
    >
    > Scientists study drift for the same reason that detectives
    > study fingerprints. The fingerprints may not be the cause
    > of anything interesting, but they may be the best evidence
    > available as to the cause of the really interesting stuff.
    --
    A man, a plan, a cat, a canal - Panama!

    Ho, ho, ho, hee, hee, hee and a couple of ha, ha, has;
    That's how we pass the day away, in the merry old land of
    Oz.
     
  4. John W Edser

    John W Edser Guest

    PostA7
    > snip< RN:- Look at the statistical distribution of
    > energies in a population. Look at quantum tunneling. Look
    > at diffusion and random walk processes. Science is filled
    > with phenomena based on random processes, statistical
    > distributions, and (yes, John Edser) with expected value
    > calculations.

    JE:- You have confused random patterns with random
    processes. Nobody has suggested that random patterns cannot
    be observed. It is what they mean and what we can validly
    suggest caused them that forms the substance of this debate

    A random pattern is any pattern that fits a certain
    criteria. All random patterns form the one, same pattern.
    OTHO, non random patterns are unique. What this dispute is
    about is _not_ the criteria for a random or non random
    _pattern_ it is what _process _can be tested cause each
    pattern type. In all cases, without exception, either a
    random or non random process can be supposed to cause any
    observed random pattern. However all non random patterns are
    only caused by a non random processes. A random process
    cannot cause a non random pattern otherwise it stands
    refuted of being a random process, i.e. just a null
    hypothesis applies to all random processes which includes
    the genetic drift process. This means random processes can
    be refuted but not verified. Note that a non random process
    can be both verified/refuted. Thus only a non random process
    is significant and only non random patterns constitute a
    significant observation within the sciences.

    Best Wishes,

    John Edser Independent Researcher PO Box 266 Church Pt NSW
    2105 Australia

    [email protected]
     
  5. John Wilkins

    John Wilkins Guest

    r norman <[email protected]_comcast.net> wrote:

    > On Wed, 7 Apr 2004 16:38:54 +0000 (UTC), Tim Tyler
    > <[email protected]> wrote:
    >
    > >r norman <[email protected]_comcast.net> wrote or quoted:
    > >
    > >> Apparently, there is a technical meaning to the
    > >> terms"AEVASIVE" and "CURSES" that is somehow relevant
    > >> to this response. Unfortunately these terms lie
    > >> completely outside my experience.
    > >
    > >[...]
    > >
    > >> Then, again, AEVASIVE might simply be the Australian
    > >> spelling for taking avoidance active, but then why the
    > >> upper case spelling?
    > >
    > >They are Peter's acronyms. A quick guide to Peter's
    > >"concEPTs":
    > >
    > >AEVASIVE: Ambi-advantageously Evolved Vital Actention
    > >System Incorporating Various Endoopiates;
    > >
    > >SHITS: Specific Hibernation Imploring Type Situations;
    > >
    > >CURSES: Conditioned-in Unconsciously Remembered Stressors
    > >Effecting Symptoms;
    >
    > Thank you. That, of course, completely clears things up.

    Yes, but what it clears up is Peter's penchant for
    meaningless acronyms.
    --
    John Wilkins [email protected]
    http://www.wilkins.id.au "Men mark it when they hit, but do
    not mark it when they miss"
    - Francis
    Bacon
     
  6. John Wilkins

    John Wilkins Guest

    Jim Menegay <[email protected]> wrote:

    > Jeffrey Turner <[email protected]> wrote:
    > > Let's do a nice little experiment with random drift.
    > > Fill a box with marbles, half blue and half red. Proceed
    > > to shake the box. How long before the red marbles drift
    > > to one side of the box and blue marbles to the other?
    > > Now, again, explain why two halves of a population with
    > > a non-adaptive trait "differentiating" them would
    > > separate into two species.
    >
    > You appear to be giving an argument against sympatric
    > speciation. Congratulations! On this subject, at least,
    > you have joined the orthodoxy. Pretty much no one believes
    > that sympatric speciation is possible.

    Oh, Jim, really? The recent work seems to suggest it is not
    only possible but occurs relatively commonly:

    Berlocher, Stewart H., and J. L. Feder. 2002. Sympatric
    speciation in phytophagous insects: moving beyond
    controversy? Annu Rev Entomol
    47:773-815.

    Dieckmann, U., and M. Doebeli. 1999. On the origin of
    species by sympatric speciation. Nature 400 (6742):354-7.

    Dres, M., and J. Mallet. 2002. Host races in plant-feeding
    insects and their importance in sympatric speciation. Philos
    Trans R Soc Lond B Biol Sci 357 (1420):471-92.

    Filchak, K. E., J. B. Roethele, and J. L. Feder. 2000.
    Natural selection and sympatric divergence in the apple
    maggot Rhagoletis pomonella. Nature 407 (6805):739-42.

    conflict. Proc Natl Acad Sci U S A 99 (16):10533-8.

    Higashi, M., G. Takimoto, and N. Yamamura. 1999. Sympatric
    speciation by

    Kawata, M. 2002. Invasion of vacant niches and
    subsequent sympatric speciation. Proc R Soc Lond B Biol
    Sci 269 (1486):55-63.

    Kephart, Susan, and Kathryn Theiss. 2004. Pollinator-
    mediated isolation in sympatric milkweeds (Asclepias): do
    floral morphology and insect behavior influence species
    boundaries? New Phytol 161 (1):265-277.

    Kondrashov, A. S. 1986. Multilocus model of sympatric
    speciation. III. Computer simulations. Theor Popul Biol
    29 (1):1-15.

    Kondrashov, A. S., and F. A. Kondrashov. 1999. Interactions
    among quantitative traits in the course of sympatric
    speciation. Nature 400 (6742):351-4.

    Kondrashov, A. S., and M. Shpak. 1998. On the origin of
    species by means of assortative mating. Proc R Soc Lond B
    Biol Sci 265 (1412):2273-8.

    Noor, M. A. 1999. Reinforcement and other consequences of
    sympatry. Heredity 83 (Pt 5):503-8.

    Rundle, H. D., L. Nagel, J. Wenrick Boughman, and D.
    Schluter. 2000. Natural selection and parallel speciation in
    sympatric sticklebacks. Science 287 (5451):306-8.

    Schliewen, U. K., D. Tautz, and S. Paabo. 1994. Sympatric
    speciation suggested by monophyly of crater lake cichlids.
    Nature 368 (6472):629-32.

    Schilthuizen, Menno. 2000. Dualism and conflicts in
    understanding speciation. BioEssays 22:1134-1141.

    Turelli, Michael, Nicholas H. Barton, and Jerry A. Coyne.
    2001. Theory and speciation. Trends in Ecology & Evolution
    16 (7):330-343.

    Via, Sara. 2001. Sympatric speciation in animals: the
    ugly duckling grows up. Trends in Ecology & Evolution 16
    (7):381-390.

    Vollmer, S. V., and S. R. Palumbi. 2002. Hybridization
    and the evolution of reef coral diversity. Science 296
    (5575):2023-5.

    Wang, R. L., J. Wakeley, and J. Hey. 1997. Gene flow and
    natural selection in the origin of Drosophila pseudoobscura
    and close relatives. Genetics 147 (3):1091-106.

    Weiblen, G. D., and G. L. Bush. 2002. Speciation in fig
    pollinators and parasites. Mol Ecol 11 (8):1573-8.

    I'd be careful about that assertion, if I were you.

    A nice and accessible review is in

    Schilthuizen, Menno. 2001. Frogs, flies, and dandelions: the
    making of species. Oxford: Oxford University Press.
    >
    > Now, lets look at the more interesting case of allopatric
    > speciation.

    More interesting to whom? :)
    >
    > First we have geographic isolation - one box of marbles,
    > half red, half blue, becomes two non-interacting boxes,
    > both with the same starting composition.
    >
    > Next we have drift. Someone, dkomo I think, gave a nice
    > model of this. In each box, replace each marble with two
    > marbles of the same color. This models Malthusian
    > reproduction. Then, randomly, remove half the marbles from
    > each box. This models the Malthusian struggle for
    > existence. But attempt to be unbiased in removing marbles.
    > Red vs blue is not a difference in adaptation. Repeat for
    > many generations for both boxes.
    >
    > There is a high (50% to be exact) probability that this
    > process will result in one of the boxes all red, and the
    > other blue. This, in itself, does not create the third
    > step in allopatric speciation - namely reproductive
    > isolation when the geographic isolation is removed.
    > Something more is needed. But it is believed by some
    > people that if you have differences in enough traits -
    > those differences caused by drift - then reproductive
    > isolation is likely.

    --
    John Wilkins [email protected]
    http://www.wilkins.id.au "Men mark it when they hit, but do
    not mark it when they miss"
    - Francis
    Bacon
     
  7. Larry Moran

    Larry Moran Guest

    On Thu, 8 Apr 2004 04:41:22 +0000 (UTC),
    John Wilkins <[email protected]> wrote:
    > Larry Moran <[email protected]> wrote:
    >
    >> On Wed, 7 Apr 2004 04:54:07 +0000 (UTC), John Edser
    >> <[email protected]> wrote:
    >> >Larry Moran wrote,
    >>
    >> >>> The hypothesis of drift cannot be verified. Full
    >> >>> stop.
    >> >>
    >> >> The hypothesis of random genetic drift and the
    >> >> hypothesis of natural selection make definite
    >> >> predictions about the outcome of allele frequencies
    >> >> over time. Both can be tested experimentally in the
    >> >> laboratory and in natural populations. Both hypotheses
    >> >> have been verified. Full stop.
    >> >
    >> > This is where you hit an ivory tower wall with Moran et
    >> > al so you have no choice but to call in an
    >> > epistemological referee. Because both hypothesis are
    >> > verified together it is impossible to suggest which one
    >> > was causative. Most Neo Darwinists will invoke Post
    >> > Modernism, delete cause and effect and effectively
    >> > shoot the referee, granting themselves a blank cheque
    >> > to say and do anything they want in the name of
    >> > "science", i.e. IMHO they resort to intellectual
    >> > thuggery in order to protect their tribal affiliations.
    >>
    >> Only some epsitemological referees deserve to be shot.
    >>
    > Now you've epsit me...

    I'd love to put you out of your misery but Austria is to far
    from here and I don't own a gun. :)

    Maybe if you came to Buffalo I could be of more help?

    Larry (who also reads talk.origins) Moran

    [mod note: First, you mean Australia; second, if you read
    t.o. how can you possibly have time to do any work? Finally,
    this jocularity should be taken to email. This ISN'T t.o.,
    after all. - JAH]
     
  8. Guy Hoelzer

    Guy Hoelzer Guest

    in article [email protected], William Morse at
    [email protected] wrote on 4/7/04 9:41 PM:

    > Guy Hoelzer <[email protected]> wrote in
    > news:[email protected]:
    >
    >> in article [email protected], William
    >> Morse at [email protected] wrote on 4/6/04 9:54 PM:
    >
    >>> There is no need to "assert" that drift is universally
    >>> at play - it _has_ to be given the mechanism of
    >>> genetics.
    >
    >> Well - genetic drift is the name we give to the
    >> stochastic sub-process influencing the dynamics of
    >> genetic populations. However, I would argue that there is
    >> a generic role for stochastic sub-processes in all robust
    >> dynamical systems. I also stick by my assertion that
    >> drift is universally at play. If by "no need to assert"
    >> you mean to disagree with my assertion, then I am
    >> interested in seeing a counter argument.
    >
    > I did not mean to disagree with your assertion - what I
    > meant was that asserting that drift is universal is like
    > asserting that 2 plus 2 is 4 - there is no need to assert
    > it because it has to occur, unless _all_ of molecular
    > biology is a snare and a delusion. Except apparently the
    > analogy does not hold since everyone will accept that 2
    > plus 2 is 4 but a number of people seem to have a
    > fundamental problem with drift.

    Exactly. I only felt the need to explicitly make this
    assertion because there is an audience in sbe that seem to
    assume the contrary.

    >>> But given the fact of excess reproduction and the same
    >>> mechanism of genetics, selection is _also_ inevitable.
    >
    >> Here I think we really disagree. Excess reproduction and
    >> the mechanism of genetics makes selection possible, but
    >> not inevitable. Selection only happens when there is
    >> heritable variation for fitness, which is not a necessary
    >> consequence of these mechanisms. This message was made
    >> explicit by Fisher's fundamental theorem of natural
    >> selection. An unavoidable consequence of natural
    >> selection is to diminish heritable variation for fitness,
    >> so the potential for natural selection goes away unless
    >> factors other than these mechanisms cause an increase in
    >> heritable variation for fitness.
    >
    >
    > Bob also noted that heritable variation is necessary, but
    > I believe that the actual mechanisms involved in
    > reproduction do make heritable variation inevitable. To be
    > more precise, the mechanisms guarantee that variation
    > exists and is heritable (let me just note that if this
    > were not true drift as we know it would not occur).
    > Perhaps the mechanisms don't _guarantee_ that the
    > variation affects fitness. But for the variation not to
    > affect fitness would require the walking of a "neutral
    > tightrope" - variation could only affect non-coding DNA,
    > amino acid sequences away from the binding site, etc.
    > Obviously much variation is in fact neutral, but certainly
    > not all. So your argument appears to be not that selection
    > won't occur, but that it will not result in evolution,
    > because it will only diminish variation for fitness.

    No. This is not my argument at all. I do think that natural
    selection is a real process and that it is an important path
    to biological adaptation. However, I am trying to make the
    argument that drift happens continuously and always,
    selection happens only sporadically and under special
    conditions. Fisher's fundamental theorem makes the point
    that selection is self-extinguishing even under the
    conditions that induce this process.

    > With regard to Fisher. I want to be careful here, because
    > I have not read Fisher, and all of the big names in the
    > field that I have read clearly know much more about
    > evolution than I do, have thought much more about
    > evolution than I have, and are generally much more aware
    > of the subtleties of their arguments than I am. It does
    > seem to me that for selection to _unavoidably_ diminish
    > heritable variation requires that (a) there exists a
    > maximum (in my sense) for the fitness measure and (b) that
    > the environment is unchanging. Now (a) is probably
    > approximately true for many fitness measures (the point
    > may make for some interesting argument) but (b) is clearly
    > false. With a changing environment, selection can in fact
    > produce variation. But note that even if selection does
    > not produce variation, _it will still occur if there is
    > excess reproduction_

    I basically agree with these points. Fisher's fundamental
    theorem was indeed derived under the typical assumption of
    an unchanging environment. I am extrapolating his result to
    make the point that selection is self-dampening (this may be
    a better term than "self-extinguishing", which I used above)
    even if the environment is changing. This tendency would
    maximize (in my sense) the extent of time periods in which
    selection is essentially not operating.

    Speaking of maximization, I don't follow your reasoning in
    asserting that there must exist a maximum fitness value if
    selection is to generically diminish heritable variation for
    fitness. I don't think that Fisher made this assumption.

    > In practice, I think the combination of drift and
    > environmental change produce initial speciation -
    > selection then drives further variation between the
    > separated populations.Perhaps this is closer to Sewall
    > Wright's point of view, with which I tend to
    > sympathize, but Wright is another of the giants that I
    > have yet to read.

    I think your views, like mine, are closer to Wright's
    than Fisher's.

    Cheers,

    Guy
     
  9. Jeffrey Turner <[email protected]> writes:

    > Steve Schaffner wrote:
    > > Three questions in human genetics for which
    > > understanding of genetic drift is crucial:
    >
    > I never said it shouldn't be studied at all, just that it
    > has nothing to do with evolution. You know, one species
    > _evolving_ into another. Darwin's classic was titled "On
    > the Origin of Species" not some blather about the
    > distribution of disease-causing alleles.

    You've said a number of things. Among others:
    1) Drift isn't important in the real world.
    2) Scientists only study drift because they can't find
    anything useful to do.
    3) Drift, and intraspecies evolution in general, shouldn't
    be called "evolution".

    I offered the examples to demonstrate that your first two
    claims were wrong (as they are).

    Your third claim represents your opinion. Since your
    proposed usage differs from the practice of everyone
    actually doing evolutionary biology, and since (as
    demonstrated by your first two claims) you don't know much
    about evolutionary biology, your opinion can safely be
    neglected. The difference in opinion is not arbitrary, by
    the way: drift is considered part of evolution because its
    study uses many of the same tools as "real" evolution, and
    because it is difficult to study molecular evolution at all
    without studying drift in the process.

    --
    Steve Schaffner [email protected] Immediate assurance is an
    excellent sign of probable lack of insight into the topic.
    Josiah Royce
     
  10. R Norman

    R Norman Guest

    On Thu, 8 Apr 2004 04:41:17 +0000 (UTC), Jeffrey Turner
    <[email protected]> wrote:

    >Larry Moran wrote:
    >
    >
    >> The current models of speciation emphasize allopatric
    >> speciation as a major player. When species arise as a
    >> result of geographical separation they do not directly
    >> complete for resources.
    >
    >Ah, there's the crux of the problem. Species do indeed
    >arise as a result of geographical separation and it is
    >that geographical separation that is the driving force.
    >The crucial quality of species is that they cannot mate
    >outside their own kind. As soon as you have a geographical
    >separation you create a separate species. It is only in
    >the context of competition for resources that it makes
    >sense to talk about whether a mutation is beneficial,
    >harmful or neutral.
    >

    This is not true. Geographical separation alone does NOT
    create a separate species. Failure to interbreed strictly
    due to physical separation does not count as a reproductive
    isolating mechanism. Once you remove the geographical
    barrier, if there is no other isolating mechanism then
    interbreeding will quickly merge the two gene pools and
    eliminate any differences that may have developed during the
    separation. The same thing happens is there is sufficient
    migration between the two incompletely isolated populations.

    What geographical separation does is eliminate the
    interbreeding that keeps the gene pool intact. Geographical
    separation also usually means small population sizes in at
    least one of the groups, increasing the probability of
    drift. And, of course, geographical separation greatly
    increases the probability that the two environments are
    sufficiently different to allow different selective forces
    to work in the two populations.
     
  11. R Norman

    R Norman Guest

    On Thu, 8 Apr 2004 16:11:43 +0000 (UTC), "John W Edser"
    <[email protected]> wrote:

    >
    >PostA7
    >> snip< RN:- Look at the statistical distribution of
    >> energies in a population. Look at quantum tunneling. Look
    >> at diffusion and random walk processes. Science is filled
    >> with phenomena based on random processes, statistical
    >> distributions, and (yes, John Edser) with expected value
    >> calculations.
    >
    >JE:- You have confused random patterns with random
    >processes. Nobody has suggested that random patterns cannot
    >be observed. It is what they mean and what we can validly
    >suggest caused them that forms the substance of this debate
    >
    >A random pattern is any pattern that fits a certain
    >criteria. All random patterns form the one, same pattern.
    >OTHO, non random patterns are unique. What this dispute is
    >about is _not_ the criteria for a random or non random
    >_pattern_ it is what _process _can be tested cause each
    >pattern type. In all cases, without exception, either a
    >random or non random process can be supposed to cause any
    >observed random pattern. However all non random patterns
    >are only caused by a non random processes. A random process
    >cannot cause a non random pattern otherwise it stands
    >refuted of being a random process, i.e. just a null
    >hypothesis applies to all random processes which includes
    >the genetic drift process. This means random processes can
    >be refuted but not verified. Note that a non random process
    >can be both verified/refuted. Thus only a non random
    >process is significant and only non random patterns
    >constitute a significant observation within the sciences.
    >
    You have confused "random patterns" with fundamentally
    random mechanisms. The fundamental process at work that
    underlies the phenomena I mentioned: tunneling,
    diffusion, radioactive decay (a new one I just added) is
    a random process.

    You have a very one-sided view of randomness and determinism
    and refuse to acknowledge what Physics has known for over
    one hundred years, now, when you consider statistical
    thermodynamics, radioactive decay, and quantum mechanics.
     
  12. Guy Hoelzer

    Guy Hoelzer Guest

    in article [email protected], Jim Menegay at
    [email protected] wrote on 4/7/04 9:41 PM:

    > Jeffrey Turner <[email protected]> wrote in message
    > news:<[email protected]>...
    >> Let's do a nice little experiment with random drift. Fill
    >> a box with marbles, half blue and half red. Proceed to
    >> shake the box. How long before the red marbles drift to
    >> one side of the box and blue marbles to the other? Now,
    >> again, explain why two halves of a population with a non-
    >> adaptive trait "differentiating" them would separate into
    >> two species.
    >
    > You appear to be giving an argument against sympatric
    > speciation. Congratulations! On this subject, at least,
    > you have joined the orthodoxy. Pretty much no one believes
    > that sympatric speciation is possible.

    This claim caught my attention, not so much because I
    disagree with the content of the argument, but because I
    think it misrepresents current conventional wisdom. I agree
    that this accurately represents the conventional wisdom of
    the 1970s, but the theoretical work of folks like Mike
    Rosenzweig effectively swayed the conventional wisdom by the
    late 1980s regarding the POSSIBILITY of sympatric
    speciation. I think the conventional wisdom these days is
    that sympatric speciation is very rare compared with
    allopatric speciation, but I think this dogma is starting to
    break down, too. Sympatric speciation has been a tough issue
    to get an empirical handle on, because there is no clear and
    distinguishing "fingerprint" that sympatric speciation is
    expected to leave behind. If, for example, most historical
    speciation events have been of the sympatric kind, what sort
    of data could be used to reveal this? The conventional
    wisdom has mainly been driven by the relative, perceived
    plausibility of competing models, which is a pretty weak
    form of argumentation because plausibility is so strongly
    influenced by preconception. It is also important to
    recognize that the traditional geographic framework for
    defining categories of speciation modes is a human
    construct. Many evolutionary biologists, including myself,
    consider the fundamental distinction to be speciation in the
    absence of presence of gene flow. Note that this framework
    lumps together sympatric and parapatric speciation at the
    process level, where both represent speciation in the face
    of gene flow. I view the geographical separation by degree
    represented by the parapatric speciation model as a
    condition that facilitates the process of sympatric
    speciation. The point I really want to make here is that
    recent theoretical work, particularly the highly regarded
    papers by Sergei Gavrilets, is rapidly raising the profile
    and plausibility of parapatric speciation.

    Cheers,

    Guy
     
  13. Jim Menegay

    Jim Menegay Guest

    Tim Tyler <[email protected]> wrote in message news:<[email protected]>...
    > I'm inclined to suggest that ... any readers (or
    > respondents) more interested in evolution than
    > epistemology should move along.

    Yes, by all means. But before moving on, I just can't resist
    giving a short explanation as to why I am a little more
    fascinated by Popper than are most people.

    It is not that I think that studying epistemology makes us
    better scientists. IMHO, scientists do a damned good job of
    sifting evidence, by and large. Edser uses the metaphor of
    the epistemologist as referee. I think it would be more
    accurate to view the epistemologist as sportscaster. His
    comentary on the action in the arena creates an illusion of
    enlightenment in some spectators, and a reaction of mild
    annoyance in others. But the commentary is completely
    ignored by the professionals fighting it out in the arena.
    As BOH and Wilkins point out, science as it is actually
    practiced is far too rich and complex to fit well into
    Popper's simplified models.

    However, there is another sense in which epistemology might
    be interesting to some evolutionary scientists. The objects
    that we study - organisms and species - are themselves
    entities that sift evidence, learn, and construct models of
    reality. Popper's models are far to simple to describe a
    human scientist, but I think that they are extremely
    illuminating in attempting to describe a bacterium, as it
    struggles to construct a useful model of the world around
    it. To understand systems, like the bacterium, that learn
    from experience (on either an individual organism or an
    evolutionary timescale), it seems to me that we have to
    imagine a space of possible models-of-reality that the
    system can construct. Concepts such as Occam's razor,
    confirming vs refuting evidence, and (relative) nullness of
    hypotheses strike me as extremely fruitful in this study.

    Popper's attempt to construct an epistemology of human
    science strikes me as a failure, but his theory applies to
    bacteria very well indeed.
     
  14. Larry Moran

    Larry Moran Guest

    On Thu, 8 Apr 2004 16:11:46 +0000 (UTC),
    John W Edser <[email protected]> wrote:
    >Larry Moran wrote,

    [snip]

    > In a theory you have to prove an allele is ONLY neutral.
    > How do you do this?

    The easiest way is to check a large sample of a population
    to see if two alleles are in Hardy-Weinberg equilibrium. Did
    you not know that?

    [snip]

    > Mr Moran simply evaded my proposition, _entirely_. Since
    > it is you and not me that insists that just a random drift
    > process can contest an win against selection then it is
    > you and not me that must answer this question:
    >
    > ___________________________________________
    > Can drift without selection cause evolution because
    > selection without drift definately can?
    >
    > PLEASE ANSWER THIS QUESTION
    > ___________________________________________
    >

    The answer is yes.

    Larry Moran
     
  15. Guy Hoelzer <ho[email protected]> wrote in
    news:[email protected]:

    > in article [email protected], William
    > Morse at [email protected] wrote on 4/7/04 9:41 PM:
    >
    >> Guy Hoelzer <[email protected]> wrote in
    >> news:[email protected]:
    >>
    >>> in article [email protected], William
    >>> Morse at [email protected] wrote on 4/6/04 9:54 PM:

    >> Bob also noted that heritable variation is necessary, but
    >> I believe that the actual mechanisms involved in
    >> reproduction do make heritable variation inevitable. To
    >> be more precise, the mechanisms guarantee that variation
    >> exists and is heritable (let me just note that if this
    >> were not true drift as we know it would not occur).
    >> Perhaps the mechanisms don't _guarantee_ that the
    >> variation affects fitness. But for the variation not to
    >> affect fitness would require the walking of a "neutral
    >> tightrope" - variation could only affect non-coding DNA,
    >> amino acid sequences away from the binding site, etc.
    >> Obviously much variation is in fact neutral, but
    >> certainly not all. So your argument appears to be not
    >> that selection won't occur, but that it will not result
    >> in evolution, because it will only diminish variation for
    >> fitness.

    > No. This is not my argument at all. I do think that
    > natural selection is a real process and that it is an
    > important path to biological adaptation. However, I am
    > trying to make the argument that drift happens
    > continuously and always, selection happens only
    > sporadically and under special conditions. Fisher's
    > fundamental theorem makes the point that selection is self-
    > extinguishing even under the conditions that induce this
    > process.

    And my point is that selection doesn't stop, it is only that
    under some (perhaps many) circumstances it keeps selecting
    the same thing. That may mean that you will only _see_ it
    sporadically, but it doesn't mean it is not occurring. If
    you offer me a choice between a and b over and over, and I
    choose b over and over without fail, does that mean no
    choice is being made?

    > Speaking of maximization, I don't follow your reasoning in
    > asserting that there must exist a maximum fitness value if
    > selection is to generically diminish heritable variation
    > for fitness. I don't think that Fisher made this
    > assumption.

    I may well be wrong, but my intuition is that if you have a
    range of values in a population (fitness) x1..xn, and you
    have a function (selection) about which the only thing you
    know is that it will increase the value, i.e. f(x) > x, you
    cannot state that the range f(x1).. f(xn) will be less than
    the range x1..xn unless there is an upper bound on f
    (xn).

    Yours,

    Bill Morse
     
  16. Jim Menegay

    Jim Menegay Guest

    Jeffrey Turner <[email protected]> wrote in message news:<[email protected]>...
    > Jim Menegay wrote:
    > > Jeffrey Turner <[email protected]> wrote:
    > >
    > >>... Now, again, explain why two halves of a population
    > >>with a non-adaptive trait "differentiating" them would
    > >>separate into two species.

    > > Here is the real reason why drift is important in the
    > > study of speciation:
    > >
    > > By counting the number of base pair differences between
    > > sibling species, and by understanding the details of how
    > > rapidly those differences arose through drift,
    > > scientists can estimate how far back in time the
    > > divergence occurred. This estimate is an important input
    > > into any attempt to explain the causality of a
    > > speciation.
    >
    > So it is important for archaeo-anthropologists to study
    > the mechanisms of radioactive decay in great detail so
    > that they can properly Carbon 14 date their finds? How can
    > butchers properly sell a pound of meat if they don't study
    > coefficients of elasticity and the their application to
    > spring scales? Hell, does your biology department offer a
    > course on auto mechanics because everyone knows that you
    > will probably have to drive a vehicle to your observation
    > site and it might break down along the way.

    Jeff, your sarcasm is certainly dazzling, but somehow, you
    forgot to mention what your point is. Unless, perhaps, it is
    something like, "Drift may be science, but it is not my kind
    of science." If I have read you right, and that is your
    point, then I have to ask:

    WHY DO YOU KEEP DISCUSSING IT?

    btw, I still like the cat, but you might consider dropping
    the munchkin chorus.
     
  17. Jim Menegay

    Jim Menegay Guest

    [email protected] (Jim Menegay) wrote in message news:<[email protected]>...
    > Pretty much no one believes that sympatric speciation is
    > possible.

    John, Tim, Guy, and whoever else is thinking of piling on:

    Gee, thanks you all. Now I have enough reading material to
    keep me busy for a while so I won't have to post. ;-)
     
  18. Jim Menegay

    Jim Menegay Guest

    "John W Edser" <[email protected]> wrote in message news:<[email protected]>...
    > PostA10

    [snip]

    > > JM:- Nature is free to choose its laws so that some of
    > > them may be
    > unverifiable.
    >
    > JE:- Yes, but you can't ever _know_ that this is the case,
    > that is my point.

    [snip]

    There is very little that you can _know_ unless you are a
    God. However, you can have well justified beliefs, and
    one of the best justifications for belief is repeated
    survival in the face of serious attempts at refutation.
    That is my point.

    John, I am embarrassed to admit that I am disputing with you
    here, and I don't properly understand your position. I'm not
    sure whether we are disputing the meaning of words, deep
    issues of philosophy, or the biological facts. Since I have
    learned that I frequently don't understand you when you
    express your position in your language, it would help me if
    you make an attempt to express your position in my language.
    Please read through the following list of "position
    statements" and indicate which most closely approximates
    your position. Then, change my wording, if necessary to
    exactly describe your position.

    1. Any claim that both drift and NS are occurring is absurd.
    ALL changes in gene frequency are caused by either
    mutation or selection. Selection IS a change in gene
    frequencies due to differences in birth or death rates.
    There can be no "drift" other than that caused by
    mutation - and mutation is not what the advocates of
    drift are talking about. If a gene increases in frequency
    by differences in birth and death rates, then it is being
    selected, regardless of whether we understand the causes
    of the difference in birth and death rates.

    2. I understand that some mutations are approximately
    neutral selectively, and I agree that Kimura's
    mathematics is correct in the same sense that Fisher's
    math is correct - it may be useful as a somewhat
    oversimplified model that provides some limited insight.
    However, it is wrong to make it sound as if Kimura is
    somehow contesting NS. Kimura is part of NS.

    3. Drift is conceptually distinguishible from NS, but it is
    scientific abdication of responsibility to actually
    hypothesize or believe in drift. Scientists are supposed
    to seek deterministic explanations for the world. A
    philosophically correct scientist will treat the so-
    called evidence for drift as an unsolved problem for
    another day, rather than actively embracing it. No
    philosophically correct scientist can adhere to an
    unverifiable hypothesis.

    4. Drift is effectively refuted. In very many cases in
    which a scientist has looked for an adaptive explanation
    for an allele fixation, such an explanation has been
    found. A scientist would be foolish to believe that this
    trend will not continue. Ultimately, almost all allele
    changes will be understood to have been caused by
    selection.

    5. Drift is absurd because it postulates selectively neutral
    mutations. That is, it assumes that the selective
    advantage is exactly zero. But it should be obvious that
    exactly zero is effectively impossible. Every mutation
    must have some small positive or negative effect, and
    therefore will be subject to selection.

    I hope that one of these approximates your position.
    Otherwise, I am very confused about what we are fighting
    about. But, once I understand what we are fighting about, I
    will fight you tooth and nail, if you wish, and if the
    stakes appear high enough. ;-)
     
  19. John W Edser

    John W Edser Guest

    PostA15

    > > JE In a theory you have to prove an allele is ONLY
    > > neutral. How do you do this?

    > LM The easiest way is to check a large sample of a
    > population to see if two alleles are in Hardy-Weinberg
    > equilibrium. Did you not know that?

    JE:- Yes I did. Did you know that the Hardy-Weinberg
    equilibrium requires an infinite population for such a proof
    and only indicates a random distribution i.e. a verified
    random PATTERN if such a proof ever existed?

    Assuming you did have an infinite population and had proven
    the allele distribution pattern was indeed neutal, what
    type of PROCESS can validly be suggested to have caused
    this pattern?

    I note that you just snipped the meat of my post which
    concerns the critical difference between a model and a
    theory.

    Is a model the same as, or different to, a theory?

    I also noted that a hypothesis was different to a theory.

    Is a hyopothesis different to, or the same as, a theory?

    > [snip]

    > > JE:- Mr Moran simply evaded my proposition, _entirely_.
    > > Since it is you and not me that insists that just a
    > > random drift process can contest an win against
    > > selection then it is you and not me that must answer
    > > this question:
    > > ___________________________________________
    > > Can drift without selection cause evolution because
    > > selection without drift definitely can?
    > >
    > > PLEASE ANSWER THIS QUESTION
    > > ___________________________________________

    > LM:- The answer is yes.

    JE:- Thank you for answering the question.

    How would you set up a real life experiment (not just a
    thought experiment) to test your proposition?

    John Edser Independent Researcher

    PO Box 266 Church Pt NSW 2105 Australia

    [email protected]

    >
    >
    >
    >
    > Larry Moran
     
  20. Jim Menegay

    Jim Menegay Guest

    "Anon." <[email protected]> wrote in message news:<[email protected]>...
    > How can you get drift with Ne=infinity? We've thought
    > about it, and some have even bee into the field and
    > sampled midlew. It's diverse, and there's a lot of it
    > about, so Ne=infinity is a good approximation. I think my
    > point is that any null hypothesis has to be referenced to
    > the species and population you're studying.

    If you define "drift" to be non-selective fixation of
    alleles, then Ne=infinity seems to rule it out. But, if you
    define "drift" as non-selective change in gene frequencies,
    then you need an even larger population to stop drift in its
    tracks - you need SQRT(Ne)= infinity. ;-)

    Other reasons for doubting the importance of drift in mildew
    are a presumably small genome with little junk, presumed
    strong expressed codon preferences making even synonymous
    substitutions non-neutral,

    It may well be that there is no significant drift in mildew,
    but this doesn't argue that drift is an inappropriate null
    hypothesis. It just means that, in this species, the null
    hypothesis is refuted.
     
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