Evolutionary questions

[jillery]

As he tends to do, Larry Moran posted on his Sandwalk blog questions
to the final of his college class:

http://sandwalk.blogspot.com/2015/05/molecular-evolution-exam-april-2015.html

My impression is they are of the "Describe the Universe. Give
examples" variety. Reading them makes me wish I taken one of his
classes.

Two of his questions are prefaced by extensive quotations. The first
is by Michael Lynch from The Origins of Genome Architecture:

***************************************************
Nothing in Evolution Makes Sense Except in the Light of Population
Genetics

Evolution is a population genetic process governed by four fundamental
forces, which jointly dictate the relative abilities of genotype
variants to expand through a species. Darwin articulated a clear but
informal description of one of those forces, selection (including
natural and sexual selection), whose central role in the evolution of
complex phenotypic traits is universally accepted, and for which an
elaborate formal theory in terms of changing genotype frequencies now
exists. The remaining three evolutionary forces, however, are
non-adaptive in the sense that they are not the function of the
fitness properties of individuals: mutation (broadly including
insertions, deletions, and duplications) is the fundamental source of
variation on which natural selection acts; recombination (including
crossing-over and gene conversion) assorts variation within and among
chromosomes; and random genetic drift insures that gene frequencies
deviate a bit from generation to generation independently of other
forces. Given the century of theoretical and empirical work devoted to
the study of evolution, the only logical conclusion is that these four
broad classes of mechanisms are, in fact, the only fundamental forces
of evolution. Their relative intensity, directionality, and variation
over time define the way in which evolution proceeds in a particular
context.
***********************************************

A question he asks is: if you agree, why isn’t population genetics
taught in introductory biology courses? ISTM that's a question worth
discussing beyond a college exam.

The second quote he uses is from Richard Dawkins from The Blind
Watchmaker:

**********************************************
Even the most ardent neutralist is quite happy to agree that natural
selection is responsible for all adaptation. All he is saying is that
most evolutionary change is not adaptation. He may well be right,
although one school of geneticists would not agree. From the
sidelines, my own hope is that the neutralists will win, because this
will make it so much easier to work out evolutionary relationships and
rates of evolution. Everybody on both sides agrees that neutral
evolution cannot lead to adaptive improvement, for the simple reason
that neutral evolution is, by definition, random, and adaptive
improvement is, by definition, non-random. Once again, we have failed
to find any alternative to Darwinian selection, as an explanation for
the feature of life that distinguishes it from non-life, namely
adaptive complexity.
***********************************************

Then he asks a technical question about Lenski's long-term E.coli
populations, which I immodestly declare to knowing the answer.

The Blind Watchmaker was my introduction to Richard Dawkins, and I
have remained an unabashed fan ever since. By highlighting this part,
Larry Moran raised a different question in my mind: Can the changes
to non-life also be reasonably described as neutral evolution, as if
the changes in life and non-life are related? If so, doesn't that
make adaptive evolution more significant to the evolution of life,
since neutral evolution happens to both?

--
Intelligence is never insulting.

[RSNorman]

On Wed, 06 May 2015 12:58:02 -0400, jillery <69jp...@gmail.com>
wrote:

<snip the second question cited here>

The whole exam is well worth discussing here. Since I tauight
introductory biology for many years (decades, actually) I'll give my
thoughts on this one.

"Real" population genetics can get hideously complex very quickly.
See, for example.
http://pespmc1.vub.ac.be/mathmpg.html
Clearly that is not what Larry means.

But I always did include pop-gen at the level of Hardy-Weinberg
equilibrium theory in my teaching because it forms the basis for
understanding the "modern" concept of evolution. Under
Hardy-Weinberg, if a population satisfies five conditions then the
gene frequencies do not change from generation to generation. So if
you break any one of the conditions, the gene frequencies can change
and you get, by definition evolution. So there are five mechanisms of
evolution: Here only four mechanismsa are given but there is an error
in that exposition: it ignores gene flow (migration) between
populations. Also it lumps sexual selection with natural selection
which is a lesser point. This list includes "recombination" which
seems to me to be really a form of chromosomal mutation. Were
evolutionary theory really based on understanding Hardy-Weinberg, then
the five mechanisms of evolution should correspond exactly with the
five conditions for Hardy-Weinberg equilibrium: random mating (no
sexual selection), large (infinite) population size (no drift), a
fixed set of alleles (no mutation), a closed and isolated population
(no migration or gene flow), and all genotypes/phenotypes contributing
equally to the gene pool (no natural selection).

So if Moran's students never learned even that much from intro
biology, I would say there was something wrong the the way intro was
taught!

Actually there are serious constraints on how much can be covered in
one year of intro biology. I taught the "organismal, ecological and
evolutionary" half. But in order to do Hardy-Weinberg for evolution,
students had to understand Mendelian genetics. And in order to
understand that, they had to understand meiosis and mitosis. So there
goes some two to three weeks of class, about 15% to 20% of the entire
semester. And we still had to go through evolutionary principles,
plant and animal systematics from a functional and evolutionary
perspective, development, plant and animal physiology, and ecology.
There is no way to get through all that in one semester and some
things simply have to go. This doesn't even include anything at all
about the protista and fungi! (Prokaryotes -- Archaea and Bacteria --
were handled in the Cell/Molecular semester). Different institutions
have different allocation strategies of what gets taught when and by
whom and different instructors have different interest and skill sets
which shapes what they cover and how thoroughly. There is also a
tendency now to teach fewer things better than to try to cover
everything too quickly for anyone to grasp, let alone retain.
Something has to give. And dropping mitosis/meiosis and Mendelian
genetics can be what gives even though it means dropping
Hardy-Weinberg and pop gen.

[RSNorman]

On Wed, 06 May 2015 12:58:02 -0400, jillery <69jp...@gmail.com>
wrote:

>As he tends to do, Larry Moran posted on his Sandwalk blog questions
>to the final of his college class:
>
>http://sandwalk.blogspot.com/2015/05/molecular-evolution-exam-april-2015.html
>
>My impression is they are of the "Describe the Universe. Give
>examples" variety. Reading them makes me wish I taken one of his
>classes.
>

All of Larry's questions are worth discussing here. Jillery cited two
particular ones, one of which I already discussed. Here I will
mention the first on the list:

1.Choose a subtopic from your essay and explain it better than you did
in your essay and/or rebut the comments and criticisms made by the
marker/grader.

I really like this and it is something I usually did in my own final
exams. If a student is unable to discuss intelligently the subject of
his or her own term paper/essay/report, then something is clearly
wrong. Ordinarily it means that the student cribbed most of it off
the internet without understanding it. Worse, it means the student
just bought a paper and turned it in without really reading it. Asking
the student to rebut the comments and criticisms is really beautiful.
It forces the students to actually read the comments and think about
them rather than just glancing at the grade and tossing the thing in
the trash.

[Ernest Major]

How one divides up the different processes that operate in
microevolution is to a degree arbitrary, but I would define (natural)
selection as differential reproductive success causally correlated with
genotype (genetic drift is the same *not* so correlated), which includes
sexual selection as well as natural selection sensu structu.

Under the heading of gene flow I would include both migration and
introgression.

Unequal crossing over and intra-allelic recombination leading to new
alleles are forms of mutation. The rest of the time recombination
doesn't change gene frequencies (unless you take a holistic Dawkinsesque
conception of a gene) so I'm tempted to leave it out altogether. On the
other hand, as selection on multiple loci is not independent,
recombination changes the degree of selection that is subsequently
applied to alleles.

Biased gene conversion I guess could be sunk under the heading of
mutation. Meiotic drive seems more like selection, but to include there
you'd have to abandon an organism-centric definition in terms of
differential reproductive success for a genocentric definition in terms
of differential replication of genes. (Transposition is another process
that could be classified as mutation or as genocentric selection.)

--
alias Ernest Major

[RSNorman]

I agree that you can define "different mechanisms" of evolution in
rather different ways. However the question is about teaching pop gen
in intro biology. There is no way to do pop gen beyond the level of
Hardy Weinberg and other very simplistic models which are based
completely on Mendelian genetics. As I indicated, it is a chore to
ensure that students even know about mitosis and meiosis and know what
alleles are. Crossover and linkage escapes a significant number. What
you describe is far too much. The only reason to do Hardy Weinberg is
to list the five conditions I cited under which NO evolution occurs to
produce the possibility of generating evolutionary change by violating
one or another of those five. And in that context, non-random mating
substitutes for sexual selection and mutation covers any and every
situation in which a new allele is introduced.

The cell biology people actually say Mendelian genetics should be
dropped completely because virtually nothing works that way. So there
go all the homework exercises where Mom has a type A blood and a
bobbed nose while Dad has type AB blood and a great big nose.

All this must be accompanied by the disclosure that it has been more
than ten years since I was in the intro biology classroom. What
happens today may be totally different than what happened in the forty
years previous.

[chris thompson]

As far as cribbed or purchased term papers go, the internet giveth and the internet taketh away:

www.turnitin.com

I tell my students that they must submit term papers electronically to save paper, which is true. It's also true that I can, and do, immediately submit those papers directly to the above service. It also cuts down the number of papers I have to read- unfortunately the plagiarized papers are very often the best papers submitted in any given semester.

Chris

[John Harshman]

I would answer "no" and "what does 'significant' mean here?

[Peter Nyikos]

I take it you have given up on smearing me as a disbeliever in
evolution on the grounds that I don't think the processes at
work in prebiotic evolution are practically congruent to the
ones in biotic [prokaryotes and beyond] evolution.

You did that a couple of years ago, and IIRC it was on the same
thread where you gave me the unbelievable tall tale that you
had NOT seen the late "el cid" and me discussing his claim
that he could make a protein ribosome in five years given
five million dollars.

By the way, Johnny, in case you have been feeling neglected
of late by me [as you were when you barged into a thread
where Ray Martinez was being voluminously criticized]
you should know that, temporarily at least, I've found the
case history of Martinez to be more interesting than yours.

I'd thought until this month that Martinez's idol, the late
Gene Scott, was just another one of those crank scholars, like
Velikovsky and Churchward, who spent a lot of time on their crank
science.

Turns out that Scott was more like the fictional Elmer Gantry
and the real life Reverend Ike.

http://www.rotten.com/library/bio/religion/dr-gene-scott

I now get the impression from the above webpage [Dana Tweedy told
me about it] that Scott was only responsible for a very limited
repertoire of arguments against evolution, which would also
account for the extreme repetitiousness of Ray's own "arguments."
Also, as I asked and you could not answer, it appears
from the same webpage that Ray got most if not all of his
pseudoscientific main interests from Scott too:

Dr. Scott spends weeks and months at a time on marvelously
conspiratorial topics: the Pyramids, Atlantis, Roswell UFO's,
Stonehenge, the Amityville poltergeists - even the
Philadelphia Experiment.

So I may not have been off the mark when I asked Ray about
Churchward's Lost Continent of Mu. You thought I was,
or at least pretended to think I was.

Peter Nyikos

[Greg Guarino]

On 5/6/2015 12:58 PM, jillery wrote:
> Can the changes
> to non-life also be reasonably described as neutral evolution, as if
> the changes in life and non-life are related?

In my inexpert opinion, unless there is a component of reproduction
involved, there is no "evolution", at least as the word is used in
biology. We may discuss "stellar evolution" or the "evolution" of our
thoughts on same-sex marriage, but without reproduction we are merely
using the same word, not describing an analogous process.

[jillery]

On Thu, 07 May 2015 12:31:56 -0400, Greg Guarino <gdgu...@gmail.com>
wrote:

I share your inexpert opinion, which is one reason why I remarked on
Dawkins' possibly unintentional conflation of the two different
meanings of evolution.

[jillery]

Dawkins' last sentence says he considers adaptive complexity a
distinguishing feature of life from non-life, and adaptive complexity
a consequence of adaptive evolution and not neutral evolution, which
makes adaptive evolution the more significant form wrt distinguishing
life from non-life.

Though I'm not sure he meant it, he also implies that neutral
evolution is a feature of non-life. Perhaps he was thinking of the
the natural progression of change of inanimate objects, like stars or
mountains, which some people call evolutionary.

[Peter Nyikos]

A trickier issue is "prebiotic evolution," by which I mean evolution
of chemical compounds and aggregates of chemical compounds culminating
in things that can fairly be called "biological organisms."

Lest we get bogged down in semantics, let me add that this last
category has to do with efficient replicators. DNA is not an efficient
replicator all by itself, nor are individual molecules of RNA.
Both require enzymes to replicate at a reasonable rate, but these enzymes
in turn need to be produced with the help of other enzymes or copies
of themselves. In "life as we know it" these enzymes are almost
exclusively proteins, but its precursors might have used ribozymes
[RNA catalysts] almost as efficiently.

Also in "life as we know it," there is an overall genome which functions
as a unit, such as our DNA. Do you think this should be a part of
the definition of "biological organisms"? If not, what would you
put in its place?

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos/

[Greg Guarino]

My level of expertise does not allow me to form an opinion on where the
"life/non-life" line might be drawn. But (so far) I hold to the idea
that for a thing to be said to evolve, replication must be involved. If
there were some forms of pre-biotic compunds that were capable of
replication, then I can imagine using the word "evolution" to describe
the changes that came about in those compounds over time.

[Peter Nyikos]

Believe it or not, "capable of replication" is not a cut and dried
issue either, which is why I put my focus on "efficient replicators."

If you put a strand of DNA or RNA into a bath containing enough
of the right kinds of nucleotides, some of those nucleotide molecules
might eventually arrange themselves into a complementary strand
[NOT a duplicate of the original] as long as the strand is not too long,
just from chance and various affinities between molecules.

Then the two strands might separate and the complementary one might then
produce a copy of the original in the same way that it was produced
while the original goes on to produce a copy of the complementary strand.

"might separate" requires a reasonably short strand; the double helix
pattern of DNA makes this almost impossible for the strands that one
has in actual chromosomes. Enzymes are required for this, very exacting
ones at that.

But perhaps the biggest devil is in the details of that "eventually."
One of the reasons Victorian biologists had trouble believing Lord
Kelvin and others that the earth was "only" about 20 million years old,
or even "only" 100 million years old [about the highest figure Lord Kelvin
seriously contemplated] was that this just didn't seem to give enough time
for even present-day highly efficient replicators (such as human beings)
to evolve from the highly efficient replicators of the Silurian period
commonly known as "primitive fish".

Now we know that we have had ca. 3500 million years to evolve from
the first prokaryotes. But those prokaryotes seem to have evolved
"from scratch" in only about 100 to 500 million years.

Dawkins once avoided a debate with Behe because -- so I have read --
he claimed not to know enough about biochemistry. So you need to
turn elsewhere for ideas about how such a tremendous leap in
organized complexity came about in such a short time.

[John Harshman]

On 5/7/15, 8:34 AM, Peter Nyikos wrote:
> On Wednesday, May 6, 2015 at 7:14:22 PM UTC-4, John Harshman wrote:
>> On 5/6/15, 9:58 AM, jillery wrote:
>
>>> The Blind Watchmaker was my introduction to Richard Dawkins, and I
>>> have remained an unabashed fan ever since. By highlighting this part,
>>> Larry Moran raised a different question in my mind: Can the changes
>>> to non-life also be reasonably described as neutral evolution, as if
>>> the changes in life and non-life are related? If so, doesn't that
>>> make adaptive evolution more significant to the evolution of life,
>>> since neutral evolution happens to both?
>>
>> I would answer "no" and "what does 'significant' mean here?

[snip tendentious, off-topic rant]

What occasioned that?

[John Harshman]

I don't think Dawkins meant that at all, and that interpretation places
undue emphasis on the word "the" in "the feature that distinguishes it
from non-life". In order to undergo neutral evolution, you need some
form of genetic inheritance in a population; in fact, you need pretty
much everything you need for selection to happen except for differences
in fitness.

So adaptive evolution can't be more significant for that reason, though
it might be more significant for other reasons. Hence my question about
the meaning of "significant".

[jillery]

On Thu, 07 May 2015 16:46:29 -0700, John Harshman

If there is undue emphasis on "the", it is from how Dawkins actually
wrote it.

>In order to undergo neutral evolution, you need some
>form of genetic inheritance in a population; in fact, you need pretty
>much everything you need for selection to happen except for differences
>in fitness.

So what *do* you think Dawkins was trying to say with his last
sentence? Even substituting "the" with "a", his assertion remains,
that adaptive evolution causes adaptive complexity and neutral
evolution doesn't.

>So adaptive evolution can't be more significant for that reason, though
>it might be more significant for other reasons. Hence my question about
>the meaning of "significant".

I suppose I should just accept your assertions as Truth From the
Pantheon, but I remain unconvinced that Dawkins didn't mean what he
actually wrote, that adaptive complexity is the main feature
distinguishing life from non-life.

I have given my meaning of "significant". If you want "the" meaning,
or even "another" meaning, GIYF.

[John Harshman]

Yes, his bad. But I think he was badly expressing what he meant, not
meaning something bad.

>> In order to undergo neutral evolution, you need some
>> form of genetic inheritance in a population; in fact, you need pretty
>> much everything you need for selection to happen except for differences
>> in fitness.
>
> So what *do* you think Dawkins was trying to say with his last
> sentence? Even substituting "the" with "a", his assertion remains,
> that adaptive evolution causes adaptive complexity and neutral
> evolution doesn't.

I think he meant to say that adaptive evolution was very important and
that non-living things don't do it.

>> So adaptive evolution can't be more significant for that reason, though
>> it might be more significant for other reasons. Hence my question about
>> the meaning of "significant".
>
> I suppose I should just accept your assertions as Truth From the
> Pantheon, but I remain unconvinced that Dawkins didn't mean what he
> actually wrote, that adaptive complexity is the main feature
> distinguishing life from non-life.

He may have meant that, now that you have qualified it with the word
"main". He thinks adaptive complexity is very important; sure.

> I have given my meaning of "significant". If you want "the" meaning,
> or even "another" meaning, GIYF.

I think your definition was unclear and/or non sequitur. Could you make
it more explicit? A quality is more significant than another if...?

To return to your original question, are we agreed that neutral
evolution doesn't happen to non-life? If so, isn't your final original
question reliant on a false premise?

[jillery]

On Fri, 08 May 2015 04:04:38 -0700, John Harshman

Why should Dawkins says these things in this context if he didn't
believe them to contrast with neutral evolution?

>>> So adaptive evolution can't be more significant for that reason, though
>>> it might be more significant for other reasons. Hence my question about
>>> the meaning of "significant".
>>
>> I suppose I should just accept your assertions as Truth From the
>> Pantheon, but I remain unconvinced that Dawkins didn't mean what he
>> actually wrote, that adaptive complexity is the main feature
>> distinguishing life from non-life.
>
>He may have meant that, now that you have qualified it with the word
>"main". He thinks adaptive complexity is very important; sure.

Now you're just quibbling. There can be only one main meaning, even
if there are other lesser meanings

>> I have given my meaning of "significant". If you want "the" meaning,
>> or even "another" meaning, GIYF.
>
>I think your definition was unclear and/or non sequitur. Could you make
>it more explicit?

Apparently not.

>A quality is more significant than another if...?

... it's the main feature. This is rather simple and straightforward
logic.

>To return to your original question, are we agreed that neutral
>evolution doesn't happen to non-life?

Are we agreed this is an implication of Dawkins' quote, however
unintended, however incorrect?

>If so, isn't your final original
>question reliant on a false premise?

I have no idea what you think is my final original question.

[John Harshman]

I think it was just an aside, not closely related to his main point.

>>>> So adaptive evolution can't be more significant for that reason, though
>>>> it might be more significant for other reasons. Hence my question about
>>>> the meaning of "significant".
>>>
>>> I suppose I should just accept your assertions as Truth From the
>>> Pantheon, but I remain unconvinced that Dawkins didn't mean what he
>>> actually wrote, that adaptive complexity is the main feature
>>> distinguishing life from non-life.
>>
>> He may have meant that, now that you have qualified it with the word
>> "main". He thinks adaptive complexity is very important; sure.
>
> Now you're just quibbling. There can be only one main meaning, even
> if there are other lesser meanings

The quality of "main" isn't about the meaning; it's about a feature. The
difference between "main" and "only" is, I think, important.

>>> I have given my meaning of "significant". If you want "the" meaning,
>>> or even "another" meaning, GIYF.
>>
>> I think your definition was unclear and/or non sequitur. Could you make
>> it more explicit?
>
> Apparently not.

Could you try?

>> A quality is more significant than another if...?
>
> ... it's the main feature. This is rather simple and straightforward
> logic.

So significance is a measure of the degree to which a quality
distinguishes life from non-life.

>> To return to your original question, are we agreed that neutral
>> evolution doesn't happen to non-life?
>
> Are we agreed this is an implication of Dawkins' quote, however
> unintended, however incorrect?

I will agree that it's an inference you can derive from his words,
though I think it's farfetched.

>> If so, isn't your final original
>> question reliant on a false premise?
>
> I have no idea what you think is my final original question.

[jillery]

On Fri, 08 May 2015 05:28:26 -0700, John Harshman

A rather remarkable aside, as it's his concluding remark.

So what *do* you think is his main point?

>>>>> So adaptive evolution can't be more significant for that reason, though
>>>>> it might be more significant for other reasons. Hence my question about
>>>>> the meaning of "significant".
>>>>
>>>> I suppose I should just accept your assertions as Truth From the
>>>> Pantheon, but I remain unconvinced that Dawkins didn't mean what he
>>>> actually wrote, that adaptive complexity is the main feature
>>>> distinguishing life from non-life.
>>>
>>> He may have meant that, now that you have qualified it with the word
>>> "main". He thinks adaptive complexity is very important; sure.
>>
>> Now you're just quibbling. There can be only one main meaning, even
>> if there are other lesser meanings
>
>The quality of "main" isn't about the meaning; it's about a feature. The
>difference between "main" and "only" is, I think, important.

Since Dawkins made no such distinction, I fail to see how it's
relevant to any implications of his words.

>>>> I have given my meaning of "significant". If you want "the" meaning,
>>>> or even "another" meaning, GIYF.
>>>
>>> I think your definition was unclear and/or non sequitur. Could you make
>>> it more explicit?
>>
>> Apparently not.
>
>Could you try?

Apparently three times isn't good enough for you. I don't know how to
accommodate to your special needs.

>>> A quality is more significant than another if...?
>>
>> ... it's the main feature. This is rather simple and straightforward
>> logic.
>
>So significance is a measure of the degree to which a quality
>distinguishes life from non-life.

Your sentence immediately above doesn't follow from your question or
my answer to it, which makes it a non sequitur.

>>> To return to your original question, are we agreed that neutral
>>> evolution doesn't happen to non-life?
>>
>> Are we agreed this is an implication of Dawkins' quote, however
>> unintended, however incorrect?
>
>I will agree that it's an inference you can derive from his words,
>though I think it's farfetched.
>
>>> If so, isn't your final original
>>> question reliant on a false premise?
>>
>> I have no idea what you think is my final original question.
>
>"If so, doesn't that make adaptive evolution more significant to the
>evolution of life, since neutral evolution happens to both?"

A premise is a prelude to a conclusion. I asserted no conclusion. As
you pointed out, I asked a question. But I'm not surprised you don't
recognize the difference.

Are you through picking at imaginary nits yet?

[Peter Nyikos]

Martinez's pseudoscience wrt pyramid power, etc. may be off-topic, but it
helps to buttress his nonsense about human ancestry and so it needs to
be dealt with. It may be that he is just parroting things he has heard
from Gene Scott; if so, that is a huge weakness of his that can be
exploited.

> What occasioned that?

My opening comments, which may be the only thing you give a rat's
ass about, were occasioned by your reply to jillery. It is relevant to
unfinished business from over two years ago, namely some para-xenophobic
suspicions you had, having to do with my contrasting attitudes towards
prebiotic versus biological evolution. This unfinished business was
exacerbated by your para-xenophobic suspicions in the last two months
wrt me and Meyer.

This latter issue is also unfinished business thanks to the way Martinez
has soaked up a lot of what little free time I have had in the last two
months.

I used to think Dana Tweedy's valuable service in keeping Martinez
in check for all these years was greatly appreciated by numerous
people whom he relieved of the burden of refuting most of Maritez's
idiocies.

Now it seems that none of these people but myself appreciate Dana's
massive perennial effort. From you and Shrubber I even get the impression
that you actually do not want any decisive victory over Martinez,
but are glad to have one alleged creationist around whom anyone can spank
as often as one wishes. Ever read the explanation of the slogan,
WAR IS PEACE in George Orwell's _1984_? That seems to like the state
of perpetual indecisive warfare with Martinez that you and Shrubber
seem to want.

Peter Nyikos

[Peter Nyikos]

On Friday, May 8, 2015 at 7:09:17 AM UTC-4, John Harshman wrote:
> On 5/7/15, 8:40 PM, jillery wrote:
> > On Thu, 07 May 2015 16:46:29 -0700, John Harshman
> > <jhar...@pacbell.net> wrote:
> >
> >> On 5/7/15, 9:53 AM, jillery wrote:
> >>> On Wed, 06 May 2015 16:09:53 -0700, John Harshman
> >>> <jhar...@pacbell.net> wrote:
> >>>
> >>>> On 5/6/15, 9:58 AM, jillery wrote:

> >>>>> The second quote he uses is from Richard Dawkins from The Blind
> >>>>> Watchmaker:
> >>>>>
> >>>>> **********************************************
> >>>>> Even the most ardent neutralist is quite happy to agree that natural
> >>>>> selection is responsible for all adaptation. All he is saying is that
> >>>>> most evolutionary change is not adaptation. He may well be right,
> >>>>> although one school of geneticists would not agree. From the
> >>>>> sidelines, my own hope is that the neutralists will win, because this
> >>>>> will make it so much easier to work out evolutionary relationships and
> >>>>> rates of evolution. Everybody on both sides agrees that neutral
> >>>>> evolution cannot lead to adaptive improvement, for the simple reason
> >>>>> that neutral evolution is, by definition, random, and adaptive
> >>>>> improvement is, by definition, non-random.

Dawkins might be amazed to learn that the word "random" doesn't mean
what he thinks it does.

Also, his analysis suffers from an absence of any definition of the
word "adaptive". A magnet attracting iron filings may be "adapting"
itself to its environment by enlarging itself, by one possible definition
of the word. Or a melting iceberg may be "adapting" itself to its
environment by turning into liquid and changing its location thereby.

> >>>>> Once again, we have failed
> >>>>> to find any alternative to Darwinian selection, as an explanation for
> >>>>> the feature of life that distinguishes it from non-life, namely
> >>>>> adaptive complexity.
> >>>>> ***********************************************

...assuming we have successfully defined "adaptive complexity." But
I'll point out some possible pitfalls below.

<small snip>

> >>>>> Larry Moran raised a different question in my mind: Can the changes
> >>>>> to non-life also be reasonably described as neutral evolution, as if
> >>>>> the changes in life and non-life are related? If so, doesn't that
> >>>>> make adaptive evolution more significant to the evolution of life,
> >>>>> since neutral evolution happens to both?
> >>>>
> >>>> I would answer "no" and "what does 'significant' mean here?
> >>>
> >>> Dawkins' last sentence says he considers adaptive complexity a
> >>> distinguishing feature of life from non-life, and adaptive complexity
> >>> a consequence of adaptive evolution and not neutral evolution, which
> >>> makes adaptive evolution the more significant form wrt distinguishing
> >>> life from non-life.

As long as you can find a definition that applies to the one and not
to the other.

> >>> Though I'm not sure he meant it, he also implies that neutral
> >>> evolution is a feature of non-life. Perhaps he was thinking of the
> >>> the natural progression of change of inanimate objects, like stars or
> >>> mountains, which some people call evolutionary.

The case of some stars is especially significant for hammering out
a definition of "adaptive" and also of "life" that will pass muster.
See below.

> >> I don't think Dawkins meant that at all, and that interpretation places
> >> undue emphasis on the word "the" in "the feature that distinguishes it
> >>from non-life".
> >
> > If there is undue emphasis on "the", it is from how Dawkins actually
> > wrote it.
>
> Yes, his bad. But I think he was badly expressing what he meant, not
> meaning something bad.

More so than even you may think. Read on.

> >> In order to undergo neutral evolution, you need some
> >> form of genetic inheritance in a population;

I haven't the foggiest reason why. Did you eventually agree that
this, too, was Dawkins's bad?

> >> in fact, you need pretty
> >> much everything you need for selection to happen except for differences
> >> in fitness.

More words to define. Let's see what careless definitions might do.

A supergiant star going supernova produces a great deal of heavy elements
in a matter of seconds. These heavy elements are "genetically inherited"
by a new generation of stars. These "descendants" of the supernova
also acquire a part of their mass from elsewhere, just as most
offspring of biological organisms get food, water, etc. from elsewhere.

The only problem is reduced fitness: none of the descendants will have
as many offspring as their parent. But in other respects they have
many advantages over their parent, including many times (sometimes
thousands of times) greater longevity. This longevity is a necessary
(but far from sufficient) condition for planets around these stars
to have life that evolves to produce life forms of staggering complexity.

> > So what *do* you think Dawkins was trying to say with his last
> > sentence? Even substituting "the" with "a", his assertion remains,
> > that adaptive evolution causes adaptive complexity and neutral
> > evolution doesn't.
>
> I think he meant to say that adaptive evolution was very important and
> that non-living things don't do it.

Many offspring of supernovas do adapt to the "need" of longevity which the
parent star conspicuously lacked by being unable to accumulate anywhere
near the mass of the parent.

> >> So adaptive evolution can't be more significant for that reason, though
> >> it might be more significant for other reasons. Hence my question about
> >> the meaning of "significant".
> >
> > I suppose I should just accept your assertions as Truth From the
> > Pantheon, but I remain unconvinced that Dawkins didn't mean what he
> > actually wrote, that adaptive complexity is the main feature
> > distinguishing life from non-life.

The complexity of the offspring of supernovas is manifestly greater
than that of the parent, in the sense of having far many more and more
varied heavy atoms. The greatest difference came in the first generation
after the big bang: stars having nothing but hydrogen and helium
explosively producing all the elements we see in the universe around us.

> He may have meant that, now that you have qualified it with the word
> "main". He thinks adaptive complexity is very important; sure.
>
> > I have given my meaning of "significant". If you want "the" meaning,
> > or even "another" meaning, GIYF.
>
> I think your definition was unclear and/or non sequitur. Could you make
> it more explicit? A quality is more significant than another if...?

Your philosophical naivete staggers me, John. Do you expect anyone
on earth to be able to give a satisfactory finish to your sentence?

Oh...wait... are you trying to use the Socratic Method on jillery?

> To return to your original question, are we agreed that neutral
> evolution doesn't happen to non-life?

Y'all's subsequent back-and-forth doesn't seem to resolve this question,
nor the next one:

> If so, isn't your final original
> question reliant on a false premise?

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina

http://www.math.sc.edu/~nyikos/

[John Harshman]

Sometimes I wonder if you are clinically insane. That wasn't intended as
a joke or even a dig. I know you can't see it, but most others can.

[John Harshman]

Based solely on that short excerpt, I think his main point was that
while most substitutions are neutral, the small fraction due to
selection are the interesting and important ones.

>>>>>> So adaptive evolution can't be more significant for that reason, though
>>>>>> it might be more significant for other reasons. Hence my question about
>>>>>> the meaning of "significant".
>>>>>
>>>>> I suppose I should just accept your assertions as Truth From the
>>>>> Pantheon, but I remain unconvinced that Dawkins didn't mean what he
>>>>> actually wrote, that adaptive complexity is the main feature
>>>>> distinguishing life from non-life.
>>>>
>>>> He may have meant that, now that you have qualified it with the word
>>>> "main". He thinks adaptive complexity is very important; sure.
>>>
>>> Now you're just quibbling. There can be only one main meaning, even
>>> if there are other lesser meanings
>>
>> The quality of "main" isn't about the meaning; it's about a feature. The
>> difference between "main" and "only" is, I think, important.
>
> Since Dawkins made no such distinction, I fail to see how it's
> relevant to any implications of his words.

You are the one who made the distinction. It makes more sense than what
he actually said.

>>>>> I have given my meaning of "significant". If you want "the" meaning,
>>>>> or even "another" meaning, GIYF.
>>>>
>>>> I think your definition was unclear and/or non sequitur. Could you make
>>>> it more explicit?
>>>
>>> Apparently not.
>>
>> Could you try?
>
> Apparently three times isn't good enough for you. I don't know how to
> accommodate to your special needs.

Where were those three times?

>>>> A quality is more significant than another if...?
>>>
>>> ... it's the main feature. This is rather simple and straightforward
>>> logic.
>>
>> So significance is a measure of the degree to which a quality
>> distinguishes life from non-life.
>
> Your sentence immediately above doesn't follow from your question or
> my answer to it, which makes it a non sequitur.

Your tendency not to try repairing my misunderstanding, just point it
out, is one of the things that makes it hard to talk to you.

>>>> To return to your original question, are we agreed that neutral
>>>> evolution doesn't happen to non-life?
>>>
>>> Are we agreed this is an implication of Dawkins' quote, however
>>> unintended, however incorrect?
>>
>> I will agree that it's an inference you can derive from his words,
>> though I think it's farfetched.
>>
>>>> If so, isn't your final original
>>>> question reliant on a false premise?
>>>
>>> I have no idea what you think is my final original question.
>>
>> "If so, doesn't that make adaptive evolution more significant to the
>> evolution of life, since neutral evolution happens to both?"
>
> A premise is a prelude to a conclusion. I asserted no conclusion. As
> you pointed out, I asked a question. But I'm not surprised you don't
> recognize the difference.
>
> Are you through picking at imaginary nits yet?

I don't understand why you always get so hostile, so fast. The premise
is "If so" and "since neutral evolution happens to both"; the conclusion
is "doesn't that make adaptive evolution more significant to the
evolution of life". And while that was stated in the form of a question,
"doesn't that" is generally considered to be a way to make a statement.

Even if that was a real question, questions can contain premises. "Have
you stopped beating your wife?", for example. Would you agree that the
question contains a false premise and is therefore invalid, i.e. can't
be answered correctly, merely rejected?

[John Harshman]

Nobody, ever in history, has meant that by "adapting".

Who are you talking to here? That wasn't Dawkins; that was me. Why would
I agree that something I said was Dawkins' bad?

>>>> in fact, you need pretty
>>>> much everything you need for selection to happen except for differences
>>>> in fitness.
>
> More words to define. Let's see what careless definitions might do.
>
> A supergiant star going supernova produces a great deal of heavy elements
> in a matter of seconds. These heavy elements are "genetically inherited"
> by a new generation of stars. These "descendants" of the supernova
> also acquire a part of their mass from elsewhere, just as most
> offspring of biological organisms get food, water, etc. from elsewhere.

True for a sufficiently meaningless definition of "genetic inheritance".
Why are you trying to destroy all the meanings in words?

> The only problem is reduced fitness: none of the descendants will have
> as many offspring as their parent. But in other respects they have
> many advantages over their parent, including many times (sometimes
> thousands of times) greater longevity. This longevity is a necessary
> (but far from sufficient) condition for planets around these stars
> to have life that evolves to produce life forms of staggering complexity.

None of that has anything to do with evolution, neutral or otherwise. Or
with reproduction. Or with genetic inheritance.

>>> So what *do* you think Dawkins was trying to say with his last
>>> sentence? Even substituting "the" with "a", his assertion remains,
>>> that adaptive evolution causes adaptive complexity and neutral
>>> evolution doesn't.
>>
>> I think he meant to say that adaptive evolution was very important and
>> that non-living things don't do it.
>
> Many offspring of supernovas do adapt to the "need" of longevity which the
> parent star conspicuously lacked by being unable to accumulate anywhere
> near the mass of the parent.

Again, if you destroy all meaning in the word "adapt", you can call
anything adaptive.

>>>> So adaptive evolution can't be more significant for that reason, though
>>>> it might be more significant for other reasons. Hence my question about
>>>> the meaning of "significant".
>>>
>>> I suppose I should just accept your assertions as Truth From the
>>> Pantheon, but I remain unconvinced that Dawkins didn't mean what he
>>> actually wrote, that adaptive complexity is the main feature
>>> distinguishing life from non-life.
>
> The complexity of the offspring of supernovas is manifestly greater
> than that of the parent, in the sense of having far many more and more
> varied heavy atoms. The greatest difference came in the first generation
> after the big bang: stars having nothing but hydrogen and helium
> explosively producing all the elements we see in the universe around us.

Yes, by one measure of complexity, second-generation stars are more
complex than first-generation stars. But by no stretch of the
imagination could this be called either reproduction or adaptive.

>> He may have meant that, now that you have qualified it with the word
>> "main". He thinks adaptive complexity is very important; sure.
>>
>>> I have given my meaning of "significant". If you want "the" meaning,
>>> or even "another" meaning, GIYF.
>>
>> I think your definition was unclear and/or non sequitur. Could you make
>> it more explicit? A quality is more significant than another if...?
>
> Your philosophical naivete staggers me, John. Do you expect anyone
> on earth to be able to give a satisfactory finish to your sentence?

They'd better if they want to talk about significance.

> Oh...wait... are you trying to use the Socratic Method on jillery?
>
>> To return to your original question, are we agreed that neutral
>> evolution doesn't happen to non-life?
>
> Y'all's subsequent back-and-forth doesn't seem to resolve this question,
> nor the next one:
>
>> If so, isn't your final original
>> question reliant on a false premise?

Sure. Jillery has departed the conversation and entered into reflexive
attack mode.

[Roger Shrubber]

I really shouldn't, but you caught me in a mood and with a drink.
I note that he has done something again, when cornered, he asserts
that his "opponent" is not serious. There's a significant parallel,
in my mind, between that and how someone else mentioned above
responds when cornered - that respondants have to say such things
because they are atheists.

It invokes the impression of a brain in conflict. There's a rational
and logical part (or facsimile thereof) dueling it out with a part
charged with maintaining the ego (and likely another part trying to
maintain status quo in general). In cartoon form, steam starts to
spew out of the ears. In Forbidden Planet, Robby the Robot would
short circuit. In Star Trek (the original) context, Nomad discovers
it has made an error between Roykirk and Kirk and must sterilize
itself, entering into an infinite loop.

Geekdom aside (hardly), our protagonists don't commit Seppuku
and reboot their self-concepts. Instead, they create mental worm-holes
to warp the space-time continuum in ways that maintain their previous
self-conceptions but fling any conflicts into the far reaches of
the universe.

[Roger Shrubber]

John Harshman wrote:
> On 5/8/15, 11:46 AM, Peter Nyikos wrote:
>> On Friday, May 8, 2015 at 7:09:17 AM UTC-4, John Harshman wrote:
>>> On 5/7/15, 8:40 PM, jillery wrote:
>>>> <jhar...@pacbell.net> wrote:
>>>>> On 5/7/15, 9:53 AM, jillery wrote:
>>>>>> On Wed, 06 May 2015 16:09:53 -0700, John Harshman

It takes a special talent to misread that, though Dawkins does
feed the opportunity.

>>>>>>>> Everybody on both sides agrees that neutral evolution
>>>>>>>> cannot lead to adaptive improvement, for the simple
>>>>>>>> reason that neutral evolution is, by definition,
>>>>>>>> random, and adaptive improvement is, by definition,
>>>>>>>> non-random.

Forgive me (or not), I disagree.
It's obvious actually. The verb "lead to" is the key.
And unlocking the key is that selection is context dependent
with the clear knowledge that contexts change in time.

Thus, it ought to be clear that neutral evolution can, as
a matter of definition, occasionally produce potential that
will only manifest in future contexts. Further, neutral
evolution works across multiple fronts simultaneously. So
clearly neutral evolution expands variation, often in ways
that will ultimately prove to be worthless or even
contraindicated. So what. The essence of biological evolution
is that excess production exists. More offspring are produced
than will (or "should") survive. A significant wastage is
already built into the equation. Many miss this point.

[Peter Nyikos]

That's neither here nor there. If you want to distinguish between adaptive
evolution, neutral evolution, and non-biological evolution, you need to
be able to define your terms so that unintended consequences don't
arise. I'm sure you know about unintended legal loopholes in laws;
scientists should be even more wary about such things than lawyers.
[Ever hear the joke about black sheep in Scotland?]

> >>>>>>> Once again, we have failed
> >>>>>>> to find any alternative to Darwinian selection, as an explanation for
> >>>>>>> the feature of life that distinguishes it from non-life, namely
> >>>>>>> adaptive complexity.
> >>>>>>> ***********************************************
> >
> > ...assuming we have successfully defined "adaptive complexity." But
> > I'll point out some possible pitfalls below.
> >
> > <small snip>
> >
> >>>>>>> Larry Moran raised a different question in my mind: Can the changes
> >>>>>>> to non-life also be reasonably described as neutral evolution, as if
> >>>>>>> the changes in life and non-life are related? If so, doesn't that
> >>>>>>> make adaptive evolution more significant to the evolution of life,
> >>>>>>> since neutral evolution happens to both?
> >>>>>>
> >>>>>> I would answer "no" and "what does 'significant' mean here?

No satisfactory explanation of that "no" appears from you below.

> >>>>> Dawkins' last sentence says he considers adaptive complexity a
> >>>>> distinguishing feature of life from non-life, and adaptive complexity
> >>>>> a consequence of adaptive evolution and not neutral evolution, which
> >>>>> makes adaptive evolution the more significant form wrt distinguishing
> >>>>> life from non-life.
> >
> > As long as you can find a definition that applies to the one and not
> > to the other.
> >
> >>>>> Though I'm not sure he meant it, he also implies that neutral
> >>>>> evolution is a feature of non-life. Perhaps he was thinking of the
> >>>>> the natural progression of change of inanimate objects, like stars or
> >>>>> mountains, which some people call evolutionary.
> >
> > The case of some stars is especially significant for hammering out
> > a definition of "adaptive" and also of "life" that will pass muster.
> > See below.

<snip for focus>

> >>>> In order to undergo neutral evolution, you need some
> >>>> form of genetic inheritance in a population;
> >

> > I haven't the foggiest [idea] why. Did you eventually agree that

> > this, too, was Dawkins's bad?
>
> Who are you talking to here? That wasn't Dawkins; that was me.

There was so much back and forth going on, and the statement seemed
so illogical to me in the light of what jillery had said about
evolution of stars and mountains earlier, that I got confused.

So tell us, what is your definition of neutral evolution? And why
does it lead to such a claim? That would, finally, begin to account
for your "no" up there.

> >>>> in fact, you need pretty
> >>>> much everything you need for selection to happen except for differences
> >>>> in fitness.
> >
> > More words to define. Let's see what careless definitions might do.
> >
> > A supergiant star going supernova produces a great deal of heavy elements
> > in a matter of seconds. These heavy elements are "genetically inherited"
> > by a new generation of stars. These "descendants" of the supernova
> > also acquire a part of their mass from elsewhere, just as most
> > offspring of biological organisms get food, water, etc. from elsewhere.
>
> True for a sufficiently meaningless definition of "genetic inheritance".
> Why are you trying to destroy all the meanings in words?

What's to destroy? The meanings have been confined to "life as we know
it" by most biologists and now it looks like Dawkins and Moran are going into
uncharted territory by trying to define "life in general". We need
to build, and I'm trying to explain what sorts of unintended applications
could arise if we are careless about defining our terms.

> > The only problem is reduced fitness: none of the descendants will have
> > as many offspring as their parent. But in other respects they have
> > many advantages over their parent, including many times (sometimes
> > thousands of times) greater longevity. This longevity is a necessary
> > (but far from sufficient) condition for planets around these stars
> > to have life that evolves to produce life forms of staggering complexity.
>
> None of that has anything to do with evolution, neutral or otherwise.

Come off it. It has plenty to do with the evolution of the universe,
almost all of which is non-biological. Once you explain what YOU
mean by "neutral evolution" I might not be saying things like that.

> Or with reproduction. Or with genetic inheritance.

Once we agree on the distinction between life and non-life, we can,
if you so wish, restrict this term to living things.

Let me give you some easy questions, and then we can go on to tougher ones.

Do you class viruses as life or non-life? How about viroids? prions?

<snip for focus>

> >> I think he meant to say that adaptive evolution was very important and
> >> that non-living things don't do it.
> >
> > Many offspring of supernovas do adapt to the "need" of longevity which the
> > parent star conspicuously lacked by being unable to accumulate anywhere
> > near the mass of the parent.
>
> Again, if you destroy all meaning in the word "adapt", you can call
> anything adaptive.

Not "anything," John, just a few things that have some interesting
resemblances to adaptation as YOU would define it.

So go ahead and define it, already. And make sure it will cover any
extraterrestrial thing that you would want to classify as life, if
you saw it.

> >>>> So adaptive evolution can't be more significant for that reason, though
> >>>> it might be more significant for other reasons. Hence my question about
> >>>> the meaning of "significant".
> >>>
> >>> I suppose I should just accept your assertions as Truth From the
> >>> Pantheon, but I remain unconvinced that Dawkins didn't mean what he
> >>> actually wrote, that adaptive complexity is the main feature
> >>> distinguishing life from non-life.
> >
> > The complexity of the offspring of supernovas is manifestly greater
> > than that of the parent, in the sense of having far many more and more
> > varied heavy atoms. The greatest difference came in the first generation
> > after the big bang: stars having nothing but hydrogen and helium
> > explosively producing all the elements we see in the universe around us.
>
> Yes, by one measure of complexity, second-generation stars are more
> complex than first-generation stars. But by no stretch of the
> imagination could this be called either reproduction or adaptive.

By no stretch of the imagination could anyone think you've defined
"reproduction" or "adaptation" in all your beating around the bush.

> >>> I have given my meaning of "significant". If you want "the" meaning,
> >>> or even "another" meaning, GIYF.
> >>
> >> I think your definition was unclear and/or non sequitur. Could you make
> >> it more explicit? A quality is more significant than another if...?
> >
> > Your philosophical naivete staggers me, John. Do you expect anyone
> > on earth to be able to give a satisfactory finish to your sentence?
>
> They'd better if they want to talk about significance.

Then you want a being with superhuman intelligence. But since you are
an atheist, I think you are out of luck here.

> > Oh...wait... are you trying to use the Socratic Method on jillery?

Nevermind. You probably wouldn't recognize the Socratic Method
if anyone used it on you.

> >> To return to your original question, are we agreed that neutral
> >> evolution doesn't happen to non-life?
> >
> > Y'all's subsequent back-and-forth doesn't seem to resolve this question,
> > nor the next one:
> >
> >> If so, isn't your final original
> >> question reliant on a false premise?
>
> Sure. Jillery has departed the conversation and entered into reflexive
> attack mode.

...pot...kettle...you expect answers to these questions from her without
ever having told YOUR definition of "neutral evolution."

Peter Nyikos

[Peter Nyikos]

You're beginning to catch on. Read my reply to John of a few
minutes ago, and you may begin to see that, although what I've
written may seem like madness, yet there is method in't.

> >>>>>>>> Everybody on both sides agrees that neutral evolution
> >>>>>>>> cannot lead to adaptive improvement, for the simple
> >>>>>>>> reason that neutral evolution is, by definition,
> >>>>>>>> random, and adaptive improvement is, by definition,
> >>>>>>>> non-random.
>
> Forgive me (or not), I disagree.
> It's obvious actually. The verb "lead to" is the key.
> And unlocking the key is that selection is context dependent
> with the clear knowledge that contexts change in time.
>
> Thus, it ought to be clear that neutral evolution can, as
> a matter of definition, occasionally produce potential that
> will only manifest in future contexts. Further, neutral
> evolution works across multiple fronts simultaneously. So
> clearly neutral evolution expands variation, often in ways
> that will ultimately prove to be worthless or even
> contraindicated.

This is all fine and dandy, once someone defines "neutral evolution"
in a way satisfactory to all here present. Jillery seems not to have
let go of the idea that neutral evolution can include the evolution
of non-living matter. Harshman seems quite insistent that it can only
refer to living things. Not remembering what Dawkins said about it
in The Blind Watchmaker, I can't tell which side he'd come down on,
but what has been quoted from him so far, seems to favor jillery.

And then there is the exchange between me and Guarino that all three
of you are ignoring, perhaps because it has to do with prebiotic
evolution, which blurs the distinction between living and non-living
matter since it starts out as clearly non-living, and then morphs
into living, with no clear dividing line.

Just WHERE in the various scenarios for prebiotic evolution would
YOU say "neutral evolution" starts to become applicable?

> So what. The essence of biological evolution
> is that excess production exists. More offspring are produced
> than will (or "should") survive. A significant wastage is
> already built into the equation. Many miss this point.

"Many" does not include anyone on this thread, methinks.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina

http://people.math.sc.edu/nyikos/
nyikos at math.sc.edu

[Roger Shrubber]

Peter Nyikos wrote:
> On Friday, May 8, 2015 at 8:19:16 PM UTC-4, John Harshman wrote:
>> On 5/8/15, 11:46 AM, Peter Nyikos wrote:


>>> Also, his analysis suffers from an absence of any definition of the
>>> word "adaptive". A magnet attracting iron filings may be "adapting"
>>> itself to its environment by enlarging itself, by one possible definition
>>> of the word. Or a melting iceberg may be "adapting" itself to its
>>> environment by turning into liquid and changing its location thereby.
>>
>> Nobody, ever in history, has meant that by "adapting".
>
> That's neither here nor there. If you want to distinguish between adaptive
> evolution, neutral evolution, and non-biological evolution, you need to
> be able to define your terms so that unintended consequences don't
> arise. I'm sure you know about unintended legal loopholes in laws;
> scientists should be even more wary about such things than lawyers.
> [Ever hear the joke about black sheep in Scotland?]

Such as might happen in the consequence of a book entitled _The Blind
Watchmaker_, as is the implied context. Dawkins defined his context.
A willful ignorance allows one to avoid the obvious, and Nyikos
complies, more than complies but propounds upon a determinedly
ignorant misconception. I grant that a determined effort to
generate obfuscation will produce enough obfuscation that authentic
elucidation will be confounded. You earn a structural victoryl

[Roger Shrubber]

Your invidious comments aside, the obvious remains obvious.
And you persist in cluelessness.

>> >>>>>>>> Everybody on both sides agrees that neutral evolution
>> >>>>>>>> cannot lead to adaptive improvement, for the simple
>> >>>>>>>> reason that neutral evolution is, by definition,
>> >>>>>>>> random, and adaptive improvement is, by definition,
>> >>>>>>>> non-random.
>>
>> Forgive me (or not), I disagree.
>> It's obvious actually. The verb "lead to" is the key.
>> And unlocking the key is that selection is context dependent
>> with the clear knowledge that contexts change in time.
>>
>> Thus, it ought to be clear that neutral evolution can, as
>> a matter of definition, occasionally produce potential that
>> will only manifest in future contexts. Further, neutral
>> evolution works across multiple fronts simultaneously. So
>> clearly neutral evolution expands variation, often in ways
>> that will ultimately prove to be worthless or even
>> contraindicated.

> This is all fine and dandy, once someone defines "neutral evolution"
> in a way satisfactory to all here present. Jillery seems not to have
> let go of the idea that neutral evolution can include the evolution
> of non-living matter. Harshman seems quite insistent that it can only
> refer to living things. Not remembering what Dawkins said about it
> in The Blind Watchmaker, I can't tell which side he'd come down on,
> but what has been quoted from him so far, seems to favor jillery.

You misread it all. It is your idiom.
Neutral evolution is simply a result. The result is that bias in
genetic potential propagates in manners disproportionate to current
selective advantage. Do spend time parsing that.

> And then there is the exchange between me and Guarino that all three
> of you are ignoring, perhaps because it has to do with prebiotic
> evolution, which blurs the distinction between living and non-living
> matter since it starts out as clearly non-living, and then morphs
> into living, with no clear dividing line.

You fantasize that your own sense of significance represents
authentic significance, all evidence to the contrary.

> Just WHERE in the various scenarios for prebiotic evolution would
> YOU say "neutral evolution" starts to become applicable?

Observationally, everywhere.

>> So what. The essence of biological evolution
>> is that excess production exists. More offspring are produced
>> than will (or "should") survive. A significant wastage is
>> already built into the equation. Many miss this point.

> "Many" does not include anyone on this thread, methinks.

And if anyone puts emphais on what "you thinks", they deserve
an associated consideration.

[Peter Nyikos]

Maybe John got discombobulated by my surreal-seeming post where I
harp on things like "neutral", "adaptive," etc. If so, I hope my
last reply to him and my previous reply to you will clear things
up for him.

I'll give him the benefit of the doubt, and assume he is NOT exclusively
referring to what I wrote in the post to which he is actually
replying here. I can certainly back up everything I wrote about his
para-xenophobia, to the point where he once more will run away,
no more able to bear his figurative reflection in a figurative
mirror than "God" was able to bear his actual reflection in
an actual mirror in "Steambath."

> > That wasn't intended as
> > a joke or even a dig. I know you can't see it, but most others can.

John will, of course, not name the tiny handful of people he really
has in mind, because he has made it abundantly clear that he is
not the least bit interested in how cowardly and/or hypocritical
and/or dishonest people with whom he is on good terms are.
And I can document such behavior for each of the people he could
plausibly construe as the "others [who]can."

That includes you, "Roger Shrubber". Was it just a coincidence
that you killfiled me in reply to the same post where I asked
you whether you were really Wade Hines?

> I really shouldn't, but you caught me in a mood and with a drink.
> I note that he has done something again, when cornered, he asserts
> that his "opponent" is not serious.

You note a figment of your imagination.

The rest of your post is even more surrealistic than the one you
did yesterday in reply to me on the thread where Ray Martinez falsely accused
me of slander and of defending slander by Dana Tweedy.

Did you see that, and see how he announced that he was quitting the
thread on account of these alleged actions, thereby using these false
accusation as an excuse for not supporting the false accusations
themselves?

I've done two replies to it so far, and am curious to see whether you have
the balls to talk about either his "swan song" for that thread or
my two replies. Next week I'll do one more reply, and one to that
surrealistic post you did, on which Martinez piggybacked his "swan song".

As for the post to which I am replying, I am snipping the rest of what you
wrote. If you really think you had something significant to say in it,
let me know, and I'll deal with it.

Peter Nyikos

[jillery]

On Fri, 08 May 2015 17:07:06 -0700, John Harshman

****************************************************
first time

>>>>>>>> Dawkins' last sentence says he considers adaptive complexity a
>>>>>>>> distinguishing feature of life from non-life, and adaptive complexity
>>>>>>>> a consequence of adaptive evolution and not neutral evolution, which
>>>>>>>> makes adaptive evolution the more significant form wrt distinguishing
>>>>>>>> life from non-life.

*****************************************************

Based on that, you should now be able to clarify your expressed
confusion about the meaning of "significant" in the context of this
topic, that a reasonable conclusion from Dawkins' quote is that he
thinks adaptive evolution is more significant than neutral evolution.

>>>>>>> So adaptive evolution can't be more significant for that reason, though
>>>>>>> it might be more significant for other reasons. Hence my question about
>>>>>>> the meaning of "significant".
>>>>>>

**********************************************************
second time

>>>>>> I suppose I should just accept your assertions as Truth From the
>>>>>> Pantheon, but I remain unconvinced that Dawkins didn't mean what he
>>>>>> actually wrote, that adaptive complexity is the main feature
>>>>>> distinguishing life from non-life.

***********************************************************

>>>>>
>>>>> He may have meant that, now that you have qualified it with the word
>>>>> "main". He thinks adaptive complexity is very important; sure.
>>>>
>>>> Now you're just quibbling. There can be only one main meaning, even
>>>> if there are other lesser meanings
>>>
>>> The quality of "main" isn't about the meaning; it's about a feature. The
>>> difference between "main" and "only" is, I think, important.
>>
>> Since Dawkins made no such distinction, I fail to see how it's
>> relevant to any implications of his words.
>
>You are the one who made the distinction.

No I did not. Once again, I remarked about an implication of Dawkins'
quote.

>It makes more sense than what
>he actually said.
>
>>>>>> I have given my meaning of "significant". If you want "the" meaning,
>>>>>> or even "another" meaning, GIYF.
>>>>>
>>>>> I think your definition was unclear and/or non sequitur. Could you make
>>>>> it more explicit?
>>>>
>>>> Apparently not.
>>>
>>> Could you try?
>>
>> Apparently three times isn't good enough for you. I don't know how to
>> accommodate to your special needs.
>
>Where were those three times?

For your convenience, I marked them explicitly. Hopefully you're
capable of looking for yourself.

>>>>> A quality is more significant than another if...?
>>>>

****************************************
third time

>>>> ... it's the main feature. This is rather simple and straightforward
>>>> logic.

***************************************

>>>
>>> So significance is a measure of the degree to which a quality
>>> distinguishes life from non-life.
>>
>> Your sentence immediately above doesn't follow from your question or
>> my answer to it, which makes it a non sequitur.
>
>Your tendency not to try repairing my misunderstanding, just point it
>out, is one of the things that makes it hard to talk to you.

Your habit of not explaining your misunderstanding, and your bald
rejection and denial of my efforts to repair your misunderstanding,
make it hard to talk to you.

>>>>> To return to your original question, are we agreed that neutral
>>>>> evolution doesn't happen to non-life?
>>>>
>>>> Are we agreed this is an implication of Dawkins' quote, however
>>>> unintended, however incorrect?
>>>
>>> I will agree that it's an inference you can derive from his words,
>>> though I think it's farfetched.
>>>
>>>>> If so, isn't your final original
>>>>> question reliant on a false premise?
>>>>
>>>> I have no idea what you think is my final original question.
>>>
>>> "If so, doesn't that make adaptive evolution more significant to the
>>> evolution of life, since neutral evolution happens to both?"
>>
>> A premise is a prelude to a conclusion. I asserted no conclusion. As
>> you pointed out, I asked a question. But I'm not surprised you don't
>> recognize the difference.
>>
>> Are you through picking at imaginary nits yet?
>
>I don't understand why you always get so hostile, so fast.

And I don't understand why you always assume so fast that I'm hostile.
Every time you make that bald assertion, I challenge you to justify
it, but then you either ignore my challenge, or just run away
altogether. From that behavior, I get the impression you reply to me
just so you post that and similar nonsense.

> The premise
>is "If so" and "since neutral evolution happens to both"; the conclusion
>is "doesn't that make adaptive evolution more significant to the
>evolution of life".

Once again, that's not a conclusion, that's a question. "If so"
identifies a hypothetical case. "since neutral evolution..." provides
a descriptive summary of the hypothetical case, which I made in detail
in the very same paragraph I asked that question, in an obviously
futile effort to forestall the picking of imagined nits.

>And while that was stated in the form of a question,
>"doesn't that" is generally considered to be a way to make a statement.
>
>Even if that was a real question, questions can contain premises. "Have
>you stopped beating your wife?", for example. Would you agree that the
>question contains a false premise and is therefore invalid, i.e. can't
>be answered correctly, merely rejected?

I disagree that my question contains a premise, either true or false.

I disagree that you have shown anything about my question to be false,
your bald assertion of your opinion notwithstanding. To the contrary,
you explicitly recognized that the falsity is a result of Dawkins'
words.

I disagree that my question is of the same class as "have you stopped
beating your wife?"

And with your continuing focus on mindless minutia, you have almost
completely obscured anything meaningful and relevant to the topic. Is
that your intent?

[jillery]

On Fri, 8 May 2015 20:50:58 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> wrote:


...nothing that has any relevance to this topic.

<mercy snip of rockhead's self-promoting noise>

[jillery]

On Fri, 8 May 2015 19:57:26 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> wrote:

>Jillery seems not to have
>let go of the idea that neutral evolution can include the evolution
>of non-living matter.

Since I never grabbed onto that idea, I have no need to let it go.

More important, your posts in this thread show that you're more
interested in posting about anything *not* related to the topic.

I already know that you know how to act like an idiot, so you don't
have to keep proving it. Just sayin'.

[John Harshman]

On 5/8/15, 7:57 PM, Peter Nyikos wrote:

> Just WHERE in the various scenarios for prebiotic evolution would
> YOU say "neutral evolution" starts to become applicable?

At the same point at which "natural selection" starts to become
applicable: when there is significant reproduction with inheritance. Of
course there is a gray area; the less certain the inheritance the less
potential there is for any sort of evolution. Perfect or near-perfect
inheritance isn't necessary, though. It seems clear to me that there is
evolution if there is replicated nucleic acid. It isn't clear to me that
there is at any hypothetical earlier stages. But maybe.

[John Harshman]

I would argue that what words mean -- and what words mean is what people
have meant by them -- is indeed relevant. Do you really not know what
"adapting" means? I suspect you do, but are just being contrarian to
show how clever you are. If we all agree that you're very, very clever,
will you stop?

>>>>>>>>> Once again, we have failed
>>>>>>>>> to find any alternative to Darwinian selection, as an explanation for
>>>>>>>>> the feature of life that distinguishes it from non-life, namely
>>>>>>>>> adaptive complexity.
>>>>>>>>> ***********************************************
>>>
>>> ...assuming we have successfully defined "adaptive complexity." But
>>> I'll point out some possible pitfalls below.
>>>
>>> <small snip>
>>>
>>>>>>>>> Larry Moran raised a different question in my mind: Can the changes
>>>>>>>>> to non-life also be reasonably described as neutral evolution, as if
>>>>>>>>> the changes in life and non-life are related? If so, doesn't that
>>>>>>>>> make adaptive evolution more significant to the evolution of life,
>>>>>>>>> since neutral evolution happens to both?
>>>>>>>>
>>>>>>>> I would answer "no" and "what does 'significant' mean here?
>
> No satisfactory explanation of that "no" appears from you below.

Pretty sure it does, but let me repeat: evolution, whether neutral,
adaptive, or something else, requires reproduction and some form of
fairly good inheritance. Stellar evolution is not evolution in the sense
we're talking about here. Despite your farfetched argument, there is no
fairly good inheritance, and not even any reproduction of stars. You
could as well say that the air reproduces because gases in it are
incorporated into living organisms. That too would be nonsensical.

Evolution is the change of allele frequencies in populations, plus some
similar processes at higher levels. One can stretch the concept of
"alleles" to other forms of inheritance, but it can't be stretched
infinitely. Neutral evolution is evolution in which the different
alleles (or analogs) do not differ in fitness. How is it possible that
you wouldn't know that?

The need for inheritance is contained in the definition of "evolution",
not "neutral evolution". Again, how is it possible you didn't know that?
And what's wrong with the claim?

>>>>>> in fact, you need pretty
>>>>>> much everything you need for selection to happen except for differences
>>>>>> in fitness.
>>>
>>> More words to define. Let's see what careless definitions might do.
>>>
>>> A supergiant star going supernova produces a great deal of heavy elements
>>> in a matter of seconds. These heavy elements are "genetically inherited"
>>> by a new generation of stars. These "descendants" of the supernova
>>> also acquire a part of their mass from elsewhere, just as most
>>> offspring of biological organisms get food, water, etc. from elsewhere.
>>
>> True for a sufficiently meaningless definition of "genetic inheritance".
>> Why are you trying to destroy all the meanings in words?
>
> What's to destroy? The meanings have been confined to "life as we know
> it" by most biologists and now it looks like Dawkins and Moran are going into
> uncharted territory by trying to define "life in general". We need
> to build, and I'm trying to explain what sorts of unintended applications
> could arise if we are careless about defining our terms.

What careless definition were you instantiating there? You failed to
say. And nobody else has proposed such a definition either. In other
words, you are all bothered about a non-problem.

>>> The only problem is reduced fitness: none of the descendants will have
>>> as many offspring as their parent. But in other respects they have
>>> many advantages over their parent, including many times (sometimes
>>> thousands of times) greater longevity. This longevity is a necessary
>>> (but far from sufficient) condition for planets around these stars
>>> to have life that evolves to produce life forms of staggering complexity.
>>
>> None of that has anything to do with evolution, neutral or otherwise.
>
> Come off it. It has plenty to do with the evolution of the universe,
> almost all of which is non-biological. Once you explain what YOU
> mean by "neutral evolution" I might not be saying things like that.

We're talking here about one meaning of "evolution", specifically
biological evolution or something closely analogous. There are many
other meanings of the word that are irrelevant here. In general, it can
be used to describe any sort of change in anything. But try to focus.

>> Or with reproduction. Or with genetic inheritance.
>
> Once we agree on the distinction between life and non-life, we can,
> if you so wish, restrict this term to living things.

I make no attempt at such a thing.

> Let me give you some easy questions, and then we can go on to tougher ones.
>
> Do you class viruses as life or non-life? How about viroids? prions?

This is a meaningless question. The line between life and non-life is
fuzzy. Viruses have some of the characteristics of life and lack others.
For our purposes, however, viruses could be considered life because they
undergo evolution (in the sense we are, I hope, using it here). I'm not
sure about viroids. Prions don't.

> <snip for focus>
>
>>>> I think he meant to say that adaptive evolution was very important and
>>>> that non-living things don't do it.
>>>
>>> Many offspring of supernovas do adapt to the "need" of longevity which the
>>> parent star conspicuously lacked by being unable to accumulate anywhere
>>> near the mass of the parent.
>>
>> Again, if you destroy all meaning in the word "adapt", you can call
>> anything adaptive.
>
> Not "anything," John, just a few things that have some interesting
> resemblances to adaptation as YOU would define it.

There are no such interesting resemblances.

> So go ahead and define it, already. And make sure it will cover any
> extraterrestrial thing that you would want to classify as life, if
> you saw it.

Adaptation might usefully defined as an increase in fitness, and fitness
as relative expected reproductive success. For this, of course, one
needs a system in which there is reproduction with fairly good
inheritance of characters that vary in fitness.

>>>>>> So adaptive evolution can't be more significant for that reason, though
>>>>>> it might be more significant for other reasons. Hence my question about
>>>>>> the meaning of "significant".
>>>>>
>>>>> I suppose I should just accept your assertions as Truth From the
>>>>> Pantheon, but I remain unconvinced that Dawkins didn't mean what he
>>>>> actually wrote, that adaptive complexity is the main feature
>>>>> distinguishing life from non-life.
>>>
>>> The complexity of the offspring of supernovas is manifestly greater
>>> than that of the parent, in the sense of having far many more and more
>>> varied heavy atoms. The greatest difference came in the first generation
>>> after the big bang: stars having nothing but hydrogen and helium
>>> explosively producing all the elements we see in the universe around us.
>>
>> Yes, by one measure of complexity, second-generation stars are more
>> complex than first-generation stars. But by no stretch of the
>> imagination could this be called either reproduction or adaptive.
>
> By no stretch of the imagination could anyone think you've defined
> "reproduction" or "adaptation" in all your beating around the bush.

Reproduction is the production of fairly good copies of an individual.
For this we need some kind of reasonably stable means to transmit
characteristics. Your stellar example has no such thing. Individual
stars don't reproduce; they merely scatter some of their materials,
which may later be collected along with those of a host of other stars
and non-stars into other stars.

>>>>> I have given my meaning of "significant". If you want "the" meaning,
>>>>> or even "another" meaning, GIYF.
>>>>
>>>> I think your definition was unclear and/or non sequitur. Could you make
>>>> it more explicit? A quality is more significant than another if...?
>>>
>>> Your philosophical naivete staggers me, John. Do you expect anyone
>>> on earth to be able to give a satisfactory finish to your sentence?
>>
>> They'd better if they want to talk about significance.
>
> Then you want a being with superhuman intelligence. But since you are
> an atheist, I think you are out of luck here.

Aren't you an atheist too, functionally?

>>> Oh...wait... are you trying to use the Socratic Method on jillery?
>
> Nevermind. You probably wouldn't recognize the Socratic Method
> if anyone used it on you.

Can we agree that you are so much more clever than anyone else, and know
so much more than anyone else, and have such confidence in your
cleverness that you don't have to make gratuitous digs at others'
understanding?

>>>> To return to your original question, are we agreed that neutral
>>>> evolution doesn't happen to non-life?
>>>
>>> Y'all's subsequent back-and-forth doesn't seem to resolve this question,
>>> nor the next one:
>>>
>>>> If so, isn't your final original
>>>> question reliant on a false premise?
>>
>> Sure. Jillery has departed the conversation and entered into reflexive
>> attack mode.
>
> ...pot...kettle...you expect answers to these questions from her without
> ever having told YOUR definition of "neutral evolution."

I believe my definition of "evolution" was implicit in what I said. But
do you now understand?

[Burkhard]

Personally I think canis maior is at it like a bitch in heat with canis
minor. But then my imagination stretches beyond all known bounds.

[jonathan]

On 5/6/2015 7:07 PM, chris thompson wrote:


>
> As far as cribbed or purchased term papers go, the internet giveth and the internet taketh away:
>
> www.turnitin.com
>
> I tell my students that they must submit term papers electronically to save paper, which is true. It's also true that I can, and do, immediately submit those papers directly to the above service. It also cuts down the number of papers I have to read- unfortunately the plagiarized papers are very often the best papers submitted in any given semester.
>



This is off topic, take a hike idiot and tell em jonny sent ya!




> Chris
>

[jonathan]

On 5/9/2015 2:47 AM, jillery wrote:
> On Fri, 8 May 2015 20:50:58 -0700 (PDT), Peter Nyikos
> <nyi...@bellsouth.net> wrote:
>
>
> ...nothing that has any relevance to this topic.
>

Look who's talking! The only thing I see
coming out of your mouth are insults
and hostility.

[jillery]

On Sat, 09 May 2015 10:51:19 -0400, jonathan <WriteI...@gmail.com>
wrote:

You make a false equivalence. Chris replied to another poster's
comment. You created an off-topic thread. Even you should be able to
recognize the difference.

[jillery]

On Sat, 09 May 2015 11:01:28 -0400, jonathan <WriteI...@gmail.com>
wrote:

>On 5/9/2015 2:47 AM, jillery wrote:
>> On Fri, 8 May 2015 20:50:58 -0700 (PDT), Peter Nyikos
>> <nyi...@bellsouth.net> wrote:
>>
>>
>> ...nothing that has any relevance to this topic.
>>
>
>
>
>Look who's talking! The only thing I see
>coming out of your mouth are insults
>and hostility.

That's because you listen with your eyes closed. Your spam would be
more coherent if you didn't mix your metaphors, and kept your mouth
shut instead.

[Peter Nyikos]

By the way, it's a good one. Would you like for me to tell it,
or would saying "Yes" jeopardize your long-standing canard that I have
no sense of humor?

> I would argue that what words mean -- and what words mean is what people
> have meant by them -- is indeed relevant. Do you really not know what
> "adapting" means? I suspect you do,

I suspect you are just trying to bluff your way out of posting
a definition. See excerpt at the end.

<snip snarky comments by you>

> >>>>>>>>> Once again, we have failed
> >>>>>>>>> to find any alternative to Darwinian selection, as an explanation for
> >>>>>>>>> the feature of life that distinguishes it from non-life, namely
> >>>>>>>>> adaptive complexity.
> >>>>>>>>> ***********************************************

Note that there is NO concession to neutral evolution here; quite
the contrary. And replacing "the" with "an" does nothing to
alleviate the problem.

> >>> ...assuming we have successfully defined "adaptive complexity." But
> >>> I'll point out some possible pitfalls below.
> >>>
> >>> <small snip>
> >>>
> >>>>>>>>> Larry Moran raised a different question in my mind: Can the changes
> >>>>>>>>> to non-life also be reasonably described as neutral evolution, as if
> >>>>>>>>> the changes in life and non-life are related? If so, doesn't that
> >>>>>>>>> make adaptive evolution more significant to the evolution of life,
> >>>>>>>>> since neutral evolution happens to both?
> >>>>>>>>
> >>>>>>>> I would answer "no" and "what does 'significant' mean here?
> >
> > No satisfactory explanation of that "no" appears from you below.
>
> Pretty sure it does, but let me repeat: evolution, whether neutral,
> adaptive, or something else, requires reproduction and some form of
> fairly good inheritance.

The extreme elasticity of "fairly good" makes this comment of little or
no value.

<snip for focus>

> >>>>>> In order to undergo neutral evolution, you need some
> >>>>>> form of genetic inheritance in a population;
> >>>
> >>> I haven't the foggiest [idea] why. Did you eventually agree that
> >>> this, too, was Dawkins's bad?
> >>
> >> Who are you talking to here? That wasn't Dawkins; that was me.
> >
> > There was so much back and forth going on, and the statement seemed
> > so illogical to me in the light of what jillery had said about
> > evolution of stars and mountains earlier, that I got confused.
> >
> > So tell us, what is your definition of neutral evolution? And why
> > does it lead to such a claim? That would, finally, begin to account
> > for your "no" up there.
>
> Evolution is the change of allele frequencies in populations, plus some
> similar processes at higher levels.

That's a huge improvement on the traditional definition, which
gives no hint of the "plus" but it still suffers from vagueness
["similar processes"].

Also relevant: read again the quote from Dawkins and
my comment immediately following its end.

I've snipped the rest of what you wrote, and call your attention to
something I posted less than an hour ago.

__________________excerpt__________

The words "reached its limit" make me wonder whether freon96
might be clinging to outmoded ideas about *Homo sapiens sapiens*
being *biologically* the present-day pinnacle of terrestrial organisms.
This was a fixure of the olden days when some organisms were considered
to be more "advanced" than others, e.g. placentals being
more "advanced" than marsupials, and humans being more "advanced"
than chimps.

Such anthropocentric ideas are being kicked out of biology,
although vestiges of them seem to linger in the extreme reluctance
of two of the most prominent biologists in talk.origins to define
the term "adaptive evolution" on another thread.

Perhaps they fear that when all hints of anthropomorphism are
expunged from it, nothing useful will remain of the distinction
between "adaptive evolution" and "neutral evolution."
================================= end of excerpt from
https://groups.google.com/forum/#!original/talk.origins/bypd3hSHoFk/bs9tz3dUxkgJ
Subject: Re: Biological Evolution Has Reached Its Limit?
Date: Mon, 11 May 2015 06:03:52 -0700 (PDT)
Message-ID: <31ee5012-812f-4e3f...@googlegroups.com>

Peter Nyikos
Professor of Math. -- standard disclaimer--
University of S. Carolina
http://people.math.sc.edu/nyikos/

[Peter Nyikos]

On Saturday, May 9, 2015 at 2:49:15 AM UTC-4, jillery wrote:
> On Fri, 8 May 2015 19:57:26 -0700 (PDT), Peter Nyikos
> <nyi...@bellsouth.net> wrote:
>
> >Jillery seems not to have
> >let go of the idea that neutral evolution can include the evolution
> >of non-living matter.
>
> Since I never grabbed onto that idea, I have no need to let it go.

I was referring to the following statement by you, and my not
having seen a definitive repudiation by you of Dawkins's
[perhaps unintended] implication:

Though I'm not sure he meant it, he also implies that neutral
evolution is a feature of non-life. Perhaps he was thinking of the
the natural progression of change of inanimate objects, like stars or
mountains, which some people call evolutionary.

> More important, your posts in this thread show that you're more
> interested in posting about anything *not* related to the topic.

Incorrect. Did you overlook the following exchange?

_____________excerpt from back-and-forth with Harshman______________

> >> To return to your original question, are we agreed that neutral
> >> evolution doesn't happen to non-life?
> >
> > Y'all's subsequent back-and-forth doesn't seem to resolve this question,
> > nor the next one:
> >
> >> If so, isn't your final original
> >> question reliant on a false premise?
>
> Sure. Jillery has departed the conversation and entered into reflexive
> attack mode.

...pot...kettle...you expect answers to these questions from her without
ever having told YOUR definition of "neutral evolution."

===================== end of excerpt

He was addressing you at the beginning of the excerpt, remember?

Peter Nyikos

[John Harshman]

On 5/11/15, 6:59 AM, Peter Nyikos wrote:
> On Saturday, May 9, 2015 at 8:19:14 AM UTC-4, John Harshman wrote:
>> On 5/8/15, 7:30 PM, Peter Nyikos wrote:
>>> On Friday, May 8, 2015 at 8:19:16 PM UTC-4, John Harshman wrote:
>>>> On 5/8/15, 11:46 AM, Peter Nyikos wrote:
>>>>> On Friday, May 8, 2015 at 7:09:17 AM UTC-4, John Harshman wrote:

>>> [Ever hear the joke about black sheep in Scotland?]
>
> By the way, it's a good one. Would you like for me to tell it,
> or would saying "Yes" jeopardize your long-standing canard that I have
> no sense of humor?

If you desperately need to tell the joke, I can't stop you.

>> I would argue that what words mean -- and what words mean is what people
>> have meant by them -- is indeed relevant. Do you really not know what
>> "adapting" means? I suspect you do,
>
> I suspect you are just trying to bluff your way out of posting
> a definition. See excerpt at the end.

Is my suspicion wrong?

>>>>>>>>>>> Once again, we have failed
>>>>>>>>>>> to find any alternative to Darwinian selection, as an explanation for
>>>>>>>>>>> the feature of life that distinguishes it from non-life, namely
>>>>>>>>>>> adaptive complexity.
>>>>>>>>>>> ***********************************************
>
> Note that there is NO concession to neutral evolution here; quite
> the contrary. And replacing "the" with "an" does nothing to
> alleviate the problem.

What problem, exactly? And if you're talking about "an" in "an
explanation", that isn't the "the" we're talking about. It's "the feature".

>>>>> ...assuming we have successfully defined "adaptive complexity." But
>>>>> I'll point out some possible pitfalls below.
>>>>>
>>>>> <small snip>
>>>>>
>>>>>>>>>>> Larry Moran raised a different question in my mind: Can the changes
>>>>>>>>>>> to non-life also be reasonably described as neutral evolution, as if
>>>>>>>>>>> the changes in life and non-life are related? If so, doesn't that
>>>>>>>>>>> make adaptive evolution more significant to the evolution of life,
>>>>>>>>>>> since neutral evolution happens to both?
>>>>>>>>>>
>>>>>>>>>> I would answer "no" and "what does 'significant' mean here?
>>>
>>> No satisfactory explanation of that "no" appears from you below.
>>
>> Pretty sure it does, but let me repeat: evolution, whether neutral,
>> adaptive, or something else, requires reproduction and some form of
>> fairly good inheritance.
>
> The extreme elasticity of "fairly good" makes this comment of little or
> no value.

I would think there would be at least some value. It's necessary to
weasel because there's a continuum here from zero inheritance to perfect
inheritance. I contend there is some gradual threshold in that continuum
at which evolution begins to become possible. (Epigenetic inheritance,
to pick a current example, is on the wrong side of that line.) Do you
disagree that there is such a continuum and such a fuzzy line?

>>>>>>>> In order to undergo neutral evolution, you need some
>>>>>>>> form of genetic inheritance in a population;
>>>>>
>>>>> I haven't the foggiest [idea] why. Did you eventually agree that
>>>>> this, too, was Dawkins's bad?
>>>>
>>>> Who are you talking to here? That wasn't Dawkins; that was me.
>>>
>>> There was so much back and forth going on, and the statement seemed
>>> so illogical to me in the light of what jillery had said about
>>> evolution of stars and mountains earlier, that I got confused.
>>>
>>> So tell us, what is your definition of neutral evolution? And why
>>> does it lead to such a claim? That would, finally, begin to account
>>> for your "no" up there.
>>
>> Evolution is the change of allele frequencies in populations, plus some
>> similar processes at higher levels.
>
> That's a huge improvement on the traditional definition, which
> gives no hint of the "plus" but it still suffers from vagueness
> ["similar processes"].

Doesn't matter, since we aren't talking about higher levels now anyway.

> Also relevant: read again the quote from Dawkins and
> my comment immediately following its end.

Why? Please make your point explicitly rather than trying to get me to
guess.

> I've snipped the rest of what you wrote, and call your attention to
> something I posted less than an hour ago.

Why? What about that excerpt is relevant here? You're talking nonsense.
And you've deleted the part where I defined adaptive evolution for you
while decrying my supposed reluctance to define adaptive evolution. Note
that the definition has exactly zero to do with anthropomorphism.

I am at a loss to understand why you snipped almost everything I said in
favor of reposting some irrelevant crap.

[Peter Nyikos]

On Saturday, May 9, 2015 at 2:49:15 AM UTC-4, jillery wrote:

> On Fri, 8 May 2015 20:50:58 -0700 (PDT), Peter Nyikos
> <nyi...@bellsouth.net> wrote:
>
>
> ...nothing that has any relevance to this topic.
>
> <mercy snip of rockhead's self-promoting noise>

Come off it. If Harshman and Shrubber had attacked you as vigorously as they
attacked me, I believe you would have responded as vigorously as I did
[even though your style would have been very different from mine].

And rightly so. You did a great job of pegging Harshman in the
following rejoinder:

__________________excerpt_______________________

>
>Your tendency not to try repairing my misunderstanding, just point it
>out, is one of the things that makes it hard to talk to you.

Your habit of not explaining your misunderstanding, and your bald
rejection and denial of my efforts to repair your misunderstanding,
make it hard to talk to you.

===========================end of excerpt

You seem to have also done a good job replying to Harshman's one-liner
in the following excerpt from the same post, where you are the first poster:

_____________________second excerpt___________________

>> A premise is a prelude to a conclusion. I asserted no conclusion. As
>> you pointed out, I asked a question. But I'm not surprised you don't
>> recognize the difference.
>>
>> Are you through picking at imaginary nits yet?
>
>I don't understand why you always get so hostile, so fast.

And I don't understand why you always assume so fast that I'm hostile.
Every time you make that bald assertion, I challenge you to justify
it, but then you either ignore my challenge, or just run away
altogether. From that behavior, I get the impression you reply to me
just so you post that and similar nonsense.

======================== end of second excerpt

Turnabout is fair play. That principle is one I have adhered to ever since I
returned to talk.origins in December 2010.

I haven't made use of that principle in my two replies so far to you today,
and I hope I will not need to use it against you in this thread.

Peter Nyikos

[jillery]

On Mon, 11 May 2015 07:18:20 -0700 (PDT), Peter Nyikos

<nyi...@bellsouth.net> wrote:

>On Saturday, May 9, 2015 at 2:49:15 AM UTC-4, jillery wrote:
>> On Fri, 8 May 2015 19:57:26 -0700 (PDT), Peter Nyikos
>> <nyi...@bellsouth.net> wrote:
>>
>> >Jillery seems not to have
>> >let go of the idea that neutral evolution can include the evolution
>> >of non-living matter.
>>
>> Since I never grabbed onto that idea, I have no need to let it go.
>
>I was referring to the following statement by you, and my not
>having seen a definitive repudiation by you of Dawkins's
>[perhaps unintended] implication:
>
> Though I'm not sure he meant it, he also implies that neutral
> evolution is a feature of non-life. Perhaps he was thinking of the
> the natural progression of change of inanimate objects, like stars or
> mountains, which some people call evolutionary.

What part of "I'm not sure he meant it" don't you understand? As with
many English words, "evolution" has multiple meanings. That Dawkins
appears to conflate two entirely different meaning makes that
implication from his quote even more remarkable. That I remarked on
it in no way implies that I agree with it. To the contrary, I have
posted many times that conflating biologic evolution with the
progression of inanimate processes is a common anti-science tactic,
similar to conflating the verb and noun meanings of "design".

>> More important, your posts in this thread show that you're more
>> interested in posting about anything *not* related to the topic.
>
>Incorrect. Did you overlook the following exchange?


>_____________excerpt from back-and-forth with Harshman______________
>
>> >> To return to your original question, are we agreed that neutral
>> >> evolution doesn't happen to non-life?
>> >
>> > Y'all's subsequent back-and-forth doesn't seem to resolve this question,
>> > nor the next one:
>> >
>> >> If so, isn't your final original
>> >> question reliant on a false premise?
>>
>> Sure. Jillery has departed the conversation and entered into reflexive
>> attack mode.
>
>...pot...kettle...you expect answers to these questions from her without
>ever having told YOUR definition of "neutral evolution."
>
>===================== end of excerpt
>
>He was addressing you at the beginning of the excerpt, remember?

Of course I didn't overlook that inane exchange. In fact, it helps to
affirm my impression that you two, intentionally or not, are both
working to derail this topic. Since I neither expressed nor implied
any basis for assuming that I thought neutral evolution happened to
non-life, Harshman's question is as much irrelevant noise as any
answers to it, as is your assertion that I ever held that idea.

As for Harshman's Parthian shot, that's what he does in almost every
thread with me for the past several years. As long as he continues to
blame for his imagined inferences, I have not hope of completing an
intelligent dialog with him.

This topic could have naturally segued to an interesting comparison of
different meanings of "evolution", but the misrepresentations by you
and Harshman pretty much poisoned the well. Whether or not that was
your intent doesn't really change the result.

[jillery]

On Mon, 11 May 2015 07:40:17 -0700 (PDT), Peter Nyikos

<nyi...@bellsouth.net> wrote:

>On Saturday, May 9, 2015 at 2:49:15 AM UTC-4, jillery wrote:
>> On Fri, 8 May 2015 20:50:58 -0700 (PDT), Peter Nyikos
>> <nyi...@bellsouth.net> wrote:
>>
>>
>> ...nothing that has any relevance to this topic.
>>
>> <mercy snip of rockhead's self-promoting noise>
>
>Come off it.

You come off it. If there is anything relevant to the OP from your
post to which I replied, or your post before that, or your post before
that, it's smothered by your irrelevant, compulsive noise. Those
posts are all about you, and how other posters wronged you, now and
years ago, and how you saved the world from their lies (the last bit
is an exaggeration but only slightly).

>If Harshman and Shrubber had attacked you as vigorously as they
>attacked me, I believe you would have responded as vigorously as I did
>[even though your style would have been very different from mine].

If I had posted in your style, I would have attacked myself for
posting like an idiot.

This is not what I call turnabout. This is what I call stating the
facts. This is what Harshman calls "reflexive attack mode" except
when he does it. This is what Harshman runs away from, while blaming
me for the vapors he succumbs to.

>I haven't made use of that principle in my two replies so far to you today,
>and I hope I will not need to use it against you in this thread.

I stand by what I wrote about Harshman and you, whether you agree or
disagree. You both almost certainly will do what you almost always
have done for years. I am used to unjustified personal attacks and
mind-numbing nonsense from both of you.

[Peter Nyikos]

On Monday, May 11, 2015 at 10:34:07 AM UTC-4, John Harshman wrote:
> On 5/11/15, 6:59 AM, Peter Nyikos wrote:
> > On Saturday, May 9, 2015 at 8:19:14 AM UTC-4, John Harshman wrote:
> >> On 5/8/15, 7:30 PM, Peter Nyikos wrote:
> >>> On Friday, May 8, 2015 at 8:19:16 PM UTC-4, John Harshman wrote:
> >>>> On 5/8/15, 11:46 AM, Peter Nyikos wrote:
> >>>>> On Friday, May 8, 2015 at 7:09:17 AM UTC-4, John Harshman wrote:
>
> >>> [Ever hear the joke about black sheep in Scotland?]
> >
> > By the way, it's a good one. Would you like for me to tell it,
> > or would saying "Yes" jeopardize your long-standing canard that I have
> > no sense of humor?
>
> If you desperately need to tell the joke, I can't stop you.

Pointless, since you have now made it clear that you are determined
to stick by your canard come hell or high water.

> >> I would argue that what words mean -- and what words mean is what people
> >> have meant by them -- is indeed relevant. Do you really not know what
> >> "adapting" means? I suspect you do,
> >
> > I suspect you are just trying to bluff your way out of posting
> > a definition. See excerpt at the end.

Applying my standards, I see that this suspicion was unfounded,
since you did make an attempt to define "adapting" in the part
I snipped. Sorry for overlooking it.

I could have toughed this one out if my conscience had allowed
me to apply YOUR standards. Jillery was not just speaking for
herself when she pegged you as follows:

__________________excerpt_______________________
>
>Your tendency not to try repairing my misunderstanding, just point it
>out, is one of the things that makes it hard to talk to you.

Your habit of not explaining your misunderstanding, and your bald
rejection and denial of my efforts to repair your misunderstanding,
make it hard to talk to you.
===========================end of excerpt

Will you ever reply to the post from which this was
taken? It's the last reply jillery did to you.

Or will you be your usual snarky self and claim that
you don't see anything in her post worth replying to?

> Is my suspicion wrong?

I can't read your mind as to what you meant by "expected
reproductive success" in your attempted definition of adaptation.

Your usual habit in such circumstances, when the roles are
reversed, is to imply that I am not really trying to clarify what I am
saying [see independent description of that behavior in excerpt above]
even while the back and forth between us is still going on.

> >>>>>>>>>>> Once again, we have failed
> >>>>>>>>>>> to find any alternative to Darwinian selection, as an explanation for
> >>>>>>>>>>> the feature of life that distinguishes it from non-life, namely
> >>>>>>>>>>> adaptive complexity.
> >>>>>>>>>>> ***********************************************
> >
> > Note that there is NO concession to neutral evolution here; quite
> > the contrary. And replacing "the" with "an" does nothing to
> > alleviate the problem.
>
> What problem, exactly? And if you're talking about "an" in "an
> explanation", that isn't the "the" we're talking about. It's "the feature".

I meant "the" just as I said, and "the feature" is what I meant, but I was
in a hurry and carelessly wrote "an" instead of "a".

Can you figure out what the problem was now, or do I have to
spoon-feed you?

> >>>>> ...assuming we have successfully defined "adaptive complexity." But
> >>>>> I'll point out some possible pitfalls below.

Do you have a clue as to what Dawkins may have had in mind with
"adaptive complexity"? It sure isn't covered by your attempted
definition of "adaptation".

> >>>>> <small snip>
> >>>>>
> >>>>>>>>>>> Larry Moran raised a different question in my mind: Can the changes
> >>>>>>>>>>> to non-life also be reasonably described as neutral evolution, as if
> >>>>>>>>>>> the changes in life and non-life are related? If so, doesn't that
> >>>>>>>>>>> make adaptive evolution more significant to the evolution of life,
> >>>>>>>>>>> since neutral evolution happens to both?
> >>>>>>>>>>
> >>>>>>>>>> I would answer "no" and "what does 'significant' mean here?
> >>>
> >>> No satisfactory explanation of that "no" appears from you below.
> >>
> >> Pretty sure it does, but let me repeat: evolution, whether neutral,
> >> adaptive, or something else, requires reproduction and some form of
> >> fairly good inheritance.
> >
> > The extreme elasticity of "fairly good" makes this comment of little or
> > no value.
>
> I would think there would be at least some value. It's necessary to
> weasel because there's a continuum here from zero inheritance to perfect
> inheritance. I contend there is some gradual threshold in that continuum
> at which evolution begins to become possible. (Epigenetic inheritance,
> to pick a current example, is on the wrong side of that line.)

Why? is it only because of the conventional wisdom that epigenetic
inheritance fizzles out after a few generations?

>Do you disagree that there is such a continuum and such a fuzzy line?

Dude, that is exactly what my provocative "misuses" of these words
["adapt," "reproduce," etc.] are based on. But I can understand
if your four-and-a-half-year-long agenda to denigrate me makes
it impossible for you to make such simple deductions.

<snip for focus>

> >>> So tell us, what is your definition of neutral evolution? And why
> >>> does it lead to such a claim? That would, finally, begin to account
> >>> for your "no" up there.
> >>
> >> Evolution is the change of allele frequencies in populations, plus some
> >> similar processes at higher levels.
> >
> > That's a huge improvement on the traditional definition, which
> > gives no hint of the "plus" but it still suffers from vagueness
> > ["similar processes"].
>
> Doesn't matter, since we aren't talking about higher levels now anyway.

YOU may not be talking about them, but I am. Without the "plus" part,
the first part of your "definition" of "evolution" is useless for talking
about common descent, unless you regard all life on earth since its
simplest beginnings as one grand population.

> > Also relevant: read again the quote from Dawkins and
> > my comment immediately following its end.
>
> Why? Please make your point explicitly rather than trying to get me to
> guess.

Behold the habit jillery wrote about in the excerpt, sugar-coated with
the word "Please". You made one guess up there, but were too lazy
to cover both possibilities. Cover the other one now.

Concluded in next reply.

Peter Nyikos

[Peter Nyikos]

On Monday, May 11, 2015 at 1:34:08 PM UTC-4, jillery wrote:
> On Mon, 11 May 2015 07:18:20 -0700 (PDT), Peter Nyikos
> <nyi...@bellsouth.net> wrote:
>
> >On Saturday, May 9, 2015 at 2:49:15 AM UTC-4, jillery wrote:
> >> On Fri, 8 May 2015 19:57:26 -0700 (PDT), Peter Nyikos
> >> <nyi...@bellsouth.net> wrote:
> >>
> >> >Jillery seems not to have
> >> >let go of the idea that neutral evolution can include the evolution
> >> >of non-living matter.
> >>
> >> Since I never grabbed onto that idea, I have no need to let it go.
> >
> >I was referring to the following statement by you, and my not
> >having seen a definitive repudiation by you of Dawkins's
> >[perhaps unintended] implication:
> >
> > Though I'm not sure he meant it, he also implies that neutral
> > evolution is a feature of non-life. Perhaps he was thinking of the
> > the natural progression of change of inanimate objects, like stars or
> > mountains, which some people call evolutionary.
>
>
> What part of "I'm not sure he meant it" don't you understand? As with
> many English words, "evolution" has multiple meanings. That Dawkins
> appears to conflate two entirely different meaning makes that
> implication from his quote even more remarkable. That I remarked on
> it in no way implies that I agree with it.

I never tried to claim such an implication. Did my words "let go of"
suggest that to you? All I meant was no explicit repudiation.

> To the contrary, I have
> posted many times that conflating biologic evolution with the
> progression of inanimate processes is a common anti-science tactic,
> similar to conflating the verb and noun meanings of "design".

I was hoping one quote from you would make my point clear,
but I see I have to trot out another:

Larry Moran raised a different question in my mind: Can the changes
to non-life also be reasonably described as neutral evolution, as if
the changes in life and non-life are related? If so, doesn't that
make adaptive evolution more significant to the evolution of life,
since neutral evolution happens to both?

I saw no move to distance yourself from this "different question"
until the post to which I am replying.

>
> >> More important, your posts in this thread show that you're more
> >> interested in posting about anything *not* related to the topic.
> >
> >Incorrect. Did you overlook the following exchange?
>
>
> >_____________excerpt from back-and-forth with Harshman______________
> >
> >> >> To return to your original question, are we agreed that neutral
> >> >> evolution doesn't happen to non-life?
> >> >
> >> > Y'all's subsequent back-and-forth doesn't seem to resolve this question,
> >> > nor the next one:
> >> >
> >> >> If so, isn't your final original
> >> >> question reliant on a false premise?
> >>
> >> Sure. Jillery has departed the conversation and entered into reflexive
> >> attack mode.
> >
> >...pot...kettle...you expect answers to these questions from her without
> >ever having told YOUR definition of "neutral evolution."
> >
> >===================== end of excerpt
> >
> >He was addressing you at the beginning of the excerpt, remember?
>
>
> Of course I didn't overlook that inane exchange. In fact, it helps to
> affirm my impression that you two, intentionally or not, are both
> working to derail this topic.

I plead not guilty. I was trying to get Harshman to see that
HE is derailing it.

> Since I neither expressed nor implied
> any basis for assuming that I thought neutral evolution happened to
> non-life, Harshman's question is as much irrelevant noise as any
> answers to it,

A simple "Yes" by you to the first question, thereby making the second
one superfluous, would not have been irrelevant noise, IMO. Do you
disagree?

<snip>

> As for Harshman's Parthian shot,

Hey! Great allusion!

> that's what he does in almost every
> thread with me for the past several years. As long as he continues to
> blame for his imagined inferences, I have not hope of completing an
> intelligent dialog with him.
>
> This topic could have naturally segued to an interesting comparison of
> different meanings of "evolution",

It's not too late. Try me.

I've snipped the rest of what you wrote. It takes two to tangle, and
I have no desire to tangle with you on this thread. [Harshman and
Shrubber are a different kettle of fish here.]

Peter Nyikos

[Roger Shrubber]

Your comments about neutral versus adaptive evolution are, so far,
embarrassing. I realize you want to "tangle" but little of your
sense of tangling is about evolution. It's more about you continuing
your hall-monitor behavior.

But let's cut through it. Adaption is evolution that occurs by
the mechanism of natural selection. Neutral evolution is change
that occurs independently of the bias of reproductive fitness.

Now there are some logical problems with those definitions if
one want to get overly pedantic but they suffice for didactic
purposes and for most other purposes as well.

The evolution of prebiotic systems can, in theory, be neutral
as well as adaptive. I can imagine cases where neutral prebiotic
evolution is even more important than it is for modern life. But
I don't know how to judge the significance of those things I
imagine to anything that mattered to abiogenesis and so they
are uninteresting.

Finally, that neutral evolution is more significant to the
changes we observe in the genetic makeup of species that have
speciated is an observational fact, provided we measure
significance by counting changes. That appears to be the most
objective metric available.

[Peter Nyikos]

How about you, Shrubber? Do you think jillery's two questions are
worth addressing?

<snip for focus>

> >> This topic could have naturally segued to an interesting comparison of
> >> different meanings of "evolution",
> >
> > It's not too late. Try me.
> >
> > I've snipped the rest of what you wrote. It takes two to tangle, and
> > I have no desire to tangle with you on this thread. [Harshman and
> > Shrubber are a different kettle of fish here.]
>
> Your comments about neutral versus adaptive evolution are, so far,
> embarrassing. I realize you want to "tangle"

You forced the issue, "Roger Shrubber", with your solidarity with
Harshman's agenda-driven remarks about me.

> but little of your
> sense of tangling is about evolution. It's more about you continuing
> your hall-monitor behavior.

Harshman has a near-monopoly on that. I could no more compete with him there
than I could compete with your ability to post canards implying bigotry
by me, and then running away when called on it.

> But let's cut through it. Adaption is evolution that occurs by
> the mechanism of natural selection.

You mean adaptive evolution, not adaptation, which you are leaving
undefined the way set theorists leave the empty set undefined.

> Neutral evolution is change
> that occurs independently of the bias of reproductive fitness.

Can't you use more direct language? What do you mean by "bias"
in this context?

> Now there are some logical problems with those definitions if
> one want to get overly pedantic but they suffice for didactic
> purposes and for most other purposes as well.
>
> The evolution of prebiotic systems can, in theory, be neutral
> as well as adaptive. I can imagine cases where neutral prebiotic
> evolution is even more important than it is for modern life. But
> I don't know how to judge the significance of those things I
> imagine to anything that mattered to abiogenesis and so they
> are uninteresting.
>
> Finally, that neutral evolution is more significant to the
> changes we observe in the genetic makeup of species that have
> speciated is an observational fact, provided we measure
> significance by counting changes. That appears to be the most
> objective metric available.

Well, looks like you've written something jillery just might want
to segue into [see her use of the word above]. I'm very busy today,
so I'll have to wait at least until tomorrow to segue into it.
But then I'll see first whether someone else segues into it in the
meantime.

Peter Nyikos

[John Harshman]

On 5/11/15, 11:43 AM, Peter Nyikos wrote:
> On Monday, May 11, 2015 at 10:34:07 AM UTC-4, John Harshman wrote:
>> On 5/11/15, 6:59 AM, Peter Nyikos wrote:
>>> On Saturday, May 9, 2015 at 8:19:14 AM UTC-4, John Harshman wrote:
>>>> On 5/8/15, 7:30 PM, Peter Nyikos wrote:
>>>>> On Friday, May 8, 2015 at 8:19:16 PM UTC-4, John Harshman wrote:
>>>>>> On 5/8/15, 11:46 AM, Peter Nyikos wrote:
>>>>>>> On Friday, May 8, 2015 at 7:09:17 AM UTC-4, John Harshman wrote:
>>
>>>>> [Ever hear the joke about black sheep in Scotland?]
>>>
>>> By the way, it's a good one. Would you like for me to tell it,
>>> or would saying "Yes" jeopardize your long-standing canard that I have
>>> no sense of humor?
>>
>> If you desperately need to tell the joke, I can't stop you.
>
> Pointless, since you have now made it clear that you are determined
> to stick by your canard come hell or high water.

Do you really want to argue about whether you have a sense of humor?

>>>> I would argue that what words mean -- and what words mean is what people
>>>> have meant by them -- is indeed relevant. Do you really not know what
>>>> "adapting" means? I suspect you do,
>>>
>>> I suspect you are just trying to bluff your way out of posting
>>> a definition. See excerpt at the end.
>
> Applying my standards, I see that this suspicion was unfounded,
> since you did make an attempt to define "adapting" in the part
> I snipped. Sorry for overlooking it.

Apology accepted. Now just let me snip out your pointless dig at my
moral values.

>> Is my suspicion wrong?
>
> I can't read your mind as to what you meant by "expected
> reproductive success" in your attempted definition of adaptation.

Have you ever read any of the literature on natural selection? Do I
really need to define "expected" and "reproductive success"? I will if I
have to, but do you really not know what those words mean in context?

>>>>>>>>>>>>> Once again, we have failed
>>>>>>>>>>>>> to find any alternative to Darwinian selection, as an explanation for
>>>>>>>>>>>>> the feature of life that distinguishes it from non-life, namely
>>>>>>>>>>>>> adaptive complexity.
>>>>>>>>>>>>> ***********************************************
>>>
>>> Note that there is NO concession to neutral evolution here; quite
>>> the contrary. And replacing "the" with "an" does nothing to
>>> alleviate the problem.
>>
>> What problem, exactly? And if you're talking about "an" in "an
>> explanation", that isn't the "the" we're talking about. It's "the feature".
>
> I meant "the" just as I said, and "the feature" is what I meant, but I was
> in a hurry and carelessly wrote "an" instead of "a".
>
> Can you figure out what the problem was now, or do I have to
> spoon-feed you?

Is the problem that you think non-life undergoes Darwinian selection? If
not, then you must spoon-feed.

>>>>>>> ...assuming we have successfully defined "adaptive complexity." But
>>>>>>> I'll point out some possible pitfalls below.
>
> Do you have a clue as to what Dawkins may have had in mind with
> "adaptive complexity"? It sure isn't covered by your attempted
> definition of "adaptation".

Well, of course not. And yellow dogs are not covered by the definition
of "yellow" either. I think I do know what he meant. I presume you do
also. He meant that life has many complex adaptations. Is it necessary
to define "complex" too?

>>>>>>>>>>>>> Larry Moran raised a different question in my mind: Can the changes
>>>>>>>>>>>>> to non-life also be reasonably described as neutral evolution, as if
>>>>>>>>>>>>> the changes in life and non-life are related? If so, doesn't that
>>>>>>>>>>>>> make adaptive evolution more significant to the evolution of life,
>>>>>>>>>>>>> since neutral evolution happens to both?
>>>>>>>>>>>>
>>>>>>>>>>>> I would answer "no" and "what does 'significant' mean here?
>>>>>
>>>>> No satisfactory explanation of that "no" appears from you below.
>>>>
>>>> Pretty sure it does, but let me repeat: evolution, whether neutral,
>>>> adaptive, or something else, requires reproduction and some form of
>>>> fairly good inheritance.
>>>
>>> The extreme elasticity of "fairly good" makes this comment of little or
>>> no value.
>>
>> I would think there would be at least some value. It's necessary to
>> weasel because there's a continuum here from zero inheritance to perfect
>> inheritance. I contend there is some gradual threshold in that continuum
>> at which evolution begins to become possible. (Epigenetic inheritance,
>> to pick a current example, is on the wrong side of that line.)
>
> Why? is it only because of the conventional wisdom that epigenetic
> inheritance fizzles out after a few generations?

Yes. Isn't that enough? Do you disagree with the conventional wisdom?

>> Do you disagree that there is such a continuum and such a fuzzy line?
>
> Dude, that is exactly what my provocative "misuses" of these words
> ["adapt," "reproduce," etc.] are based on. But I can understand
> if your four-and-a-half-year-long agenda to denigrate me makes
> it impossible for you to make such simple deductions.

No, your misuses have nothing to do with the fuzzy line, as they are all
very, very far from any place one could reasonably draw such a line. My
agenda is not to denigrate you. It just happens that you say a lot of
stupid things. While I find your web personality repellant, that's not
what I generally focus on.

>>>>> So tell us, what is your definition of neutral evolution? And why
>>>>> does it lead to such a claim? That would, finally, begin to account
>>>>> for your "no" up there.
>>>>
>>>> Evolution is the change of allele frequencies in populations, plus some
>>>> similar processes at higher levels.
>>>
>>> That's a huge improvement on the traditional definition, which
>>> gives no hint of the "plus" but it still suffers from vagueness
>>> ["similar processes"].
>>
>> Doesn't matter, since we aren't talking about higher levels now anyway.
>
> YOU may not be talking about them, but I am. Without the "plus" part,
> the first part of your "definition" of "evolution" is useless for talking
> about common descent, unless you regard all life on earth since its
> simplest beginnings as one grand population.

That's a non sequitur. Most evolutionary processes occur within
populations. All you need to add to produce common descent is some way
to split one population into two. And one could argue that splitting
generally occurs by within-population processes.

Could you explain yourself in greater detail here?

[chris thompson]

It's sad when someone tries as hard as you do, and still...well.

Chris

[Roger Shrubber]

Are you daft? I did answer them well enough below. And rather than
parse what I wrote you attempt to tell me I meant something different
than what I wrote.

> <snip for focus>
>
>>>> This topic could have naturally segued to an interesting comparison of
>>>> different meanings of "evolution",
>>>
>>> It's not too late. Try me.
>>>
>>> I've snipped the rest of what you wrote. It takes two to tangle, and
>>> I have no desire to tangle with you on this thread. [Harshman and
>>> Shrubber are a different kettle of fish here.]
>>
>> Your comments about neutral versus adaptive evolution are, so far,
>> embarrassing. I realize you want to "tangle"
>
> You forced the issue, "Roger Shrubber", with your solidarity with
> Harshman's agenda-driven remarks about me.

Only in your imagination.

>> but little of your
>> sense of tangling is about evolution. It's more about you continuing
>> your hall-monitor behavior.
>
> Harshman has a near-monopoly on that. I could no more compete with him there
> than I could compete with your ability to post canards implying bigotry
> by me, and then running away when called on it.

Buy a mirror.

>> But let's cut through it. Adaption is evolution that occurs by
>> the mechanism of natural selection.
>
> You mean adaptive evolution, not adaptation, which you are leaving
> undefined the way set theorists leave the empty set undefined.

Are you really this stupid?
When the frequency of alleles is changing due to the bias of
selective advantages to those alleles, that's adaption in action.
Adaption and adaptive evolution are synonymous. Are you completely
new to discussions of evolution? Dawkins and his adaptionist ways,
as opposed to Gould, is an oft discussed issue.

>> Neutral evolution is change
>> that occurs independently of the bias of reproductive fitness.
>
> Can't you use more direct language? What do you mean by "bias"
> in this context?

Are you attempting to misunderstand? Selection. That's the bias
I refer to. As opposed to neutral evolution where the changes
occur due to just chance.

Read some Dawkins. Read some Gould. Or maybe take an "Introduction
to Biology" course. They cover often basic terminology, at least
for students who are willing to learn.

>> Now there are some logical problems with those definitions if
>> one want to get overly pedantic but they suffice for didactic
>> purposes and for most other purposes as well.
>>
>> The evolution of prebiotic systems can, in theory, be neutral
>> as well as adaptive. I can imagine cases where neutral prebiotic
>> evolution is even more important than it is for modern life. But
>> I don't know how to judge the significance of those things I
>> imagine to anything that mattered to abiogenesis and so they
>> are uninteresting.
>>
>> Finally, that neutral evolution is more significant to the
>> changes we observe in the genetic makeup of species that have
>> speciated is an observational fact, provided we measure
>> significance by counting changes. That appears to be the most
>> objective metric available.
>
> Well, looks like you've written something jillery just might want
> to segue into [see her use of the word above]. I'm very busy today,
> so I'll have to wait at least until tomorrow to segue into it.
> But then I'll see first whether someone else segues into it in the
> meantime.

See, you are more worried about what people will do than the issues
at hand.

[jillery]

On Mon, 11 May 2015 12:08:28 -0700 (PDT), Peter Nyikos

That may be what you meant, but why do you expect me to repudiate
something, explicitly or otherwise, I never advocated?

>> To the contrary, I have
>> posted many times that conflating biologic evolution with the
>> progression of inanimate processes is a common anti-science tactic,
>> similar to conflating the verb and noun meanings of "design".
>
>I was hoping one quote from you would make my point clear,
>but I see I have to trot out another:
>
> Larry Moran raised a different question in my mind: Can the changes
> to non-life also be reasonably described as neutral evolution, as if
> the changes in life and non-life are related? If so, doesn't that
> make adaptive evolution more significant to the evolution of life,
> since neutral evolution happens to both?
>
>I saw no move to distance yourself from this "different question"
>until the post to which I am replying.

Yes, that's my question. I see no reason to distance myself from it.
Why do you think I should? How do you think I have?

What I distanced myself from is Harshman's incorrect interpretation of
my question. Your statement above makes sense only if you agree with
Harshman's strawman. In that case, you nullify your pleas of
innocence.

>> >> More important, your posts in this thread show that you're more
>> >> interested in posting about anything *not* related to the topic.
>> >
>> >Incorrect. Did you overlook the following exchange?
>>
>>
>> >_____________excerpt from back-and-forth with Harshman______________
>> >
>> >> >> To return to your original question, are we agreed that neutral
>> >> >> evolution doesn't happen to non-life?
>> >> >
>> >> > Y'all's subsequent back-and-forth doesn't seem to resolve this question,
>> >> > nor the next one:
>> >> >
>> >> >> If so, isn't your final original
>> >> >> question reliant on a false premise?
>> >>
>> >> Sure. Jillery has departed the conversation and entered into reflexive
>> >> attack mode.
>> >
>> >...pot...kettle...you expect answers to these questions from her without
>> >ever having told YOUR definition of "neutral evolution."
>> >
>> >===================== end of excerpt
>> >
>> >He was addressing you at the beginning of the excerpt, remember?
>>
>>
>> Of course I didn't overlook that inane exchange. In fact, it helps to
>> affirm my impression that you two, intentionally or not, are both
>> working to derail this topic.
>
>I plead not guilty. I was trying to get Harshman to see that
>HE is derailing it.

If so, your methods were too subtle. You have never been one to shy
away from a direct approach. You'll confuse everybody if you start
now.

>> Since I neither expressed nor implied
>> any basis for assuming that I thought neutral evolution happened to
>> non-life, Harshman's question is as much irrelevant noise as any
>> answers to it,
>
>A simple "Yes" by you to the first question, thereby making the second
>one superfluous, would not have been irrelevant noise, IMO. Do you
>disagree?

It's unclear what questions you're referring to, or even what you're
asking, but Harshman almost never accepts a simple "yes" or "no" from
me.

><snip>
>
>> As for Harshman's Parthian shot,
>
>Hey! Great allusion!

Bob Casanova provides lots of them, royalty free.

>> that's what he does in almost every
>> thread with me for the past several years. As long as he continues to
>> blame for his imagined inferences, I have not hope of completing an
>> intelligent dialog with him.
>>
>> This topic could have naturally segued to an interesting comparison of
>> different meanings of "evolution",
>
>It's not too late. Try me.

No problem. Just post something that doesn't include irrelevant
references to other posters and other topics. Try some
self-discipline, if only as a refreshing change of pace.

>I've snipped the rest of what you wrote. It takes two to tangle,

The standard phrase is Tango, as in the dance, usually performed by
two people as a couple, hence the witticism. Unfortunately, in almost
all of Harshman's replies to me, it simply doesn't matter what I post,
which suggests that a better metaphor would be a more common but
solitary activity.

>and
>I have no desire to tangle with you on this thread. [Harshman and
>Shrubber are a different kettle of fish here.]

If you don't want to tangle, or even Tango, with me on this thread, or
any other thread, stop injecting my nym into your replies to other
posters, and stop snipping my replies to your comments.

[Peter Nyikos]

On Monday, May 11, 2015 at 10:34:07 AM UTC-4, John Harshman wrote:
> On 5/11/15, 6:59 AM, Peter Nyikos wrote:

Picking up where I left off yesterday:

> > I've snipped the rest of what you wrote, and call your attention to
> > something I posted less than an hour ago.
>
> Why? What about that excerpt is relevant here? You're talking nonsense.
> And you've deleted the part where I defined adaptive evolution for you

...while leaving an anthropocentric-sounding "expected" in your
attempted definition:

Adaptation might usefully defined as an increase in fitness,
and fitness as relative expected reproductive success.

Try harder next time.

By the way, I'm sure you realize that you did not define "adaptation" per se,
but only "adaptive evolution." Your definition says nothing whatsoever about
whether an individual is well or poorly adapted to the environment it happens
to find itself in at a given moment. I learned more about THAT at the age of
seven from a picture in _Life_ magazine's "The Pageant of Life" than I could
ever learn from anything I've seen from you or Shrubber on the topic.

> while decrying my supposed reluctance to define adaptive evolution. Note
> that the definition has exactly zero to do with anthropomorphism.

anthropomorphism vs. anthropocentrism...I don't think there's enough
difference to be worth quibbling about. Do you?

> I am at a loss to understand why you snipped almost everything I said in
> favor of reposting some irrelevant crap.

There you go again, counting your chickens before they are hatched
("irrelevant crap") by failing to put yourself in the shoes of
the person you are debating with. If you only had thought about how
many times you either pretended not to understand what I was writing,
or actually did not understand it, you might not have gone off
half-cocked like you did just now.

> > __________________excerpt__________
> >
> > The words "reached its limit" make me wonder whether freon96
> > might be clinging to outmoded ideas about *Homo sapiens sapiens*
> > being *biologically* the present-day pinnacle of terrestrial organisms.
> > This was a fixure of the olden days when some organisms were considered
> > to be more "advanced" than others, e.g. placentals being
> > more "advanced" than marsupials, and humans being more "advanced"
> > than chimps.
> >
> > Such anthropocentric ideas are being kicked out of biology,
> > although vestiges of them seem to linger in the extreme reluctance
> > of two of the most prominent biologists in talk.origins to define
> > the term "adaptive evolution" on another thread.
> >
> > Perhaps they fear that when all hints of anthropomorphism are
> > expunged from it, nothing useful will remain of the distinction
> > between "adaptive evolution" and "neutral evolution."
> > ================================= end of excerpt from
> > https://groups.google.com/forum/#!original/talk.origins/bypd3hSHoFk/bs9tz3dUxkgJ
> > Subject: Re: Biological Evolution Has Reached Its Limit?
> > Date: Mon, 11 May 2015 06:03:52 -0700 (PDT)
> > Message-ID: <31ee5012-812f-4e3f...@googlegroups.com>
> >
> > Peter Nyikos
> > Professor of Math. -- standard disclaimer--
> > University of S. Carolina
> > http://people.math.sc.edu/nyikos/

Well, at least you didn't delete what you snarkily called "crap".

Peter Nyikos

[John Harshman]

On 5/12/15, 7:11 AM, Peter Nyikos wrote:
> On Monday, May 11, 2015 at 10:34:07 AM UTC-4, John Harshman wrote:
>> On 5/11/15, 6:59 AM, Peter Nyikos wrote:
>
> Picking up where I left off yesterday:
>
>>> I've snipped the rest of what you wrote, and call your attention to
>>> something I posted less than an hour ago.
>>
>> Why? What about that excerpt is relevant here? You're talking nonsense.
>> And you've deleted the part where I defined adaptive evolution for you
>
> ...while leaving an anthropocentric-sounding "expected" in your
> attempted definition:
>
> Adaptation might usefully defined as an increase in fitness,
> and fitness as relative expected reproductive success.
>
> Try harder next time.

How is it possible for a mathematician not to know what "expected" means
here, or am I confusing you with a statistician? By "expected" I refer
to the result we would see if averaged over a great number of trials,
each of them with potentially confounding stochastic variation.

> By the way, I'm sure you realize that you did not define "adaptation" per se,
> but only "adaptive evolution." Your definition says nothing whatsoever about
> whether an individual is well or poorly adapted to the environment it happens
> to find itself in at a given moment. I learned more about THAT at the age of
> seven from a picture in _Life_ magazine's "The Pageant of Life" than I could
> ever learn from anything I've seen from you or Shrubber on the topic.

I confess to wondering what that picture could possibly have been.

An adaptation is whatever results in increased expected reproductive
success. (Again, "expected" is merely there to account for stochastic
variation in actual results.) How else would you determine goodness or
poorness of adaptation?

>> while decrying my supposed reluctance to define adaptive evolution. Note
>> that the definition has exactly zero to do with anthropomorphism.
>
> anthropomorphism vs. anthropocentrism...I don't think there's enough
> difference to be worth quibbling about. Do you?

Doesn't matter, as both are irrelevant here.

>> I am at a loss to understand why you snipped almost everything I said in
>> favor of reposting some irrelevant crap.
>
> There you go again, counting your chickens before they are hatched
> ("irrelevant crap") by failing to put yourself in the shoes of
> the person you are debating with. If you only had thought about how
> many times you either pretended not to understand what I was writing,
> or actually did not understand it, you might not have gone off
> half-cocked like you did just now.

Does that mean you're about to explain yourself? Goodie. Oh, it appears
that you are not. Dang.

It's still crap, though. Nothing you say there has anything to do with
what I said. Have you ever taken a course in statistics? Do you know
what "expectation" means there?

[Peter Nyikos]

On Monday, May 11, 2015 at 11:54:05 PM UTC-4, Roger Shrubber wrote:
> Peter Nyikos wrote:
> > On Monday, May 11, 2015 at 3:44:07 PM UTC-4, Roger Shrubber wrote:
> >> Peter Nyikos wrote:
> >>> On Monday, May 11, 2015 at 1:34:08 PM UTC-4, jillery wrote:
> >>>> On Mon, 11 May 2015 07:18:20 -0700 (PDT), Peter Nyikos
> >>>> <nyi...@bellsouth.net> wrote:
> >>>>
> >>>>> On Saturday, May 9, 2015 at 2:49:15 AM UTC-4, jillery wrote:
> >>>>>> On Fri, 8 May 2015 19:57:26 -0700 (PDT), Peter Nyikos
> >>>>>> <nyi...@bellsouth.net> wrote:
> >>>>>>
> >>>>>>> Jillery seems not to have
> >>>>>>> let go of the idea that neutral evolution can include the evolution
> >>>>>>> of non-living matter.
> >>>>>>
> >>>>>> Since I never grabbed onto that idea, I have no need to let it go.
> >>>>>
> >>>>> I was referring to the following statement by you, and my not
> >>>>> having seen a definitive repudiation by you of Dawkins's
> >>>>> [perhaps unintended] implication:
> >>>>>
> >>>>> Though I'm not sure he meant it, he also implies that neutral
> >>>>> evolution is a feature of non-life. Perhaps he was thinking of the
> >>>>> the natural progression of change of inanimate objects, like stars or
> >>>>> mountains, which some people call evolutionary.

<snip for focus>

> >>> Larry Moran raised a different question in my mind: Can the changes
> >>> to non-life also be reasonably described as neutral evolution, as if
> >>> the changes in life and non-life are related? If so, doesn't that
> >>> make adaptive evolution more significant to the evolution of life,
> >>> since neutral evolution happens to both?
> >>>
> >>> I saw no move to distance yourself from this "different question"
> >>> until the post to which I am replying.
> >
> > How about you, Shrubber? Do you think jillery's two questions are
> > worth addressing?
>
> Are you daft? I did answer them well enough below.

Your naked opinion "well enough" is noted.

> And rather than
> parse what I wrote you attempt to tell me I meant something different
> than what I wrote.

Where?

> > <snip for focus>
> >
> >>>> This topic could have naturally segued to an interesting comparison of
> >>>> different meanings of "evolution",
> >>>
> >>> It's not too late. Try me.
> >>>
> >>> I've snipped the rest of what you wrote. It takes two to tangle, and
> >>> I have no desire to tangle with you on this thread. [Harshman and
> >>> Shrubber are a different kettle of fish here.]
> >>
> >> Your comments about neutral versus adaptive evolution are, so far,
> >> embarrassing. I realize you want to "tangle"
> >
> > You forced the issue, "Roger Shrubber", with your solidarity with
> > Harshman's agenda-driven remarks about me.
>
> Only in your imagination.

His questioning my sanity has been part of an agenda of denigration
that he began with an utterly baseless "opinion" about me within a
month after I resumed posting in December 2010, and has been indulged
in numerous times since. You fed enthusiastically into his questioning.
Do you deny any of this?

> >> but little of your
> >> sense of tangling is about evolution. It's more about you continuing
> >> your hall-monitor behavior.
> >
> > Harshman has a near-monopoly on that. I could no more compete with him there
> > than I could compete with your ability to post canards implying bigotry
> > by me, and then running away when called on it.
>
> Buy a mirror.

People have been showing me the backs of what they imply to be mirrors
since 1992, but when I ask them to show me the front, they invariably
fail to do so. You've taken the first step, and now I'm calling your
bluff: show me the business side of the "mirror" of which you speak.

Contrast that behavior with the NUMEROUS times I have held up
the business side of a mirror to Harshman, and he behaved exactly
as I described in the post where I replied to your feed-in to his
despicable post.

You'll never have the guts to reply to THAT post of mine in detail, will you?
I challenged you to reply to at least one of a pair of posts on
"Unanswered challenges by Casanova of Martinez in re immutabilism vs. the horse family tree"
and those were even less difficult for you to reply to.

Concluded in next reply, which will be solidly on topic.

Peter Nyikos

[Peter Nyikos]

On Monday, May 11, 2015 at 11:54:05 PM UTC-4, Roger Shrubber wrote:
> Peter Nyikos wrote:
> > On Monday, May 11, 2015 at 3:44:07 PM UTC-4, Roger Shrubber wrote:

Picking up where I left off in the first reply:

> >> But let's cut through it. Adaption is evolution that occurs by
> >> the mechanism of natural selection.
> >
> > You mean adaptive evolution, not adaptation, which you are leaving
> > undefined the way set theorists leave the empty set undefined.
>
> Are you really this stupid?

I'm "stupid" enough to be able to say the following to Harshman about
an hour ago:

"By the way, I'm sure you realize that you did not define "adaptation" per se,
but only "adaptive evolution." Your definition says nothing whatsoever about
whether an individual is well or poorly adapted to the environment it happens
to find itself in at a given moment. I learned more about THAT at the age of
seven from a picture in _Life_ magazine's "The Pageant of Life" than I could
ever learn from anything I've seen from you or Shrubber on the topic."

> When the frequency of alleles is changing due to the bias of
> selective advantages to those alleles, that's adaption in action.

You do a great job of talking around "adaptation". The caption to that
picture in "The Pageant of Life" did a great job of giving people a
feel for the concept.

> Adaption and adaptive evolution are synonymous. Are you completely
> new to discussions of evolution? Dawkins and his adaptionist ways,
> as opposed to Gould, is an oft discussed issue.

Thanks for confirming that evolutionary theory has become too pragmatic
to discuss the concept which laymen associate with the term.

A jackass whose herd has been wiped out but for him, coming onto a
herd of horses consisting temporarily of mares, is superbly adapted
to having first-generation offspring. But he does nothing in the
long run for the adaptive evolution of his kind.

By the way, the above paragraph actually meets both concepts
(the evolutionary-theoretic and the layman's halfway) then
talks only about the former, which is much easier to talk
about than the latter because it is so one-dimensional.

> >> Neutral evolution is change
> >> that occurs independently of the bias of reproductive fitness.
> >
> > Can't you use more direct language? What do you mean by "bias"
> > in this context?
>
> Are you attempting to misunderstand? Selection. That's the bias
> I refer to. As opposed to neutral evolution where the changes
> occur due to just chance.

"just chance" is a slippery concept. Genetic drift seems to
cover it, but then the reproductive fitness of the population
that changes by chance may be no greater than that of
a population that changed due to selection.

Otherwise, most evolution could not be neutral, eh?

> Read some Dawkins. Read some Gould. Or maybe take an "Introduction
> to Biology" course. They cover often basic terminology, at least
> for students who are willing to learn.

I've read all of the above, but when words like "bias" are used
in isolation from the context, and it's been years since I last
read them, I have to wonder just what is being talked about.

> >> Now there are some logical problems with those definitions if
> >> one want to get overly pedantic but they suffice for didactic
> >> purposes and for most other purposes as well.
> >>
> >> The evolution of prebiotic systems can, in theory, be neutral
> >> as well as adaptive. I can imagine cases where neutral prebiotic
> >> evolution is even more important than it is for modern life. But
> >> I don't know how to judge the significance of those things I
> >> imagine to anything that mattered to abiogenesis and so they
> >> are uninteresting.
> >>
> >> Finally, that neutral evolution is more significant to the
> >> changes we observe in the genetic makeup of species that have
> >> speciated is an observational fact, provided we measure
> >> significance by counting changes. That appears to be the most
> >> objective metric available.
> >
> > Well, looks like you've written something jillery just might want
> > to segue into [see her use of the word above]. I'm very busy today,
> > so I'll have to wait at least until tomorrow to segue into it.
> > But then I'll see first whether someone else segues into it in the
> > meantime.
>
> See, you are more worried about what people will do than the issues
> at hand.

I like for discussions to be fruitful. Whenever discussion degenerates
to a bunch of one-on-one interactions, with people in one interaction
ignoring everything being said in the other interactions, then the words "dysfunctional" and "miasma" come to my mind.

Evidently you are of the opposite opinion, just like Harshman.

Peter Nyikos
Professor of Mathematics
people.math.sc.edu/nyikos

[Roger Shrubber]

And you delete it. Precious.

O wad some Pow'r the giftie gie us, To see oursels as ithers see us!
Here's your mirror.

Once upon a time in the land of talk.origins there was no Santa Claus.
Boys and girls chased feral chickens through flux tubes whilst
professors swilled beer at the Panda's Thumb. It was a golden age, a
time of innocence, a time before Santa Claus.

And then one day, riding his sleigh with eight tiny topological papers,
the Bad Santa Claus rode into town. He pulled up into the center of town
and announced, "You people are in a bad way! I have just come from
cleaning up talk.abortion, which was a real sewer, and now I'm going to
clean up things here."

People looked at each, shook their heads, and said "Who is this guy,
anyway." A spy was sent over to talk.abortion to ask about Santa Claus
but he didn't learn much. "They wouldn't talk to me," he said, "but they
just giggled a lot when I mentioned Santa Claus."

Then Santa said, "I'm making a list of who's naughty and who's nice.
Don't think you can fool me - I know your type." Then he proceeded to
tell everybody that the Cheese Kid, aka the Dean, was a crypto
abortionist because the Kid said something that sounded like something
said by somebody else long ago and far away and Santa never forgets.

And then Santa made lists. And he published them. And he made more
lists. And he published them. And he told the world who was naughty and
who was nice. Only the funny thing is, there wasn't anybody on the nice
list. And Santa said, "You children have been bad, bad, bad." And he
gave them all coal for Christmas, except that the coal was brown and
squishy and didn't smell too good.

The town folk didn't think much of these doings and they started to jump
and shout and make all kinds of outlandish noise. The Bad Santa didn't
mind that at'all - it was just to his liking. People were coming around
to his way of doing things.

The folks that started arguing with Santa started turning into elves.
Not nice elves, mind you, but Santa type elves. There was the Chocolate
Kid, and the Paul brothers, and the Irishman, and Big John and I don't
know who all. Even the Pastor got into the act. Santa would start a fire
and pretty soon the flames would be rising high. Then the elves would
dance around the fire and they would throw stuff into the fire too, and
the flames would burn even higher.

All the little boys and girls stood back and watched Santa and his evil
elves dance around the fire and they looked at each other and said,
"Whatever happened to the feral chickens."
http://richardhartersworld.com/cri/1998/elves.html

Now if you'll excuse me, I have to get my ears trimmed.

[Roger Shrubber]

Peter Nyikos wrote:
> On Monday, May 11, 2015 at 11:54:05 PM UTC-4, Roger Shrubber wrote:
>> Peter Nyikos wrote:
>>> On Monday, May 11, 2015 at 3:44:07 PM UTC-4, Roger Shrubber wrote:
>
> Picking up where I left off in the first reply:
>
>>>> But let's cut through it. Adaption is evolution that occurs by
>>>> the mechanism of natural selection.
>>>
>>> You mean adaptive evolution, not adaptation, which you are leaving
>>> undefined the way set theorists leave the empty set undefined.
>>
>> Are you really this stupid?
>
> I'm "stupid" enough to be able to say the following to Harshman about
> an hour ago:
>
> "By the way, I'm sure you realize that you did not define "adaptation" per se,
> but only "adaptive evolution." Your definition says nothing whatsoever about
> whether an individual is well or poorly adapted to the environment it happens
> to find itself in at a given moment. I learned more about THAT at the age of
> seven from a picture in _Life_ magazine's "The Pageant of Life" than I could
> ever learn from anything I've seen from you or Shrubber on the topic."

You may not like what the word means in biology, but it retains that
meaning. There's a context and it's relative fitness. There is no
absolute fitness. There is no absolute sense of adapted. You want it
to be different but that's your peculiar problem.

As for your confessed learning disability, it explains much. But it's
really just your ego in the way.

>> When the frequency of alleles is changing due to the bias of
>> selective advantages to those alleles, that's adaption in action.
>
> You do a great job of talking around "adaptation". The caption to that
> picture in "The Pageant of Life" did a great job of giving people a
> feel for the concept.

You like these private conversations you have with yourself. I imagine
you'll repost them a few more times for your reading pleasure.

>> Adaption and adaptive evolution are synonymous. Are you completely
>> new to discussions of evolution? Dawkins and his adaptionist ways,
>> as opposed to Gould, is an oft discussed issue.
>
> Thanks for confirming that evolutionary theory has become too pragmatic
> to discuss the concept which laymen associate with the term.
>
> A jackass whose herd has been wiped out but for him, coming onto a
> herd of horses consisting temporarily of mares, is superbly adapted
> to having first-generation offspring. But he does nothing in the
> long run for the adaptive evolution of his kind.
>
> By the way, the above paragraph actually meets both concepts
> (the evolutionary-theoretic and the layman's halfway) then
> talks only about the former, which is much easier to talk
> about than the latter because it is so one-dimensional.

Your skill at producing misconceptions is truly impressive to you.

>>>> Neutral evolution is change
>>>> that occurs independently of the bias of reproductive fitness.
>>>
>>> Can't you use more direct language? What do you mean by "bias"
>>> in this context?
>>
>> Are you attempting to misunderstand? Selection. That's the bias
>> I refer to. As opposed to neutral evolution where the changes
>> occur due to just chance.
>
> "just chance" is a slippery concept. Genetic drift seems to
> cover it, but then the reproductive fitness of the population
> that changes by chance may be no greater than that of
> a population that changed due to selection.
>
> Otherwise, most evolution could not be neutral, eh?

You seem to be laboring with this misconception about
absolute fitness. Maybe you learned it that way when you
were seven. It's time to grow up and toss it aside.

>> Read some Dawkins. Read some Gould. Or maybe take an "Introduction
>> to Biology" course. They cover often basic terminology, at least
>> for students who are willing to learn.
>
> I've read all of the above, but when words like "bias" are used
> in isolation from the context, and it's been years since I last
> read them, I have to wonder just what is being talked about.

The context is evolution and adaption. That's enough context
for anyone who isn't just trying to be difficult and thinks
with some awareness of population genetics.

I care somewhat about what John thinks about evolutionary biology.
I don't care what he thinks about you. Oh, and about that mirror.

[John Harshman]

Some sort of group selection, manifest destiny sort of thing?

>>>>> Neutral evolution is change
>>>>> that occurs independently of the bias of reproductive fitness.
>>>>
>>>> Can't you use more direct language? What do you mean by "bias"
>>>> in this context?
>>>
>>> Are you attempting to misunderstand? Selection. That's the bias
>>> I refer to. As opposed to neutral evolution where the changes
>>> occur due to just chance.
>>
>> "just chance" is a slippery concept. Genetic drift seems to
>> cover it, but then the reproductive fitness of the population
>> that changes by chance may be no greater than that of
>> a population that changed due to selection.
>>
>> Otherwise, most evolution could not be neutral, eh?
>
> You seem to be laboring with this misconception about
> absolute fitness. Maybe you learned it that way when you
> were seven. It's time to grow up and toss it aside.

I'm not sure that's his misconception. But perhaps a bit more
explanation would help him. I will throw some words.

There is sometimes a distinction made between expected fitness, an
abstract property correlated with genotype, and realized fitness, the
actual reproductive success of a real organism. In Peter's example, the
jackass actually has zero realized fitness, since his offspring will be
sterile. Let's change him to a horse to make the example more
interesting; then he has high realized fitness, but his expected
fitness, based on his genotype, may not be different from the average.
He has achieved high reproductive success because of an environmental
feature (lucking upon a herd of mares) that isn't correlated with
genotype, all of which we habitually label as "chance". Any one
individual, exemplar of a genotype, may have realized fitness much less
or much more than his expected fitness because of "chance" factors. We
can't predict the outcome of any particular individual's reproduction.
Only in the mass can we predict the average reproductive success of a
genotype. When two genotypes have equal expected success, changes in
their relative frequencies are said to be neutral.

Given the various "chance" factors involved, the realized fitnesses of
individuals of various genotypes may not correspond to the expected
fitnesses of their genotypes. Many individuals of lower expected fitness
will have greater reproductive success than many individuals of higher
expected fitness. You can consider realized fitness as a random variable
with a distribution around the expected fitness, if that helps.

Peter, did that help? This is all standard biology, not my invention.

[Peter Nyikos]

On Tuesday, May 12, 2015 at 11:59:04 AM UTC-4, Roger Shrubber wrote:
> Peter Nyikos wrote:
> > On Monday, May 11, 2015 at 11:54:05 PM UTC-4, Roger Shrubber wrote:
> >> Peter Nyikos wrote:

> >>> How about you, Shrubber? Do you think jillery's two questions
> >>> are worth addressing?
> >>
> >> Are you daft? I did answer them well enough below.
> >
> > Your naked opinion "well enough" is noted.
> >
> >> And rather than parse what I wrote you attempt to tell me I meant
> >> something different than what I wrote.
> >
> > Where?
>
> And you delete it. Precious.

It appeared in my second reply, fat lot of good that did you.

> >>> <snip for focus>
> >>>
> >>>>>> This topic could have naturally segued to an interesting
> >>>>>> comparison of different meanings of "evolution",
> >>>>>
> >>>>> It's not too late. Try me.
> >>>>>
> >>>>> I've snipped the rest of what you wrote. It takes two to
> >>>>> tangle, and I have no desire to tangle with you on this
> >>>>> thread. [Harshman and Shrubber are a different kettle of fish
> >>>>> here.]
> >>>>
> >>>> Your comments about neutral versus adaptive evolution are, so
> >>>> far, embarrassing. I realize you want to "tangle"
> >>>
> >>> You forced the issue, "Roger Shrubber", with your solidarity
> >>> with Harshman's agenda-driven remarks about me.
> >>
> >> Only in your imagination.
> >
> > His questioning my sanity has been part of an agenda of
> > denigration that he began with an utterly baseless "opinion" about me
> > within a month after I resumed posting in December 2010, and has been
> > indulged in numerous times since. You fed enthusiastically into his
> > questioning. Do you deny any of this?

Of course, you did not. Your jillery-style comeback was all bluff.

> >>>> but little of your sense of tangling is about evolution. It's
> >>>> more about you continuing your hall-monitor behavior.
> >>>
> >>> Harshman has a near-monopoly on that. I could no more compete
> >>> with him there than I could compete with your ability to post
> >>> canards implying bigotry by me, and then running away when called
> >>> on it.
> >>
> >> Buy a mirror.
> >
> > People have been showing me the backs of what they imply to be
> > mirrors since 1992, but when I ask them to show me the front, they
> > invariably fail to do so. You've taken the first step, and now I'm
> > calling your bluff: show me the business side of the "mirror" of
> > which you speak.
>
> O wad some Pow'r the giftie gie us, To see oursels as ithers see us!

The "ithers" in this newsgroup are anywhere from zero to about half a dozen,
depending on how sincere they are about what they claim to see.
I'm referring to the ones who think about me the way you claim to.

> Here's your mirror.

Like the most warped of funhouse mirrors. If this is the best you
can do, the words "Physician, heal thyself!" come to mind.

> Once upon a time in the land of talk.origins there was no Santa Claus.

But there was a mother in whose whose mouth Roger Shrubber put some inane
comments, thereby demonstrating his lack of imagination.

To humor the talentless Shrubber, I treated this fictional mother like
royalty. The result was a comeback that Shrubber has not only
been afraid to talk about to this day, he can't seem to use its
style to cultivate a more subtle and intelligent form of humor.

And so, he just regurgitates something the late Richard Harter
composed, and which perfectly illustrates the contempt Shrubber has for
those who hunger and thirst for justice.

I don't know enough about Harter to tell whether he shared this contempt
of Shrubber's. But Harshman is one who does. Both remind me of the
words of C.S. Lewis:

We laugh at honour and are shocked to find traitors in our midst.
--in: _The Abolition of Man_, end of first chapter.

Peter Nyikos

[Peter Nyikos]

On Tuesday, May 12, 2015 at 12:14:03 PM UTC-4, Roger Shrubber wrote:
> Peter Nyikos wrote:
> > On Monday, May 11, 2015 at 11:54:05 PM UTC-4, Roger Shrubber wrote:
> >> Peter Nyikos wrote:
> >>> On Monday, May 11, 2015 at 3:44:07 PM UTC-4, Roger Shrubber wrote:
> >
> > Picking up where I left off in the first reply:
> >
> >>>> But let's cut through it. Adaption is evolution that occurs by
> >>>> the mechanism of natural selection.
> >>>
> >>> You mean adaptive evolution, not adaptation, which you are leaving
> >>> undefined the way set theorists leave the empty set undefined.
> >>
> >> Are you really this stupid?
> >
> > I'm "stupid" enough to be able to say the following to Harshman about
> > an hour ago:
> >
> > "By the way, I'm sure you realize that you did not define "adaptation" per se,
> > but only "adaptive evolution." Your definition says nothing whatsoever about
> > whether an individual is well or poorly adapted to the environment it happens
> > to find itself in at a given moment. I learned more about THAT at the age of
> > seven from a picture in _Life_ magazine's "The Pageant of Life" than I could
> > ever learn from anything I've seen from you or Shrubber on the topic."
>
> You may not like what the word means in biology,

Correction: what it means to specialists in evolutionary theory.

> but it retains that
> meaning. There's a context and it's relative fitness. There is no
> absolute fitness.

I said "well or poorly adapted to the environment" -- do you really
think I thought there are no degrees of "well" and "poor," that
these are black and white concepts?

If so, you are probably affected by what I call "para-xenophobia"
which causes you to read things I say as though I were as stupid
as Bill or Ray.

>There is no absolute sense of adapted. You want it
> to be different but that's your peculiar problem.

Did you think I would pull a John Harshman and claim you are terrible at
guessing motivations WITHOUT giving a clue as to where your misunderstanding
lies?

If so, you were mistaken.

> As for your confessed learning disability, it explains much. But it's
> really just your ego in the way.

Are you thinking that because you think you've nailed me on something,
I've confessed to a learning disability?

If so, are you deliberately feigning Ray-type illogic to help make
Ray's seeming lies and slanders look a little more like innocent
illogic and a little less like deliberate lies of someone who knows
that what he is saying is false?

> >> When the frequency of alleles is changing due to the bias of
> >> selective advantages to those alleles, that's adaption in action.
> >
> > You do a great job of talking around "adaptation". The caption to that
> > picture in "The Pageant of Life" did a great job of giving people a
> > feel for the concept.
>
> You like these private conversations you have with yourself.

I was addressing YOU, you surrealist.

> I imagine
> you'll repost them a few more times for your reading pleasure.

Do you think that para-xenophobic taunts like these are an adequate substitute
for refuting my observation that you talked AROUND the concept
of adaptation without touching the many-faceted concept that layman
understand with a ten foot pole?

> >> Adaption and adaptive evolution are synonymous. Are you completely
> >> new to discussions of evolution? Dawkins and his adaptionist ways,
> >> as opposed to Gould, is an oft discussed issue.
> >
> > Thanks for confirming that evolutionary theory has become too pragmatic
> > to discuss the concept which laymen associate with the term.
> >
> > A jackass whose herd has been wiped out but for him,

even better: who has wandered far from others of his species

> > coming onto a
> > herd of horses consisting temporarily of mares, is superbly adapted
> > to having first-generation offspring. But he does nothing in the
> > long run for the adaptive evolution of his kind.
> >
> > By the way, the above paragraph actually meets both concepts

> > (the evolutionary-theoretic and the layman's) halfway then

> > talks only about the former, which is much easier to talk
> > about than the latter because it is so one-dimensional.

...and so convenient for people forced to play the publish-or-perish game.

> Your skill at producing misconceptions is truly impressive to you.

The "to you" is yet another way of masking the fact that you
are powerless to explain why the word "adaptation" HAS to
be understood in the anemic, one-dimensional way to which professional
evolutionary biologists of 2015 confine themselves.

<snip of things to be dealt with later>

> >>> Well, looks like you've written something jillery just might want
> >>> to segue into [see her use of the word above]. I'm very busy today,
> >>> so I'll have to wait at least until tomorrow to segue into it.
> >>> But then I'll see first whether someone else segues into it in the
> >>> meantime.
> >>
> >> See, you are more worried about what people will do than the issues
> >> at hand.

That was another non sequitur by you. Did you think I would pull a
Harshman in reply to this one too? The following should have alerted
you to how far off-base your surrealistic sentence would be even
without that cocksure "See,"

> > I like for discussions to be fruitful. Whenever discussion degenerates
> > to a bunch of one-on-one interactions, with people in one interaction
> > ignoring everything being said in the other interactions, then the words
> > "dysfunctional" and "miasma" come to my mind.
> >
> > Evidently you are of the opposite opinion, just like Harshman.
>
> I care somewhat about what John thinks about evolutionary biology.
> I don't care what he thinks about you. Oh, and about that mirror.

I'd be far more concerned about that scratch in your record, if I
were you.

Peter Nyikos

[Roger Shrubber]

Peter Nyikos wrote:
> On Tuesday, May 12, 2015 at 12:14:03 PM UTC-4, Roger Shrubber wrote:
>> Peter Nyikos wrote:
>>> On Monday, May 11, 2015 at 11:54:05 PM UTC-4, Roger Shrubber wrote:


>>> By the way, the above paragraph actually meets both concepts
>>> (the evolutionary-theoretic and the layman's) halfway then
>>> talks only about the former, which is much easier to talk
>>> about than the latter because it is so one-dimensional.
>

> ....and so convenient for people forced to play the publish-or-perish game.

>
>> Your skill at producing misconceptions is truly impressive to you.
>
> The "to you" is yet another way of masking the fact that you
> are powerless to explain why the word "adaptation" HAS to
> be understood in the anemic, one-dimensional way to which professional
> evolutionary biologists of 2015 confine themselves.
>
> <snip of things to be dealt with later>

Again, the fact that you want a concept to address something other
than what it does, and has, represented in biology is your peculiar
problem. If you think you have a handle on some concept that is
more significant than "adaption" as biologists use it, by all
means post something coherent in support of your concept. And,
if you can, provide an objective means to measure it. And provide
an update to the standard concepts of population genetics that
references your new concept.

Lacking that, you should recognize that you appear to be an
incorrigible blowhard that is acting like people do when they
are clueless but nevertheless think they are superior to those
they are conversing with.

>>>>> Well, looks like you've written something jillery just might want
>>>>> to segue into [see her use of the word above]. I'm very busy today,
>>>>> so I'll have to wait at least until tomorrow to segue into it.
>>>>> But then I'll see first whether someone else segues into it in the
>>>>> meantime.
>>>>
>>>> See, you are more worried about what people will do than the issues
>>>> at hand.
>
> That was another non sequitur by you. Did you think I would pull a
> Harshman in reply to this one too? The following should have alerted
> you to how far off-base your surrealistic sentence would be even
> without that cocksure "See,"

I don't know what "pulling a Harshman" is. The phrasing seems to be
engineered to slander but avoid actually saying anything to actually
communicate what you mean. Hmmm. I guess you were pulling a Nyikos.

>>> I like for discussions to be fruitful. Whenever discussion degenerates
>>> to a bunch of one-on-one interactions, with people in one interaction
>>> ignoring everything being said in the other interactions, then the words
>> > "dysfunctional" and "miasma" come to my mind.
>>>
>>> Evidently you are of the opposite opinion, just like Harshman.
>>
>> I care somewhat about what John thinks about evolutionary biology.
>> I don't care what he thinks about you. Oh, and about that mirror.
>
> I'd be far more concerned about that scratch in your record, if I
> were you.

Number 9, number 9, number 9, number 9, number 9, number 9

[jillery]

As are your compulsive and baseless assertions. My comebacks are well
documented.

[Peter Nyikos]

On Tuesday, May 12, 2015 at 10:29:02 PM UTC-4, jillery wrote:
> On Tue, 12 May 2015 17:40:22 -0700 (PDT), Peter Nyikos
> <nyi...@bellsouth.net> wrote:
>
> >On Tuesday, May 12, 2015 at 11:59:04 AM UTC-4, Roger Shrubber wrote:
> >> Peter Nyikos wrote:
> >> > On Monday, May 11, 2015 at 11:54:05 PM UTC-4, Roger Shrubber wrote:
> >> >> Peter Nyikos wrote:

> >> >>>>> I've snipped the rest of what you wrote. It takes two to
> >> >>>>> tangle, and I have no desire to tangle with you on this
> >> >>>>> thread. [Harshman and Shrubber are a different kettle of fish
> >> >>>>> here.]

You, on the other hand, consistently seem to be spoiling for a
fight with me. Is this a mistaken opinion of mine?

> >> >>>> Your comments about neutral versus adaptive evolution are, so
> >> >>>> far, embarrassing. I realize you want to "tangle"
> >> >>>
> >> >>> You forced the issue, "Roger Shrubber", with your solidarity
> >> >>> with Harshman's agenda-driven remarks about me.
> >> >>
> >> >> Only in your imagination.
> >> >
> >> > His questioning my sanity has been part of an agenda of
> >> > denigration that he began with an utterly baseless "opinion" about me
> >> > within a month after I resumed posting in December 2010, and has been
> >> > indulged in numerous times since. You fed enthusiastically into his
> >> > questioning. Do you deny any of this?
> >
> >Of course, you did not. Your jillery-style comeback was all bluff.
>
>
> As are your compulsive and baseless assertions.

This is an example of what I was referring to just now with "...spoiling
for a fight..."

> My comebacks are well
> documented.

Yes, I could document literally hundreds of similar one liners from you.
And I'm sure you can too.

But you may have overlooked the fact that I wrote "-style" as opposed
to "-substance," about which I wrote nothing.

Peter Nyikos

[jillery]

On Tue, 12 May 2015 19:48:15 -0700 (PDT), Peter Nyikos

<nyi...@bellsouth.net> wrote:

>On Tuesday, May 12, 2015 at 10:29:02 PM UTC-4, jillery wrote:
>> On Tue, 12 May 2015 17:40:22 -0700 (PDT), Peter Nyikos
>> <nyi...@bellsouth.net> wrote:
>>
>> >On Tuesday, May 12, 2015 at 11:59:04 AM UTC-4, Roger Shrubber wrote:
>> >> Peter Nyikos wrote:
>> >> > On Monday, May 11, 2015 at 11:54:05 PM UTC-4, Roger Shrubber wrote:
>> >> >> Peter Nyikos wrote:
>
>> >> >>>>> I've snipped the rest of what you wrote. It takes two to
>> >> >>>>> tangle, and I have no desire to tangle with you on this
>> >> >>>>> thread. [Harshman and Shrubber are a different kettle of fish
>> >> >>>>> here.]
>
>You, on the other hand, consistently seem to be spoiling for a
>fight with me. Is this a mistaken opinion of mine?

What happened to "it takes two"? Apparently you don't apply such
banalities to yourself. And where's your noise-free, relevant
contribution to this topic? You seem to be giving all of your
compulsions free reign. That's a poor way to show your intent to
avoid entanglements.

[Peter Nyikos]

On Tuesday, May 12, 2015 at 2:09:04 PM UTC-4, John Harshman wrote:
> On 5/12/15, 9:11 AM, Roger Shrubber wrote:
> > Peter Nyikos wrote:
> >> On Monday, May 11, 2015 at 11:54:05 PM UTC-4, Roger Shrubber wrote:
> >>> Peter Nyikos wrote:

<snip of things dealt with in reply to Shrubber>

> >> A jackass whose herd has been wiped out but for him, coming onto a
> >> herd of horses consisting temporarily of mares, is superbly adapted
> >> to having first-generation offspring. But he does nothing in the
> >> long run for the adaptive evolution of his kind.
> >>
> >> By the way, the above paragraph actually meets both concepts
> >> (the evolutionary-theoretic and the layman's halfway) then
> >> talks only about the former, which is much easier to talk
> >> about than the latter because it is so one-dimensional.

What follows is an illustration of how you two ("Shrubber" and you,
Harshman) assume that, just because I didn't spend 1000+ lines
talking about all the fine points of fitness, I only know
what you see typed in far fewer lines.

Fact is, I learned a lot about fitness back in the 1990's
in sci.bio.evolution, discussing fine points with some
knowledgeable people, including Felsenstein, for whom
"knowledgeable" is a laughable understatement.

[Sic transit gloria mundi: now all those people are gone,
and s.b.e. is even less of a going concern than sci.bio.paleontology;
for two months, when last I looked, there had not been a single
post to that ng.]

> > Your skill at producing misconceptions is truly impressive to you.
>
> Some sort of group selection, manifest destiny sort of thing?

Keep telling such things to yourself, John, and you might just
start to believe them.

[Shrubber:]

> >>>>> Neutral evolution is change
> >>>>> that occurs independently of the bias of reproductive fitness.
> >>>>
> >>>> Can't you use more direct language? What do you mean by "bias"
> >>>> in this context?
> >>>
> >>> Are you attempting to misunderstand? Selection. That's the bias
> >>> I refer to. As opposed to neutral evolution where the changes
> >>> occur due to just chance.
> >>
> >> "just chance" is a slippery concept. Genetic drift seems to
> >> cover it, but then the reproductive fitness of the population
> >> that changes by chance may be no greater than that of
> >> a population that changed due to selection.
> >>
> >> Otherwise, most evolution could not be neutral, eh?

Shrubber is so bent on denigrating me, he may not even

have realized that he was ducking my question when he wrote:

> > You seem to be laboring with this misconception about
> > absolute fitness. Maybe you learned it that way when you
> > were seven. It's time to grow up and toss it aside.
>
> I'm not sure that's his misconception. But perhaps a bit more
> explanation would help him. I will throw some words.

And you don't seem to realize that you, too, are not addressing
the question I asked "Shrubber."

> There is sometimes a distinction made between expected fitness, an
> abstract property correlated with genotype, and realized fitness, the
> actual reproductive success of a real organism.

The distinction is so elementary, the only question is how many
generations must go by before it counts as "expected fitness".

But maybe that is the wrong question to ask, because this
abstract property may belong exclusively to theoretical
biology, and never darkens the door of biologists in the
form of observing a habitat for n generations. Correct?

> In Peter's example, the
> jackass actually has zero realized fitness, since his offspring will be
> sterile. Let's change him to a horse to make the example more
> interesting; then he has high realized fitness, but his expected
> fitness, based on his genotype, may not be different from the average.
> He has achieved high reproductive success because of an environmental
> feature (lucking upon a herd of mares) that isn't correlated with
> genotype, all of which we habitually label as "chance". Any one
> individual, exemplar of a genotype, may have realized fitness much less
> or much more than his expected fitness because of "chance" factors. We
> can't predict the outcome of any particular individual's reproduction.
> Only in the mass can we predict the average reproductive success of a
> genotype. When two genotypes have equal expected success, changes in
> their relative frequencies are said to be neutral.
>
> Given the various "chance" factors involved, the realized fitnesses of
> individuals of various genotypes may not correspond to the expected
> fitnesses of their genotypes. Many individuals of lower expected fitness
> will have greater reproductive success than many individuals of higher
> expected fitness. You can consider realized fitness as a random variable
> with a distribution around the expected fitness, if that helps.
>
> Peter, did that help? This is all standard biology, not my invention.

Sort of. Put together with another post of yours, I surmise
that the anthropocentric-sounding "expected" can be replaced
with "average".

That, and the ducking of my question by both of you, goes
a long way towards justifying something over which you
originally went ballistic:

Perhaps they fear that when all hints of anthropomorphism
are expunged from it, nothing useful will remain of the distinction
between "adaptive evolution" and "neutral evolution."

All that remeains is to add "anthropocentrism and" before
"anthropomorphism," and I'm home free. Correct?

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://www.math.sc.edu/~nyikos/
nyikos "at" math.sc.edu

[John Harshman]

On 5/14/15, 6:43 AM, Peter Nyikos wrote:
> On Tuesday, May 12, 2015 at 2:09:04 PM UTC-4, John Harshman wrote:
>> On 5/12/15, 9:11 AM, Roger Shrubber wrote:
>>> Peter Nyikos wrote:
>>>> On Monday, May 11, 2015 at 11:54:05 PM UTC-4, Roger Shrubber wrote:
>>>>> Peter Nyikos wrote:
>
> <snip of things dealt with in reply to Shrubber>
>
>>>> A jackass whose herd has been wiped out but for him, coming onto a
>>>> herd of horses consisting temporarily of mares, is superbly adapted
>>>> to having first-generation offspring. But he does nothing in the
>>>> long run for the adaptive evolution of his kind.
>>>>
>>>> By the way, the above paragraph actually meets both concepts
>>>> (the evolutionary-theoretic and the layman's halfway) then
>>>> talks only about the former, which is much easier to talk
>>>> about than the latter because it is so one-dimensional.

<snip boast about Joe Felsenstein>

You seem to misunderstand what expected fitness is. It has nothing to do
with multiple generations, just statistical expectation. The point about
sterile offspring not contributing to fitness is an unrelated matter.

> But maybe that is the wrong question to ask, because this
> abstract property may belong exclusively to theoretical
> biology, and never darkens the door of biologists in the
> form of observing a habitat for n generations. Correct?

Again, n generations would be irrelevant. It's observing lots of cases
involving the genotype that counts. Those cases might be over many
generations or thy might be all within a single generation; doesn't
matter. And of course the expected fitness is an abstraction estimated
from real data, just as any mean or other estimated statistical quantity
is an abstraction.

>> In Peter's example, the
>> jackass actually has zero realized fitness, since his offspring will be
>> sterile. Let's change him to a horse to make the example more
>> interesting; then he has high realized fitness, but his expected
>> fitness, based on his genotype, may not be different from the average.
>> He has achieved high reproductive success because of an environmental
>> feature (lucking upon a herd of mares) that isn't correlated with
>> genotype, all of which we habitually label as "chance". Any one
>> individual, exemplar of a genotype, may have realized fitness much less
>> or much more than his expected fitness because of "chance" factors. We
>> can't predict the outcome of any particular individual's reproduction.
>> Only in the mass can we predict the average reproductive success of a
>> genotype. When two genotypes have equal expected success, changes in
>> their relative frequencies are said to be neutral.
>>
>> Given the various "chance" factors involved, the realized fitnesses of
>> individuals of various genotypes may not correspond to the expected
>> fitnesses of their genotypes. Many individuals of lower expected fitness
>> will have greater reproductive success than many individuals of higher
>> expected fitness. You can consider realized fitness as a random variable
>> with a distribution around the expected fitness, if that helps.
>>
>> Peter, did that help? This is all standard biology, not my invention.
>
> Sort of. Put together with another post of yours, I surmise
> that the anthropocentric-sounding "expected" can be replaced
> with "average".

Yes. I will note that it's only anthropocentric-sounding if you don't
know the usage.

> That, and the ducking of my question by both of you, goes
> a long way towards justifying something over which you
> originally went ballistic:
>
> Perhaps they fear that when all hints of anthropomorphism
> are expunged from it, nothing useful will remain of the distinction
> between "adaptive evolution" and "neutral evolution."
>
> All that remeains is to add "anthropocentrism and" before
> "anthropomorphism," and I'm home free. Correct?

No. I have no idea how you arrived at this supposed "fear".

And I'm not sure what question I ducked. Was it "Otherwise, most
evolution could not be neutral, eh?" If so, the problem is that the
question appears nonsensical and impossible to answer. One would have to
untangle the layers of misconception involved in it and explain why it
can't be answered, which Roger and I each attempted to do in a small
way. It would help if you tried to explain again what you were trying to
ask. Roger was saying that it seemed contaminated with some notion of
"the good of the species". Fitness is not a population property, but a
property of genotypes or individuals. Fitness of one genotype is
generally measured relative to other genotypes in the population.
Fitness of a population is seldom considered and would be hard to
measure; what would you compare it to? And I was trying to point out
that stochastic effects not due to genotype are not what we mean by
"fitness". But even with that, I don't understand the question.

Then again, if it's some other question you meant, what was it?

[John Harshman]

On 5/14/15, 6:43 AM, Peter Nyikos wrote:

> Sort of. Put together with another post of yours, I surmise
> that the anthropocentric-sounding "expected" can be replaced
> with "average".

I'm only slightly uncomfortable with that. An average is a calculated
value from a sample. It's an estimate of the expected value. But we
often conflate estimates with "true" values.

[Peter Nyikos]

On Thursday, May 14, 2015 at 10:08:59 AM UTC-4, John Harshman wrote:
> On 5/14/15, 6:43 AM, Peter Nyikos wrote:
> > On Tuesday, May 12, 2015 at 2:09:04 PM UTC-4, John Harshman wrote:
> >> On 5/12/15, 9:11 AM, Roger Shrubber wrote:

> > [Shrubber:]
> >>>>>>> Neutral evolution is change
> >>>>>>> that occurs independently of the bias of reproductive fitness.
> >>>>>>
> >>>>>> Can't you use more direct language? What do you mean by "bias"
> >>>>>> in this context?
> >>>>>
> >>>>> Are you attempting to misunderstand? Selection. That's the bias
> >>>>> I refer to. As opposed to neutral evolution where the changes
> >>>>> occur due to just chance.
> >>>>
> >>>> "just chance" is a slippery concept. Genetic drift seems to
> >>>> cover it, but then the reproductive fitness of the population
> >>>> that changes by chance may be no greater than that of
> >>>> a population that changed due to selection.
> >>>>
> >>>> Otherwise, most evolution could not be neutral, eh?

<snip for focus>

> >> There is sometimes a distinction made between expected fitness, an
> >> abstract property correlated with genotype, and realized fitness, the
> >> actual reproductive success of a real organism.
> >
> > The distinction is so elementary, the only question is how many
> > generations must go by before it counts as "expected fitness".
>
> You seem to misunderstand what expected fitness is. It has nothing to do
> with multiple generations, just statistical expectation.

Statistics is not, and never can be, an exact science. You
can observe a genotype over one generation, or over many
generations, and the statistical expectations can become
wildly different-- due, perhaps, to changes in the environment.

> The point about
> sterile offspring not contributing to fitness is an unrelated matter.

I see you are using a concept of "individual fitness" that only
counts one's own offspring. But since that is just a raw datum
for assessing expected fitness, it is of no interest in and
of itself to biologists. Correct?

> > But maybe that is the wrong question to ask, because this
> > abstract property may belong exclusively to theoretical
> > biology, and never darkens the door of biologists in the
> > form of observing a habitat for n generations. Correct?
>
> Again, n generations would be irrelevant. It's observing lots of cases
> involving the genotype that counts. Those cases might be over many
> generations or thy might be all within a single generation; doesn't
> matter. And of course the expected fitness is an abstraction estimated
> from real data, just as any mean or other estimated statistical quantity
> is an abstraction.

Yes, it looks like we are on the same page here, but that still
does not answer the question I posed to Shrubber. Let's see
whether what you wrote further down does that.
<snip for focus>

> > Put together with another post of yours, I surmise
> > that the anthropocentric-sounding "expected" can be replaced
> > with "average".
>
> Yes. I will note that it's only anthropocentric-sounding if you don't
> know the usage.
>
> > That, and the ducking of my question by both of you, goes
> > a long way towards justifying something over which you
> > originally went ballistic:
> >
> > Perhaps they fear that when all hints of anthropomorphism
> > are expunged from it, nothing useful will remain of the distinction
> > between "adaptive evolution" and "neutral evolution."
> >
> > All that remeains is to add "anthropocentrism and" before
> > "anthropomorphism," and I'm home free. Correct?
>
> No. I have no idea how you arrived at this supposed "fear".

Irrelevant question, but I'm humoring you by answering it:

From the way you both talked around the terms without ever
defining them. Even when I pointed this out in re the impasse
between you and jillery on the two questions you asked her
about "neutral evolution," you STILL didn't define
"neutral evolution" in reply to me.

> And I'm not sure what question I ducked. Was it "Otherwise, most
> evolution could not be neutral, eh?" If so, the problem is that the
> question appears nonsensical and impossible to answer.

Shrubber has gone on record as saying most evolution IS
neutral, no?

Don't just look at the question in isolation; look at the
back and forth that preceded it.

<snarky comments of a nature skewered by jillery, snipped>

> Fitness is not a population property, but a
> property of genotypes or individuals. Fitness of one genotype is
> generally measured relative to other genotypes in the population.
> Fitness of a population is seldom considered and would be hard to
> measure;

"Average number of offspring per member" would seem to do the trick.

> what would you compare it to?

Why bother comparing it to anything? But I'll humor you below.

> And I was trying to point out
> that stochastic effects not due to genotype are not what we mean by
> "fitness".

So "survival of the fittest" has nothing to do with which of
several competing species is more likely to thrive, eh?

An example I came across recently: spotted owls being threatened
by barred owls.

An example I've known about since the age of 12: *Odontomachus,*
*Pheidole* and *Iridomyrmex humilis* on the island of Madeira.

[However, it appears that the author, of a classic book on ants,
prematurely decided on which genera were doomed.]

> But even with that, I don't understand the question.

Did what I wrote help?

Peter Nyikos

[John Harshman]

Your scattershot approach brings up several questions in a confusing
way. Yes, environmental change can alter selection coefficients. Yes,
statistics is, um, statistical. But it isn't the number of generations
that counts. It's the number of data points, i.e. individuals in this
case. It doesn't matter whether those individuals belong to many
generations or one. The change over time and/or space in selective
environment is a separate matter altogether.

>> The point about
>> sterile offspring not contributing to fitness is an unrelated matter.
>
> I see you are using a concept of "individual fitness" that only
> counts one's own offspring. But since that is just a raw datum
> for assessing expected fitness, it is of no interest in and
> of itself to biologists. Correct?

I don't know what you're trying to say there. Are you talking about kin
selection, or what?

I have defined it several times. Here, again: change in allele
frequencies not dependent on genotype. Strictly speaking, I suppose
that's a definition of drift, not neutral evolution, but close enough.
(Depending on population size, allele that are either slightly
beneficial or deleterious can behave in the same manner as neutral alleles.)

>> And I'm not sure what question I ducked. Was it "Otherwise, most
>> evolution could not be neutral, eh?" If so, the problem is that the
>> question appears nonsensical and impossible to answer.
>
> Shrubber has gone on record as saying most evolution IS
> neutral, no?

Yes. I agree that it is, if we're talking about sheer numbers of
fixations. Do you disagree? But I don't see what that has to do with the
question.

> Don't just look at the question in isolation; look at the
> back and forth that preceded it.
>
> <snarky comments of a nature skewered by jillery, snipped>

You are now taking perfectly reasonable requests for clarification as
"snarky". Why not just clarify?

>> Fitness is not a population property, but a
>> property of genotypes or individuals. Fitness of one genotype is
>> generally measured relative to other genotypes in the population.
>> Fitness of a population is seldom considered and would be hard to
>> measure;
>
> "Average number of offspring per member" would seem to do the trick.

Perhaps. Nobody does that, though. What would we compare that fitness
to? For individual fitness, we could compare it to that of other members
of the population. Would you attempt to compare different species?

>> what would you compare it to?
>
> Why bother comparing it to anything? But I'll humor you below.

What's the point of fitness if it isn't relative to something?

>> And I was trying to point out
>> that stochastic effects not due to genotype are not what we mean by
>> "fitness".
>
> So "survival of the fittest" has nothing to do with which of
> several competing species is more likely to thrive, eh?

Indeed not. First, it's a term invented by Herbert Spencer and not
generally used by modern biologists, for several reasons. Second, if it
refers to anything in modern biology, it's about individual genotypes.
Third, I don't see how that question relates to my statement.

> An example I came across recently: spotted owls being threatened
> by barred owls.

That isn't natural selection; it's interspecific competition. You might
consider competition to be an evolutionary process (and under some
circumstances I do) but it would be operating at the macroevolutionary
level and would have nothing to do with fitness as commonly understood.

Now of course both owl populations are presumably exerting a selective
environment on the other, with effects on the fitness of various
genotypes within each population. And if there is no relevant,
selectable genetic variation in the populations, no evolution (in that
sense of allele frequency change) will occur. Extinction might happen,
which is a macroevolutionary process analogous to fixation of one allele
in a population. But that sort of thing isn't described as fitness.
Perhaps you want to talk about levels of evolution?

> An example I've known about since the age of 12: *Odontomachus,*
> *Pheidole* and *Iridomyrmex humilis* on the island of Madeira.
>
> [However, it appears that the author, of a classic book on ants,
> prematurely decided on which genera were doomed.]
>
>> But even with that, I don't understand the question.
>
> Did what I wrote help?

No, I'm afraid not. You seem to be going off on all sorts of tangents.
If that isn't the case, I haven't been able to figure out your unifying
theme.

[Peter Nyikos]

Harshman's gradualistic explanations seem to have reached a critical
mass, to where the time seems to be ripe to finally address the OP.

On Wednesday, May 6, 2015 at 12:59:22 PM UTC-4, jillery wrote:
> As he tends to do, Larry Moran posted on his Sandwalk blog questions
> to the final of his college class:
>
> http://sandwalk.blogspot.com/2015/05/molecular-evolution-exam-april-2015.html

<snip>

> Two of his questions are prefaced by extensive quotations. The first
> is by Michael Lynch from The Origins of Genome Architecture:
>
> ***************************************************
> Nothing in Evolution Makes Sense Except in the Light of Population
> Genetics

A statement with which I disagree, but I'll only touch on it
indirectly in this post. Later posts are a different matter.

> Evolution is a population genetic process governed by four fundamental
> forces, which jointly dictate the relative abilities of genotype
> variants to expand through a species.

Note that: "through a species". No mention of competition between species,
which (as Harshman has assured me) has nothing to do with fitness and does
not come under the rubric of "natural selection" nor under population
genetics.

Harshman actually posted to that Sandwalk webpage and said
something he may want to repeat here. But I'm more interested
in something Moran said in reply to him:

Speciation, in general, is important but it
has almost nothing to do with population genetics.
Species sorting is not a population genetics phenomenon.


[...]

> Given the century of theoretical and empirical work devoted to
> the study of evolution, the only logical conclusion is that these four
> broad classes of mechanisms are, in fact, the only fundamental forces
> of evolution.

...but if one confines oneself to population genetics, it's worse than
looking at the grin and not the whole Cheshire Cat.

The four fundamental forces that were identified are selection, mutation,
recombination, and random genetic drift. Except for recombination,
these are the fundamental factors operating on the grand scale of
speciation and beyond to the whole "tree of life," of which popultation
genetics has nothing to say.

> ***********************************************
>
> A question he asks is: if you agree, why isn't population genetics
> taught in introductory biology courses?

Is it a fact that it is not? The standard introductory biology
text used by my university has a whole section on population genetics.
But I don't know whether it is actually part of the syllabus.

> ISTM that's a question worth
> discussing beyond a college exam.

Yes, and only one person on that (VERY LONG) blogpage had anything
to say about it: "Simon Gunkel," who wrote: "It's not taught in
introductory courses, because apparently maths scares students."

I agree with that to some extent: IMHO only someone majoring in statistics
(or math, with a keen interest in discrete math) could really get excited
about the subject as a freshman, but these students can very quickly aim
for the upper level courses that treat it in the kind of depth it deserves.
Meanwhile, they can read about it in their backbreaking-size [1] textbook
even if the course makes no mention of it.

But IMHO the real reason is more pragmatic. Population genetics is a
specialized topic with little hope of appealing to the average
freshman, who is either taking it to fulfill a requirement
[often because the freshman is a pre-med major
whose main goal is raking in big bucks as an MD]
or got excited about biology long ago but is thirsting for
the panorama of knowledge a great naturalist like Agassiz could
impart on that level. Population genetics just can't compete
with other topics in that respect.

[1] The combined weight of standard science major texts in calculus,
biology, and chemistry is already enough to make students leave
their textbooks in their dorm rooms. No wonder hardly anyone looks
at the textbook while waiting for slower students to finish beginning-
of-class quizzes.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina

http://people.math.sc.edu/nyikos/
nyikos "AT" math.sc.edu

[John Harshman]

On 5/18/15, 9:55 AM, Peter Nyikos wrote:
> Harshman's gradualistic explanations seem to have reached a critical
> mass, to where the time seems to be ripe to finally address the OP.
>
> On Wednesday, May 6, 2015 at 12:59:22 PM UTC-4, jillery wrote:
>> As he tends to do, Larry Moran posted on his Sandwalk blog questions
>> to the final of his college class:
>>
>> http://sandwalk.blogspot.com/2015/05/molecular-evolution-exam-april-2015.html
>
> <snip>
>
>> Two of his questions are prefaced by extensive quotations. The first
>> is by Michael Lynch from The Origins of Genome Architecture:
>>
>> ***************************************************
>> Nothing in Evolution Makes Sense Except in the Light of Population
>> Genetics
>
> A statement with which I disagree, but I'll only touch on it
> indirectly in this post. Later posts are a different matter.
>
>> Evolution is a population genetic process governed by four fundamental
>> forces, which jointly dictate the relative abilities of genotype
>> variants to expand through a species.
>
> Note that: "through a species". No mention of competition between species,
> which (as Harshman has assured me) has nothing to do with fitness and does
> not come under the rubric of "natural selection" nor under population
> genetics.

I never said that interspecific competition has nothing to do with
fitness. Competition is a feature of a species' environment and can
affect the fitness of individuals in that species just like any other
feature of the environment. However, if there is no selectable variation
in that species relevant to the competition, which I think is often the
case, then it has nothing to do with fitness.

> Harshman actually posted to that Sandwalk webpage and said
> something he may want to repeat here. But I'm more interested
> in something Moran said in reply to him:
>
> Speciation, in general, is important but it
> has almost nothing to do with population genetics.
> Species sorting is not a population genetics phenomenon.

These are two different statements. I'd say that speciation does have
quite a bit to do with population genetics. But he's right about the
second one. What I said, if I remember, is that there are
macroevolutionary processes that aren't covered by population genetics.

>> Given the century of theoretical and empirical work devoted to
>> the study of evolution, the only logical conclusion is that these four
>> broad classes of mechanisms are, in fact, the only fundamental forces
>> of evolution.
>
> ...but if one confines oneself to population genetics, it's worse than
> looking at the grin and not the whole Cheshire Cat.

I wouldn't say that. I'd say that population genetics is actually the
majority of the cat.

> The four fundamental forces that were identified are selection, mutation,
> recombination, and random genetic drift. Except for recombination,
> these are the fundamental factors operating on the grand scale of
> speciation and beyond to the whole "tree of life," of which popultation
> genetics has nothing to say.

Here, I don't know what you mean. Those four forces are specifically and
entirely within-population and thus entirely within the purview of
population genetics. Macroevolutionary forces are something else
entirely, though one can make analogies.

>> ***********************************************

I have nothing to say about whether pop gen should be covered in intro
biology courses.

[John Harshman]

On 5/18/15, 9:55 AM, Peter Nyikos wrote:

And might I say that I'm overjoyed to see an on-topic post?

[Burkhard]

John Harshman wrote:
> On 5/18/15, 9:55 AM, Peter Nyikos wrote:
>
> And might I say that I'm overjoyed to see an on-topic post?
>

Pffft, why don't you marry him?

<hark! is that the sound of a thread derailing?>

[jillery]

On Mon, 18 May 2015 09:55:43 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> wrote:

>Harshman's gradualistic explanations seem to have reached a critical
>mass, to where the time seems to be ripe to finally address the OP.

I suppose you're right, if by "gradualistic" you mean increasingly
pedantic and off-topic.

Perhaps population genetics is taught as a specialized topic because
it's reserved for specialized students who go on to careers biological
sciences. If a population genetics class was specifically designed for
introductory classes, for those who needed a grounding in biology but
not as a specific career, that might satisfy Michael Lynch and Larry
Moran. After all, the math of Hardy-Weinberg and genetic drift isn't
that hard, even I can do it.

[erik simpson]

Well, you just threw a tie across that tracks. Let's see...

[Peter Nyikos]

On Monday, May 18, 2015 at 3:23:45 PM UTC-4, John Harshman wrote:
> On 5/18/15, 9:55 AM, Peter Nyikos wrote:
> > Harshman's gradualistic explanations seem to have reached a critical
> > mass, to where the time seems to be ripe to finally address the OP.
> >
> > On Wednesday, May 6, 2015 at 12:59:22 PM UTC-4, jillery wrote:
> >> As he tends to do, Larry Moran posted on his Sandwalk blog questions
> >> to the final of his college class:
> >>
> >> http://sandwalk.blogspot.com/2015/05/molecular-evolution-exam-april-2015.html

<snip>

> >> Evolution is a population genetic process governed by four fundamental
> >> forces, which jointly dictate the relative abilities of genotype
> >> variants to expand through a species.
> >
> > Note that: "through a species". No mention of competition between species,
> > which (as Harshman has assured me) has nothing to do with fitness and does
> > not come under the rubric of "natural selection" nor under population
> > genetics.

I gave two examples of competition between species, but in my second
example I conflated two:

1. *Odontomachus haematoda*, var. insularis, a Ponerine ant, versus
*Pheidole megacephala*, a Myrmicine ant, on the island of Bermuda;

2. *Pheidole megacephala* versus *Iridomyrmex humilis*, a Dolichoderine ant,

on the island of Madeira.

Source: the classic _Of Ants And Men_, by Caryl P. Haskins

> I never said that interspecific competition has nothing to do with
> fitness. Competition is a feature of a species' environment and can
> affect the fitness of individuals in that species just like any other
> feature of the environment. However, if there is no selectable variation
> in that species relevant to the competition, which I think is often the
> case, then it has nothing to do with fitness.

Sorry, I was trying to be concise and stand corrected.

<snip for focus>

> > The four fundamental forces that were identified are selection, mutation,
> > recombination, and random genetic drift. Except for recombination,
> > these are the fundamental factors operating on the grand scale of
> > speciation and beyond to the whole "tree of life," of which popultation
> > genetics has nothing to say.
>
> Here, I don't know what you mean. Those four forces are specifically and
> entirely within-population and thus entirely within the purview of
> population genetics. Macroevolutionary forces are something else
> entirely, though one can make analogies.

"analogies" is the wrong word; "generalizations" [from intra-population
forces to essentially the same forces on a much larger scale] is much
better. But I think I'd better narrow it down to two when going to
speciation and beyond: mutation and natural selection, their intended
meaning understood by everyone except autistic people and contrarians.

> I have nothing to say about whether pop gen should be covered in intro
> biology courses.

Fine with me.

Peter Nyikos

[John Harshman]

On 5/18/15, 1:21 PM, Peter Nyikos wrote:
> On Monday, May 18, 2015 at 3:23:45 PM UTC-4, John Harshman wrote:
>> On 5/18/15, 9:55 AM, Peter Nyikos wrote:
>>> Harshman's gradualistic explanations seem to have reached a critical
>>> mass, to where the time seems to be ripe to finally address the OP.
>>>
>>> On Wednesday, May 6, 2015 at 12:59:22 PM UTC-4, jillery wrote:
>>>> As he tends to do, Larry Moran posted on his Sandwalk blog questions
>>>> to the final of his college class:
>>>>
>>>> http://sandwalk.blogspot.com/2015/05/molecular-evolution-exam-april-2015.html
>
> <snip>
>
>>>> Evolution is a population genetic process governed by four fundamental
>>>> forces, which jointly dictate the relative abilities of genotype
>>>> variants to expand through a species.
>>>
>>> Note that: "through a species". No mention of competition between species,
>>> which (as Harshman has assured me) has nothing to do with fitness and does
>>> not come under the rubric of "natural selection" nor under population
>>> genetics.
>
> I gave two examples of competition between species, but in my second
> example I conflated two:
>
> 1. *Odontomachus haematoda*, var. insularis, a Ponerine ant, versus
> *Pheidole megacephala*, a Myrmicine ant, on the island of Bermuda;
>
> 2. *Pheidole megacephala* versus *Iridomyrmex humilis*, a Dolichoderine ant,
> on the island of Madeira.
>
> Source: the classic _Of Ants And Men_, by Caryl P. Haskins

And I'm sure they're very fine examples. Did you want to draw a lesson
of some sort for evolution?

>> I never said that interspecific competition has nothing to do with
>> fitness. Competition is a feature of a species' environment and can
>> affect the fitness of individuals in that species just like any other
>> feature of the environment. However, if there is no selectable variation
>> in that species relevant to the competition, which I think is often the
>> case, then it has nothing to do with fitness.
>
> Sorry, I was trying to be concise and stand corrected.
>
> <snip for focus>
>
>>> The four fundamental forces that were identified are selection, mutation,
>>> recombination, and random genetic drift. Except for recombination,
>>> these are the fundamental factors operating on the grand scale of
>>> speciation and beyond to the whole "tree of life," of which popultation
>>> genetics has nothing to say.
>>
>> Here, I don't know what you mean. Those four forces are specifically and
>> entirely within-population and thus entirely within the purview of
>> population genetics. Macroevolutionary forces are something else
>> entirely, though one can make analogies.
>
> "analogies" is the wrong word; "generalizations" [from intra-population
> forces to essentially the same forces on a much larger scale] is much
> better.

> But I think I'd better narrow it down to two when going to
> speciation and beyond: mutation and natural selection, their intended
> meaning understood by everyone except autistic people and contrarians.

I disagree strongly. There are no such "exactly the same" forces. What
is mutation at at the species level? What is migration at the species
level? What is drift at the species level? What is selection at the
species level? (Yes, there is something we call species selection, but
it requires analogizing gene pools, reproductive success, and such.)

Go ahead, make a case.

[RSNorman]

On Mon, 18 May 2015 09:55:43 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> wrote:

Since I actually did teach intro biology for many decades I do have
some strong opinions on teaching pop gen in that course. That is why
I wrote a rather long post on just that topic early in this thread. In
fact it was the first response posted less than three hours after
jillery started the thread.
Message-ID: <t0pkkalvhem1nguuq...@4ax.com>
I won't repeat the whole of my arguments here but the real issue is
the length of time it takes to introduce even elementary pop gen
(Hardy Weinberg) vs. the relative return considering the enormous
scope of topics to be covered.

As to the significance of the subject to evolutionary biology, it is
both the most important thing and simultaneously it really is not that
necessary except for a few points. Certainly it was the work of the
early population geneticists, Fisher and then Sewell Wright and
Haldane, that formed the core of the "modern evolutionary synthesis"
in the mid 20th century. It provides the solid foundation for the
overwhelming power of selection and, later, for the action of genetic
drift. Of course mechanisms by which selection and mutation can work
are outside the subject. Still pretty much all of microevolution is
based on population genetics.

Still, it is not the be-all and end-all of evolution. Two points have
already been raised here. First, competition is not part of pop gen.
But fitness certainly is. Both intraspecific and interspecific
competition are enormously important but their importance is only to
the extent that they influence fitness. Intraspecific competition is
easy to envision: one individual is simply more fit than another.
However competition with another species simply fits in the category
of being able to function, survive and reproduce, within the
environment since the biologic environment includes all the other
species in the community. And the effect of variations in fitness is
to allow one particular genetic type to expand "through a species."
That in no way excludes interspecific competition: it is just that the
evolutionary change occurs within each species. In practice,
coevolution rules so that several species all interact with each other
and changing the genetic structure of one species changes the
environment for the others so that they also change. Pop gen includes
all that. However the real evolutionary biological interest is in the
particulars of how organism change to adapt. Air/water breathing and
flying/swimming/walking/creeping are all best explained by the details
of the development of particular organs of particular shapes and
abilities and not by simply saying "well some changes produce higher
fitness". It is just what specific changes that we care about.

Second, there most definition are concepts of speciation beyond pop
gen. For example, the concept of reproductive isolation, so critical
to the whole modern concept of species, is not part of pop gen per se.
Second, there are enormous arguments in evolutionary biology about
levels of selection but certainly factors like group selection and
species sorting are beyond ordinary pop gen. Larry Moran had some
serious issues here about the notion of macroevolution. He insists
that macroevolution is more than just microevolution piled higher and
deeper: it involves other concepts at work. This went against the
prevailing sentiment here (see the t.o. archive at
http://www.talkorigins.org/faqs/macroevolution.html
I would guess that this type of disagreement is evident in what you
cite about John and Larry commenting on each other in the Sandwalk
site.

[Roger Shrubber]

Even within the simple notions of population genetics, selection, and
fitness, one must work with the concepts rather than against them.

Fitness is defined as allele frequency after / allele frequency before,
or absolute allele count after / absolute allele count before.

What is not defined is the "correct" time frame to evaluate before
and after.

Other species make up the environment and the environment is dynamic.
That dynamic nature is a given. We know through archetype examples
of ecology that many species cycle in boom/bust sequences.
Simplistically, lots of coyotes eat most of the rabbits and then
the coyotes starve. The grass grows back because there are few rabbits,
the rabbits increase due to the plentiful grass and low predation,
the grass suffers, the coyotes increase, turn turn turn.

One can address fitness short term where some alleles cycle with
the cycling environment, or average over many cycles. One can even
(re)discover variations of r/k selection theory. But it all still
fits within population genetics, unless one is working to misunderstand
things so that they can, for example, manufacture a press release
about how they have overturned the neoDarwinian synthesis.

And as I recall, this was covered in first year biology, at least
quickly.

[John Harshman]

On 5/18/15, 1:54 PM, RSNorman wrote:

> Both intraspecific and interspecific
> competition are enormously important but their importance is only to
> the extent that they influence fitness.

On this one point I disagree. Interspecific competition can also be
important as a macroevolutionary process, as it can affect extinction
probabilities, and so the composition of the biota and evolutionary
trends, even in the absence of any relevant intrapopulation genetic
variation.

> Second, there most definition are concepts of speciation beyond pop
> gen. For example, the concept of reproductive isolation, so critical
> to the whole modern concept of species, is not part of pop gen per se.

Still, the processes by which reproductive isolation evolves are
population genetic.

> Second, there are enormous arguments in evolutionary biology about
> levels of selection but certainly factors like group selection and
> species sorting are beyond ordinary pop gen. Larry Moran had some
> serious issues here about the notion of macroevolution. He insists
> that macroevolution is more than just microevolution piled higher and
> deeper: it involves other concepts at work. This went against the
> prevailing sentiment here (see the t.o. archive at
> http://www.talkorigins.org/faqs/macroevolution.html
> I would guess that this type of disagreement is evident in what you
> cite about John and Larry commenting on each other in the Sandwalk
> site.

No, on that point Larry and I agree.

[RSNorman]

I stand (although I am actually seated) corrected on your point about
interspecific competition acting as a macroevolutionary process
provided I also am corrected on your point about accepting, along with
Larry, that macroevolution includes factors beyond those acting in
microevolution.

Yes, the changes within each of two populations that ultimately
results in reproductive isolation occur because of population
genetics. However crossing that threshold into isolation is the
critical factor in speciation and pop gen does not define nor compute
just how that threshold is arrived at. It only says "change happens".
Speciation requires "change specifically that causes X". That is the
point I was trying to make about adaptation. Pop gen says "change
happens and the population becomes better adapted to survive and
reproduce." Far more interesting biology says "change happens to make
a faster swimmer or a tougher hide or a camouflaging color pattern,"
concepts beyond the scope of pop gen.

[RSNorman]

I seriously doubt that population genetics had anything at all to do
with that coverage in intro biology. My impression is that pop gen
says "given the allele frequencies in this generation, this population
size, and these fitness coefficients for each genotype, here are the
expected values (possibly with standard deviations) for the allele
frequencies in the next generation. Time is included if only by
generation number. Fitness is not defined as allele counts before and
after reproduction but rather the ability of each genotype to
contribute to the gene pool for the next generation.

That the environment constantly changes and that it interacts strongly
with the changes that pop gen does calculate forms exactly the complex
system that jonathan is so enamored about.

What you describe in terms of population cycles and r/K selection
theory is what constitutes population ecology, not population
genetics. Of course, to coin a phrase, "nothing in biology makes
sense except in the light of evolution." And it is also true that
ecology and evolution are often lumped together into one department or
branch of biology separate from the two other legs: cell/molecular and
organismal. Still the two kinds of population studies, ecology and
genetics, are rather distinct. No doubt the fact that both areas are
highly mathematical struck sufficient fear into your class that they
got confused.

[Roger Shrubber]

http://en.wikipedia.org/wiki/Fitness_(biology)#Measures_of_fitness

If it isn't defined by the measure I am indeed confused. Perhaps you
could expand on why you don't think it is defined by the ratio.

Although the above suggests the calculation is done after one generation
I disagree somewhat although I'm muddled things.

The standard formulas for pop gen involving fitness use the number for a
single generation in their models. But I argue that at a conceptual
level, if you work with the foundational concepts, there is a useful
sense that averages over the realities of species interactions. It
does not require reinventing the foundational concepts.

> That the environment constantly changes and that it interacts strongly
> with the changes that pop gen does calculate forms exactly the complex
> system that jonathan is so enamored about.
>
> What you describe in terms of population cycles and r/K selection
> theory is what constitutes population ecology, not population
> genetics. Of course, to coin a phrase, "nothing in biology makes
> sense except in the light of evolution." And it is also true that
> ecology and evolution are often lumped together into one department or
> branch of biology separate from the two other legs: cell/molecular and
> organismal. Still the two kinds of population studies, ecology and
> genetics, are rather distinct. No doubt the fact that both areas are
> highly mathematical struck sufficient fear into your class that they
> got confused.

I don't recall the fear or suggesting that people were confused, my
own sloppy presentation aside. The relevance of r/K selection is to
the cycling whereby there are a systematic shift in standard fitness,
where one can predictably suggest that fitness will vary over time
in a manner that nevertheless can reach a stable equilibrium. Or you
can get destabilizing selection but such situations don't tend to
last long, as they are unstable and all that.

[John Harshman]

Are you in fact also corrected?

> Yes, the changes within each of two populations that ultimately
> results in reproductive isolation occur because of population
> genetics. However crossing that threshold into isolation is the
> critical factor in speciation and pop gen does not define nor compute
> just how that threshold is arrived at. It only says "change happens".
> Speciation requires "change specifically that causes X". That is the
> point I was trying to make about adaptation. Pop gen says "change
> happens and the population becomes better adapted to survive and
> reproduce."

I hope pop gen doesn't say that. It should be about individual
reproductive success and the spread of alleles within a population, not
about making the population better. The spread of alleles by selection
might or might not make a population better adapted to survive and

reproduce.

> Far more interesting biology says "change happens to make
> a faster swimmer or a tougher hide or a camouflaging color pattern,"
> concepts beyond the scope of pop gen.

Are you saying that selective environment (or the response to it) is
outside the scope of population genetics? I'd say rather that it's a
crucial variable.

[RSNorman]

On Mon, 18 May 2015 18:57:55 -0400, Roger Shrubber

It is past my bedtime and I will take up the notion of fitness
sometime tomorrow evening when I get a chance. The definition you
offer is a conceptual one about the numbers of individuals provided
that selection is the only factor. That is, it is a way of describing
the probability of contributing to the next generation. It is like
saying that the probability of getting heads in a coin toss is the
number of heads you get divided by the total number of tosses.

As to the r/K and cycling business, the key point of my response was
that you have switched from population genetics to population ecology,
a different subject. The "fear of being confused" was my attempt at
jocularity relating to the comment Peter cited about biology students
general fear of anything mathematical.

[RSNorman]

On Mon, 18 May 2015 16:10:16 -0700, John Harshman

I am not one of those who claim that macroevolution is nothing more
than microevolution carried out to a greater or longer extent.

And when I say that pop gen says populations become better adapted,
all I meant was that if there are two alleles (or genotypes) one with
higher fitness and one with lower fitness, then the population will
change so that there will be an increase in the total fitness of the
population averaged over all the types. Since fitness is a measure of
the ability to survive and reproduce, then the ability to survive and
reproduce increases. Most people would then think that the population
becomes "better" but, no, pop gen does not include the notion of
'good' or 'bad'.

As for my final point, the ability of individuals to respond or behave
in different environments is important. It is just that the
particulars of why fitness differs -- speed of locomotion, toughness
of hide, ability to hide from predators -- none of that matters. It
only matters that some members of the population have greater fitness
than others and the types with greater fitness will grow in relative
number.

[John Harshman]

Me neither, as I think we have already agreed.

> And when I say that pop gen says populations become better adapted,
> all I meant was that if there are two alleles (or genotypes) one with
> higher fitness and one with lower fitness, then the population will
> change so that there will be an increase in the total fitness of the
> population averaged over all the types. Since fitness is a measure of
> the ability to survive and reproduce, then the ability to survive and
> reproduce increases. Most people would then think that the population
> becomes "better" but, no, pop gen does not include the notion of
> 'good' or 'bad'.

I was thinking of the commonly expressed possibility that an allele may
increase the fitness of an individual but end up reducing the species
population, i.e. natural selection in conflict with group selection. In
other words, it's possible for an allele that increases individual
fitness to cause reduced population fitness.

> As for my final point, the ability of individuals to respond or behave
> in different environments is important. It is just that the
> particulars of why fitness differs -- speed of locomotion, toughness
> of hide, ability to hide from predators -- none of that matters. It
> only matters that some members of the population have greater fitness
> than others and the types with greater fitness will grow in relative
> number.

So you mean that popu gen just treats environments as numerical factors
unconnected with the characteristics we find interesting?

[RSNorman]

On Mon, 18 May 2015 21:35:21 -0700, John Harshman

That selfish gene destroying the group does, in fact, increase the
average fitness of the population. It is just that the population as
a whole will decline, probably eventually to zero as the individuals
all come to conform to the new standard.

And, yes, all I meant about selection is that pop gen is purely
numbers on a piece of paper (or in a computer). It is sort of like
economics describing statistics about income distribution without
including any notion of the desperation of those at one end and the
greed of those at the other. The numbers are very definitely
important but they are just part of the story. (Yes, I know that real
economists also treat more than just the numbers, too.)

[John Harshman]

It's not a selfish gene, by the usual definition of the term. I suppose
it depends on how you define group fitness, but it must result in
individuals in the group having, on average, lower reproductive success
than before the appearance of the allele, or the population won't go down.

[RSNorman]

On Tue, 19 May 2015 06:24:54 -0700, John Harshman

<jhar...@pacbell.net> wrote:

>On 5/19/15, 5:42 AM, RSNorman wrote:
>> On Mon, 18 May 2015 21:35:21 -0700, John Harshman
>> <jhar...@pacbell.net> wrote:
>>
>>> On 5/18/15, 8:22 PM, RSNorman wrote:

<snip out all the debris>

>>>> And when I say that pop gen says populations become better adapted,
>>>> all I meant was that if there are two alleles (or genotypes) one with
>>>> higher fitness and one with lower fitness, then the population will
>>>> change so that there will be an increase in the total fitness of the
>>>> population averaged over all the types. Since fitness is a measure of
>>>> the ability to survive and reproduce, then the ability to survive and
>>>> reproduce increases. Most people would then think that the population
>>>> becomes "better" but, no, pop gen does not include the notion of
>>>> 'good' or 'bad'.
>>>
>>> I was thinking of the commonly expressed possibility that an allele may
>>> increase the fitness of an individual but end up reducing the species
>>> population, i.e. natural selection in conflict with group selection. In
>>> other words, it's possible for an allele that increases individual
>>> fitness to cause reduced population fitness.
>>>
>>

>> That selfish gene destroying the group does, in fact, increase the
>> average fitness of the population. It is just that the population as
>> a whole will decline, probably eventually to zero as the individuals
>> all come to conform to the new standard.
>
>It's not a selfish gene, by the usual definition of the term. I suppose
>it depends on how you define group fitness, but it must result in
>individuals in the group having, on average, lower reproductive success
>than before the appearance of the allele, or the population won't go down.
>

No, not by the usual definition. I used the words carelessly. I
meant the selfishness that acts to destroy altruism or other
cooperative activities.

We we engaging in little pedantic arguments here but in one sense, the
selfish or non-cooperative individuals can thrive and grow in number
even as the generous and sharing ones die out. The total population
shrinks but the population of the nasty remainders does not. So is
that lower reproductive success or not? If that surviving population
can't withstand attacks from outside because of lack of mutual
cooperation, then that must introduce a new kind of group fitness
quite distinct from averaging the individual fitness of the group
members. I have been out of the professional biology loop for too
long, now, to know just how pop gen handles such things.

[Bob Casanova]

On Mon, 18 May 2015 12:57:01 -0700 (PDT), the following
appeared in talk.origins, posted by erik simpson
<eastsi...@gmail.com>:

I hope it wasn't a regimental-striped one.
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[John Harshman]

Those are generally known as cheater genes, or something similar.
Selfish genes benefit the genes, not the individuals. Cheater genes
benefit the individual, not the population.

> We we engaging in little pedantic arguments here but in one sense, the
> selfish or non-cooperative individuals can thrive and grow in number
> even as the generous and sharing ones die out. The total population
> shrinks but the population of the nasty remainders does not. So is
> that lower reproductive success or not?

If you're talking about average or whole-population fitness, then yes.

> If that surviving population
> can't withstand attacks from outside because of lack of mutual
> cooperation, then that must introduce a new kind of group fitness
> quite distinct from averaging the individual fitness of the group
> members. I have been out of the professional biology loop for too
> long, now, to know just how pop gen handles such things.

No, the inability to withstand attacks would (assuming there were ever
any attacks) cause lower average reproductive success for the
individuals in the population, and so is not a new kind of fitness.

[RSNorman]

On Tue, 19 May 2015 10:49:46 -0700, John Harshman

I suppose the group benefit of cooperation could be handled by some
sort of frequency dependent selection: as the percentage of cheaters
(I do learn from being corrected!) increases the fitness of every
member of the population will decrease. Isn't this an example of
selection above the level of the individual? (Not that that is
anything wrong with that notion.)

[John Harshman]

No, I don't think frequency-dependent selection is above the level of
the individual. Each individidual is simply part of the environment of
other individuals. Now I suppose the group benefit could be thought of
as an increase in the mean fitness of group members, and the mean is a
group property. But on the other hand the mean is just an aggregate of
individual fitnesses, and cooperation would act by increasing the
fitnesses of some individuals while possible reducing the fitnesses of
others. And a cheater would have greater than mean fitness, even if his
actions reduced the mean.

A completely altruistic allele can spread through a population only by
drift, and thus any selection would occur only at the group level. Any
such allele that drifted to fixation within a group would tend to
increase that group's size at the expense of other groups. There's your
group selection. Cheater alleles spread through ordinary selection. And
there might be cheater-punishing alleles or enforcement alleles that
might be selected for in an altruistic group and might help maintain (or
even spread?) altruistic alleles.