Dawkins on Kimura



Guy Hoelzer <[email protected]> wrote in message news:<[email protected]>...
> in article [email protected], Jim Menegay
> at [email protected] wrote on 4/6/04 9:54 PM:
>
> > John's argument, as I understand it, is that an unknown
> > deterministic process could conceivably make the same
> > predictions as the hypothesis of drift.
>
> This is certainly true, although I see no need to invoke
> an "unknown" deterministic process. As I have pointed out
> to John before, natural selection could serve this role.

It appears that I have neglected your priority on the idea
of drift as a null hypothesis. Sorry about that. I probably
read what you wrote, then "forgot" about it.

> Indeed, I have argued several times on sbe that the
> general proposition that selection is responsible for the
> shape of biodiversity is entirely untestable because
> detailed selection models could be constructed to predict
> any biodiversity pattern that could possibly be observed.
> In contrast, the general proposition that drift is
> responsible for the shape of biodiversity is more testable
> because drift is expected to act in the same way all of
> the time. While drift can stumble onto any particular
> pattern in principle, we have a clear expectation of the
> likelihood of such an occurrence, which allows us to
> reject drift as a reasonable sole explanation for observed
> data. There is no such general expectation that has ever
> been proposed for selection, which makes it impossible to
> directly reject a selection-only model for any
> observation. At best we can tenuously (indirectly) reject
> selection as a reasonable explanation for data that fit
> the drift-only model very well.

Exactly! NS explanations have degrees of freedom not present
in the drift null hypothesis. Hence Occam favors drift if
both explain the data.

> > He may well be right about this. Therefore, it seems
> > tactically correct to me to concede his point, but then
> > to point out the philosophical and epistemological
> > silliness of his argument.
>
> Having gone further than concession, and actively making
> this argument myself, has had no effect on John's
> argumentation that I can see.

I never claimed to wisdom ...
 
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.

>>> 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.

> 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?

> 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?

[snip]

Guy
 
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.

> Thus, there is no requirement that the new species has to
> have an "edge" on the previous species. You seem to be
> confining your thoughts to a particular form of speciation
> where a parent species gradually transforms into a new
> species over time with no splitting. At least I think
> that's what you mean.

Well, it enters into what we mean by "previous." If a new
ecosystem arises does it make sense to talk about a
"previous" species? A species may "bud" off an existing
species by creating a new niche - or even taking over a
niche from another species - or it may outcompete its
progenitor in the same niche.

Genetic drift is a process whose importance seems to lie on
a scale somewhere between individuals and species. As long
as drift is going on, we're necessarily talking about
genetic frequencies within a species. The only way for a
genetic mutation to work its way through a population is for
the individuals who carry that mutation to reproduce at a
rate higher than their fraction of the population. That is,
they must have disproportional reproductive success. So how
do you distinguish, in the absence of an a priori measure of
fitness, whether a mutation is neutral or adaptive if the
carriers of that mutation are having outsized reproductive
success? (Ah, that pins down the nearly neutral theory!) And
when a mutation does make it through the population, do you
have a new species or not? That is, at what point can you
say that the offspring could not, at least in theory,
reproduce with the parents? Making these distinctions in

Will absolutely neutral mutations propagate through a
species with millions of individuals? It seems unlikely to
happen in a finite amount of time. Can you give an example?

--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.
 
On Wed, 7 Apr 2004 16:38:53 +0000 (UTC), 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.
>

Let's do a better little experiment that truly encapsulates
random drift. Fill a box with marbles, half blue and half
red. Shake the box to mix them thoroughly. Now draw 6
marbles from the box. Rebuild the full population in the box
from these six, in the same proportion and check to see
whether you still have half blue and half red.

Two geographically separated (allopatric) populations can
accumulate non-adaptive differences in mating behavior
(cricket calling songs, firefly flashing pattern, etc), or
non-adaptive differences in details of reproductive
structures (many arthropods) or cellular recognition factors
in egg and sperm (all prezygotic species isolating
mechanisms) or else chromosomal mutations that result in
hybrid breakdown or sterility or incompatibility (all
postzygotic species isolating mechanisms). This would result
in two species.
 
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.

Now, lets look at the more interesting case of allopatric
speciation.

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.
 
Jeffrey Turner <[email protected]> wrote in message news:<[email protected]>...
> ... 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.

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.
 
On Wed, 7 Apr 2004 16:38:54 +0000 (UTC), Tim Tyler <[email protected]>
wrote:

>r norman <rsn_@_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;
>
>*****: Specific Hibernation Imploring Type Situations;
>
>CURSES: Conditioned-in Unconsciously Remembered Stressors
>Effecting Symptoms;

Thank you. That, of course, completely clears things up.
 
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...

--
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
 
PostA10
> > > > JM:- The hypothesis of drift cannot be verified.
> > > > Full stop.

> > JE:- Well, sbe is still waiting? Where exactly did you
> > "point out the philosophical and epistemological
> > silliness of his argument" within this reply?

> JM:- Within this reply I did not. Look within the first
> post containing the
quote
> "The hypothesis of drift cannot be verified. Full stop.".
> You should reread that post. It makes several arguments
> that you are being silly.

JM:- Jim, you never replied to my critiqueof your position.
If something cannot be verified it has not been tested even
if it can be refuted because nobody understood in the first
place what it was they thought they were testing. It is easy
to say all observations verify x by definition and then look
for one that does not. This tells you nothing about what you
are testing! Drift cannot be verified but it can be refuted.
This means you only know what drift isn't and not what it
actually is as a process.

> JM:- The strongest one, to my mind, and the one you
> completely missed, has to do with epistemologists trying
> to constrain Nature, rather than constraining scientists.

JE:- Nature as a _concept_ is anything that we want it to be
unless you can prove:

1) Knowledge of nature is inherited.
2) God given.

Thus all concepts of what nature is are just guesses about
what exists. You have to separate testable from non testable
guesses. All testable guesses "constrain Nature" via at
least one absolute assumption of nature, otherwise concepts
of it cannot be tested. A scientist is thus confined to
testing finite propositions of what nature may or may not,
be. He/she must fairly test, i.e. test without bias, all
testable propositions on the table. To be testable, a
proposition must be verified/refuted. It has to have _both
_of these qualities and not just one of them as a valid
testable THEORY of nature

> 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. Thus this proposition is thrown as a non
testable proposition by any competent epistemological
referee. Science leaves such propositions to the intuitive
mystic mind where it may or may not, do some good.

> JM:- That is, an unverifiable hypothesis may turn out to
> be the correct description of Nature's law.

JE:- Incorrect. You can never know this until it can
be verified!

> JM:- Therefore, a wise epistemologist does not try to
> forbid scientists from advancing unverifiable
> hypotheses. To do so would be to place some of Nature's
> laws as being forever forbidden to scientific belief.
> That would be silly.

JE:- No, it is silly to think you know what you don't know.
The null hypothesis has its uses and misuses. It is misused
if it seeks to replace a non null hypothesis, i.e. you
cannot know what it is you are testing using the null
hypothesis but you do know when you use a non null
hypothesis. Thus the null hypothesis is just that, ONLY a
hypothesis and not a theory of nature. All hypothesis are
parts of a theory. There is no such animal as a null theory.

> JM:- But an epistemologist is quite correct in advising
> scientists not to propose unrefutable hypotheses. Such
> hypotheses can never correspond to a law of Nature. For an
> unrefutable hypothesis is not a "law" at all - it doesn't
> forbid any conceivable empirical evidence. Any such
> unrefutable "law" of Nature must be vacuous - it forbids
> nothing and hence can explain nothing.

JE:- For a theory to be testable it must be BOTH verifiable
and refutable. Drift as a null hypothesis is simply another
gene centric misuse to be added to a long list other model
misuses, when it seeks to replace selection because only
selection is:

3) NOT a hypothesis but a theory.
4) Can be BOTH verified and refuted.

Respectfully,

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email protected]
 
PostA11
> > JE:- This is because it is impossible to divide these 6
> > among NS and drift! This is simply because drift is just
> > a random process. The reason why drift cannot validly
> > contest selection is simply because random variation
> > patterns have always in the past, are today, and will
> > always in the future, only form a part of a _testable_
> > non random process like selection within the sciences.

> LM:- The mutations are neutral, deleterious, or
> beneficial. It's quite possible to estimate the
> relative frequency of each type from known data. All
> three types are subject to random genetic drift but
> only the deleterious and beneficial mutations are
> affected by natural selection.

JE:- Yes, they are just estimates and neutrality is just
assumed within a MODEL. Ok that is fine for just a model. A
model cannot stand alone, it must help understand a testable
theory of nature. Because you are a specialist in model
building why does that give you the right to misuse your
mode to replace a valid , testable theory of nature?

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

>> JE:-
> > Selection can cause evolution without drift but drift
> > cannot cause evolution without selection. All drift can
> > do without selection is allow for the dissipation of
> > Darwinian selectees.

> LM:- Most evolution at the level of the gene is due to
> random genetic drift and not natural selection. In real
> populations it's impossible for natural selection to
> operate in the absence of random genetic drift. This is
> why most beneficial alleles are eliminated from the
> population before they can become fixed and it's why
> some deleterious alleles become fixed in spite of the
> fact that they are associated with negative fitness.
> Any change in the frequency of a neutral allele cannot
> possibly be due to natural selection acting on that
> allele.

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 definately can?

PLEASE ANSWER THIS QUESTION
___________________________________________

Best Wishes,

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email protected]
 
PostA12
> > > JM:-
> >>The hypothesis of drift cannot be verified. Full stop.

> > LM:- 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.

> > JE:- 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.

> BOH:- I rathr think that, unlike you, professional
> biologists are aware of the possibility of multiple
> causation. Stop full.

JE:- "Stop full" Have you been drinking that awful Norwegian
Vodka again?

Multiple testable causations YES, multiple non testable
causations, NO.

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email protected]
 
PostA13
> > JW:- Oh for heavens' sakes, John. Of *course* Darwin
> > cited others - he cited Malthus, in particular, as the
> > source of the inspiration, but he *never* did *any*
> > experiments on natural selection. None.

> > JE:- I have never denied that "Darwin cited others".
> > Obviously, none of us are an intellectual island.
> > However, it was not so much that these others
> > contributed but what Darwin creatively did with
> > it. Where the famed Owen only saw fixed species because
> > of religious bias Darwin saw non separated variants.
> > Why? Because Darwin was only a naive naturalist (a
> > rank amateur) as far as Owen was concerned. It was
> > Huxley that had to take on the likes of Owen et al
> > who given the chance, would have happily used their
> > "authority" to crush Darwin. Darwin preferred to
> > avoid such demeaning tribal politics and just
> > concentrate on the science.

> JW:- Owen actually tended towards species transitional
> forms, and was working on an evolutionary accoutn when
> Darwin went public. And Owen also afforded Darwin
> professional standing. History is more complicated than
> simple moral tales permits. Huxley used Darwin to
> establish his own professional standing in Owen's own
> territory, and so crystallised Owen against Darwin. Had
> Huxley not been convinced (and as a transcendentalist he
> was more likely on a naive reading to reject Darwin than
> Owen), Owen would have become Darwin's main defender in
> all probability. As it was, he tried to take credit for
> many of Darwin's ideas in an early [anonymous - nobody
> said he was a *nice* man] review of the Origin.

JE:- I acknowledge your historical supremicy on this
subject. However, the principles of what I said still stand.
Darwin left the politics to the politicians while he got on
with the science. Owen and Huxley were more politicians than
scientsists.

> JW:- And variant forms of species were commonplace from
> 1840 onwars. Henrui Milne Edwards and Alphonse de Candolle
> both stressed subspecific variation, and several
> continental ornithologists did too. The "species question"
> as it was then called focused on whether there was, in
> fact, warrant for the Cuvierian notion that species were
> logical classes "in the mind of God".

JE:- Varients were seen by those that had eyes to see them
but were not interpreted as varients between species but
within species. The same percept was regarded in an OPPOSING
theory of causation using Darwin's concept of variation.
Before Darwin, sepecies were absolute assumptions. After
Darwin they became relative assumptions. Most of the worlds
population is still reeling from this simple revelation.

> > JE:- Where Malthus could only see death and destruction

> JW:- This is also false. Malthus thought that economic
> selection would generate fitter individuals (in the pre-
> Fisherian sense of "fit").

JE:- Yes, and Herbert Spencer agreed so after Muller the
fascist racist right had to have WW2 as a "natural"
Darwinian act, according to ******. Malthus could not
differentiate competition by default from competition intent
but Darwin could. This difference was massive.

> > Darwin saw natural selection. Mathus, Owen and Darwin
> > all "saw" the same things as perceptual patterns but not
> > as concepts (processes that may have caused these
> > patterns). Malthus and Owen passed on their perceptions
> > to Darwin but not, thankfully, their concepts. Darwin
> > created his own concepts, which unlike theirs, were
> > rigorous i.e. testable against nature. So did Mendel
> > before Darwin and many others. You only have two
> > choices: dictate what nature is or provide contestable
> > theories of what nature might be and throw out the
> > poorer view/views via the Popperian process of
> > refutation. Science can only deal with the latter.
> > Authority, misused, imposes the former. When status and
> > power are concerned uncivilised men are psychologically
> > driven to use any means possible to maintain
> > it. Such behaviour remains predictable from basic
> > evolutionary theory.

> JW:- This is vastly overstated and oversimplified.

JE:- OK That is all the room I have ... Please make specific
criticisms to save verbiage.

>snip<

> > JW:- He did experiments on *artificial* selection, on
> > dispersal by seed, on earthworm activity, on plant
> > tropism and carnivorism. But nothing on natural
> > selection.

> > JE:- What experiments on natural selection would you
> > suggest he could have done at that time, that he did
> > not do?

JE:- No answer?

> > JW:- Moreover, nearly all the evidence he adduces to
> > support natural selection is based on or directly the
> > work or observation of others, although he does, of
> > course, cite his own experiences during the Beagle
> > voyage. Without that external support, nobody would have
> > taken his hypothesis seriously.

> > JE:- Yes "Without that external support, nobody would
> > have taken his hypothesis seriously" e.g. Wallace. This
> > does not mean that Darwin was right or wrong it, just
> > means tribal based prejudice predictably, remains
> > endemic and can only be removed by the prerequisite of
> > testability , i.e. scientific ideas must be able to be
> > verified/refuted or they are not admitted.

> JW:- And again, I partly agree. But you had better get the
> history right if you want to mount a historical argument.
> Don't rely on textbook histories. They are like flowers,
> designed to propagate ideas, not support them, and like
> flowers they often mislead the pollinators.

JE:- Like everything else history is open to interpretation.
What matters to me is the process that allows this.

Do you agree that: "scientific ideas must be able to be
verified/refuted or they are not admitted" ?

Regards,

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email protected]
 
PostA14
> > JM:-
> > > The hypothesis of drift cannot be verified. Full stop.

> > LM:- 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.

> > JE:- 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. [snip]

> JM:- Larry and I are in agreement regarding the evidence
> for drift, how that evidence should be interpreted, ....

JE:- Dear oh dear...

You said:- The hypothesis of drift cannot be verified. Full
stop

Larry said: Both hypotheses have been verified. Full stop.

Do I need glasses? Larry and yourself stand in contradiction
to each other.

Prof. Felsenstein stated that all models are non testable.
Dr G. Hoelzer stated that all models are testable.

Where is the referee? Having tea? Is Evolutionary theory
just a Mad Hatter's Tea Party? If so, say hello to the White
Rabbit for me....

Respectfully, John Edser

Independent Researcher PO Box 266 Church Pt NSW 2105
Australia

[email protected]
 
PostA14
> >> Within gene centric Neo Darwinism this is not the case
> >> but it is the case within organism centric Darwinism.
> >> Thus, Darwinism remains today's evolutionary authority
> >> and today's Neo Darwinism.

> >I can't parse this.

JE:- If you snip everything that is required then of course
it does not make sense.

Best Wishes,

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email protected]
 
PostA9
> > The evidence that you cite fully convinces me that drift
> > is taking place, but, by its very nature, it can never
> > convince John.

> LM:- I agree. According to Edser's silly philosophy
> nothing in science can ever be verified - including
> natural selection.

JE:- Incorrect.

Because NS is a non random process it can be
verified/refuted. Because Drift is only a random process it
can only be refuted but cannot be verified.

Simple.

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email protected]
 
Guy Hoelzer wrote:
> in article [email protected], Anon. at
> [email protected] wrote on 4/7/04
> 9:38 AM:
>
>
>>>> I think claiming that any allele frequency changes are
>>>> due to drift will get you laughed at (well it would do
>>>> if most mildew biologists weren't too polite).
>>>
>>>
>>> While getting laughed at would not be pleasant for me,
>>> I think it would be far more damaging to the
>>> scientific credibility of mildew biologists. I don't
>>> know any personally, but you make them sound like an
>>> unthinking lot.
>>>
>>
>> How can you get drift with Ne=infinity? We've thought
>> about it, and some have even bee into the field and
>> sampled midlew.
>
>
> I did not know you were into mildew, Bob.
>
In my past life, but now I've got better. :)

>
>> 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.
>>
>
>
> I don't think this point has any traction in this
> instance because...
>
>
>
>> Of course, there are other stochastic events - founder
>> effects and bottlenecks, and these can occur (and indeed
>> probably do have a significant effect on the
>> populations).
>
>
> ... every system exists in a spatial and temporal context
> that invariably reduces local Ne to values that are way
> lower than infinity (I will sarcastically add "by at
> least half" to further make my point). Despite evidence
> to the contrary from my own bathroom, I will continue to
> argue that there is a finite amount of mildew.
>
Actual local population sizes are huge, and there is a lot
of migration (especially early in the season). We're talking
a mild infection being about 10 colonies (=individuals) per
leaf, and there are a lot of leaves in a field.

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
 
Larry Moran wrote:
> On Wed, 7 Apr 2004 16:38:55 +0000 (UTC), Anon.
> <[email protected]> wrote:
>
> [snip]
>
>
>>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.
>>
>>Of course, there are other stochastic events - founder
>>effects and bottlenecks, and these can occur (and indeed
>>probably do have a significant effect on the populations).
>
>
> Random genetic drift is the process of change in allele
> frequency due solely to chance. It includes founder
> effects and bottlenecks. You may have been assuming that
> trandom genetic drift was only due

>
> I assume someone has sampled mildew for heterozygosity?

Difficult: it's haploid. :)

If so, I assume
> that the local population contains a large number of
> alleles of different genes. How did this happen? Are all
> of these alleles examples that are in the process of
> becoming fixed or eliminated by natural selection?
>
LD: see below.

> I assume that someone has sampled mildew from different
> parts of the country? Is the frequency of alleles
> identical in these samples? Why not?
>
Selection? There's a large selective pressure, because it
grows on barley, a commerically (and culturally!) important
crop, and one of the major defences is single genes with
large effects. The mildew can overcome these with changes at
single genes (this is the gene-for-gene system, for those
that know it). Hence, it breaks down the rsistance very
quickly (3-5 years). This lead to a rapid cycling in the
resistance geens used, so the mildew's environment was
changing every year. Hence, an increase in the use of of
resistance gene leads to increased selection pressure, and a
change in the population.

large LD being set up.

> In evolutionary terms, a true population is a group of
> individuals where every individual has an equal chance of
> mating with every other individual. The term for this is
> "panmitic." Most species consist of many populations where
> gene flow is restricted in one way or another. I doubt
> very much whether the effective population size of mildew
> is anywhere near infinity. Aren't mildew species usually
> sub-divided into sub-species and isolates?
>
I suspect that the sub-species are "true" species, as for
the isolates,

be passed around the world.

As for gene flow, it goes everywhere. There is immigration
of British mildew to Denmark, and the northern French
population is a mixture of southern English and central
French populations.

Bob

--
Bob O'Hara

Dept. of Mathematics and Statistics
L.E. 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
 
Tim Tyler wrote:
> Anon. <[email protected]> wrote
> or quoted:
>
>
>>How can you get drift with Ne=infinity?
>
>
> You can't even measure relative allele frequencies then.
>
>
>>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. [...]
>
>
> Is there any mildew on islands anywhere?
>
Yes - the Orkneys. It gets there from Scotland.

> It seems like drift could produce effects there - which
> could then re-invade the ancestral population.
>
Difficult - it would be like a drop in the ocean. The
mainland population is just too big.

The nearest you're going to get to drift is founder effects,
caused by selective sweeps.

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
 
On Thu, 8 Apr 2004 04:41:24 +0000 (UTC),
William Morse <[email protected]> wrote:

[snip]

> 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 you but I'd just like to raise a
minor point that has always bothered me. I don't think that
(b) is clearly false in the sense you mean. In most cases
the environment doesn't change very much or, if it does,
species track their preferred environment.

But selection can still produce variation. The reason why
selection can still produce variation in an unchanging
environment is because no species is perfectly adapted to
its environment (IMHO). I assume that you require a
*changing* environment because you disagree with me. You
probably assume that after some time in a constant
environment the species will become so well-adapted that
further change by selection can't happen. That's why you
require a *changing* environment. Am I right?

It seems to be a common perception that species will rapidly
become perfectly adapted to their environment and that's why
*change* in environment seems to be required for further
adaptation. I've never understood the rationale for this
assumption. Are there any modern examples of species that
are presently so perfectly adapted to their environment so
that natural selection is insignificant?

> 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 don't think environmental change is a requirement for
speciation. Most cases of speciation in the fossil record
show that the daughter species and the parent species co-
exist for millions of years in (presumably) the same
environment. (This is one of the main tenets of punctuated
equilibria.) Furthermore, I also don't think it's necessary
to postulate that "selection drives further variation
between the populations" as you say. The populations could
just as easily diverge by drift, although the data in the
fossil record suggests that stasis is very common.

If I understand you correctly, you're postulating speciation
by cladogenesis followed by subsequent gradual divergence
due to natural selection. Is this a correct interpretation?

Larry Moran
 
Steve Schaffner wrote:
> Jeffrey Turner <[email protected]> writes:
>>Larry Moran wrote:
>>
>>>I can understand why you aren't interested in things like
>>>pseudogenes, genome organization, molecular evolution,
>>>and the source of variation within a population but I'm
>>>having trouble understanding why you feel the need to be
>>>so insulting about the interests of many evolutionary
>>>biologists.
>>
>>Because there's a chance that you can still do something
>>useful with your life and not just pick at intellectual
>>navel lint 'til you're pushing up the daisies instead of
>>contemplating them.
>
>
> 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.

> the distribution of disease-causing alleles, the history
> of human populations, and the detection of loci under
> positive selection. That's leaving aside the basic
> scientific goal of understanding what's going on, of
> course. Do you have some reason for posting attacks on the
> most basic motivation for doing science in a science
> newsgroup?

I have no objection to doing science, but do not play
baseball and call it ice hockey.

--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.
 
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