Dawkins on Kimura



William Morse <[email protected]> wrote or quoted:

> And I will further note that non-adaptive lock-ins are unlikely to represent very many traits in
> old, widespread, morphologically stable species, because such species are still subject to
> competition from other species and have been for a long time. So they cannot afford too much extra
> baggage.

What if - after not very long - all their competition comes from other organisms with the
same lock-in?

I fully expect this is the case regarding a number of old, widespread and stable adaptations - such
as the genetic code.

I don't want to give too much weight to non-adaptive traits - but frozen accidents are
certainly possible.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove lock to reply.
 
in article [email protected], Jim Menegay at
[email protected] wrote on 3/4/04 8:39 AM:

> Guy Hoelzer <[email protected]> wrote in message news:<[email protected]>...
>
>> [snip] IMHO, if Dawkins and his followers continue to ignore the overwhelming evidence of
>> adaptive "evolution" in complex dynamical systems that seemingly lack the basic ingredients for
>> the process of natural selection (e.g., populations of reproducing agents), they will look
>> increasingly like closed-minded zealots as time goes on. [snip]
>
> This interests me, but puzzles me. What does "adaptive" mean in this context? I have a picture of
> a system (without reproducing parts) getting better at something - presumably something that is in
> its own best interests. But I don't see in what sense a dynamical system can be said to have
> interests.

I agree with your intuition about how to conceive of adaptation as something not limited to
biological populations. Note that I think of this hierarchically, so that any explanation of self-
interest in the bigger picture should apply fully to our narrower understanding of self-interest in
the biological context. I see non-equilibrial thermodynamics as explaining the notion of self-
interest most generally.

Your concern about the nature of self-interest in non-biological, dynamical systems is
understandable; but interestingly I think that most evolutionary biologists would have a similar
problem with the notion of self-interest at the level of populations of biological organisms, which
is exactly the level at which they are most comfortable with the notion of natural selection as the
adaptive process. The general claim of the theory of complex adaptive systems, as I see it, is that
they emerge (manifest) because they serve a thermodynamic imperative. The teleological aspect of
service thus imbues all dynamical systems with self-interest in a sense that does not require
anything like cognition.

> Also, I wonder what "complex" means in this context. Presumably, dynamical systems that are not
> complex don't exhibit this phenomenon of adaptive evolution.

Well -- the theory as I understand it suggests that there cannot be such a thing as a simple
dynamical system. Complexity (decentralized control in networks of interacting parts) is claimed to
be a co-requisite for the emergence of systematic (coherent) functional activity.

> But what is complexity? Does it come from the large number of dimensions in the state space? The
> strangeness of the attractors? Our lack of understanding of how the system works?

It is emphatically not about our lack of understanding, although it can be harder to understand the
inner workings of complex systems than it is to understand simple relations. I hope my explanation
above suggests the conceptual links of complexity with dimensionality and strange attractors.

> (Or did I misunderstand the "e.g."? Are you saying that a population of reproducing, but non-
> mutating, agents will evolve adaptively? One model of this, of course, would be Daisy World.)

No; you seem to have understood my "e.g." correctly, although I agree with your point.

Cheers,

Guy
 
Guy Hoelzer <[email protected]> wrote in message news:<[email protected]>...
> in article [email protected], Jim Menegay at
> [email protected] wrote on 3/4/04 8:39 AM:
>
> > Guy Hoelzer <[email protected]> wrote in message
> > news:<[email protected]>...
> >
> >> [snip] IMHO, if Dawkins and his followers continue to ignore the
> >> overwhelming evidence of adaptive "evolution" in complex dynamical systems
> >> that seemingly lack the basic ingredients for the process of natural
> >> selection (e.g., populations of reproducing agents), they will look
> >> increasingly like closed-minded zealots as time goes on. [snip]
> >
> > This interests me, but puzzles me. What does "adaptive" mean in this context?
> > I have a picture of a system (without reproducing parts) getting better at
> > something - presumably something that is in its own best interests. But I
> > don't see in what sense a dynamical system can be said to have interests.
>
> I agree with your intuition about how to conceive of adaptation as something
> not limited to biological populations. Note that I think of this
> hierarchically, so that any explanation of self-interest in the bigger picture
> should apply fully to our narrower understanding of self-interest in the
> biological context. I see non-equilibrial thermodynamics as explaining the
> notion of self-interest most generally.
>
> Your concern about the nature of self-interest in non-biological, dynamical
> systems is understandable; but interestingly I think that most evolutionary
> biologists would have a similar problem with the notion of self-interest at the
> level of populations of biological organisms, which is exactly the level at
> which they are most comfortable with the notion of natural selection as the
> adaptive process. The general claim of the theory of complex adaptive systems,
> as I see it, is that they emerge (manifest) because they serve a thermodynamic
> imperative. The teleological aspect of service thus imbues all dynamical
> systems with self-interest in a sense that does not require anything like
> cognition.

But would you say that the motion of the planets around the sun is a kind of self-
interest because it serves a gravitational imperative? I don't think so.

NeoDarwinism is sometimes characterized by the slogan that "Genes mutate,
individuals are selected, and species evolve". It might be added that the end
result of this evolution is that the typical individual is adapted. But,
"adaptation" for a complex system must apply to the same entity that evolves -
namely the system itself. There are no lower level entities. Are you saying that
NeoPrigoginism's slogan would be "Systems evolve, systems become adapted"? Or,
are you saying that complex systems are automatically adaptive (adapted?) - they
don't need to evolve to become adapted? As you can see, I am struggling here to
come up with some analogy with Evolution/NaturalSelection that lets me categorize
your viewpoint and usee of the word "adapt".

Let me suggest that thermodynamic systems far from equilibrium sometimes exhibit
a kind of "self organization" and you might say that they have an interest in
maintaining that organization. I am still a little uncomfortable with using the
word "adaptive" to describe this hypothetical behavior by a complex system. It
seems to be little more than a kind of (meta)stability. I am also not yet
convinced that the inevitable appearance of this kind of behavior is backed by
"overwhelming evidence"
>
> > Also, I wonder what "complex" means in this context. Presumably, dynamical
> > systems that are not complex don't exhibit this phenomenon of adaptive
> > evolution.
>
> Well -- the theory as I understand it suggests that there cannot be such a
> thing as a simple dynamical system. Complexity (decentralized control in
> networks of interacting parts) is claimed to be a co-requisite for the
> emergence of systematic (coherent) functional activity.

You are apparently reading different texts than I am. My sources use the term
dynamical system for simple systems such as pendula and two-body orbital
mechanics problems. But this is merely a quibble over terminology.

>
> > But what is complexity? Does it come from the large number of dimensions in
> > the state space? The strangeness of the attractors? Our lack of understanding
> > of how the system works?
>
> It is emphatically not about our lack of understanding, although it can be
> harder to understand the inner workings of complex systems than it is to
> understand simple relations. I hope my explanation above suggests the
> conceptual links of complexity with dimensionality and strange attractors.
>
> > (Or did I misunderstand the "e.g."? Are you saying that a population of
> > reproducing, but non-mutating, agents will evolve adaptively? One model of
> > this, of course, would be Daisy World.)
>
> No; you seem to have understood my "e.g." correctly, although I agree with
> your point.

I'm happy that you agree with me, but I'm not sure I successfully communicated my
point. Daisy World is a crock IMHO. Lovelock created an artificial model to
illustrate the kinds of mechanisms that might lead to a Gaian homeostasis. But it
would be just as easy to create a model of a world that doesn't exhibit
homeostasis - that is actively unstable.
 
Tim Tyler <[email protected]> wrote in message news:<[email protected]>...
> Jim Menegay <[email protected]> wrote or quoted:
> > Guy Hoelzer <[email protected]> wrote in message
> > news:<[email protected]>...
>
> > > [snip] IMHO, if Dawkins and his followers continue to
> > > ignore the overwhelming evidence of adaptive
> > > "evolution" in complex dynamical systems that
> > > seemingly lack the basic ingredients for the process
> > > of natural selection (e.g., populations of reproducing
> > > agents), they will look increasingly like closed-
> > > minded zealots as time goes on. [snip]
> >
> > This interests me, but puzzles me. What does "adaptive"
> > mean in this context? I have a picture of a system
> > (without reproducing parts) getting better at something
> > - presumably something that is in its own best
> > interests. But I don't see in what sense a dynamical
> > system can be said to have interests.
>
> A brain is a complex adaptive system - it changes over
> time in a manner that matches and reflects elements in its
> environment.
>
> You don't have to be able to self-reproduce to be able to
> adapt - since there are other ways of adapting besides
> natural selection -
> e.g. learning.

But the brain is an evolved mechanism. Sure, systems that
have been constructed by evolution or by intelligent design
can be adaptive. The adaptiveness of such systems arises
from their genesis, not from their complexity. I thought
that the issue was whether there is some sort of compulsion
or tendency of complex systems to become adaptive.
 
[email protected] (Larry Moran) wrote in message news:<[email protected]>...
> On Wed, 3 Mar 2004 16:51:17 +0000 (UTC), Anon.
> <[email protected]> wrote:
> > Larry Moran wrote:
>
> [snip]
>
> >> Two points ...
> >>
> >> 1. Genetic diversity cannot be an adaptation since this
> >> requires a form of group selection that has been
> >> thoroughly discredited. If a species accidently
> >> possesses more diversity then it will be the lucky
> >> survivor when the environment changes. This is more
> >> like evolution by chance that real adaptation.
> >>
> > Two points ...
> > 1. Inbreeding depression is a form of lack of genetic
> > diversity that can increase the chance that a
> > population goes extinct. This will generally work at
> > low effective population sizes.
>
> This is correct but that's not the point. The point is
> whether you can *select* for diversity within a population
> based on the assumption that it will become useful at some
> future date.

This discussion involves an intricate interplay of
several ideas
1. Species selection vs individual selection.
2. Selection vs drift
3. Long term vs short term.

I hope I don't complicate things more by introducing a
fourth issue - the dreaded Haldane's dilemma.

My take on HD is that it points out that selection has a lot
of work to do killing off the unfit, and only a finite time
to do it. Selective deaths are a scarce resource, and
natural selection is unlikely to waste them on trivial
things like optimizing the size of an elephant's ears -
especially since there has only been a short time since
African and Indian elephants diverged.

That is, I am taking HD as an argument against extreme
adaptationism.

But HD is also applicable to the question of long term vs
short term. If a trait is disadvantageous in the short
term, but advantageous in the long term, should we expect
the trait to persist in a population? Sure, why not,
suggests HD, as long as the short term disadvantage is
small in comparison with the other issues that selection
has to deal with.

That is, I am suggesting here that the orthodox belief in
the idea that the short term always trumps the long term is
probably wrong. Long term advantageous traits, for example a
mutation rate slightly larger than the short term optimum,
can be selected for in the face of a short term
disadvantage.

Consider the population just after one of the sporadic long
term events. For example, look at it just after a major
attack by a new virus. The survivors were lucky in having a
high mutation rate that let them "respond" to the attack. So
the population at this point in time will have a high
mutation rate. But, this high mutation rate is
disadvantageous in the short term, so we can expect it to
decline under selection. But HD says that the rate of
decline will be finite. If the trait of a high mutation rate
is not totally extinguished by short term selection before
the next big virus attack, then long term selective pressure
can win over short term selective pressure. And, if it
doesn't win, then it could be claimed that there wasn't
really any long term advantage to begin with.
 
> >> Two points ...
> >>
> >>1. Genetic diversity cannot be an adaptation since this
> >> requires a form
> >> of group selection that has been thoroughly
> >> discredited. If a
species
> >> accidently possesses more diversity then it will be
> >> the lucky
survivor
> >> when the environment changes. This is more like
> >> evolution by chance that real adaptation.

> > Two points ...
> > 1. Inbreeding depression is a form of lack of genetic
> > diversity that can increase the chance that a
> > population goes extinct. This will generally work at
> > low effective population sizes.

> This is correct but that's not the point. The point is
> whether you can *select* for diversity within a population
> based on the assumption that it will become useful at some
> future date.

JM:- This discussion involves an intricate interplay of
several ideas
1. Species selection vs individual selection.
2. Selection vs drift
3. Long term vs short term.

JE:- Why did you exclude "Organism Fitness Mutualism" (OFM)?

The main reason as to why "you can *select* for diversity
within a population based on the assumption that it will
become useful at some future date" is because it increases
_mutualised_ fitness.

When forms make associations that benefit each form in
absolute fitness but do not necessarily benefit them
equally, then selection must increase the diversity between
mutualised forms. This is because there is little point
forming an OFM association when they are mostly the same.
OFM is a form of unconscious trade. It is best to trade with
those who do things better and differently. IMO, the most
obvious example of OFM selecting for increased diversity is
in the evolution of

attempting to explain the evolution of non hermaphrodite

resulting is a 50% _gene centric_ loss. Of course if you
only use Darwinian fitness this "loss" is only a
possibility, i.e. it is not measured as an actual loss. In
Darwinian fitness terms a potential loss can only be
measured by a reduction of _fertile_

evolution and Darwinian fitness any potential loss must
have resolved itself to become, an absolute parental
fitness GAIN.

The more intense OFM becomes, the more selective pressure
that is applied to each, separate, Darwinian entity to
increase heritable diversity for each entity within each OFM
group. I stress:

THIS IS NOT GROUP SELECTION.

L. Moran et al, do not understand how group selection
differs from Darwinian selection. This is proven when b
within Hamilton's rule was not understood by them to be
group selective in the classical sense of the word.

JM:- I hope I don't complicate things more by introducing a
fourth issue - the dreaded Haldane's dilemma. My take on HD
is that it points out that selection has a lot of work to
do killing off the unfit, and only a finite time to do it.
Selective deaths are a scarce resource, and natural
selection is unlikely to waste them on trivial things like
optimizing the size of an elephant's ears - especially
since there has only been a short time since African and
Indian elephants diverged. That is, I am taking HD as an
argument against extreme adaptationism. But HD is also
applicable to the question of long term vs short term. If a
trait is disadvantageous in the short term, but
advantageous in the long term, should we expect the trait
to persist in a population? Sure, why not, suggests HD, as
long as the short term disadvantage is small in comparison
with the other issues that selection has to deal with. That
is, I am suggesting here that the orthodox belief in the
idea that the short term always trumps the long term is
probably wrong.

JE:- You should go back in sbe archives and read the long
tortuous discussions between Walter ReMine and Prof.
Felsenstein on Haldane's Dilemma. Haldane is the source of
two major Neo Darwinistic errors re: model _misuse_:

1) Haldane's Dilemma

2) His discussion of OFA that preceded Hamilton's views on
the same subject.

Haldane's Dilemma: The discussion was based on Haldane's
simplified model that predicted that not enough time existed
to allow man and chimp to evolve from a common ancestor.
Haldane based his calculations on an _inflated_ size re: the
human genome. His assumption of the probable size of the
human genome was many more times bigger than it was actually
proven to be. Since the discovery of the relatively small
size of the human genome, the "Haldane's Dilemma" story has
been reduced to just a waste caused by crossing gene centric
bridges before you come to them. Given the actual size of
the human genome and the tiny differences that exist between
it and the chimp genome, more than enough time has passed to
evolve chimps and men from a common ancestor, using
Haldane's assumptions. Thus it just is red faces all round
on this issue.

ReMine (a creationist) who had written a large book on the
subject and was attempting to hit evolutionary theory over
the head with Haldane's dilemma, refused to admit that he
was wrong. Prof. Felsenstein refused to admit that the
dilemma was unreal to start with ,
i.e. was a just a waste of time and resources caused by the
_misuse_ of Haldane's oversimplified view of nature.

The most important issue re: Haldane's Dilemma remains NON
DISCUSSED. The dilemma was wrong because Haldane's
inflated size for the human genome, was wrong. Why did
gene centric Neo Darwinists consider such a huge genome a
necessity? Simply because they needed such a huge genome
if just additive epistasis (which just means no epistasis
at all!) was allowed as "heritable". Fisher's model
deleted all gene fitness epistasis. It redefined "non
additive" epistasis as "inherited" but "non heritable" and
thus "non selectable". We are stuck with Fisher to this
very day. The fact is, the failure of Haldane's dilemma
points to Fisher's failure re: what is and what is not
validly regarded as "heritable". If non additive
information can be "heritable" and thus "selectable" then
the human genome can be compressed like a zip file.

OFA: In the now famous pub discussion, Haldane did not
include any value for cmax. This discussion pre-empted
Hamilton by many years. Hamilton made the same mistake of
not including a maximal value for c within his famous rule.
In both cases, only relative fitness was included allowing
for totally erroneous arguments to occupy evolutionary
theory for over 50 years re: the evolution of OFA within
nature. OFA could not be supported by Hamilton's rule
because OFA can only be diagnosed from OFM using the sign of
c. Within Hamilton's rule. the sign of c remains _arbitrary_
. Thus at all times OFM OR OFA can be validly supposed to be
operating within Hamilton's rule. Thus the rule was entirely
misused to support OFA within nature after group selection
failed to do so. To this day, no theory of nature has been
proposed that supports OFA. Gene centric Neo Darwinists have
had to resort to redefining nature as just their simplified
model view while wheeling in Post Modern epistemology to
justify such nonsense.

Respectfully,

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email protected]
 
Jim Menegay <[email protected]> wrote or quoted:

> Daisy World is a crock IMHO. Lovelock created an
> artificial model to illustrate the kinds of mechanisms
> that might lead to a Gaian homeostasis. But it would be
> just as easy to create a model of a world that doesn't
> exhibit homeostasis - that is actively unstable.

...if true, that would impact Lovelock's thesis not in the
slightest.

He only suggested that the planet spends most of its time in
a homeostatic equilibrium orchestrated by living organisms.

The possibility of processes that drive the state away from
equilibrium is acknoledged - but they will only manifest
themselves noticably during times of instability - and
dynamical systems are likely to spend most of their times in
stable states if these exist.

Indeed, the existence of such unstable processes simply echo
the warnings from the Gaia enthusiasts that the Earth will
only stomach being pushed so far before it flips into a new
state - possibly one less habitable by the forces causing
the instability in the first place.

Also check out the properties of daisy world:

It suggests that white dasies reflect away more heat - and
in hot times will spread selfishly - and have the effect of
cooling down the whole planet.

Note that the local effect and the global one are both
derived from the same bit of physics: reflecting away heat
cools you down.

If the model was changed - by wiping out the Sun and having
the heat source inside the planet - then black dasies will
survives better when it is too hot - since they will
radiate heat away from themselves better. However a planet
covered with black dasies will also cool down faster by
radiating heat.

The fact that the model survives this sort of modification
suggests there is a general principle at work - /sometimes/
acting locally really does produce similar effects globally.

Some other examples where this might happen include reducing
levels of pollution, and dealing with resource shortages.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.
 
Jim Menegay <[email protected]> wrote or quoted:
> Tim Tyler <[email protected]> wrote in message
> news:<[email protected]>...
> > Jim Menegay <[email protected]> wrote or quoted:
> > > Guy Hoelzer <[email protected]> wrote in message
> > > news:<[email protected]>...

> > > > IMHO, if Dawkins and his followers continue to
> > > > ignore the overwhelming evidence of adaptive
> > > > "evolution" in complex dynamical systems that
> > > > seemingly lack the basic ingredients for the process
> > > > of natural selection (e.g., populations of
> > > > reproducing agents), they will look increasingly
> > > > like closed-minded zealots as time goes on.
> > >
> > > This interests me, but puzzles me. What does
> > > "adaptive" mean in this context? I have a picture of a
> > > system (without reproducing parts) getting better at
> > > something - presumably something that is in its own
> > > best interests. But I don't see in what sense a
> > > dynamical system can be said to have interests.
> >
> > A brain is a complex adaptive system - it changes over
> > time in a manner that matches and reflects elements in
> > its environment.
> >
> > You don't have to be able to self-reproduce to be able
> > to adapt - since there are other ways of adapting
> > besides natural selection -
> > e.g. learning.
>
> But the brain is an evolved mechanism. Sure, systems
> that have been constructed by evolution or by
> intelligent design can be adaptive. The adaptiveness of
> such systems arises from their genesis, not from their
> complexity. [...]

Water poured onto a rocky landscape exhibits a "good fit"
with the contours of the landscape - and preserves it in the
face of deformations of that landscape.

For me, that's the essence of an adaptive system: it's
exactly the same sort of process that genes in organisms are
performing on their fitness landscapes.

> I thought that the issue was whether there is some sort of
> compulsion or tendency of complex systems to become
> adaptive.

Guy was saying that not all adaptive systems were the
product of evolution.

That seems a bit different to whether there's a tendency for
some class of systems to come to exhibit adaptive behaviour.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.
 
[email protected] (Larry Moran) wrote in
news:[email protected]:

> On Wed, 3 Mar 2004 16:51:14 +0000 (UTC), William Morse
> <[email protected]> wrote:
>> [email protected] (Larry Moran) wrote in
>> news:[email protected]:
>
> [snip]
>
>>> Hmmmm .... I would have thought that ear size in
>>> elephants and skin color in humans were excellent
>>> example of drift. Don't you see how difficult it is to
>>> make general rules? Your decision about what the
>>> "default" hypothesis should be depends to a great extent
>>> on your original biases. This is exactly the point that
>>> Lewontin and Gould made in their original paper. If you
>>> tend to emphasize natural selection in your thinking
>>> about evolution then you will look to adaptive
>>> explanations ahead of non-adaptive explanations.
>>
>> I will stand by my example of ear size in elephants - my
>> reference is a book entitled "Why Elephants Have Big
>> Ears" - which despite its title was written by Chris
>> Lavers, not Rudyard Kipling :) In another follow on this
>> thread you questioned why Indian elephants have smaller
>> ears. Lavers notes that both Indian elephants and African
>> forest elephants - both of which have smaller ears than
>> African savanna elephants - inhabit forests with lower
>> temperatures than the savanna. He also notes that woolly
>> mammoths had tiny ears.
>
> I have't read the book.
>
> How does one distinguish between a just-so story and a
> valid explanation? If it turned out that Asian elephants
> had big ears and African elephants had small ones do you
> think that someone would come up with an adaptionist
> explanation? I do. That's the problem. With sufficient
> imagination one can conjure up an adaptionist explanation
> for almost anything that happens in biology. This isn't a
> very good reason for preferring adaptionist explanations
> over chance and accident - expecially since we know for a
> fact that chance plays the major role at the molecular
> level. Why shouldn't it play a major role at the
> morphological level as well?

How major a role? Darwin's logic is fairly incontrovertible
here - if organisms produce more offspring than can survive
(which they do), and if there is heritable variation
between those offspring (which there is) then _if_ that
variation results in a differential fitness (which appears
to be the crux of our disagreement) there _will be
selection_ for the morphological trait. Drift plays the
major role at the molecular level because most changes at
that level _are_ selectively neutral. I can change an
alanine for a valine far from a binding site and selection
won't (at first) see it. But AFAIK drift hasn't made much
of a dent in the binding site of hemoglobin, to give only
one obvious example.

Now while it is true that adaptationists are prone to
conjuring up explanations for observed morphological traits,
that doesn't make those explanations wrong, it just makes
them untested. Ideally one would like to alter the ear genes
for African elephants, stick a bunch of small- eared ones in
an otherwise identical savanna environment, and see if they
survive as well as big eared ones, but even if we could
perform the experiment we would have to wait 20000 years for
results, and even postdocs might get a little antsy :)
Luckily for us mother nature has performed some of these
experiments for us. Pangolins, aardvarks, anteaters, and
echidnas are all mammals but otherwise quite unrelated -
except that they share the same ecological niche and share
numerous morphological traits. Take a good look sometime at
pictures of the heads of deer and kangaroos, which also only
distantly share a common ancestor, and use quite different
mechanisms of locomotion (score one for contingency!), but
share a similar niche. A zoologist can look at the teeth of
an animal and tell you what it eats, can look at its skin
and tell you what climate it inhabits, can look at its eyes
and tell you whether it is predator or prey. So how are
these morphological traits _not_ adaptations?

The argument for drift is a much tougher row to hoe. You've
got all the tools of molecular biology that prove that drift
occurs, but on a morphological basis how do you prove a
negative? And even if you do, where is the glory? The
adaptationist gets to come up with a great (if unprovable)
story, while the stochasticist is left with endless strings
of purines and pyrimidenes which mostly cannot (yet) be
linked to morphology and behavior.

(snip intro to this)

> So, is it possible that variation in skin color is due to
> selection in some parts of the world (Northern Europe) but
> drift elsewhere?

Certainly (although my argument is that "some parts of the
world" includes all of Europe, Africa, Asia and Australia) .
Drift happens. Selection happens. Calamity (aka ****)
happens :) If Arlin Stoltzfus were still contributing to
sbe he would be telling us that mutation pressure happens.
Evolution doesn't care which of the above is leading to
changes in gene frequencies. What I was trying to define
with my "default assumptions" was traits that were
_primarily_ shaped by one or the other
- but there are no magic force fields that protect
reproducing organisms from any of the above effects.

(snip)

> (A minor quibble ... natural selection also has a major
> stochastic component. Most beneficial mutations are
> eliminated from the population. The best you can do is
> calulate the "probability" that a given allele will become
> fixed if you know the selection coefficient.)

Agreed. One of the reasons that zebra mussels have been able
to spread so rapidly in North American fresh waters is their
ability to fix to a substrate. This ability is common in
mussels throughout the world, but there are no native North
American freshwater mussels that can do this. Even I have
difficulty in coming up with a Just So story to explain this
- it may well be due to "bad luck".

Yours,

Bill Morse
 
Tim Tyler <[email protected]> wrote in
news:[email protected]:

> William Morse <[email protected]> wrote or quoted:
>
>> And I will further note that non-adaptive lock-ins are
>> unlikely to represent very many traits in old,
>> widespread, morphologically stable species, because such
>> species are still subject to competition from other
>> species and have been for a long time. So they cannot
>> afford too much extra baggage.
>
> What if - after not very long - all their competition
> comes from other organisms with the same lock-in?
>
> I fully expect this is the case regarding a number of
> old, widespread and stable adaptations - such as the
> genetic code.
>
> I don't want to give too much weight to non-adaptive
> traits - but frozen accidents are certainly possible.

In another follow on this thread you mentioned that you
might be accused of arguing both sides of the point. I think
that you _have_ been doing that, and doing a right good job
of it! One of Darwin's many good points was his ability to
see both sides of an argument - you also seem to have this
ability. I will now try to evince the same.

One of the key features of evolution is that it builds on
previous successes, vs. reinventing the wheel at every step.
The downside of this is that it is hard to go back. I seem
to recall a recent article about a clade of insects
(dragonflies maybe?) reinventing flight after having lost
it. This was news because it almost never happens. So yes
there will be frozen accidents. Lavers in discussing
elephant ears notes that elephants don't sweat, perhaps
because their ancestors lost the ability during an aquatic
phase (don't let Larry Moran know this!). Their big ears may
only be a "contingent" adaptation.

Yours,

Bill Morse
 
Tim Tyler <[email protected]> wrote in message news:<[email protected]>...
> Jim Menegay <[email protected]> wrote or quoted:
>
> > The standard way of thoroughly discrediting group
> > selection is to point out that selection at the level of
> > individuals would "trump" the much weaker process at the
> > group level. But in this case particularly, that
> > argument doesn't seem to apply. What could a selfish
> > individual possibly do that would subvert the species
> > from carrying out its strategy of genetic diversity?
>
> It's going to look as though I am playing both sides of
> this - but:
>

> rate.
>
> Individuals can control their mutation rates to some
> extent - by choosing to what extent they invest in clean-
> burn technology, and clean-up technology.
>
> According to genetic-algorithm folklore, a population will
> best explore the fitness landscape if there's about one
> mutation per individual per generation. I figure this is
> what species selection would probably favour.
>
> However, individuals benefit most from avoiding mutations
> completely - since often mutataions lead to broken
> offspring.
>
> In some single-celled organisms, I've read [sorry no
> reference today] that the individual gets its way. The
> mutation rate is *much* lower (by a couple of orders of
> magnitude) than it should be if the species wanted to be
> able to evolve rapdily in the face of a changing
> environment.
>
> Here, the individuals could do something to stop diversity
> arising - namely lower their mutation rates to *extremely*
> low levels.
>
> Apparently, sometimes that's exactly what they do.

But it is the individual that benefits if it has a high
mutation rate and it lucks out by coming up with just the
mutation that is needed.

Hmmm... But the species also benefits in some sense. All the
other low mutation rate individuals in the population have
the opportunity to recombine with the mutant. So, they may
have some reason to encourage the altruistic mutator and to
provide some kind of compensation.

What do you know... They do compensate. They assume a share
of the risks of mutation; their descendents will
occasionally get a double dose of

creates a kind of reciprocity between high mutation-rate
individuals and low mutation-rate individuals.

This idea is new to me, but it can't be new. Has anyone seen
anything like this in the literature.
 
Jim Menegay <[email protected]> wrote or quoted:

> This discussion involves an intricate interplay of
> several ideas
> 1. Species selection vs individual selection.
> 2. Selection vs drift
> 3. Long term vs short term.
>
> I hope I don't complicate things more by introducing a
> fourth issue - the dreaded Haldane's dilemma.
>
> My take on HD is that it points out that selection has a
> lot of work to do killing off the unfit, and only a
> finite time to do it. Selective deaths are a scarce
> resource [...]

Selective deaths /may/ be a scarse resource - so it's a good
thing that evolution can *also* produce adaptations via
differential reproductive success.

> and natural selection is unlikely to waste them on trivial
> things like optimizing the size of an elephant's ears -
> especially since there has only been a short time since
> African and Indian elephants diverged.

I'm pretty convinced that the large ears of African
elephants exist because they /are/ adaptive - primarily in
the role of a thermoregulation device. Asian elephants are
significantly smaller *and* generally live further north -
in a cooler climate.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.
 
On Sat, 6 Mar 2004 23:03:05 +0000 (UTC),
Jim Menegay <[email protected]> wrote:

[snip]

> I hope I don't complicate things more by introducing a
> fourth issue
> - the dreaded Haldane's dilemma.

You did complicate things by introducing "Haldane's
dilemma."

The discussion will now diverge into meaningless debate
about a non-existent phenomenon that is of no practical
interest to modern evolutionary biologists.

What is it with "Haldane's dilemma", anyways? I can
understand why anti-science idiots would want to use it a
club to beat on evolution but why would any real scientist
pay attention?

Larry Moran
 
> JM:- I hope I don't complicate things more by introducing
> a fourth issue
> - the dreaded Haldane's dilemma.

LM:- You did complicate things by introducing "Haldane's
dilemma." The discussion will now diverge into
meaningless debate about a non-existent phenomenon that
is of no practical interest to modern evolutionary
biologists. What is it with "Haldane's dilemma", anyways?
I can understand why anti-science idiots would want to
use it a club to beat on evolution but why would any real
scientist pay attention?

JE:- Because the dilemma discloses other incorrect but
hidden assumptions of gene centric Neo Darwinism, e.g. the
deletion within over simplified models of actual genetic
epistasis via its redefinition to mean "additive genetic
epistasis". Reducing the human genome to only allow
additive information as "heritable" forces the genome to
become huge compared to the size that it actually is.
Haldane's dilemma reflects this "unsatisfactory" situation.
The relatively small size of the human genome remains a
total shock to gene centric Neo Darwinists because they
cannot fit all their known heritable information into it.
This is why you hardly ever find the discussion of the size
of the human genome in sbe. People are very sensitive about
what it proves re: their assumptions of what must be
heritable within nature (not just within their models of
nature). EITHER Nature refutes Neo Darwinism on this point
or if you prefer Post Modern epistemology: Neo Darwinism
refutes nature. Of course you can always do what GH
suggested: just forget about Popperian refutability within
the sciences. If you add to this what Prof. Felsenstein
suggested: remove all reference to cause and effect within
the sciences then the transition is complete. All we sane
taxpayers have to do now is lock them all up in one room
with their toys and throw away the key....

Regards,

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email protected]
 
With all this discussion about non-adaptive phenotypic variation, it
seems relevant to point out a talk that will be given here in Helsinki
next week. I know some of you won't be able to attend, but I think it's
worth pointing out that someone is working on the problem. The
speaker's homepage is <http://www.bio.ic.ac.uk/research/iowens/>.

Bob

--
Bob O'Hara Department 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: www.jnr-eeb.org

ARE NEUTRAL MECHANISMS IMPORTANT IN PHENOTYPIC EVOLUTION?

Prof Ian P. F. Owens

Department of Biological Sciences and NERC Centre for
Population Biology, Imperial College London, Silwood Park,
Ascot, Berkshire SL5 7PY, UK

Theory suggests that, in addition to selection, evolutionary
change can also occur via neutral mechanisms, such as
founder effects and genetic drift. Such neutral mechanisms
are repeatedly invoked to explain otherwise puzzling aspects
of biology, particularly in the context of small, isolated
populations and conservation biology. But how strong is the
evidence that neutral mechanisms really are important in the
evolution of phenotypic diversity in wild populations? I
will begin by reviewing the previous studies that have
tested for the action of neutral mechanisms in wild
populations. I will then describe the model system that we
have used to study this problem - an island-colonizing
passerine bird called the silvereye. This species was used
by Mayr to support his original founder effect model and has
repeatedly been used in discussions of island evolution.
Recently we have used the uniquely well documented pattern
of pattern of island colonization by this species to perform
a replicated test of the relative roles of founder effects,
drift and selection in generating rapid morphological
differentiation.
 
On Mon, 8 Mar 2004 04:12:39 +0000 (UTC),
William Morse <[email protected]> wrote:
> [email protected] (Larry Moran) wrote in
> news:[email protected]:

[snip]

>> How does one distinguish between a just-so story and a
>> valid explanation? If it turned out that Asian elephants
>> had big ears and African elephants had small ones do you
>> think that someone would come up with an adaptionist
>> explanation? I do. That's the problem. With sufficient
>> imagination one can conjure up an adaptionist explanation
>> for almost anything that happens in biology. This isn't a
>> very good reason for preferring adaptionist explanations
>> over chance and accident - expecially since we know for a
>> fact that chance plays the major role at the molecular
>> level. Why shouldn't it play a major role at the
>> morphological level as well?
>
> How major a role?

If we compare homologous genes from different species the
vast majority of differences appear to be neutral with
respect to fitness. Thus, it appears that random genetic
drift is responsible for most of evolution when measured by
actual changes in the fixation of new alleles. This doesn't
take into account the role of negative selection in
eliminating detrimental alleles but that's not what we're
discussing. One question is whether positive natural
selection accounts for a significant proportion of change at
the molecular level. This doesn't seem likely.

What about the mechanism of evolution for alleles that have
an obvious phenotype? Is it only natural selection or drift
involved? I don't know what you might consider a "major"
role. Right now I'd be happy just to see adaptionist admit
to the possibility that some morphological traits can be
fixed by accident.

> Darwin's logic is fairly incontrovertible here - if
> organisms produce more offspring than can survive (which
> they do), and if there is heritable variation between
> those offspring (which there is) then _if_ that variation
> results in a differential fitness (which appears to be the
> crux of our disagreement) there _will be selection_ for
> the morphological trait.

Yes, this is the crux of the disagreement. The question is
whether a given morphological trait is associated with a
difference in fitness. I argue that this should not be
automatically assumed. It is equally likely that (many)
morphological traits are effectively neutral.

> Drift plays the major role at the molecular level because
> most changes at that level _are_ selectively neutral. I
> can change an alanine for a valine far from a binding site
> and selection won't (at first) see it. But AFAIK drift
> hasn't made much of a dent in the binding site of
> hemoglobin, to give only one obvious example.

Nobody is arguing that positive natural selection doesn't
exist at the molecular level. However, I hope we can agree
that most change in the sequences of genes is not due to
adaptation. The question is whether this observation should
apply to nucleotide substitutions that give rise to visible
phenotypes or whether it is confined to substitutions that
don't have any obviously visible phenotype.

> Now while it is true that adaptationists are prone to
> conjuring up explanations for observed morphological
> traits, that doesn't make those explanations wrong, it
> just makes them untested.

Correct, they aren't "wrong." However, a problem arises when
adaptionists completely ignore the possibility that the
morphological trait may not be due to adaptation at all.
There seems to be an implicit assumption that all
morphological traits must be explained by adaptation. In
fact, most adaptionists seem to think of "evolution" as a
synonym for "natural selection." I argue that this bias may
prevent adaptionists from considering alternative
explanations and this isn't a good thing.

> Ideally one would like to alter the ear genes for African
> elephants, stick a bunch of small-eared ones in an
> otherwise identical savanna environment, and see if they
> survive as well as big eared ones, but even if we could
> perform the experiment we would have to wait 20000 years
> for results, and even postdocs might get a little antsy
> :) Luckily for us mother nature has performed some of
> these experiments for us. Pangolins, aardvarks, anteaters,
> and echidnas are all mammals but otherwise quite unrelated
> - except that they share the same ecological niche and
> share numerous morphological traits. Take a good look
> sometime at pictures of the heads of deer and kangaroos,
> which also only distantly share a common ancestor, and use
> quite different mechanisms of locomotion (score one for
> contingency!), but share a similar niche. A zoologist can
> look at the teeth of an animal and tell you what it eats,
> can look at its skin and tell you what climate it
> inhabits, can look at its eyes and tell you whether it is
> predator or prey. So how are these morphological traits
> _not_ adaptations?

Everyone agrees that there are morphological and molecular
traits that are adaptive. Just because these exist is no
reason to assume that ALL morphological and molecular
changes are adaptive.

> The argument for drift is a much tougher row to hoe.
> You've got all the tools of molecular biology that prove
> that drift occurs, but on a morphological basis how do you
> prove a negative? And even if you do, where is the glory?
> The adaptationist gets to come up with a great (if
> unprovable) story, while the stochasticist is left with
> endless strings of purines and pyrimidenes which mostly
> cannot (yet) be linked to morphology and behavior.

I agree that just-so stories are seductive. Does that mean
they are good science?

> (snip intro to this)
>
>> So, is it possible that variation in skin color is due to
>> selection in some parts of the world (Northern Europe)
>> but drift elsewhere?
>
> Certainly (although my argument is that "some parts of the
> world" includes all of Europe, Africa, Asia and Australia)
> . Drift happens. Selection happens. Calamity (aka ****)
> happens :) If Arlin Stoltzfus were still contributing to
> sbe he would be telling us that mutation pressure happens.
> Evolution doesn't care which of the above is leading to
> changes in gene frequencies. What I was trying to define
> with my "default assumptions" was traits that were
> _primarily_ shaped by one or the other
> - but there are no magic force fields that protect
> reproducing organisms from any of the above effects.

Why does there have to be a "default assumption" when we
know for a fact that both random genetic drift and natural
selection play important roles in evolution?

> (snip)
>
>> (A minor quibble ... natural selection also has a major
>> stochastic component. Most beneficial mutations are
>> eliminated from the population. The best you can do is
>> calulate the "probability" that a given allele will
>> become fixed if you know the selection coefficient.)
>
> Agreed. One of the reasons that zebra mussels have been
> able to spread so rapidly in North American fresh waters
> is their ability to fix to a substrate. This ability is
> common in mussels throughout the world, but there are no
> native North American freshwater mussels that can do this.
> Even I have difficulty in coming up with a Just So story
> to explain this
> - it may well be due to "bad luck".

I'm glad we can agree on something ... :)

Larry Moran
 
On Mon, 8 Mar 2004 16:37:44 +0000 (UTC),
John Edser <[email protected]> wrote:
>Larry Moran wrote

>> You did complicate things by introducing "Haldane's
>> dilemma." The discussion will now diverge into
>> meaningless debate about a non-existent phenomenon that
>> is of no practical interest to modern evolutionary
>> biologists. What is it with "Haldane's dilemma", anyways?
>> I can understand why anti-science idiots would want to
>> use it a club to beat on evolution but why would any real
>> scientist pay attention?
>
> Because the dilemma discloses other incorrect but hidden
> assumptions of gene centric Neo Darwinism, e.g. the
> deletion within over simplified models of actual genetic
> epistasis via its redefinition to mean "additive genetic
> epistasis". Reducing the human genome to only allow
> additive information as "heritable" forces the genome to
> become huge compared to the size that it actually is.
> Haldane's dilemma reflects this "unsatisfactory"
> situation. The relatively small size of the human genome
> remains a total shock to gene centric Neo Darwinists
> because they cannot fit all their known heritable
> information into it. This is why you hardly ever find the
> discussion of the size of the human genome in sbe. People
> are very sensitive about what it proves re: their
> assumptions of what must be heritable within nature (not
> just within their models of nature). EITHER Nature refutes
> Neo Darwinism on this point or if you prefer Post Modern
> epistemology: Neo Darwinism refutes nature. Of course you
> can always do what GH suggested: just forget about
> Popperian refutability within the sciences. If you add to
> this what Prof. Felsenstein suggested: remove all
> reference to cause and effect within the sciences then the
> transition is complete. All we sane taxpayers have to do
> now is lock them all up in one room with their toys and
> throw away the key....

Like I said, why would any real scientist pay attention to
this nonsense?

Larry Moran
 
>> You did complicate things by introducing "Haldane's
>> dilemma." The discussion will now diverge into
>> meaningless debate about a non-existent phenomenon that
>> is of no practical interest to modern evolutionary
>> biologists. What is it with "Haldane's dilemma", anyways?
>> I can understand why anti-science idiots would want to
>> use it a club to beat on evolution but why would any real
>> scientist pay attention?

> JE:- Because the dilemma discloses other incorrect but
> hidden assumptions of gene centric Neo Darwinism, e.g. the
> deletion within over simplified models of actual genetic
> epistasis via its redefinition to mean "additive genetic
> epistasis". Reducing the human genome to only allow
> additive information as "heritable" forces the genome to
> become huge compared to the size that it actually is.
> Haldane's dilemma reflects this "unsatisfactory"
> situation. The relatively small size of the human genome
> remains a total shock to gene centric Neo Darwinists
> because they cannot fit all their known heritable
> information into it. This is why you hardly ever find the
> discussion of the size of the human genome in sbe. People
> are very sensitive about what it proves re: their
> assumptions of what must be heritable within nature (not
> just within their models of nature). EITHER Nature refutes
> Neo Darwinism on this point or if you prefer Post Modern
> epistemology: Neo Darwinism refutes nature. Of course you
> can always do what GH suggested: just forget about
> Popperian refutability within the sciences. If you add to
> this what Prof. Felsenstein suggested: remove all
> reference to cause and effect within the sciences then the
> transition is complete. All we sane taxpayers have to do
> now is lock them all up in one room with their toys and
> throw away the key....

LM:- Like I said, why would any real scientist pay attention
to this nonsense?

JE:- To evade any discussion of consistent and chronic Neo
Darwinian misuse of oversimplified models within mostly
public funded evolutionary theory research so that
researcher's can keep their jobs.

Best Wishes,

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email protected]

John Edser
 
Larry Moran <[email protected]> wrote or quoted:

[Material from John Edser]

> Like I said, why would any real scientist pay attention to
> this nonsense?

Ignore it then. That's what I've been doing for a long time
now.

Let the newcomers play with John. Between them they seem to
do a fine job of filling the forum with Edserisms - without
the other folk joining in as well.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.
 
Tim Tyler wrote:
> Anon. <[email protected]> wrote
> or quoted:
>
>
>>Of course, drift may also be an explanation, but I believe
>>that we can only separate out the contributions of the
>>different causes empirically.
>
>
> It may be hard to do - but should be possible in
> principle:
>
> If you used a large population and "stirred" it well, the
> effects of drift would become very small compared to
> selection.

I don't think this accurately describes drift.

Of course there is a difference between a "stirred" and an
"unstirred" population.

But for the first approximation, I'd extend smoothly from
the fact the stirring-as-we-understand-it-now is done
through acts of intercourse, and acts of intercourse are
best approximations for two individual to occupy the *same
locus in space* (and time).

individuals, hum, that makes the chessboard interesting :)

We can, can't we, think in terms of pollinating individuals.
At some point, the distributions of gametes plays by mass
rules that strictly speaking can transcend case-enumerated
local topology of spacetime ??

So I'd want "stirring" to erase space-like rather than time-
like information, what imo is your own option. Would you
believe me confused ?

My most profound opinion (tm) on the matter is :

"Stirring erases tachyons" while erased tachyons is the
substance of the irreducible gap from model to reality - in
your defavor :)

>
> You could similarly create circumstances that emphasised
> drift - small populations - with death striking young
> individuals at random.

I see, so what we are really looking at is the idea of
*evolutionary selection sport* with champion styles of
species, for optimizing gain out of episodes of widespread
simultaneous selection over large territories. You'd have
"Shroedinger intervals" for drift-in-your-observation to
occur, and contrasting years/moments/maps of sharp to very
sharp selection aka "collapses".

I say "maps" because I'd tend to imagine to mother Earth, an
age-old pre-consciousness of its own geographic portrait,
because events of simultaneous selection occur over its
geographic portrait, and these events are also (a good half)
the motor of evolution (iov)

>
> These sorts of experiments or observations should - in
> principle - have the power to tease out the effects of
> drift and selection empirically - and distinguish between
> hypotheses about to what extent the forces contribute to
> the forms of organisms.
>
> In theory, drift can help populations escape local maxima
> that selection would leave them stuck on. Quantifying that
> effect seems like an important task for the participants
> in the drift vs selection debate.

There is a geographic, quasi-tectonic (look at bird-
migrations) magnetic-field-like component to observable
genetic drift channels.
 
You must log in or register to reply here.
Top Bottom Back