Complexity

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

Quoted message said:

Tim Tyler said:

Larry Moran <[email hidden]> wrote or
quoted:

[snip]

Quoted message said:

Quoted message said:

Hmmm ... I think I see your objection. You want a
precise definition of evolutionary change so you can
objectively analyze the mechanisms. I've been assuming
all along that changes are most easily quantified by
adding up mutations in DNA but you don't seem to accept
that particular measure.

It's a great measure - but not the /only/ one - and as I
mentioned in another post, it has some definite flaws as
a metric of evolutionary change.

What are the flaws ... other than the fact that it leads
to a conclusion you don't like?

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

Quoted message said:

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I am not my mind. I am not my body. I am not my DNA
sequence ;-)

What the heck does this mean? I sounds like new-age
doublespeak.

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

Quoted message said:

Quoted message said:

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It was obvious to me. If a new set of limbs is due to 74
different base substitutions in DNA then that's how you
measure it and compare it to, for example, 74 single
neutral base substitutions. I think you want to
substitute a subjective measure where a new set of limbs
has a much higher score because it's more significant to
your way of thinking. This is a new idea to me. Do you
have a clear quantitative way of calculating the score
of morphological changes or is this just a sleight-of-
hand way of trying to argue in favor of the supremacy of
natural selection?

I hope not the latter ;-)

Me too, but I'm not holding my breath. :-)

Quoted message said:

Quanifying phenotypic change is difficult.

That's probably why it isn't very useful. It's too
subjective and it ignores all the other kinds of
evolutionary change.

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

Quoted message said:

Quoted message said:

However, the phenotypes of living organisms still form a
tree where qualities very along the branches.

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

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

Quoted message said:

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Taxonomists don't *have* to look at an organisms' DNA
sequence to begin to answer questions about which other
organisms it is most closely related to.

That's correct. It's quite possible to look at a subset of
all evolutionary change in order to work out some of the
history. This applies to morphological change as well as
to DNA/protein sequence change. Do you have a point?

Quoted message said:

As for general-purpose metrics - there are several of
them. Length, lifespan, mass and number of cell types are
all fairly useful means of quantifying evolutionary
change.

Now were getting a bit silly .....

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

Quoted message said:

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BTW, I'm not conceding that all morphological change is
due to natural selection. Do you have a quantifiable
measure of the amount of morphological change that's due
to natural selection?

My impression is that this depends in a big way on the
effective population size.

In "small" populations, the founder effect is the
main force.

In "large" populations, the founder effect is of low
relevance, and selective forces tend to dominate as
causes of phenotypic change.

Do you have a quantifiable measure of the amount of
morphological change that's due to natural selection?

Quoted message said:

This is *only* if you ignore neutral mutations, of
course.

What does this mean? I'm asking for a way to distinguish
between morphological change that's due to natural
selection and morphological change that's neutral. How can
you "ignore" neutral mutations when you can't even
identify them?

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

Quoted message said:

Quoted message said:

*If* you use a metric that measures raw genome hamming
distance, random noise is indeed the cause of most
changes.

"Random noise" is a loaded phrase that reveals a great
deal about your biases.

Quoted message said:

However, random noise is like radio static - interesting
if you are wondering how far away the transmitter is -
but if you are trying to listen to the radio program, it
just gets in the way.

I'm interested in molecular evolution and deep phylogeny.
Natural selection just gets in the way of such studies and
may even invalidate them. Natural selection is sort of
like radio static to me - I have to put up with it but I
try to ignore it whenever possible. However, in spite of
my personal interests I would never try and define natural
selection out of existence just because I'm not very
interested in it. That would not be scientific.

Very well said.

Regards,

Guy

[email hidden] (Larry Moran) wrote in
:"]news:[email hidden]:

Quoted message said:

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

(snip)

Quoted message said:

Quoted message said:

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

Quoted message said:

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

Quoted message said:

Quoted message said:

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

Quoted message said:

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

A very wise man has said the following:

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

The same wise man also suggested the following definition:

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

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

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

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

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

Quoted message said:

Quoted message said:

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

Quoted message said:

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

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

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

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

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

Quoted message said:

Quoted message said:

But in either case:

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

Quoted message said:

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

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

delta q = pq/2N

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

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

Quoted message said:

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

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

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

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

Yours,

Bill Morse

Phil Roberts said:

John Wilkins said:

Phil Roberts said:

I agree with you about logic. One of the brightest among
us (Aristotle for instance) managed to cognize the order
in the manner in which we cognize order. But unlike my
read of you so far, I believe who ever this individual
was, he had intellectual acuities that went far beyond
rote learning and trial and error, the so-called
"darwinian" approach as you have deemed it, I believe.

Well, all I can say is that there is no way I can
conceive of for this to occur, apart from noetic rays or
clairvoyance or divine revelation.

Nah! It just presupposes that there's a little more to
reasoning than rote learning, that perceptiveness,
intuitiveness, brilliant insights that just pop up with
Aha! experiences are central to scientific progress, and
that most of this occurres at subconscious levels and
about which little is currently understood. But I think
Hume at least gave us a nudge forward in his recognition
of the centrality of the role of comparing. We'll just
have to agree to disagree on this. But your contention
that my claim that a central feature of reaoning is 'the
capacity to cognize abstruse similarity and difference'
requires invoking divine creation to explain its presence
is one hell of a stretch, if you don't mind my saying so.

Then how do you account for that ability? In other words,
where does the cognitive power come from? Why do brains work
when they model their environment? I can't think of any
other ways to ask that critical question...

Quoted message said:

Quoted message said:

I am not in this sense a Kantian (which is whence we get
the pure and practical reason distinction, and the means
and end contrast).

Actually, the paradigm for the rationalty of ends is not
the categorical imperative but rather 'the equal weight'
criterion:

I wasn't referring to the categorical imperative. ...

Quoted message said:

Notice that this criterion entails two assumptions:

1. That rationality entails self-interest.
2. That within the perimeter of self-interest,
rationality entails VALUATIVE OBJECTIVITY.

I believe 1 is highly suspect, as exemplified in the
Parfit quote on self-interest I posted last time.

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

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

<snip Luce and Rafffia>

Quoted message said:

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The rationality here is one of a course of action to be
taken in a situation of agreed value and conflict of
interest. But this is a very limited form of
rationality.

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

I'm a bit lost here. How is one to be objective in
valuation? Is there a gold standard? In biology, valuative
assessments (by biologists about the organisms, not by the
organisms themselves) are always relative to alternatives -
strategies, genes, forms, traits, whatever - in the
competitive population. There is nothing to be objective
about a priori, only ever post hoc, although there are
clearly objective physical facts; how they play out is
generally unknown ahead of time.

Quoted message said:

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This is why game theory is applicable to evolution - the
"rational egoism" is specified in a very specific sense
- of maximising the number of copies of a gene. But this
does not transfer to social behaviors directly. Social
action is not selfish because we can model genes as if
they were selfish (something Dawkins notes quite
explicitly in the Afterword to the 1989 edition of The
Selfish Gene).

But this gene selfishness should almost always translate
to plain old selfishness. The exceptions are "limited" and
"special". IOW, far from resolving the enigma of human
morality, as Wilson seemed to be implying in the last
chapter of Sociobiology, our fomral models have ONLY
SERVED TO DEEPEN THE MYSTERY.

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

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

Quoted message said:

This is tricky stuff, but in general you should be able to
get lots of instrumental valueing of others out of
intellignece, but extremely limited intrinsic valuing of
others (immediate kin) out of natural selection, at least
to the extent that natural selection operates in the
manner in which it has been mathematically modeled. Humans
are wildly outside the parameters predicted by these
models by the way, which is precisely why Dawkins has
thrown up his hands and declared the need for a full
fledged addendum to the theory in order to accomodate the
benevolent selfishness found in man (e.g., concern for a
bird with a broken wing) and to a lesser extent, in
species phylogenetically proximal to man.

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

Quoted message said:

Quoted message said:

Genes can be considered *as if* they were selfish
players in a game, and the end result of this selection
can be apparently altruistic behavior on the part of the
organisms, due to kin selection, and the fact that
iterated Prisoner's Dilemmas (uncommunicative dilemmas
where either one player loses out or both do less well
than the optimum) will, if the initial population is
suitably composed, evolve into equilibrium of "[censored] for
tat" strategies.

This is all pretty old stuff. Axelrod is the authority
most often cited that I'm aware of.

Yep. Sorry for patronising you, but it's hard to know what
people know over the internet.

Quoted message said:

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

OK. What anomalies, in detail? Are they anomalies from the
environment of evolutionary adaptedness (EEA) or are they
anomalies in modern society (agrarian and later), which is
not at all what we adapted to when our strategies went to
fixation for whatever reason?

Quoted message said:

Quoted message said:

In short, cooperation can evolve through the
maximisation of genetic fitness. It won't always, but
there is absolutely no justification for the direct
transference of selfishness from the level of the gene
to that of the individual or social group, contrary to
Ghiselin's sarcastic and cynical comment, "scratch an
altruist and watch a hypocrite bleed). It's all about
keeping your levels straight when determining the
interest bearers.

Agreed. But when do we get to start talking about the
subject I am interested in, anomalies in our species
valuative profile.

Quoted message said:

Quoted message said:

9/11 poses nothing we didn't already know from a couple
of millenia of documented fanaticism. It just hit
America hard, that's all (from a theoretical
perspective; it hit me hard as I had friends near
there, and I had just been there a couple of months
prior). There is no anomaly to deal with, but a well-
known fact of cultural dynamics.

True. But I'm not looking at 9/11 though my fellow human
being glasses, but rather through my natural scientist
glasses. There's one hell of a difference between what I
have come to expect from my fellow man and what I have a
right to expect from an organism designed by natural
selection. The latter is not a free ride, but comes
equipped with some fairly SEVERE CONSTRAINTS on what we
have a right to expect. If flying planes into buildings is
evidence to you of genes that have been endlessly honed to
maximnize reproductive success, maybe you ought to think
about going into a different occupation, John. 🙂

Certainly I won't try to maximise *my* genes that way. But
we want an explanation of the modules (damn! I used that
term!) that, when placed into the modern situation, generate
that behavior. I believe that what is adaptive is not the
behavior, but the strategy that makes cultural "kin" take
the place of genetic kin. Once upon a time (i.e., in the
EEA) there would be no distinction between genetic
relationship and cultural identity. It follows that if we
evolved our defence of culture as a way of defending our
genetic relatives, when the two were coterminous, the mere
fact that modern social evolution has prised the two apart
is irrelevant.

Quoted message said:

What would an organism have to do before you finally got
around to considering its behavior anomalous? Or are you
suggesting we simply adopt nat selection as an
unfalisifiable dogma. Hey. If we're going to start a
religion here, I got dibs on being the Pope. 🙂

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

Larry Moran said:

Anon. said:

Larry Moran said:

On Sun, 23 May 2004 18:07:23 +0000 (UTC), A non.
<[email hidden]> wrote:

[snip]

Quoted message said:

Quoted message said:

>I think I can still use my same question: Doesn't that
>depend on how you measure evolutionary change? It's not
>clear to me that we have to measure it at the sequence
>level.

I didn't say you *have* to measure it at the sequence
level. I just said that when you take into account ALL
evolutionary change, including change at the sequence
level, then drift is the main mechanism.

To measure "all evolutionary change" you have to measure
both phenotypic and genotypic change. How do you put these
onto the same scale? You have to weight them somehow, and
it's not clear to me that there is a unique way of doing
this - it will depend on your ideas about the relative
importance of the genotypic and phenotypic levels in
evolution. You can, I think, get either selection, or
drift, (or contingency?) as being the most important
mechanism, depending on how you weight them.

Why not give it a try? We already have an effective and
quantitatvie way of measuring evolution by looking at
changes in DNA sequence. If you want to find a more
effective measure then let's see what you come up with.

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

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

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

So

Quoted message said:

far, all I've seen is some warm fuzzy feeling that
"phenotypic change" should get a higher score in order to
restore the supremacy of natural selection as a mechanism
of evolution. Can you turn that subjective feeling into a
scientific definition that we can examine?

That's a mis-representation - I'm not arguing that
phenotypic change should get a highe score, but rather that
there is no obvious single score, so whatever measure you
use is subjective. Why remove phenotypic traits from
evolution?

Quoted message said:

Let's take the evolution of humans and chimps as an
example. We already know that they differ by about 2% in
DNA sequence. How would you evaluate the "phenotypic
changes" along each lineage in order to arrive at some
quantitative measure of the amount of evolution in each
species from the time of the last common ancestor? How
much of that is due to natural selection?

That's actually something I'm starting to work on. Over
short time scales, one can compare Fst and Qst (e.g.
Palo et al. 2003 Molecular Ecology, 12: 1963-1978) but
some more work needs to be done to find a more
quantitaive formulation. I've started work with a
colleague on the variation between species, but I'm not
sure how that will pan out.

Bob

--
Bob O'Hara

Dept. of Mathematics and Statistics
P.O. Box 4 (Yliopistonkatu 5) FIN-00014 University of
Helsinki Finland Telephone: +358-9-191 23743 Mobile:
+358 50 599 0540 Fax: +358-9-191 22 779 WWW:
rni.helsinki.fi~bohOpen ↗ Journal of Negative
Results - EEB: jnr-eeb.orgjnr-eeb.orgOpen ↗

On Thu, 27 May 2004 16:40:40 +0000 (UTC),

William Morse said:

[email hidden] (Larry Moran) wrote in
:"]news:[email hidden]:

Quoted message said:

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

(snip)

Quoted message said:

Quoted message said:

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

Quoted message said:

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

Quoted message said:

Quoted message said:

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

Quoted message said:

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

A very wise man has said the following:

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

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

Quoted message said:

The same wise man also suggested the following definition:

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

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

Quoted message said:

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

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

Quoted message said:

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

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

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

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

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

Quoted message said:

Quoted message said:

Quoted message said:

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

Quoted message said:

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

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

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

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

Quoted message said:

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

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

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

Quoted message said:

Quoted message said:

Quoted message said:

But in either case:

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

Quoted message said:

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

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

delta q = pq/2N

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

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

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

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

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

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

Quoted message said:

Quoted message said:

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

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

I like that ... can I use it?

Quoted message said:

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

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

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

Quoted message said:

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

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

You mean we have to find a new niche?

Larry Moran

On Thu, 27 May 2004 16:40:43 +0000 (UTC),

Anon. said:

Larry Moran said:

On Tue, 25 May 2004 23:48:33 +0000 (UTC), Anon.
<[email hidden]> wrote:

[snip]

Quoted message said:

Quoted message said:

Why not give it a try? We already have an effective and
quantitatvie way of measuring evolution by looking at
changes in DNA sequence. If you want to find a more
effective measure then let's see what you come up with.

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

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

Quoted message said:

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

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

Quoted message said:

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

So

Quoted message said:

far, all I've seen is some warm fuzzy feeling that
"phenotypic change" should get a higher score in order to
restore the supremacy of natural selection as a mechanism
of evolution. Can you turn that subjective feeling into a
scientific definition that we can examine?

That's a mis-representation - I'm not arguing that
phenotypic change should get a highe score, but rather
that there is no obvious single score, so whatever measure
you use is subjective. Why remove phenotypic traits from
evolution?

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

Quoted message said:

Quoted message said:

Let's take the evolution of humans and chimps as an
example. We already know that they differ by about 2% in
DNA sequence. How would you evaluate the "phenotypic
changes" along each lineage in order to arrive at some
quantitative measure of the amount of evolution in each
species from the time of the last common ancestor? How
much of that is due to natural selection?

That's actually something I'm starting to work on. Over
short time scales, one can compare Fst and Qst (e.g. Palo
et al. 2003 Molecular Ecology, 12: 1963-1978) but some
more work needs to be done to find a more quantitaive
formulation. I've started work with a colleague on the
variation between species, but I'm not sure how that will
pan out.

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

Larry Moran

John Edser said:

Quoted message said:

Quoted message said:

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

Quoted message said:

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

Quoted message said:

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

Any change that isn't heritable.

Quoted message said:

Quoted message said:

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

Quoted message said:

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

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

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

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

Bob

--
Bob O'Hara

Dept. of Mathematics and Statistics
P.O. Box 4 (Yliopistonkatu 5) FIN-00014 University of
Helsinki Finland Telephone: +358-9-191 23743 Mobile:
+358 50 599 0540 Fax: +358-9-191 22 779 WWW:
rni.helsinki.fi~bohOpen ↗ Journal of Negative
Results - EEB: jnr-eeb.orgjnr-eeb.orgOpen ↗

Quoted message said:

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

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

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

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

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

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

Quoted message said:

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

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

Quoted message said:

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

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

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

Regards,

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

PO Box 266 Church Pt NSW 2105 Australia

[email hidden]

Quoted message said:

Quoted message said:

Quoted message said:

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

Quoted message said:

Quoted message said:

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

Quoted message said:

Quoted message said:

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

BOH:- Any change that isn't heritable.

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

Quoted message said:

Quoted message said:

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

Quoted message said:

Quoted message said:

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

Quoted message said:

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

Quoted message said:

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

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

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

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

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

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

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

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

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

Best Wishes,

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email hidden]

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

Quoted message said:

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

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

P

Larry Moran <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler said:

Larry Moran <[email hidden]> wrote or
quoted:

Quoted message said:

Tim Tyler <[email hidden]> wrote:
> Larry Moran <[email hidden]> wrote
> or quoted:

Quoted message said:

Quoted message said:

Quoted message said:

>> I've been assuming all along that changes are most
>> easily quantified by adding up mutations in DNA but
>> you don't seem to accept that particular measure.
>
> It's a great measure - but not the /only/ one - and
> as I mentioned in another post, it has some definite
> flaws as a metric of evolutionary change.

What are the flaws ... other than the fact that it
leads to a conclusion you don't like?

The ones I mentioned in another post - namely a neutral
mutation counts as the same quantity of evolutionary
change as a mutation that causes speciation.

This is contrary to common sense relating to the
relative significance of such changes in evolution.

That "significance" is subjective. You may think that some
heritable changes are more significant than others but
that perspective isn't shared by all scientists.

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

Quoted message said:

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

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

Quoted message said:

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

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

* Shortest program to transform between the genomes in
question;

...you could use:

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

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

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

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

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

Quoted message said:

Quoted message said:

Quoted message said:

> I am not my mind. I am not my body. I am not my DNA
> sequence ;-)

What the heck does this mean? I sounds like new-age
doublespeak.

The smiley was intended to indicate that this was
a joke.

However there was a hint of seriousness: evolution is
about more than just DNA sequences. Attempt to measure
it *only* in terms of DNA and much of its richness will
be omitted.

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

As I wrote (above) of your preferred metric:

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

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

Consider neutral mutations to have the same significance as
other types if you so choose - but don't think that that's
the *only* valid way of measuring the rate of evolution.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

On Sat, 29 May 2004 23:42:11 +0000 (UTC),

Tim Tyler said:

Larry Moran <[email hidden]> wrote
or quoted:

Quoted message said:

Tim Tyler said:

Larry Moran <[email hidden]> wrote or
quoted:

[snip]

Quoted message said:

Quoted message said:

> Hmmm ... I think I see your objection. You want a
> precise definition of evolutionary change so you can
> objectively analyze the mechanisms. I've been assuming
> all along that changes are most easily quantified by
> adding up mutations in DNA but you don't seem to
> accept that particular measure.

It's a great measure - but not the /only/ one - and as
I mentioned in another post, it has some definite flaws
as a metric of evolutionary change.

What are the flaws ... other than the fact that it leads
to a conclusion you don't like?

The ones I mentioned in another post - namely a neutral
mutation counts as the same quantity of evolutionary
change as a mutation that causes speciation.

This is contrary to common sense relating to the relative
significance of such changes in evolution.

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

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

Quoted message said:

Quoted message said:

Quoted message said:

I am not my mind. I am not my body. I am not my DNA
sequence ;-)

What the heck does this mean? I sounds like new-age
doublespeak.

The smiley was intended to indicate that this was a joke.

However there was a hint of seriousness: evolution is
about more than just DNA sequences. Attempt to measure it
*only* in terms of DNA and much of its richness will be
omitted.

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

Larry Moran

On Sat, 29 May 2004 23:42:07 +0000 (UTC),

Guy Hoelzer said:

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

Quoted message said:

Tim Tyler said:

Larry Moran <[email hidden]> wrote or
quoted:

[snip]

Quoted message said:

> Hmmm ... I think I see your objection. You want a
> precise definition of evolutionary change so you can
> objectively analyze the mechanisms. I've been assuming
> all along that changes are most easily quantified by
> adding up mutations in DNA but you don't seem to accept
> that particular measure.

It's a great measure - but not the /only/ one - and as I
mentioned in another post, it has some definite flaws as
a metric of evolutionary change.

What are the flaws ... other than the fact that it leads
to a conclusion you don't like?

It seems to me that Tim and Larry are talking past each
other. I think the cryptic difference underlying there
differences have to do with the level of evolutionary
interest. Tim is focusing on the evolution of populations
of organisms in which DNA sequences are only tangentially
relevant, while Larry is focusing on the evolution of
populations of DNA sequences in which the organisms are
only tangential vehicles (sensu Dawkins).

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

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

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

Quoted message said:

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

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

[snip]

Quoted message said:

Quoted message said:

That's probably why it isn't very useful. It's too
subjective and it ignores all the other kinds of
evolutionary change.

DNA sequences may be objectively determined, but they too
ignore all other kinds of evolutionary change at the
organismal level (e.g., cultural evolution, epigenetic
effects, developmental effects of sequence rearrangements
that do not involve changes in nucleotide identities).

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

Quoted message said:

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

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

[snip]

Quoted message said:

Quoted message said:

Quoted message said:

However, the phenotypes of living organisms still form a
tree where qualities very along the branches.

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

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

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

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

Quoted message said:

Quoted message said:

Quoted message said:

Taxonomists don't *have* to look at an organisms' DNA
sequence to begin to answer questions about which other
organisms it is most closely related to.

That's correct. It's quite possible to look at a subset
of all evolutionary change in order to work out some of
the history. This applies to morphological change as well
as to DNA/protein sequence change. Do you have a point?

Quoted message said:

As for general-purpose metrics - there are several of
them. Length, lifespan, mass and number of cell types
are all fairly useful means of quantifying evolutionary
change.

Now were getting a bit silly .....

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

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

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

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

Larry Moran

Hi Larry,

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

Quoted message said:

Guy Hoelzer said:

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

Quoted message said:

On Wed, 26 May 2004 23:12:56 +0000 (UTC), Tim Tyler
<[email hidden]> wrote:
> Larry Moran <[email hidden]> wrote or
> quoted:

[snip]

>> Hmmm ... I think I see your objection. You want a
>> precise definition of evolutionary change so you can
>> objectively analyze the mechanisms. I've been assuming
>> all along that changes are most easily quantified by
>> adding up mutations in DNA but you don't seem to
>> accept that particular measure.
>
> It's a great measure - but not the /only/ one - and as
> I mentioned in another post, it has some definite flaws
> as a metric of evolutionary change.

What are the flaws ... other than the fact that it leads
to a conclusion you don't like?

It seems to me that Tim and Larry are talking past each
other. I think the cryptic difference underlying there
differences have to do with the level of evolutionary
interest. Tim is focusing on the evolution of populations
of organisms in which DNA sequences are only tangentially
relevant, while Larry is focusing on the evolution of
populations of DNA sequences in which the organisms are
only tangential vehicles (sensu Dawkins).

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

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

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

Quoted message said:

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

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

Quoted message said:

Quoted message said:

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

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

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

Quoted message said:

Quoted message said:

Quoted message said:

That's probably why it isn't very useful. It's too
subjective and it ignores all the other kinds of
evolutionary change.

DNA sequences may be objectively determined, but they too
ignore all other kinds of evolutionary change at the
organismal level (e.g., cultural evolution, epigenetic
effects, developmental effects of sequence rearrangements
that do not involve changes in nucleotide identities).

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

Quoted message said:

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

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

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

Quoted message said:

Quoted message said:

Quoted message said:

> However, the phenotypes of living organisms still form
> a tree where qualities very along the branches.

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

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

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

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

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

Quoted message said:

Quoted message said:

Quoted message said:

> Taxonomists don't *have* to look at an organisms' DNA
> sequence to begin to answer questions about which other
> organisms it is most closely related to.

That's correct. It's quite possible to look at a subset
of all evolutionary change in order to work out some of
the history. This applies to morphological change as
well as to DNA/protein sequence change. Do you have a
point?

> As for general-purpose metrics - there are several of
> them. Length, lifespan, mass and number of cell types
> are all fairly useful means of quantifying evolutionary
> change.

Now were getting a bit silly .....

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

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

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

Quoted message said:

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

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

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

Regards,

Guy Hoelzer

"Larry Moran" <[email hidden]> wrote in message
"]news:[email hidden]...

Quoted message said:

On Thu, 20 May 2004 02:13:22 +0000 (UTC), Phil Roberts,

Jr. said:

Larry Moran said:

On Wed, 19 May 2004 05:33:01 +0000 (UTC), Phil Roberts,
Jr. <[email hidden]> wrote:

<snip>

Quoted message said:

What's the problem? Intelligence may have been selected
(adaptive) but not all of the many consequences of that
intelligence (behavior) are necessarily adaptations by
themselves. The overall benefit of being intelligent may
have been a selective advantage but that doesn't mean that
every single act of an intellignet human has to be an
adaptation.

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

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

P

[email hidden] (Larry Moran) wrote in
:"]news:[email hidden]:

Quoted message said:

William Morse said:

[email hidden] (Larry Moran) wrote in
:"]news:[email hidden]:

Quoted message said:

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

(snip)

Quoted message said:

Quoted message said:

The same wise man also suggested the following
definition:

Quoted message said:

Quoted message said:

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

Quoted message said:

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

Quoted message said:

Quoted message said:

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

Quoted message said:

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

Touche!

Quoted message said:

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

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

See my comments below.

Quoted message said:

Quoted message said:

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

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

Quoted message said:

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

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

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

(snip)

Quoted message said:

Quoted message said:

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

Quoted message said:

Quoted message said:

delta q = pq/2N

Quoted message said:

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

Quoted message said:

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

Quoted message said:

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

Quoted message said:

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

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

Quoted message said:

Quoted message said:

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

I like that ... can I use it?

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

Quoted message said:

Quoted message said:

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

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

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

Quoted message said:

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

You are right - there are only first prizes :-)

Quoted message said:

Quoted message said:

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

Quoted message said:

You mean we have to find a new niche?

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

Yours,

Bill Morse

Larry Moran said:

Anon. said:

Larry Moran said:

On Tue, 25 May 2004 23:48:33 +0000 (UTC), Anon.
<[email hidden]> wrote:

[snip]

Quoted message said:

Quoted message said:

Why not give it a try? We already have an effective and
quantitatvie way of measuring evolution by looking at
changes in DNA sequence. If you want to find a more
effective measure then let's see what you come up with.

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

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

:-) I think that's why I'm exiled in a maths and stats
:department.

Quoted message said:

Quoted message said:

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

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

One can actually use the same method as I've already
described: the transistion matrix will be for transitions
within a population (i.e. showing how the allele
frequencies change).

Quoted message said:

Quoted message said:

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

So

Quoted message said:

far, all I've seen is some warm fuzzy feeling that
"phenotypic change" should get a higher score in order to
restore the supremacy of natural selection as a mechanism
of evolution. Can you turn that subjective feeling into a
scientific definition that we can examine?

That's a mis-representation - I'm not arguing that
phenotypic change should get a highe score, but rather
that there is no obvious single score, so whatever measure
you use is subjective. Why remove phenotypic traits from
evolution?

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

As others are arguing with you, we might consider changes in
phenotype to be a more important part of evolution, unless
one adopts a militant gene's eye view. The magnitude of
effects of point mutations on a phenotpye can vary widely,
and I think this should be acknowledged.

Bob

--
Bob O'Hara

Dept. of Mathematics and Statistics
P.O. Box 4 (Yliopistonkatu 5) FIN-00014 University of
Helsinki Finland Telephone: +358-9-191 23743 Mobile:
+358 50 599 0540 Fax: +358-9-191 22 779 WWW:
rni.helsinki.fi~bohOpen ↗ Journal of Negative
Results - EEB: jnr-eeb.orgjnr-eeb.orgOpen ↗

John Edser said:

Quoted message said:

Quoted message said:

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

Quoted message said:

Quoted message said:

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

Quoted message said:

Quoted message said:

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

BOH:- Any change that isn't heritable.

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

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

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

Quoted message said:

Quoted message said:

Quoted message said:

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

Quoted message said:

Quoted message said:

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

Quoted message said:

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

Quoted message said:

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

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

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

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

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

OK, so my point is that drift is the difference between
observed and [mathematical] expectation of the change in
allele frequency (the expectation coming from a model of
selection, using the conventioal definition of fitness): the
total number of fertile offspring is the sum of the expected
number, and the drift effect. Your definition conflates the
effects of selection and drift, by defining fitness in terms
of the obseved number. Any random variation in the number of
offspring that we would ascribe to drift you would include
in the fitness measure, and hence would ascribe to
selection.

Bob

--
Bob O'Hara

Dept. of Mathematics and Statistics
P.O. Box 4 (Yliopistonkatu 5) FIN-00014 University of
Helsinki Finland Telephone: +358-9-191 23743 Mobile:
+358 50 599 0540 Fax: +358-9-191 22 779 WWW:
rni.helsinki.fi~bohOpen ↗ Journal of Negative
Results - EEB: jnr-eeb.orgjnr-eeb.orgOpen ↗

John Edser said:

Quoted message said:

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

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

Is the expected value of any conceivable use?

Quoted message said:

JE:- Dr O'Hara has misrepresented my position. Drift is
_included_ as temporal variation (random variation over
time) within Darwinian selective events. Mutation is
included as random variation within genetic space.
Darwinian evolution by natural selection has, from its
inception, required variation that is assumed to be
random. Only _non_ random forms of variation can validly
compete against Darwinian selection for evolutionary
causation. Sampling error is not one of them.

Isn't it just obvious that an "expected value" is just an
approximation of "the actual number of offspring" which I
stress (yet again) is the TOTAL (requiring a time frame to
complete) of only FERTILE forms reproduced into ONE
population by EACH Darwinian selectee (one fertile form)?

Please note that Dr O'Hara, refused to address the problem
that I addressed in detail: setting up a _controlled_
experiment to test if random patterns can _alone_, cause
"evolution".

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

Quoted message said:

AGAIN: Please state what would be EXCLUDED from such an
_amazingly_ wide acceptance of what Dr Moran insists can
_scientifically_ constitute "evolution", i.e. would Dr
Moran please provide at least one example of a _non_
evolutionary change within a biological system.

PLEASE COMMENT ON THE BELOW:-
1) Drift defined as evolution is not testable because any
random pattern can validly be assumed to be caused by
either a random or non random process.

Quoted message said:

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

If then...

Quoted message said:

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

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

Quoted message said:

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

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

Beginner

Quoted message said:

Quoted message said:

Quoted message said:

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

Quoted message said:

BOH:- Any change that isn't heritable.

Quoted message said:

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

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

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

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

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

Quoted message said:

Quoted message said:

Quoted message said:

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

Quoted message said:

Quoted message said:

Quoted message said:

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

Quoted message said:

Quoted message said:

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

Quoted message said:

Quoted message said:

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

Quoted message said:

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

Quoted message said:

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

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

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

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

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

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

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

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

Regards,

John Edser Independent Researcher

PO Box 266 Church Pt NSW 2105 Australia

[email hidden]