Wide Spread

[Glenn]

"The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment. "

https://www.annualreviews.org/doi/10.1146/annurev-conmatphys-062910-140509

What say the morons?

[RonO]

Since you've read it you can give us a summary because few of us are
going to pay the $32.00 to read it.

Ron Okimoto

[Glenn]

There's one moron's 2 sense.

https://arxiv.org/pdf/1011.4125.pdf

[erik simpson]

The arxiv version is free:

https://arxiv.org/pdf/1011.4125.pdf

It's not exactly new, but comparatively recent. It wouldn't hurt DrDr to read
it, but I doubt he would. I'm not certain it's had the bad effect on medicine
that the authors are concerned about. Most researchers aren't listening to
input from general prectitioners anyway, particularly cranky ones, and most are
reptilefeatherians anyway (thank God).

I've heard it said that "all medicine is snecdotal", which is certainly unfair,
but most medicine as practised isn't depending on the cutting edge. The
discussion of working past the "modern synthesis" is particularly interesting.
You Know Who might find it revealing that attention has been and is being given
to the "woefully inadequate TOE". There even stuff in there for complexity
theory fans.

[jillery]

On Sat, 7 Mar 2020 20:09:38 -0800 (PST), erik simpson
<eastsi...@gmail.com> wrote:

>On Saturday, March 7, 2020 at 7:15:02 PM UTC-8, Ron O wrote:
>> On 3/7/2020 8:58 PM, Glenn wrote:
>> >
>> > "The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment."
>> >
>> > https://www.annualreviews.org/doi/10.1146/annurev-conmatphys-062910-140509
>> >
>> > What say the morons?
>> >
>>
>> Since you've read it you can give us a summary because few of us are
>> going to pay the $32.00 to read it.
>>
>> Ron Okimoto
>
>The arxiv version is free:
>
>https://arxiv.org/pdf/1011.4125.pdf
>
>It's not exactly new, but comparatively recent. It wouldn't hurt DrDr to read
>it, but I doubt he would. I'm not certain it's had the bad effect on medicine
>that the authors are concerned about. Most researchers aren't listening to
>input from general prectitioners anyway, particularly cranky ones, and most are
>reptilefeatherians anyway (thank God).
>

>I've heard it said that "all medicine is [a]necdotal", which is certainly unfair,

>but most medicine as practised isn't depending on the cutting edge. The
>discussion of working past the "modern synthesis" is particularly interesting.
>You Know Who might find it revealing that attention has been and is being given
>to the "woefully inadequate TOE". There even stuff in there for complexity
>theory fans.

Since you mention drdr bonzo, I can't resist noting the irony of the
following:

*************************************
...on the other hand, the lack of appreciation for the RAPIDITY AND
PERVASIVENESS [emphasis mine] of evolution has, within a lifetime,
destroyed the effectiveness of numerous antibiotics, and probably is
responsible for the limited success of the treatment
of cancer.
*************************************

According to the authors, it's assumptions that evolution is too slow
and limited which causes multiple drug resistance, failed cancer
treatments, and harm to children. It would have been even more
delicious if they mentioned HIV and malaria, but this will do. They
sound like reptifeatharians to me.

How clever of Glenn, to act the double-agent, to post this cite as if
it refutes those he calls "morons", when in fact it identifies the
authors as among those "morons". I should have recognized his genius
before.

--
You're entitled to your own opinions.
You're not entitled to your own facts.

[RonO]

QUOTE:
We envisage a readership with a wide range of knowledge and interest in
evolutionary biology. To the biologist interested in practical issues,
we ask that you do not dismiss the seemingly useless and na¨ıve issues
that we necessarily raise.
END QUOTE:

That also excludes the willfully ignorant.

How does this help IDiots out? You might want to state what you get out
of this paper.

They make a case that biology has a physical nature. No big whooop.
They point out that we don't know everything. No big secrect though we
do know more than we did when they published this paper. Woese was a
pretty sharp guy. I don't know about Goldenfeld.

The new synthesis is incomplete. Again, no big whoop or surprise. It
is still incomplete.

These guys are proposing that we look at the issues in a different way
from what they perceive is the norm. They could be onto something, but
the problem is that it is difficult to do what they want to do. This
doesn't mean that it should not be tried, but that it will be some time
before anyone does it.

If you look at genetic papers on epistasis and nonadditive genetic
variation you will know that researchers have constantly looked into
gene interactions, but we are just beginning to develop the tools to
really look into the issue. In my experience most of the papers do not
find a significant component for epistasis in the systems that they look
at. My take is that we lack the means to detect it at the level that it
is occurring. I would hope that there are very few geneticists that do
not understand that life is a boad load of gene interactions, but we
haven't been able to tease them out very well. Just check out the last
30 years of papers on nonadditive genetics. Population genetics and the
new synthesis have concentrated on the additive genetic variation
because that is the part that we can easily study. The literature will
tell you that geneticists have constantly attempted to look at the
nonadditive fraction, but it was pretty much impossible before
computers, and we need to understand a lot more about cell physiology
and basic biochemistry before we can attack the problem even with the
current super computers. It has not been ignored, the classic example
of obvious gene interaction Pea Comb and Rose comb creating Walnut comb
in chickens was in most genetics and even college level biology texts
and likely still is though I haven't checked it out in over a decade.
That gene interaction was described by Bateson and Punnett pretty much
at the beginning of modern genetics over 100 years ago.

So where does this get IDiots? What do you think will happen when we
are able to do the type of research that they think should be done?

So what besides your usual god of the gaps argument are you making?

Ron Okimoto

[Kalkidas]

Yeah, after all, they've only had 160 years of intense indoctrination to
explain "the evolutionary process" to us rubes. Give it time. ;-)

[RonO]

On 3/7/2020 9:57 PM, Glenn wrote:

[RonO]

How do you determine what articles are available from arxiv?

Ron Okimoto

[erik simpson]

I use Unpaywall, which has a Firefox extension. It dispays a litle green
padlock with the hasp undone if there's an available source. Otherwise you can
Google stuff, but Unpaywall saves a lot of looking.

[RonO]

Thanks.

Ron Okimoto

[Bob Casanova]

On Sat, 7 Mar 2020 18:58:05 -0800 (PST), the following
appeared in talk.origins, posted by Glenn
<GlennS...@msn.com>:

>
>"The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment. "
>
>https://www.annualreviews.org/doi/10.1146/annurev-conmatphys-062910-140509
>
>What say the morons?

Mirror, mirror...
--

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

[Burkhard]

great tip! I use google scholar, and then check the "versions" link,
which normally lists also all the free ones, but this sounds even faster

[Peter Nyikos]

On Saturday, March 7, 2020 at 10:00:03 PM UTC-5, Glenn wrote:

> "The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment. "

This may come as a surprise to some people, especially where medicine
is concerned, because of the overwhelming pre-med orientation of
biology departments all over the USA. But "pre-med" is pre-MD, not
pre-Ph.D. in biology (with emphasis on medical research) which is where
actual progress in medicine is concentrated AFAIK.


Here is what I wrote on another thread about some of those disastrous
consequences:

Modern society is suffering from an advanced state of bureaucratization
and "nanny state" crony capitalism. The inevitable end, I fear,
is an almost exclusive emphasis on instant scientific/technological solutions.

There has been a devaluation of all pure (as opposed to applied)
science. Our biology department has long ago ceased to offer the
courses (still on the books) on ornithology and mammals. Clemson
may still have those, but all courses and even clubs in paleontology
are things of the past (at least 5 years in the past).

Already when I was an undergraduate, I got fed up with the
way my college's biology department was pre-med oriented,
even in the course in general zoology, and switched my
major from biology to mathematics. It's even worse here, now.

That was over half a century ago, btw.

> https://www.annualreviews.org/doi/10.1146/annurev-conmatphys-062910-140509

Co-authored by Carl Woese, a truly great naturalist whose like we
are not likely to see again in today's climate of intellectual exhaustion
and compartmentalization.

This article was published a bit less than two years before his death.

I have printed out the paper and will be giving it a great deal of careful
study. I hope by Friday I will be able to give some worthwhile comments on
more than just the abstract.


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

[Peter Nyikos]

This is interesting, since I got it right here on my office computer,
immediately. Evidently Ron O does not work for an institution that
gives its faculty (or the business equivalent) access to the journal.

> There's one moron's 2 sense.

I'm surprised that Alan Kleinman, who has nicknamed Ron O moRON, hasn't
shown up on this thread yet. Yet Erik Simpson wrote about "DrDr" here
back on the 7th. More importantly, note what the part you quoted from
the abstract says about the baleful effects of the failure to
understand evolutionary biology on medicine.


> https://arxiv.org/pdf/1011.4125.pdf

The html version of the article looks great, and a fringe benefit of my
university's subscription is that the pdf for the finished article is prettier
than the one available via arxiv.org.

Additional trivia: the arxiv.org version predates the paper itself,
so there may have been a few changes here and there before the
printed version.


Peter Nyikos

[John Harshman]

On 3/11/20 9:27 AM, Peter Nyikos wrote:
> On Saturday, March 7, 2020 at 10:00:03 PM UTC-5, Glenn wrote:
>
>> "The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment."
>
> This may come as a surprise to some people, especially where medicine
> is concerned, because of the overwhelming pre-med orientation of
> biology departments all over the USA. But "pre-med" is pre-MD, not
> pre-Ph.D. in biology (with emphasis on medical research) which is where
> actual progress in medicine is concentrated AFAIK.

I have not experienced this overwhelming pre-med orientation. I've had
premeds in undergraduate biology classes both as an undergrad myself and
as a TA. But never in the majority and never all that many and never
driving the curriculum. Where do you draw your conclusions from?

> Here is what I wrote on another thread about some of those disastrous
> consequences:
>
> Modern society is suffering from an advanced state of bureaucratization
> and "nanny state" crony capitalism. The inevitable end, I fear,
> is an almost exclusive emphasis on instant scientific/technological solutions.
>
> There has been a devaluation of all pure (as opposed to applied)
> science. Our biology department has long ago ceased to offer the
> courses (still on the books) on ornithology and mammals. Clemson
> may still have those, but all courses and even clubs in paleontology
> are things of the past (at least 5 years in the past).
>
> Already when I was an undergraduate, I got fed up with the
> way my college's biology department was pre-med oriented,
> even in the course in general zoology, and switched my
> major from biology to mathematics. It's even worse here, now.
>
> That was over half a century ago, btw.
>
>> https://www.annualreviews.org/doi/10.1146/annurev-conmatphys-062910-140509
>
> Co-authored by Carl Woese, a truly great naturalist whose like we
> are not likely to see again in today's climate of intellectual exhaustion
> and compartmentalization.
>
> This article was published a bit less than two years before his death.
>
> I have printed out the paper and will be giving it a great deal of careful
> study. I hope by Friday I will be able to give some worthwhile comments on
> more than just the abstract.

Is the Annual Review of Condensed Matter Physics really the right place
for an article on evolutionary biology? Are the reviewers and editors of
that journal really the right peer reviewers?

[Bill Jefferys]

It might not be so far-fetched here.

Reading the abstract, this is a discussion of life in the context of far-from-equilibrium thermodynamics, a physical regime that allows (and even requires) that localized, complex systems will arise spontaneously in thermodynamic systems that are far from equilibrium, due to the flow of energy from regions that have a concentrated amount of it (e.g., stars) to those that have hardly energy (e.g., deep empty space). Objects that are in the way (e.g., the Earth) intercept a portion of the energy releases by the stars and in the process of dumping it into outer space, all sorts of interesting physics happens, including life.

My colleague at the University of Texas, Ilya Prigogine, a chemist and physics, won the Nobel Prize in Chemistry in 1977 for work in this area. He called these structures, that spontaneously arise in this process, "dissipative structures."

https://en.wikipedia.org/wiki/Ilya_Prigogine

Bill

[Glenn]

What's "cornplexity"?
https://link.springer.com/chapter/10.1007/978-3-663-01511-6_10

[j.nobel...@gmail.com]

On Wednesday, March 11, 2020 at 9:45:02 PM UTC-4, John Harshman wrote:

> On 3/11/20 9:27 AM, Peter Nyikos wrote:
> > On Saturday, March 7, 2020 at 10:00:03 PM UTC-5, Glenn wrote:
> >
> >> "The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment."
> >
> > This may come as a surprise to some people, especially where medicine
> > is concerned, because of the overwhelming pre-med orientation of
> > biology departments all over the USA. But "pre-med" is pre-MD, not
> > pre-Ph.D. in biology (with emphasis on medical research) which is where
> > actual progress in medicine is concentrated AFAIK.
>
> I have not experienced this overwhelming pre-med orientation. I've had
> premeds in undergraduate biology classes both as an undergrad myself and
> as a TA. But never in the majority and never all that many and never
> driving the curriculum. Where do you draw your conclusions from?

The term "overwhelming" renders this subjective but I've known many
to express similar sentiment. And it extends beyond the root biology
curriculum. Some schools have for instance adopted Organic Chemistry
for Biology Majors, and even Physics for Biology majors. Interestingly,
those seeking a Biochemistry degree have to take Organic Chemistry for
organic chemists, same with those seeking a Genetics degree. The
explanation is that if you are training to be scientist, you want to
actually learn organic chemistry but if you are actually a pre-med
you just need to memorize some stuff in order to do well on the MCATS.

The "for biology majors" in the course title is mostly "for premeds".
(not entirely true as which courses are required vary across many
degrees).

I've also been 1 degree removed from discussions about what to include
in the 1st year biology class, the "weed out" class. Those focused on
the pre-med track want to keep it heavily memorization based and do
indeed drive the significance of those things thought to be including
in medical school entrance exams. These fight with various biological
disciplines over how to best introduce concepts critical to their
discipline. At minimum, there is a significant tension and compromise
towards the premed agenda.

[Bill Rogers]

When I was a pre-med I took P-Chem and organic chem for the chemists, and physics for the physics majors because even though the courses were harder, the classes were smaller, the students were nicer, and they did not have the high stress, competitive feeling about them that the pre-med courses had.

[j.nobel...@gmail.com]

I've heard that sentiment as well, and something like it that countered
that the organic chemistry for chemistry majors was actually easier
(for them) because it was geared towards a theoretical understanding
rather than rote memorization of a bunch of named reactions. For many,
it's easier to understand the general principles first, then understand
the contexts in which they apply, organizing things by the higher
concept.

Same with choices of calculus courses for that matter. There was an
option to take a course that was very rule based to cover differential
and integral calculus that was little more than presentation of
tables and dragging people through examples.

It sadly leaves some people with the impression that they understand
things that they really do not, not that such a pair of docs would
apply to anyone you might encounter around here.

[Alan Kleinman MD PhD]

Too bad you didn't learn how to exercise those skills, if you had, you might have recognized that evolutionary competition is an example of the first law of thermodynamics. And DNA evolution is an example of the second law of thermodynamics.

[Peter Nyikos]

On Wednesday, March 11, 2020 at 9:45:02 PM UTC-4, John Harshman wrote:

> On 3/11/20 9:27 AM, Peter Nyikos wrote:
> > On Saturday, March 7, 2020 at 10:00:03 PM UTC-5, Glenn wrote:

> >> "The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment."

This was not the first sentence in the abstract; it was the fourth.

John, if you recall my thread, TOWARDS A SCIENTIFIC THEORY OF MACROEVOLUTION,
you may surmise from the first three sentences of the abstract why I am highly
motivated to read the paper in detail:

Evolution is the fundamental physical process that gives rise to
biological phenomena. Yet it is widely treated as a subset of population
genetics, and thus its scope is artificially limited. As a result, the
key issues of how rapidly evolution occurs and its coupling to ecology
have not been satisfactorily addressed and formulated.

By the way, I believe Alan Kleinman is all too happy to have the subject
of evolution continue to be "widely treated as a subset of population genetics."
Do you share this attitude with him?

> >
> > This may come as a surprise to some people, especially where medicine
> > is concerned, because of the overwhelming pre-med orientation of
> > biology departments all over the USA. But "pre-med" is pre-MD, not
> > pre-Ph.D. in biology (with emphasis on medical research) which is where
> > actual progress in medicine is concentrated AFAIK.
>
> I have not experienced this overwhelming pre-med orientation. I've had
> premeds in undergraduate biology classes both as an undergrad myself and
> as a TA.

At the University of California in Berkeley, no?

> But never in the majority and never all that many and never
> driving the curriculum. Where do you draw your conclusions from?

From colleges and universities without the Brahmin status of UC-Berkeley.

>
> > Here is what I wrote on another thread about some of those disastrous
> > consequences:
> >
> > Modern society is suffering from an advanced state of bureaucratization
> > and "nanny state" crony capitalism. The inevitable end, I fear,
> > is an almost exclusive emphasis on instant scientific/technological solutions.
> >
> > There has been a devaluation of all pure (as opposed to applied)
> > science. Our biology department has long ago ceased to offer the
> > courses (still on the books) on ornithology and mammals. Clemson
> > may still have those, but all courses and even clubs in paleontology
> > are things of the past (at least 5 years in the past).

Note, John, that you cannot judge the orientation of departments by looking
up the course catalogue. We have courses in our own department
that haven't run for two decades or more.

Our Department of Biological sciences had an interdisciplinary
undergraduate semester course up until a bit over a decade ago, on the
geological and biological history of the earth. The person who
last taught it retired the following year, and the follow-up semester course
was not taught by anyone, and neither course has not been taught since.

I'd have to look them up, but I wouldn't be the least bit surprised
if the courses are still in the undergraduate master catalogue.

> > Already when I was an undergraduate, I got fed up with the
> > way my college's biology department was pre-med oriented,
> > even in the course in general zoology, and switched my
> > major from biology to mathematics. It's even worse here, now.
> >
> > That was over half a century ago, btw.
> >
> >> https://www.annualreviews.org/doi/10.1146/annurev-conmatphys-062910-140509
> >
> > Co-authored by Carl Woese, a truly great naturalist whose like we
> > are not likely to see again in today's climate of intellectual exhaustion
> > and compartmentalization.
> >
> > This article was published a bit less than two years before his death.
> >
> > I have printed out the paper and will be giving it a great deal of careful
> > study. I hope by Friday I will be able to give some worthwhile comments on
> > more than just the abstract.
>
> Is the Annual Review of Condensed Matter Physics really the right place
> for an article on evolutionary biology?

How should I know? This is the first time I have heard of the journal,
but from Ron O's inability to access it, I would surmise that it
is fairly prestigious. Do you disagree?

> Are the reviewers and editors of
> that journal really the right peer reviewers?

If you are attempting to cast aspersions on the article,
or on Woese himself, you are hamstrung by your laziness
into making the attempt look pathetic.

Note the "If". In fact, I wouldn't even bring up the possibility at all,
were not your questions too provocative to be the product of disinterested inquiry.

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

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

[j.nobel...@gmail.com]

Even by your "standards" the first is an obtuse statement. The second
claim, however, can be partially rehabilitated. Using TdS <= -dQ as one
statement of the second law, one can note that any change in entropy
must be paid for by an adequate supply of Q (energy). Essentially, you
have to plug the refrigerator in for it to cool.

This particular constraint is of course not problematic for systems
far from equilibrium where the flow of energy is relatively large
compared to the temporary reduction in entropy in dissipative structures.

This is formalized in some treatments of statistical mechanics. It's
standard fair for basic fluid dynamics. And apparently, it's misunderstood
by people whose understanding of probability is limited to introductory
courses.

[Peter Nyikos]

On Thursday, March 12, 2020 at 7:10:03 PM UTC-4, Peter Nyikos wrote:

> Our Department of Biological sciences had an interdisciplinary
> undergraduate semester course up until a bit over a decade ago, on the
> geological and biological history of the earth. The person who
> last taught it retired the following year, and the follow-up semester course
> was not taught by anyone, and neither course has not been taught since.

Haste makes waste: the "not" that is fourth from the end does not belong.

By the way, there is also a geology department, but it doesn't offer
that kind of interdisciplinary course either. There are all too
many topics that fall into the cracks between departments,
and never see the light of day.

Also into cracks within a department. The subject of change
of variables in multivariate calculus has consistently
fallen into the crack between it and the course in vector calculus,
except when I teach the latter, ever since the multivariate
calculus course went from five days a week to three days a week,
about thirty years ago.

As for the Inverse Function Theorem and the Implicit Function Theorem,
there are several cracks into which they can fall, and AFAIK they
have always fallen into them in the four decades I have been here.


[I miss Richard Norman. He'd know exactly what I am talking about here;
I don't know whether anyone else who is still active in talk.origins can.]


Peter Nyikos
Professor of Mathematics -- standard disclaimer--

[John Harshman]

On 3/12/20 4:09 PM, Peter Nyikos wrote:
> On Wednesday, March 11, 2020 at 9:45:02 PM UTC-4, John Harshman wrote:
>> On 3/11/20 9:27 AM, Peter Nyikos wrote:
>>> On Saturday, March 7, 2020 at 10:00:03 PM UTC-5, Glenn wrote:
>
>>>> "The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment."
>
> This was not the first sentence in the abstract; it was the fourth.
>
> John, if you recall my thread, TOWARDS A SCIENTIFIC THEORY OF MACROEVOLUTION,
> you may surmise from the first three sentences of the abstract why I am highly
> motivated to read the paper in detail:
>
> Evolution is the fundamental physical process that gives rise to
> biological phenomena. Yet it is widely treated as a subset of population
> genetics, and thus its scope is artificially limited. As a result, the
> key issues of how rapidly evolution occurs and its coupling to ecology
> have not been satisfactorily addressed and formulated.
>
> By the way, I believe Alan Kleinman is all too happy to have the subject
> of evolution continue to be "widely treated as a subset of population genetics."
> Do you share this attitude with him?

Of course there's more to it than that. Why are you bringing Kleinman
into it?

>>> This may come as a surprise to some people, especially where medicine
>>> is concerned, because of the overwhelming pre-med orientation of
>>> biology departments all over the USA. But "pre-med" is pre-MD, not
>>> pre-Ph.D. in biology (with emphasis on medical research) which is where
>>> actual progress in medicine is concentrated AFAIK.
>>
>> I have not experienced this overwhelming pre-med orientation. I've had
>> premeds in undergraduate biology classes both as an undergrad myself and
>> as a TA.
>
> At the University of California in Berkeley, no?

No. U. of Chicago.

>> But never in the majority and never all that many and never
>> driving the curriculum. Where do you draw your conclusions from?
>
> From colleges and universities without the Brahmin status of UC-Berkeley.

So your contention is that this is a phenomenon of lower-caste
universities only? I must say that I didn't encounter it in the
California State University system either.

Then again, I do recall a lot of comment in the 1990s when Stanford
de-accessioned all their natural history collections. What you're
talking about here might be the rise of molecular biology and the
relative decline of organismal biology in many institutions. But not
Berkeley, not CSU, and not U. of Chicago. My condolences if it applies
to your school.

Your conclusion calls for a broader sample.

>>> Here is what I wrote on another thread about some of those disastrous
>>> consequences:
>>>
>>> Modern society is suffering from an advanced state of bureaucratization
>>> and "nanny state" crony capitalism. The inevitable end, I fear,
>>> is an almost exclusive emphasis on instant scientific/technological solutions.
>>>
>>> There has been a devaluation of all pure (as opposed to applied)
>>> science. Our biology department has long ago ceased to offer the
>>> courses (still on the books) on ornithology and mammals. Clemson
>>> may still have those, but all courses and even clubs in paleontology
>>> are things of the past (at least 5 years in the past).
>
> Note, John, that you cannot judge the orientation of departments by looking
> up the course catalogue. We have courses in our own department
> that haven't run for two decades or more.

I never have. But so far all you have is anecdote, which as you know is
not the singular of data.

It's an Annual Review, though I suspect not one of the more widely
available ones. Those tend to have shorter and more obvious titles, like
Annu. Rev. Genetics, Annu. Rev. Geology, Annu. Rev. Ecology and
Systematics, etc. Why would you imagine that Ron would lack access to
prestigious journals, especially? I would think the opposite.

>> Are the reviewers and editors of
>> that journal really the right peer reviewers?
>
> If you are attempting to cast aspersions on the article,
> or on Woese himself, you are hamstrung by your laziness
> into making the attempt look pathetic.
>
> Note the "If". In fact, I wouldn't even bring up the possibility at all,
> were not your questions too provocative to be the product of disinterested inquiry.

There is a history of physicists trying to help out biologists by
telling them they're doing it all wrong, and publishing these helpful
articles in journals that biologists don't read. I speculate that we
might have something of the sort here. You know, like publishing
articles on evolution in something called "Statistics in Medicine".

[erik simpson]

Oh, Peter, you are so smart, and we are so stupid. If you could just tell us
a little about Advanced Math we would be so grateful.

[*Hemidactylus*]

I do also miss Richard Norman, but not for the Inverse Function Theorem and
the Implicit Function Theorem.

[Bill Jefferys]

It is technically called a "typo".

Bill

[erik simpson]

I apologize for my previous post. Your boasting is tiresome, but my remarks
were unhelpful.

[Glenn]

In scientific papers that are checked, edited and reviewed? Unlikely.
And I caught it on first read. This suggests:
>
https://en.wikipedia.org/wiki/Satiric_misspelling
https://en.wikipedia.org/wiki/Sensational_spelling
https://en.wikipedia.org/wiki/Catachresis
https://en.wikipedia.org/wiki/Cacography
https://en.wikipedia.org/wiki/Typographical_error

Could be unconscious or intentional? Freudian?

[Bill Jefferys]

Technically, "typos".

Bill

[Mark Isaak]

On 3/12/20 4:31 PM, John Harshman wrote:
> On 3/12/20 4:09 PM, Peter Nyikos wrote:
>> On Wednesday, March 11, 2020 at 9:45:02 PM UTC-4, John Harshman wrote:

>>> [...]

>>> Is the Annual Review of Condensed Matter Physics really the right place
>>> for an article on evolutionary biology?
>>
>> How should I know? This is the first time I have heard of the journal,
>> but from Ron O's inability to access it, I would surmise that it
>> is fairly prestigious. Do you disagree?
>
> It's an Annual Review, though I suspect not one of the more widely
> available ones. Those tend to have shorter and more obvious titles, like
> Annu. Rev. Genetics, Annu. Rev. Geology, Annu. Rev. Ecology and
> Systematics, etc. Why would you imagine that Ron would lack access to
> prestigious journals, especially? I would think the opposite.

Wikipedia's "Annual Reviews" article has a full list. One you list
above, incidentally, has been renamed "Annual Review of Ecology,
Evolution, and Systematics." The longest title is "Annual Review of
Organizational Psychology and Organizational Behavior".

I just checked the catalog of San Jose State University, which is
probably on the small side for universities, and it does not have _Ann
Rev of Condensed Matter Physics_.

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"Omnia disce. Videbis postea nihil esse superfluum."
- Hugh of St. Victor

[Burkhard]

Edinburgh has it - it seems t be a younger one, first volume is from 2010

[Peter Nyikos]

On Thursday, March 12, 2020 at 7:35:04 PM UTC-4, John Harshman wrote:
> On 3/12/20 4:09 PM, Peter Nyikos wrote:
> > On Wednesday, March 11, 2020 at 9:45:02 PM UTC-4, John Harshman wrote:
> >> On 3/11/20 9:27 AM, Peter Nyikos wrote:
> >>> On Saturday, March 7, 2020 at 10:00:03 PM UTC-5, Glenn wrote:
> >
> >>>> "The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment."
> >
> > This was not the first sentence in the abstract; it was the fourth.
> >
> > John, if you recall my thread, TOWARDS A SCIENTIFIC THEORY OF MACROEVOLUTION,
> > you may surmise from the first three sentences of the abstract why I am highly
> > motivated to read the paper in detail:
> >
> > Evolution is the fundamental physical process that gives rise to
> > biological phenomena. Yet it is widely treated as a subset of population
> > genetics, and thus its scope is artificially limited. As a result, the
> > key issues of how rapidly evolution occurs and its coupling to ecology
> > have not been satisfactorily addressed and formulated.
> >
> > By the way, I believe Alan Kleinman is all too happy to have the subject
> > of evolution continue to be "widely treated as a subset of population genetics."
> > Do you share this attitude with him?
>
> Of course there's more to it than that.

True to form, you do not say what that "more" is, whereas I have
gone on record as supporting the thesis that it is almost
totally lacking in macroevolutionary and, especially, mega-evolutionary theory.

> Why are you bringing Kleinman into it?

Because he is an ardent supporter of the thesis that microevolutionary
theory is the way to understand evolution. I know of no other regular
here who is as *explicit* about that as he is, though many seem to believe
that the Modern Synthesis [known to creationists as Neo-Darwinism]
is all the evolutionary theory that is needed to explain the
vast panoply of life on earth.

> >>> This may come as a surprise to some people, especially where medicine
> >>> is concerned, because of the overwhelming pre-med orientation of
> >>> biology departments all over the USA. But "pre-med" is pre-MD, not
> >>> pre-Ph.D. in biology (with emphasis on medical research) which is where
> >>> actual progress in medicine is concentrated AFAIK.
> >>
> >> I have not experienced this overwhelming pre-med orientation. I've had
> >> premeds in undergraduate biology classes both as an undergrad myself and
> >> as a TA.
> >
> > At the University of California in Berkeley, no?
>
> No. U. of Chicago.

I've been at the U. of Chicago on a postdoc, and it is at least as Brahmin
in its undergraduate curriculum as UC-Berkeley. Every student back then
had to go through a personal interview to be admitted. The intellectual
sophistication of the undergrads there was a world apart from that
of those in University of Illinois at Urbana, itself a leading university.

> >> But never in the majority and never all that many and never
> >> driving the curriculum. Where do you draw your conclusions from?
> >
> > From colleges and universities without the Brahmin status of UC-Berkeley.
>
> So your contention is that this is a phenomenon of lower-caste
> universities only?

Any below Brahmin status: see above about U.Illinois.

> I must say that I didn't encounter it in the
> California State University system either.
>
> Then again, I do recall a lot of comment in the 1990s when Stanford
> de-accessioned all their natural history collections. What you're
> talking about here might be the rise of molecular biology and the
> relative decline of organismal biology in many institutions. But not
> Berkeley, not CSU, and not U. of Chicago. My condolences if it applies
> to your school.

Your condolences are taken for what they are worth. Especially since
you don't include Stanford on your list, yet its prestige is far above
that of CSU -- isn't it?

>
> Your conclusion calls for a broader sample.

So does yours.

> >>> Here is what I wrote on another thread about some of those disastrous
> >>> consequences:
> >>>
> >>> Modern society is suffering from an advanced state of bureaucratization
> >>> and "nanny state" crony capitalism. The inevitable end, I fear,
> >>> is an almost exclusive emphasis on instant scientific/technological solutions.
> >>>
> >>> There has been a devaluation of all pure (as opposed to applied)
> >>> science. Our biology department has long ago ceased to offer the
> >>> courses (still on the books) on ornithology and mammals. Clemson
> >>> may still have those, but all courses and even clubs in paleontology
> >>> are things of the past (at least 5 years in the past).
> >
> > Note, John, that you cannot judge the orientation of departments by looking
> > up the course catalogue. We have courses in our own department
> > that haven't run for two decades or more.
>
> I never have. But so far all you have is anecdote,

By that warped standard, so do you.

Stop acting as if you don't know what "paywalled" (to the tune of over
$30, no less!) means.

It isn't paywalled here. So much for your condolences.

> >> Are the reviewers and editors of
> >> that journal really the right peer reviewers?
> >
> > If you are attempting to cast aspersions on the article,
> > or on Woese himself, you are hamstrung by your laziness
> > into making the attempt look pathetic.
> >
> > Note the "If". In fact, I wouldn't even bring up the possibility at all,
> > were not your questions too provocative to be the product of disinterested inquiry.
>
> There is a history of physicists trying to help out biologists by
> telling them they're doing it all wrong, and publishing these helpful
> articles in journals that biologists don't read.

As usual, you give no hint of where this history is to be found.

In contrast, I have a copy of a classic article on quaternions
by Sir Edmund Whittaker, in which he wrote about how the
underlying thought processes that inspired Hamilton were
vindicated by some of the revolutionary physical theories of the
first half of the 20th century.

Each area of science and mathematics has its own thought processes,
which are like the part of the iceberg of research that is hidden
below the surface. They can be referred to as the little-understood
tools of the trade.

In my branch of topology, for example, we would
be lost without highly fictitious pictures of the spaces we describe,
to which we can refer as needed to work out the actual reasoning
about their structures. And we generally do have to refer to them
many times in the course of writing a research paper.

The article of Goldenfeld and Woese makes for very difficult
reading in its first few pages, but my impression is that they
are trying to convey some sense of the tools of the trade
of condensed matter physics that they believe to be useful
in a deeper understanding of biological evolution.


As an analogy, here is a bit of what Whittaker writes:

Meanwhile, the workers in quantum theory were coming
to realize that Hamilton's dynamical conceptions
must form the basis of all rules of quantification.
And in 1925 the other side of his work -- his noncommutative algebra --
was brought into quantum theory by Werner Heisenberg,
Max Born, and Pascual Jordan, who showed that the
ordinary Hamiltonian equations of dynamics were still
valid in quantum theory, provided the symbols
representing the coordinates and momenta in classical
dynamics were interpreted as operators whose products
did not commute.
-- "William Rowan Hamilton," in the anthology
_Mathematics_ by Samuel Rapport and Helen Wright,
New York University Press, 1963, pp.66-77.

There's more, but duty calls. Catch you next week.


<snip philistine speculation by an unemployed biologist here>

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

U. of South Carolina at Columbia
http://people.math.sc.edu/nyikos/

[Alan Kleinman MD PhD]

Microevolution is the only kind of evolution observed. And even that, biologists have failed to correctly explain the physics and mathematics. Perhaps in your imagination, fossils tell you otherwise. Why doesn't Nomathos explain the mathematics of those kinds of genetic transformations? If you can't come up with the math to explain macroevolution, we can call it Nomathian evolution.
<snip>

[John Harshman]

On 3/13/20 3:28 PM, Peter Nyikos wrote:
> On Thursday, March 12, 2020 at 7:35:04 PM UTC-4, John Harshman wrote:
>> On 3/12/20 4:09 PM, Peter Nyikos wrote:
>>> On Wednesday, March 11, 2020 at 9:45:02 PM UTC-4, John Harshman wrote:
>>>> On 3/11/20 9:27 AM, Peter Nyikos wrote:
>>>>> On Saturday, March 7, 2020 at 10:00:03 PM UTC-5, Glenn wrote:
>>>
>>>>>> "The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment."
>>>
>>> This was not the first sentence in the abstract; it was the fourth.
>>>
>>> John, if you recall my thread, TOWARDS A SCIENTIFIC THEORY OF MACROEVOLUTION,
>>> you may surmise from the first three sentences of the abstract why I am highly
>>> motivated to read the paper in detail:
>>>
>>> Evolution is the fundamental physical process that gives rise to
>>> biological phenomena. Yet it is widely treated as a subset of population
>>> genetics, and thus its scope is artificially limited. As a result, the
>>> key issues of how rapidly evolution occurs and its coupling to ecology
>>> have not been satisfactorily addressed and formulated.
>>>
>>> By the way, I believe Alan Kleinman is all too happy to have the subject
>>> of evolution continue to be "widely treated as a subset of population genetics."
>>> Do you share this attitude with him?
>>
>> Of course there's more to it than that.
>
> True to form, you do not say what that "more" is, whereas I have
> gone on record as supporting the thesis that it is almost
> totally lacking in macroevolutionary and, especially, mega-evolutionary theory.

True to form, you attack me even when I'm agreeing with you. Why must
you be so continuously unpleasant?

>> Why are you bringing Kleinman into it?
>
> Because he is an ardent supporter of the thesis that microevolutionary
> theory is the way to understand evolution. I know of no other regular
> here who is as *explicit* about that as he is, though many seem to believe
> that the Modern Synthesis [known to creationists as Neo-Darwinism]
> is all the evolutionary theory that is needed to explain the
> vast panoply of life on earth.

No he isn't. He supports the thesis that his bizarre, simple math is the
way to understand evolution, and that most evolution is impossible.

>>>>> This may come as a surprise to some people, especially where medicine
>>>>> is concerned, because of the overwhelming pre-med orientation of
>>>>> biology departments all over the USA. But "pre-med" is pre-MD, not
>>>>> pre-Ph.D. in biology (with emphasis on medical research) which is where
>>>>> actual progress in medicine is concentrated AFAIK.
>>>>
>>>> I have not experienced this overwhelming pre-med orientation. I've had
>>>> premeds in undergraduate biology classes both as an undergrad myself and
>>>> as a TA.
>>>
>>> At the University of California in Berkeley, no?
>>
>> No. U. of Chicago.
>
> I've been at the U. of Chicago on a postdoc, and it is at least as Brahmin
> in its undergraduate curriculum as UC-Berkeley. Every student back then
> had to go through a personal interview to be admitted. The intellectual
> sophistication of the undergrads there was a world apart from that
> of those in University of Illinois at Urbana, itself a leading university.

Sure. But what is the relevance here?

>>>> But never in the majority and never all that many and never
>>>> driving the curriculum. Where do you draw your conclusions from?
>>>
>>> From colleges and universities without the Brahmin status of UC-Berkeley.
>>
>> So your contention is that this is a phenomenon of lower-caste
>> universities only?
>
> Any below Brahmin status: see above about U.Illinois.

OK, thanks for clarifying.

>> I must say that I didn't encounter it in the
>> California State University system either.
>>
>> Then again, I do recall a lot of comment in the 1990s when Stanford
>> de-accessioned all their natural history collections. What you're
>> talking about here might be the rise of molecular biology and the
>> relative decline of organismal biology in many institutions. But not
>> Berkeley, not CSU, and not U. of Chicago. My condolences if it applies
>> to your school.
>
> Your condolences are taken for what they are worth. Especially since
> you don't include Stanford on your list, yet its prestige is far above
> that of CSU -- isn't it?

What list?

>> Your conclusion calls for a broader sample.
>
> So does yours.

I merely offer counter-anecdotes to yours. The proper conclusion is that
neither of us can support any sort of general conclusion.

>>>>> Here is what I wrote on another thread about some of those disastrous
>>>>> consequences:
>>>>>
>>>>> Modern society is suffering from an advanced state of bureaucratization
>>>>> and "nanny state" crony capitalism. The inevitable end, I fear,
>>>>> is an almost exclusive emphasis on instant scientific/technological solutions.
>>>>>
>>>>> There has been a devaluation of all pure (as opposed to applied)
>>>>> science. Our biology department has long ago ceased to offer the
>>>>> courses (still on the books) on ornithology and mammals. Clemson
>>>>> may still have those, but all courses and even clubs in paleontology
>>>>> are things of the past (at least 5 years in the past).
>>>
>>> Note, John, that you cannot judge the orientation of departments by looking
>>> up the course catalogue. We have courses in our own department
>>> that haven't run for two decades or more.
>>
>> I never have. But so far all you have is anecdote,
>
> By that warped standard, so do you.

Quite so. But why is it a warped standard?

What? You are very confused about what this conversation has been about.

>>>> Are the reviewers and editors of
>>>> that journal really the right peer reviewers?
>>>
>>> If you are attempting to cast aspersions on the article,
>>> or on Woese himself, you are hamstrung by your laziness
>>> into making the attempt look pathetic.
>>>
>>> Note the "If". In fact, I wouldn't even bring up the possibility at all,
>>> were not your questions too provocative to be the product of disinterested inquiry.
>>
>> There is a history of physicists trying to help out biologists by
>> telling them they're doing it all wrong, and publishing these helpful
>> articles in journals that biologists don't read.
>
> As usual, you give no hint of where this history is to be found.

You aren't acquainted with it? Fred Hoyle? The famous Asilomar Conference?

> In contrast, I have a copy of a classic article on quaternions
> by Sir Edmund Whittaker, in which he wrote about how the
> underlying thought processes that inspired Hamilton were
> vindicated by some of the revolutionary physical theories of the
> first half of the 20th century.
>
> Each area of science and mathematics has its own thought processes,
> which are like the part of the iceberg of research that is hidden
> below the surface. They can be referred to as the little-understood
> tools of the trade.
>
> In my branch of topology, for example, we would
> be lost without highly fictitious pictures of the spaces we describe,
> to which we can refer as needed to work out the actual reasoning
> about their structures. And we generally do have to refer to them
> many times in the course of writing a research paper.

How is this digression relevant?

> The article of Goldenfeld and Woese makes for very difficult
> reading in its first few pages, but my impression is that they
> are trying to convey some sense of the tools of the trade
> of condensed matter physics that they believe to be useful
> in a deeper understanding of biological evolution.

Yes, I think that's what they're doing.

> As an analogy, here is a bit of what Whittaker writes:
>
> Meanwhile, the workers in quantum theory were coming
> to realize that Hamilton's dynamical conceptions
> must form the basis of all rules of quantification.
> And in 1925 the other side of his work -- his noncommutative algebra --
> was brought into quantum theory by Werner Heisenberg,
> Max Born, and Pascual Jordan, who showed that the
> ordinary Hamiltonian equations of dynamics were still
> valid in quantum theory, provided the symbols
> representing the coordinates and momenta in classical
> dynamics were interpreted as operators whose products
> did not commute.
> -- "William Rowan Hamilton," in the anthology
> _Mathematics_ by Samuel Rapport and Helen Wright,
> New York University Press, 1963, pp.66-77.
>
> There's more, but duty calls. Catch you next week.
>
>
> <snip philistine speculation by an unemployed biologist here>

Another gratuitous insult? You can't help yourself.

[Alan Kleinman MD PhD]

At least I know that doubling population size does not double the probability of a beneficial mutation occurring. Perhaps you want to give it a shot at explaining why it takes a billion replications for each evolutionary step in the Kishony and Lenski experiments?
<snip>

[jillery]

He sounds testy to me.

--
You're entitled to your own opinions.
You're not entitled to your own facts.

[j.nobel...@gmail.com]

Hold the fort. "At least I know that doubling population size does
not double the probability of a benefitial mutatiion occurring. "

What crazy context does DrDr pretend applies?



\
various various various various
" "

[jillery]

On Sat, 14 Mar 2020 01:52:51 -0700 (PDT), j.nobel...@gmail.com

wrote:

>On Friday, March 13, 2020 at 9:10:03 PM UTC-4, Alan Kleinman MD PhD wrote:
>> On Friday, March 13, 2020 at 5:45:03 PM UTC-7, John Harshman wrote:
>
>
>> > No he isn't. He supports the thesis that his bizarre, simple math is the
>> > way to understand evolution, and that most evolution is impossible.
>>
>> At least I know that doubling population size does not double the
>> probability of a beneficial mutation occurring. Perhaps you want to
>> give it a shot at explaining why it takes a billion replications
>> for each evolutionary step in the Kishony and Lenski experiments?
>
>Hold the fort. "At least I know that doubling population size does
>not double the probability of a benefitial mutatiion occurring. "
>
>What crazy context does DrDr pretend applies?

Welcome to the world of evolutionary theory as defined by drdr bonzo.

[John Harshman]

It all depends on what "the probability of a benefitial mutatiion"
means. If he's talking about the probability that at least one
beneficial mutation happens, he's right. If the probability is small, it
approximately doubles, but as the probability increases, it departs
farther and farther from doubling. Suppose, for example, that the
original probability is .75; doubling the population clearly can't
double the probability.

Then again, if we're talking about the expected number of beneficial
mutations, doubling the population certainly doubles that.

It's just his canned response to me. You can ignore it.

[erik simpson]

It may also hinge on whatever definition he's using for "probability",
"population", "beneficial", "replications", and maybe even "doubling". But most
likely it's just what he pulled out of the can.

[Glenn]

On Saturday, March 14, 2020 at 5:30:03 AM UTC-7, John Harshman wrote:

Can I also ignore all the claims about fixation occurring at higher rates in smaller populations than in larger populations?

[jillery]

On Sat, 14 Mar 2020 09:47:48 -0700 (PDT), Glenn <GlennS...@msn.com>
wrote:

You can, and it's almost certain you have, but you shouldn't. It
would also help if you learned the difference between fixation rate
and mutation rate.

[jillery]

The "beneficial" qualifer is invalid in this context.

[Oxyaena]

On 3/13/2020 6:28 PM, Peter Nyikos wrote:
> On Thursday, March 12, 2020 at 7:35:04 PM UTC-4, John Harshman wrote:
>> On 3/12/20 4:09 PM, Peter Nyikos wrote:
>>> On Wednesday, March 11, 2020 at 9:45:02 PM UTC-4, John Harshman wrote:
>>>> On 3/11/20 9:27 AM, Peter Nyikos wrote:
>>>>> On Saturday, March 7, 2020 at 10:00:03 PM UTC-5, Glenn wrote:
>>>
>>>>>> "The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment."
>>>
>>> This was not the first sentence in the abstract; it was the fourth.
>>>
>>> John, if you recall my thread, TOWARDS A SCIENTIFIC THEORY OF MACROEVOLUTION,
>>> you may surmise from the first three sentences of the abstract why I am highly
>>> motivated to read the paper in detail:
>>>
>>> Evolution is the fundamental physical process that gives rise to
>>> biological phenomena. Yet it is widely treated as a subset of population
>>> genetics, and thus its scope is artificially limited. As a result, the
>>> key issues of how rapidly evolution occurs and its coupling to ecology
>>> have not been satisfactorily addressed and formulated.
>>>
>>> By the way, I believe Alan Kleinman is all too happy to have the subject
>>> of evolution continue to be "widely treated as a subset of population genetics."
>>> Do you share this attitude with him?
>>
>> Of course there's more to it than that.
>
> True to form, you do not say what that "more" is, whereas I have
> gone on record as supporting the thesis that it is almost
> totally lacking in macroevolutionary and, especially, mega-evolutionary theory.

You still haven't even answered how your bullshit "mega-evolutionary
theory" more adequately explains facts of biology than regular
evolutionary theory does. For example, your favorite racing horse, the
Cambrian Explosion, is already *easily* explainable by such concepts as
evolutionary arms races between predator and prey and the subsequent
opening up of novel niches never before seen in the history of life on
earth.

>
>
>> Why are you bringing Kleinman into it?
>
> Because he is an ardent supporter of the thesis that microevolutionary
> theory is the way to understand evolution. I know of no other regular
> here who is as *explicit* about that as he is, though many seem to believe
> that the Modern Synthesis [known to creationists as Neo-Darwinism]
> is all the evolutionary theory that is needed to explain the
> vast panoply of life on earth.

You need to be less vague here, why is the modern theory insufficient to
account for the "vast panoply of life on earth?" Don't tell me
aliensdidit like your outrageous "eumetazoans are separate from the rest
of life on earth" just so story.

[snip unwarranted condescension]

>
>
> <snip philistine speculation by an unemployed biologist here>

This is an uncalled for insult here, you *really* need to knock these off.



--
"I would rather be the son of an ape than be descended from a man afraid
to face the truth." - TH Huxley

https://peradectes.wordpress.com/

[Oxyaena]

On 3/11/2020 12:27 PM, Peter Nyikos wrote:
> On Saturday, March 7, 2020 at 10:00:03 PM UTC-5, Glenn wrote:
>
>> "The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment."
>

> This may come as a surprise to some people, especially where medicine
> is concerned, because of the overwhelming pre-med orientation of
> biology departments all over the USA. But "pre-med" is pre-MD, not
> pre-Ph.D. in biology (with emphasis on medical research) which is where
> actual progress in medicine is concentrated AFAIK.
>
>

> Here is what I wrote on another thread about some of those disastrous
> consequences:
>
> Modern society is suffering from an advanced state of bureaucratization
> and "nanny state" crony capitalism. The inevitable end, I fear,
> is an almost exclusive emphasis on instant scientific/technological solutions.
>
> There has been a devaluation of all pure (as opposed to applied)
> science. Our biology department has long ago ceased to offer the
> courses (still on the books) on ornithology and mammals. Clemson
> may still have those, but all courses and even clubs in paleontology
> are things of the past (at least 5 years in the past).
>

> Already when I was an undergraduate, I got fed up with the
> way my college's biology department was pre-med oriented,
> even in the course in general zoology, and switched my
> major from biology to mathematics. It's even worse here, now.
>
> That was over half a century ago, btw.
>
>> https://www.annualreviews.org/doi/10.1146/annurev-conmatphys-062910-140509
>
> Co-authored by Carl Woese, a truly great naturalist whose like we
> are not likely to see again in today's climate of intellectual exhaustion
> and compartmentalization.
>
> This article was published a bit less than two years before his death.
>
> I have printed out the paper and will be giving it a great deal of careful
> study. I hope by Friday I will be able to give some worthwhile comments on
> more than just the abstract.
>

Strange to see such an elitist as yourself moan the rise of gatekeeping
credentialism.

[John Harshman]

But what about "benefitial"? If what you're saying is that he doesn't
consider the selection coefficient at all, and what he's actually
talking about is the probability of some particular mutation, neither
any beneficial mutation or some mutation with regard to whether or not
it's beneficial, then yes.

[jillery]

On Sat, 14 Mar 2020 11:12:42 -0700, John Harshman

I have to look that up.

> If what you're saying is that he doesn't
>consider the selection coefficient at all, and what he's actually
>talking about is the probability of some particular mutation, neither
>any beneficial mutation or some mutation with regard to whether or not
>it's beneficial, then yes.

What I am saying is, "beneficial" is a quality set by the environment,
and different environments have different probabilities for any
nonspecific mutation being beneficial in it. At the same time,
fixation rates of neutral mutations, and mutation rates of all
mutations, are independent of the environment. I can't tell if that
means the same thing you said above.

drdr bonzo's math doesn't account for different environments, or for
different fixation rates of beneficial mutations and harmful
mutations. These are some of the reasons why his math doesn't apply
to real-world evolutionary examples.

[Mark Isaak]

Sounds like it should refer to Benigno Fitial, former governor of the
Northern Mariana Islands, who was impeached in 2013 and, in 2015,
pleaded guilty to misconduct in public office and conspiracy to commit
theft of services. A "benefitial mutatiion" sounds rather ominous.

[Glenn]

Is your claim that I don't know the difference a fact, or your opinion?

Is it a fact that you know what Alan meant?

Does a specific mutation, say a point mutation in a specific location, occur twice as often in a doubled population size? Is this not what Alan meant?

Come on now, you're on a roll.

[jillery]

"bene fete" might be a good celebration, perhaps in honor of Benigno
Fitial. So a "bene fetial mutation" might be what happened when he
was convicted.

[jillery]

On Sat, 14 Mar 2020 19:38:31 -0700 (PDT), Glenn <GlennS...@msn.com>

>Is your claim that I don't know the difference a fact, or your opinion?

What does it matter to you?

>Is it a fact that you know what Alan meant?

The evidence suggests neither of you know what he's talking about and
are proud of it.

>Does a specific mutation, say a point mutation in a specific location, occur twice as often in a doubled population size? Is this not what Alan meant?

You would have to ask him what he meant, but your question above
refers to a different topic from what he posted.

>Come on now, you're on a roll.

Kaiser or onion? I hope they don't stain.

[John Harshman]

Dr.Dr.'s math doesn't account for selection at all. It deals only with
mutation probabilities. Doesn't matter whether the mutations are
deleterious, advantageous, or neutral. Doesn't matter what the
environment is. It's about mutation, period.

> drdr bonzo's math doesn't account for different environments, or for
> different fixation rates of beneficial mutations and harmful
> mutations. These are some of the reasons why his math doesn't apply
> to real-world evolutionary examples.

True. It applies to bizarre populations in which population size doesn't
change and each individual dies right after reproducing one offspring.

[jillery]

On Sat, 14 Mar 2020 21:13:29 -0700, John Harshman

Exactly. And that's why the "beneficial" qualifer is invalid in this
context.

>> drdr bonzo's math doesn't account for different environments, or for
>> different fixation rates of beneficial mutations and harmful
>> mutations. These are some of the reasons why his math doesn't apply
>> to real-world evolutionary examples.
>
>True. It applies to bizarre populations in which population size doesn't
>change and each individual dies right after reproducing one offspring.

[John Harshman]

I wouldn't use the word "invalid". Any qualifier would be valid. Green
mutations, mutations in a box, mutations with a fox, they're all valid.
The qualifier is merely irrelevant. Unless you interpret as "only
beneficial mutations".

[Oxyaena]

Mutations in my socks....

[jillery]

On Sun, 15 Mar 2020 06:25:19 -0700, John Harshman

Incorrect. The probability of any specific mutation, whether green,
box, or fox, is much smaller than the probability of any mutation in
general. Drdr bonzo's argument assumes that the mutations which
historically did occur are the mutations which had to occur. That's
how he justifies his application of the multiplication rule of
probability, to conclude that the appearance of any beneficial trait,
ex. drug resistance, requires billions of duplications. That's one
reason why he can't account for evolutionary change in real-world
populations within relatively few generations.

[John Harshman]

Dr.Dr. is computing the probability of a specific mutation.

> Drdr bonzo's argument assumes that the mutations which
> historically did occur are the mutations which had to occur. That's
> how he justifies his application of the multiplication rule of
> probability, to conclude that the appearance of any beneficial trait,
> ex. drug resistance, requires billions of duplications. That's one
> reason why he can't account for evolutionary change in real-world
> populations within relatively few generations.

Sure. But why does that make use of the word "beneficial", or even
"benefitial", invalid?

No, forget I asked. This isn't worth any more argument. Sorry for
bringing it up.

[jillery]

On Sun, 15 Mar 2020 08:48:28 -0700, John Harshman

Correct, but computing a specific mutation doesn't apply to
evolutionary change in real-world populations, as I pointed out
immediately below.

>> Drdr bonzo's argument assumes that the mutations which
>> historically did occur are the mutations which had to occur. That's
>> how he justifies his application of the multiplication rule of
>> probability, to conclude that the appearance of any beneficial trait,
>> ex. drug resistance, requires billions of duplications. That's one
>> reason why he can't account for evolutionary change in real-world
>> populations within relatively few generations.
>
>Sure. But why does that make use of the word "beneficial", or even
>"benefitial", invalid?

As I said, applying *any* specific qualifier means his math doesn't
apply to evolutionary change in real-world populations.

>No, forget I asked. This isn't worth any more argument. Sorry for
>bringing it up.

I wasn't arguing. I assumed you knew all this, and were merely
providing an opportunity to summarize what has been chewed over many
times by many posters over many years. Silly me.

[Glenn]

Can you clarify, and comment on this:

https://www.pnas.org/content/109/13/4950

[Alan Kleinman MD PhD]

It's a context that j.nibble.dribble isn't aware of or understand.
>
>
>
> \
> various various various various
> " "

[Alan Kleinman MD PhD]

And neither does half a banana understand but perhaps Elmer PhuD will explain.

[Alan Kleinman MD PhD]

On Saturday, March 14, 2020 at 5:30:03 AM UTC-7, John Harshman wrote:

> On 3/14/20 1:52 AM, j.nobel...@gmail.com wrote:
> > On Friday, March 13, 2020 at 9:10:03 PM UTC-4, Alan Kleinman MD PhD wrote:
> >> On Friday, March 13, 2020 at 5:45:03 PM UTC-7, John Harshman wrote:
> >
> >
> >>> No he isn't. He supports the thesis that his bizarre, simple math is the
> >>> way to understand evolution, and that most evolution is impossible.
> >>
> >> At least I know that doubling population size does not double the
> >> probability of a beneficial mutation occurring. Perhaps you want to
> >> give it a shot at explaining why it takes a billion replications
> >> for each evolutionary step in the Kishony and Lenski experiments?
> >
> > Hold the fort. "At least I know that doubling population size does
> > not double the probability of a benefitial mutatiion occurring. "
> >
> > What crazy context does DrDr pretend applies?
>
> It all depends on what "the probability of a benefitial mutatiion"
> means. If he's talking about the probability that at least one
> beneficial mutation happens, he's right. If the probability is small, it
> approximately doubles, but as the probability increases, it departs
> farther and farther from doubling. Suppose, for example, that the
> original probability is .75; doubling the population clearly can't
> double the probability.

Let's make it simpler for Elmer PhuD. Let's make it the probability of any mutation occurring, not just beneficial mutations. And your problem is that your understanding of probability theory doesn't even reach the level of a lower division undergraduate student. You don't understand the difference between complementary and additive events.

>
> Then again, if we're talking about the expected number of beneficial
> mutations, doubling the population certainly doubles that.

Does that mean you are finally ready to explain the physics and mathematics of the evolution occurring in the Kishony and Lenski experiments based on your understanding of probability theory? Please do so PhuD evolutionary biologist.

>
> It's just his canned response to me. You can ignore it.

Ignore it if you don't want to understand the physics and mathematics of evolution occurring in the Kishony and Lenski experiments and how antimicrobial drug resistance evolves and why cancer treatments fail. Elmer, you really have a contribution to make to society and it is not a good one. Elmer Phud, you really are a blithering and harmful idiot.

[Alan Kleinman MD PhD]

Son of Homer, I'm using the correct definitions. People who understand probability theory (which you don't) publish my papers.

[Alan Kleinman MD PhD]

Glenn, you have to understand, these reptifeatharians don't want to understand these mathematical facts of life. They don't fit with their delusions.

[Alan Kleinman MD PhD]

Elmer Phud, the math applies to any particular mutation, not just beneficial mutations. And your linearization of the probability curve may be necessary for a poorly trained lower-division undergraduate but after all, you are a PhuD evolutionary biologist. So, in your mind, you think that when you roll a die twice, your probability of getting a least a single 1 occurring is 1/6 + 1/6 = 1/3?

[Alan Kleinman MD PhD]

Elmer Phud, you still haven't learned the difference between competition and adaptation (DNA evolution). What exactly do they teach you when you get a PhuD in evolutionary biology? It certainly isn't science and mathematics.

>
> > drdr bonzo's math doesn't account for different environments, or for
> > different fixation rates of beneficial mutations and harmful
> > mutations. These are some of the reasons why his math doesn't apply
> > to real-world evolutionary examples.
>
> True. It applies to bizarre populations in which population size doesn't
> change and each individual dies right after reproducing one offspring.

You reptifeatharians are the slowest learners I've ever encountered.

[Alan Kleinman MD PhD]

That's right, and the probability of a specific mutation occurring is a function of the mutation rate and the number of replications of the particular variant. That's how you do the mathematics of adaptation (DNA evolution). There are several different ways you can understand this. You can look at this computation as the mathematics which describes a single step on an evolutionary trajectory. Or you can think of it a step in a random walk of a Markov chain.

This is not the mathematics of competition where you think I should apply your limited understanding of selection. Competition (which Darwin calls the struggle for existence) and adaptation (DNA evolution) are distinct physical processes with different governing mathematical behaviors. The reason why I continue to press you to study and understand the Kishony and Lenski experiments is that these two experiments well demonstrate the difference between DNA evolution in competitive and non-competitive environments. Competitive environments slows the DNA evolution process.

>
> > Drdr bonzo's argument assumes that the mutations which
> > historically did occur are the mutations which had to occur. That's
> > how he justifies his application of the multiplication rule of
> > probability, to conclude that the appearance of any beneficial trait,
> > ex. drug resistance, requires billions of duplications. That's one
> > reason why he can't account for evolutionary change in real-world
> > populations within relatively few generations.
>
> Sure. But why does that make use of the word "beneficial", or even
> "benefitial", invalid?

Beneficial mutations improve the fitness of those variants that get those particular mutations in a particular environment. There are many other mutations occurring in other variants that don't improve fitness for those variants in that environment. These different variants give rise to different lineages on their own particular evolutionary trajectories. The ability of those lineages to continue on there particular evolutionary trajectories depends on their ability to replicate.

>
> No, forget I asked. This isn't worth any more argument. Sorry for
> bringing it up.

Don't forget it, try to understand it.

[jillery]

The above are two of your willfully stupid canned responses. That
means your dancing is based on the can-can, but your particular
explanations are more accurately called the can't-can't.

[Alan Kleinman MD PhD]

The fundamental error that Lenski and his team make in understanding their experiment is that they don't make the distinction between competition and adaptation. They understand that competition slows adaptation, they say this in the first line in the abstract:
"When large asexual populations adapt, competition between simultaneously segregating mutations slows the rate of adaptation and restricts the set of mutations that eventually fix."

Competition doesn't improve fitness, competition removes the less fit variants from the population as the more fit variants consume the resources available in that limited carrying capacity environment. In order for there to be an improvement in fitness, some member of the population must get a beneficial mutation and there may be more than one beneficial mutation for any evolutionary step. But different beneficial mutations will lead to different lineages on their own particular evolutionary trajectories. And the probability of the next beneficial mutation occurring depends on the particular variant's ability to replicate. I show how to do this mathematics in the following publication:
https://www.researchgate.net/publication/335243441_Fixation_and_Adaptation_in_the_Lenski_E_coli_Long_Term_Evolution_Experiment

The fundamental error that evolutionary biologists make is that fixation is the principal step in evolution. Fixation is neither necessary nor sufficient for DNA evolution to occur. If DNA evolution is occurring in a limited carrying capacity environment such as the Lenski experiment, it slows that evolutionary process. This is clearly demonstrated by the much larger carrying capacity environment used in the Kishony experiment where evolution occurs much more rapidly without fixation occurring.

[Vincent Maycock]

On Mon, 16 Mar 2020 04:53:36 -0700 (PDT), Alan Kleinman MD PhD
<klei...@sti.net> wrote:

[...]

>Competition doesn't improve fitness, competition removes the less fit variants from the population

If you remove the less fit variants, shouldn't what's left be "more
fit" compared to a population where those less fit variants have not
been removed?

Also, in the Kishony experiment aren't we seeing evolution occurring
in response to more than one selection pressure (the different levels
of antibiotic) at the same time? Or do you consider the different
levels of antibiotic to be the same selection pressure?

[Alan Kleinman MD PhD]

On Monday, March 16, 2020 at 8:20:03 AM UTC-7, Vincent Maycock wrote:
> On Mon, 16 Mar 2020 04:53:36 -0700 (PDT), Alan Kleinman MD PhD
> <klei...@sti.net> wrote:
>
> [...]
> >Competition doesn't improve fitness, competition removes the less fit variants from the population
>
> If you remove the less fit variants, shouldn't what's left be "more
> fit" compared to a population where those less fit variants have not
> been removed?

There are two ways of considering fitness. Relative fitness (fitness of one variant with respect to other variants) pertains to competition. Absolute fitness (fecundity) pertains to DNA adaptation.

>
> Also, in the Kishony experiment aren't we seeing evolution occurring
> in response to more than one selection pressure (the different levels
> of antibiotic) at the same time? Or do you consider the different
> levels of antibiotic to be the same selection pressure?

Kishony is only using a single selection pressure and varying the intensity of selection such that a single mutation can give improved fitness and allows the growth of that variant in the next higher level of drug concentration. There is a clinical medical lesson here, don't use antimicrobials at low concentration. This is oftentimes done when using antimicrobials prophylactically. Ask Rogers what happened when they tried to irradicate malaria by putting chloroquine in table salt.

[Peter Nyikos]

On Thursday, March 12, 2020 at 7:35:04 PM UTC-4, erik simpson wrote:
> On Thursday, March 12, 2020 at 4:25:03 PM UTC-7, Peter Nyikos wrote:
> > On Thursday, March 12, 2020 at 7:10:03 PM UTC-4, Peter Nyikos wrote:
> >
> > > Our Department of Biological sciences had an interdisciplinary
> > > undergraduate semester course up until a bit over a decade ago, on the
> > > geological and biological history of the earth. The person who
> > > last taught it retired the following year, and the follow-up semester course
> > > was not taught by anyone, and neither course has not been taught since.
> >
> > Haste makes waste: the "not" that is fourth from the end does not belong.
> >
> > By the way, there is also a geology department, but it doesn't offer
> > that kind of interdisciplinary course either. There are all too
> > many topics that fall into the cracks between departments,
> > and never see the light of day.
> >
> > Also into cracks within a department. The subject of change
> > of variables in multivariate calculus has consistently
> > fallen into the crack between it and the course in vector calculus,
> > except when I teach the latter, ever since the multivariate
> > calculus course went from five days a week to three days a week,
> > about thirty years ago.
> >
> > As for the Inverse Function Theorem and the Implicit Function Theorem,
> > there are several cracks into which they can fall, and AFAIK they
> > have always fallen into them in the four decades I have been here.
> >
> >
> > [I miss Richard Norman. He'd know exactly what I am talking about here;
> > I don't know whether anyone else who is still active in talk.origins can.]
> >
> >
> > Peter Nyikos
> > Professor of Mathematics -- standard disclaimer--
> > University of South Carolina
> > http://www.math.sc.edu/~nyikos/
>
> Oh, Peter, you are so smart, and we are so stupid. If you could just tell us
> a little about Advanced Math we would be so grateful.

I just did, depending on what your definition of Advanced Math is.
If the Inverse Function Theorem and the Implicit Function Theorem
are old-hat to you, I can take you all the way up to the cutting
edge of current research if you wish.

But I get the feeling, from your choice of words, that you are
not the least bit interested in learning any advanced math. Correct?


Peter Nyikos

PS "several cracks into which they can fall" includes the detail that they have
never been taught in any of the undergraduate OR graduate courses where it
would be appropriate to teach them, AFAIK. I can check with our resident
expert on the subject if you wish. But something tells me you don't wish it.

[Alan Kleinman MD PhD]

Not only is the son of Homer not interested, but you also don't need multivariate calculus to describe the physics and mathematics of evolution.

[Vincent Maycock]

On Mon, 16 Mar 2020 08:45:35 -0700 (PDT), Alan Kleinman MD PhD

<klei...@sti.net> wrote:

>On Monday, March 16, 2020 at 8:20:03 AM UTC-7, Vincent Maycock wrote:
>> On Mon, 16 Mar 2020 04:53:36 -0700 (PDT), Alan Kleinman MD PhD
>> <klei...@sti.net> wrote:
>>
>> [...]
>> >Competition doesn't improve fitness, competition removes the less fit variants from the population
>>
>> If you remove the less fit variants, shouldn't what's left be "more
>> fit" compared to a population where those less fit variants have not
>> been removed?
>
>There are two ways of considering fitness. Relative fitness (fitness of one variant with respect to other variants) pertains to competition. Absolute fitness (fecundity) pertains to DNA adaptation.

We were talking about competition, not absolute fitness.

>> Also, in the Kishony experiment aren't we seeing evolution occurring
>> in response to more than one selection pressure (the different levels
>> of antibiotic) at the same time? Or do you consider the different
>> levels of antibiotic to be the same selection pressure?
>
>Kishony is only using a single selection pressure and varying the intensity of selection such that a single mutation can give improved fitness and allows the growth of that variant in the next higher level of drug concentration. There is a clinical medical lesson here, don't use antimicrobials at low concentration. This is oftentimes done when using antimicrobials prophylactically. Ask Rogers what happened when they tried to irradicate malaria by putting chloroquine in table salt.

Okay; same selection pressure, but different beneficial mutations? Or
does one beneficial mutation lead to resistance to differing amounts
of antibiotics?

[Oxyaena]

Sarcasm eludes you as usual, I see.

>
>
> Peter Nyikos
>
> PS "several cracks into which they can fall" includes the detail that they have
> never been taught in any of the undergraduate OR graduate courses where it
> would be appropriate to teach them, AFAIK. I can check with our resident
> expert on the subject if you wish. But something tells me you don't wish it.
>

--
"All opinions are not equal. Some are a very great deal more robust,
sophisticated and well supported in logic and argument than others." -
Douglas Adams

https://peradectes.wordpress.com/

[Peter Nyikos]

On Friday, March 13, 2020 at 6:50:03 PM UTC-4, Alan Kleinman MD PhD wrote:

> On Friday, March 13, 2020 at 3:30:03 PM UTC-7, Peter Nyikos wrote:
> > On Thursday, March 12, 2020 at 7:35:04 PM UTC-4, John Harshman wrote:

> > > On 3/12/20 4:09 PM, Peter Nyikos wrote:
> > > > On Wednesday, March 11, 2020 at 9:45:02 PM UTC-4, John Harshman wrote:
> > > >> On 3/11/20 9:27 AM, Peter Nyikos wrote:
> > > >>> On Saturday, March 7, 2020 at 10:00:03 PM UTC-5, Glenn wrote:
> > > >
> > > >>>> "The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment."
> > > >
> > > > This was not the first sentence in the abstract; it was the fourth.
> > > >
> > > > John, if you recall my thread, TOWARDS A SCIENTIFIC THEORY OF MACROEVOLUTION,
> > > > you may surmise from the first three sentences of the abstract why I am highly
> > > > motivated to read the paper in detail:
> > > >
> > > > Evolution is the fundamental physical process that gives rise to
> > > > biological phenomena. Yet it is widely treated as a subset of population
> > > > genetics, and thus its scope is artificially limited. As a result, the
> > > > key issues of how rapidly evolution occurs and its coupling to ecology
> > > > have not been satisfactorily addressed and formulated.
> > > >
> > > > By the way, I believe Alan Kleinman is all too happy to have the subject
> > > > of evolution continue to be "widely treated as a subset of population genetics."
> > > > Do you share this attitude with him?
> > >
> > > Of course there's more to it than that.
> >
> > True to form, you do not say what that "more" is, whereas I have
> > gone on record as supporting the thesis that it is almost
> > totally lacking in macroevolutionary and, especially, mega-evolutionary theory.

> >
> >
> > > Why are you bringing Kleinman into it?
> >
> > Because he is an ardent supporter of the thesis that microevolutionary
> > theory is the way to understand evolution. I know of no other regular
> > here who is as *explicit* about that as he is, though many seem to believe
> > that the Modern Synthesis [known to creationists as Neo-Darwinism]
> > is all the evolutionary theory that is needed to explain the
> > vast panoply of life on earth.
>

> Microevolution is the only kind of evolution observed.

Yes: where direct observation is concerned, we are the victims of
an acute case of sampling bias, and humans are likely to be victims for the next
million years or so.

That is NO EXCUSE for us, the living, to abandon all hope of understanding macroevolution.

With your attitude, Einstein's theory of General Relativity should never
have been formulated.

And there are any number of quantum theorists whose life would be made
a lot simpler if it HAD never been formulated.



> And even that, biologists have failed to correctly explain the physics and mathematics.

That is also true of a non-biologist Dr. Dr., and I'm not talking about
Dr. Dr. Howler Monkey, who claimed that one of his Drs. was a Ph.D.
in some branch of biology. I'm talking about the Dr. Dr. whose two
doctorates are in engineering (Ph.D.?) and medical practice (MD).
I assume you know who I am talking about.


> Perhaps in your imagination, fossils tell you otherwise.

Your last sentence is taken from your obfuscation-loving imagination.
I never claimed, nor would I ever claim, that fossils can explain
the math and physics of evolution, any more than you should claim
that your medical practice explains it.

Are you enough of a crank to think that it DOES explain it, and that
your 2014 and 2016 papers are pure gravy?


> Why doesn't Nomathos explain the mathematics of those kinds of genetic transformations?

You are the true Nomathos here, otherwise your paper that you had
to publish in a vanity press journal would not have been rejected
by _Statistics in Medicine_. The reviewers there probably laughed at your conceit
in thinking that the Haldane equations that you used as window dressing
explained the Kishony and Lenski experiments without you having
to connect the dots.


> If you can't come up with the math to explain macroevolution, we can call it Nomathian evolution.

I already did it, liar. I used YOUR math in the 2014 and 2016 papers
to give a mathematical scenario for reptiles evolving feathers
in 40 million years from scales. You never dared to challenge
my mathematics.

So your nickname "Nomathos" for me is an out and out scam, disguising
your true intent, which is to shame me into doing YOUR work of connecting
the dots for the Kishony and Lenski experiments.

And if you think you can shame me into doing that, you are badly
in need of psychiatric counseling.

That reminds me: you might as well earn your keep here in t.o. by using your
medical training to explain the phenomenon of Jonathan never sleeping
for over a year. One person "diagnosed" that as Jonathan being in a manic
bipolar state all that time. Do you think he may have been right about that?


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

[Oxyaena]

On 3/12/2020 7:13 PM, j.nobel...@gmail.com wrote:
> On Thursday, March 12, 2020 at 6:20:05 PM UTC-4, Alan Kleinman MD PhD wrote:
>> On Thursday, March 12, 2020 at 2:25:03 PM UTC-7, Bill Rogers wrote:

>>> On Thursday, March 12, 2020 at 3:00:04 PM UTC-4, j.nobe...@gmail.com wrote:
>>>> On Wednesday, March 11, 2020 at 9:45:02 PM UTC-4, John Harshman wrote:
>>>>> On 3/11/20 9:27 AM, Peter Nyikos wrote:
>>>>>> On Saturday, March 7, 2020 at 10:00:03 PM UTC-5, Glenn wrote:
>>>>>>
>>>>>>> "The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology, and the global environment."
>>>>>>

>>>>>> This may come as a surprise to some people, especially where medicine
>>>>>> is concerned, because of the overwhelming pre-med orientation of
>>>>>> biology departments all over the USA. But "pre-med" is pre-MD, not
>>>>>> pre-Ph.D. in biology (with emphasis on medical research) which is where
>>>>>> actual progress in medicine is concentrated AFAIK.
>>>>>
>>>>> I have not experienced this overwhelming pre-med orientation. I've had
>>>>> premeds in undergraduate biology classes both as an undergrad myself and
>>>>> as a TA. But never in the majority and never all that many and never
>>>>> driving the curriculum. Where do you draw your conclusions from?
>>>>
>>>> The term "overwhelming" renders this subjective but I've known many
>>>> to express similar sentiment. And it extends beyond the root biology
>>>> curriculum. Some schools have for instance adopted Organic Chemistry
>>>> for Biology Majors, and even Physics for Biology majors. Interestingly,
>>>> those seeking a Biochemistry degree have to take Organic Chemistry for
>>>> organic chemists, same with those seeking a Genetics degree. The
>>>> explanation is that if you are training to be scientist, you want to
>>>> actually learn organic chemistry but if you are actually a pre-med
>>>> you just need to memorize some stuff in order to do well on the MCATS.
>>>>
>>>> The "for biology majors" in the course title is mostly "for premeds".
>>>> (not entirely true as which courses are required vary across many
>>>> degrees).
>>>>
>>>> I've also been 1 degree removed from discussions about what to include
>>>> in the 1st year biology class, the "weed out" class. Those focused on
>>>> the pre-med track want to keep it heavily memorization based and do
>>>> indeed drive the significance of those things thought to be including
>>>> in medical school entrance exams. These fight with various biological
>>>> disciplines over how to best introduce concepts critical to their
>>>> discipline. At minimum, there is a significant tension and compromise
>>>> towards the premed agenda.
>>>
>>> When I was a pre-med I took P-Chem and organic chem for the chemists, and physics for the physics majors because even though the courses were harder, the classes were smaller, the students were nicer, and they did not have the high stress, competitive feeling about them that the pre-med courses had.
>>
>> Too bad you didn't learn how to exercise those skills, if you had, you
>> might have recognized that evolutionary competition is an example of
>> the first law of thermodynamics. And DNA evolution is an example of
>> the second law of thermodynamics.
>
> Even by your "standards" the first is an obtuse statement. The second
> claim, however, can be partially rehabilitated. Using TdS <= -dQ as one
> statement of the second law, one can note that any change in entropy
> must be paid for by an adequate supply of Q (energy). Essentially, you
> have to plug the refrigerator in for it to cool.

What Alan doesn't get is that life is not an isolated system, nor is
earth. Life needs food to survive, the cord for life is food, and the
plug in is the sun, we get our energy from the sun, as that energy
source won't run out for at the very least several hundred million more
years to come, probably longer.

>
> This particular constraint is of course not problematic for systems
> far from equilibrium where the flow of energy is relatively large
> compared to the temporary reduction in entropy in dissipative structures.
>
> This is formalized in some treatments of statistical mechanics. It's
> standard fair for basic fluid dynamics. And apparently, it's misunderstood
> by people whose understanding of probability is limited to introductory
> courses.

[jillery]

On Mon, 16 Mar 2020 04:53:36 -0700 (PDT), Alan Kleinman MD PhD
<klei...@sti.net> wrote:

>On Sunday, March 15, 2020 at 1:55:03 PM UTC-7, Glenn wrote:
>> On Friday, March 13, 2020 at 6:10:03 PM UTC-7, Alan Kleinman MD PhD wrote:
>> > On Friday, March 13, 2020 at 5:45:03 PM UTC-7, John Harshman wrote:
>> > > On 3/13/20 3:28 PM, Peter Nyikos wrote:
>> > > > On Thursday, March 12, 2020 at 7:35:04 PM UTC-4, John Harshman wrote:
>> >
>> > >
>> > > >> Why are you bringing Kleinman into it?
>> > > >
>> > > > Because he is an ardent supporter of the thesis that microevolutionary
>> > > > theory is the way to understand evolution. I know of no other regular
>> > > > here who is as *explicit* about that as he is, though many seem to believe
>> > > > that the Modern Synthesis [known to creationists as Neo-Darwinism]
>> > > > is all the evolutionary theory that is needed to explain the
>> > > > vast panoply of life on earth.
>> > >
>> > > No he isn't. He supports the thesis that his bizarre, simple math is the
>> > > way to understand evolution, and that most evolution is impossible.
>> >
>> > At least I know that doubling population size does not double the probability of a beneficial mutation occurring.
>>
>> Can you clarify, and comment on this:
>>
>> https://www.pnas.org/content/109/13/4950
>
>The fundamental error that Lenski and his team make in understanding their experiment is that they don't make the distinction between competition and adaptation. They understand that competition slows adaptation, they say this in the first line in the abstract:
>"When large asexual populations adapt, competition between simultaneously segregating mutations slows the rate of adaptation and restricts the set of mutations that eventually fix."

Your quote above explicitly shows Lenski making a distinction between
competition and adaptation. This proves false your first sentence
above.

>Competition doesn't improve fitness, competition removes the less fit variants from the population as the more fit variants consume the resources available in that limited carrying capacity environment. In order for there to be an improvement in fitness, some member of the population must get a beneficial mutation and there may be more than one beneficial mutation for any evolutionary step. But different beneficial mutations will lead to different lineages on their own particular evolutionary trajectories. And the probability of the next beneficial mutation occurring depends on the particular variant's ability to replicate. I show how to do this mathematics in the following publication:
>https://www.researchgate.net/publication/335243441_Fixation_and_Adaptation_in_the_Lenski_E_coli_Long_Term_Evolution_Experiment
>
>The fundamental error that evolutionary biologists make is that fixation is the principal step in evolution. Fixation is neither necessary nor sufficient for DNA evolution to occur. If DNA evolution is occurring in a limited carrying capacity environment such as the Lenski experiment, it slows that evolutionary process. This is clearly demonstrated by the much larger carrying capacity environment used in the Kishony experiment where evolution occurs much more rapidly without fixation occurring.

[jillery]

FWIW Eric apologized for his remark above in a post less that two
hours later.

[Peter Nyikos]

On Monday, March 16, 2020 at 6:50:03 AM UTC-4, Alan Kleinman MD PhD wrote:
> On Saturday, March 14, 2020 at 5:30:03 AM UTC-7, John Harshman wrote:
> > On 3/14/20 1:52 AM, j.nobel...@gmail.com wrote:
> > > On Friday, March 13, 2020 at 9:10:03 PM UTC-4, Alan Kleinman MD PhD wrote:
> > >> On Friday, March 13, 2020 at 5:45:03 PM UTC-7, John Harshman wrote:
> > >
> > >
> > >>> No he isn't. He supports the thesis that his bizarre, simple math is the
> > >>> way to understand evolution, and that most evolution is impossible.
> > >>
> > >> At least I know that doubling population size does not double the
> > >> probability of a beneficial mutation occurring. Perhaps you want to
> > >> give it a shot at explaining why it takes a billion replications
> > >> for each evolutionary step in the Kishony and Lenski experiments?
> > >
> > > Hold the fort. "At least I know that doubling population size does
> > > not double the probability of a benefitial mutatiion occurring. "
> > >
> > > What crazy context does DrDr pretend applies?
> >
> > It all depends on what "the probability of a benefitial mutatiion"
> > means. If he's talking about the probability that at least one
> > beneficial mutation happens, he's right. If the probability is small, it
> > approximately doubles, but as the probability increases, it departs
> > farther and farther from doubling.

You've won a victory here, Kleinman, with an assist from the entity
whose posts appear via the email address j.nobel.daggett.
Harshman has been forced to backpedal on his unequivocal misdirection
to the effect that you were off base in writing the absolutely
correct thing that you did.

> > Suppose, for example, that the
> > original probability is .75; doubling the population clearly can't
> > double the probability.

See, Harshman is now in full agreement with you. But that didn't stop
his groupies from frantically doing damage control: they have sent up one
thick cloud of smoke after another to spin-doctor what you wrote
into something you never wrote.

>
> Let's make it simpler for Elmer PhuD. Let's make it the probability of any mutation occurring, not just beneficial mutations. And your problem is that your understanding of probability theory doesn't even reach the level of a lower division undergraduate student. You don't understand the difference between complementary and additive events.

Like one of his generals told Hannibal: you know how to win victories,
but you don't know how to follow them up. You are stuck back in the
idiocy Harshman wrote while shooting from the hip, rather than
capitalizing on the way he backpedaled after the "daggett" entity
supported him in *ad* *hominem* fashion.

Apparently, the entity's support made him stop and think about what he
had foolishly written.

> >
> > Then again, if we're talking about the expected number of beneficial
> > mutations, doubling the population certainly doubles that.

Perhaps you didn't realize that Harshman is playing dumb here.
He must know that the standard claim about you is that you
write about single, targeted mutations, in exactly the way you wrote
above. So he is still doing damage control here.

> Does that mean you are finally ready to explain the physics and mathematics of the evolution occurring in the Kishony and Lenski experiments based on your understanding of probability theory? Please do so PhuD evolutionary biologist.
> >
> > It's just his canned response to me. You can ignore it.

Ironically enough, the last thing you wrote above is perfectly
described by this one-liner that Harshman wrote BEFORE it.

I told you once before about Hannibal's general, when you won
a victory over Ron O. You really ought to take what the general said to heart.

> Ignore it if you don't want to understand the physics and mathematics of evolution occurring in the Kishony and Lenski experiments and how antimicrobial drug resistance evolves and why cancer treatments fail. Elmer, you really have a contribution to make to society and it is not a good one. Elmer Phud, you really are a blithering and harmful idiot.

Just to make sure YOU aren't describing yourself as missed opportunities
for contribution to society go, I'd advise you to think seriously about what
I wrote about Jonathan in my earlier reply to you today. If that "diagnosis"
had a chance of being correct, an awful lot of Jonathan's flaky behavior would
fall into place.

Peter Nyikos
Professor, Dept. of Mathematics

U. of South Carolina -- standard disclaimer --
http://people.math.sc.edu/nyikos/

[Alan Kleinman MD PhD]

On Monday, March 16, 2020 at 10:15:03 AM UTC-7, Vincent Maycock wrote:
> On Mon, 16 Mar 2020 08:45:35 -0700 (PDT), Alan Kleinman MD PhD
> <klei...@sti.net> wrote:
>
> >On Monday, March 16, 2020 at 8:20:03 AM UTC-7, Vincent Maycock wrote:
> >> On Mon, 16 Mar 2020 04:53:36 -0700 (PDT), Alan Kleinman MD PhD
> >> <klei...@sti.net> wrote:
> >>
> >> [...]
> >> >Competition doesn't improve fitness, competition removes the less fit variants from the population
> >>
> >> If you remove the less fit variants, shouldn't what's left be "more
> >> fit" compared to a population where those less fit variants have not
> >> been removed?
> >
> >There are two ways of considering fitness. Relative fitness (fitness of one variant with respect to other variants) pertains to competition. Absolute fitness (fecundity) pertains to DNA adaptation.
>
> We were talking about competition, not absolute fitness.

So what do you think happens with the notion of relative fitness when a variant gets fixed in the population?

>
> >> Also, in the Kishony experiment aren't we seeing evolution occurring
> >> in response to more than one selection pressure (the different levels
> >> of antibiotic) at the same time? Or do you consider the different
> >> levels of antibiotic to be the same selection pressure?
> >
> >Kishony is only using a single selection pressure and varying the intensity of selection such that a single mutation can give improved fitness and allows the growth of that variant in the next higher level of drug concentration. There is a clinical medical lesson here, don't use antimicrobials at low concentration. This is oftentimes done when using antimicrobials prophylactically. Ask Rogers what happened when they tried to irradicate malaria by putting chloroquine in table salt.
>
> Okay; same selection pressure, but different beneficial mutations? Or
> does one beneficial mutation lead to resistance to differing amounts
> of antibiotics?

There can be and usually are different mutations that can give increasing resistance (improved fitness) to different variants. So, let's say mutation A1 gives sufficient resistance that the variant can grow in the first (lowest drug concentration region). Then a second mutation must occur on one of those variants that already has A1 to give a further improvement in fitness so as to grow in the second drug region (the next higher concentration). Call that mutation B1. Now, a different lineage taking a different evolutionary trajectory might require mutations A2 and then B2 respectively in order to improve fitness to that selection pressure.

But you had better have lots of A1s and A2s to have a reasonable probability of the B1 or B2 mutations occurring on some member that would benefit from that particular mutation.

[Alan Kleinman MD PhD]

Why don't you make an attempt to understand how microevolution works and the mechanisms of genetic transformation before you go off on your fantasy trips? At least physicians would have a better understanding of how drug-resistance evolves and why cancer treatments fail.

>
>
>
> > And even that, biologists have failed to correctly explain the physics and mathematics.
>
> That is also true of a non-biologist Dr. Dr., and I'm not talking about
> Dr. Dr. Howler Monkey, who claimed that one of his Drs. was a Ph.D.
> in some branch of biology. I'm talking about the Dr. Dr. whose two
> doctorates are in engineering (Ph.D.?) and medical practice (MD).
> I assume you know who I am talking about.

Whatever Nomathos. And my PhD is in mechanical engineering. If you want to read my PhD thesis, I solved an inverse non-linear partial differential equation.

>
>
> > Perhaps in your imagination, fossils tell you otherwise.
>
> Your last sentence is taken from your obfuscation-loving imagination.
> I never claimed, nor would I ever claim, that fossils can explain
> the math and physics of evolution, any more than you should claim
> that your medical practice explains it.

Then, what makes you think that macroevolution is a real thing? Do you really think there were 10s or 100s of billions of replications of some reptile lineage to accumulate the mutations necessary to grow feathers? And that it occurred in some magical environment as stable as a laboratory?

>
> Are you enough of a crank to think that it DOES explain it, and that
> your 2014 and 2016 papers are pure gravy?

Whether you like it or not, those papers give the correct mathematics of DNA evolution. It is just that simple. Face the facts Nomathos, you studied the wrong area of mathematics necessary to understand evolution.

>
>
> > Why doesn't Nomathos explain the mathematics of those kinds of genetic transformations?
>
> You are the true Nomathos here, otherwise your paper that you had
> to publish in a vanity press journal would not have been rejected
> by _Statistics in Medicine_. The reviewers there probably laughed at your conceit
> in thinking that the Haldane equations that you used as window dressing
> explained the Kishony and Lenski experiments without you having
> to connect the dots.

Nomathos, Haldane (and Hoyle) were doing the mathematics of competition, not DNA evolution. You should have done your homework.

>
>
> > If you can't come up with the math to explain macroevolution, we can call it Nomathian evolution.
>
> I already did it, liar. I used YOUR math in the 2014 and 2016 papers
> to give a mathematical scenario for reptiles evolving feathers
> in 40 million years from scales. You never dared to challenge
> my mathematics.

It's the magic of mathematics, you don't have to correlate it with reality. Just plug numbers into equations you don't understand and you think you have your answer. You must be hitting the pálinka again.

>
> So your nickname "Nomathos" for me is an out and out scam, disguising
> your true intent, which is to shame me into doing YOUR work of connecting
> the dots for the Kishony and Lenski experiments.

Sleep it off Nomathos.

>
> And if you think you can shame me into doing that, you are badly
> in need of psychiatric counseling.

We all know that you have no shame. But if you know a psychiatrist that can cure boredom, let me know because you have given me a severe case.

>
> That reminds me: you might as well earn your keep here in t.o. by using your
> medical training to explain the phenomenon of Jonathan never sleeping
> for over a year. One person "diagnosed" that as Jonathan being in a manic
> bipolar state all that time. Do you think he may have been right about that?

My advice to Jonathan is to read one of your posts before going to bed, it is sure to cure his insomnia.

[Alan Kleinman MD PhD]

Do you really want to start playing scientist? Life should be abounding in Death Valley according to your argument.

[Alan Kleinman MD PhD]

Check his math further down in his paper, half a banana.

[Alan Kleinman MD PhD]

I don't think he was playing. But who knows, perhaps he is learning. You know hope springs eternal.

>
>
> > Does that mean you are finally ready to explain the physics and mathematics of the evolution occurring in the Kishony and Lenski experiments based on your understanding of probability theory? Please do so PhuD evolutionary biologist.
> > >
> > > It's just his canned response to me. You can ignore it.
>
> Ironically enough, the last thing you wrote above is perfectly
> described by this one-liner that Harshman wrote BEFORE it.
>
> I told you once before about Hannibal's general, when you won
> a victory over Ron O. You really ought to take what the general said to heart.

OK general, how should we follow up?

>
>
> > Ignore it if you don't want to understand the physics and mathematics of evolution occurring in the Kishony and Lenski experiments and how antimicrobial drug resistance evolves and why cancer treatments fail. Elmer, you really have a contribution to make to society and it is not a good one. Elmer Phud, you really are a blithering and harmful idiot.
>
> Just to make sure YOU aren't describing yourself as missed opportunities
> for contribution to society go, I'd advise you to think seriously about what
> I wrote about Jonathan in my earlier reply to you today. If that "diagnosis"
> had a chance of being correct, an awful lot of Jonathan's flaky behavior would
> fall into place.

Flaky behavior is spreading faster than the coronavirus. I even bought an extra can of hair spray so I would be prepared. You never know when you might need it.

[jillery]

The above is an example of Nyikos the peter siding completely with
drdr bonzo in a willfully stupid attempt to discredit Harshman and his
alleged groupies.

>> > Suppose, for example, that the
>> > original probability is .75; doubling the population clearly can't
>> > double the probability.
>
>See, Harshman is now in full agreement with you. But that didn't stop
>his groupies from frantically doing damage control: they have sent up one
>thick cloud of smoke after another to spin-doctor what you wrote
>into something you never wrote.

If Harshman's exception above was drdr bonzo's point, then it's very
odd drdr bonzo never mentioned that exception himself.

>> Let's make it simpler for Elmer PhuD. Let's make it the probability of any mutation occurring, not just beneficial mutations. And your problem is that your understanding of probability theory doesn't even reach the level of a lower division undergraduate student. You don't understand the difference between complementary and additive events.
>
>Like one of his generals told Hannibal: you know how to win victories,
>but you don't know how to follow them up. You are stuck back in the
>idiocy Harshman wrote while shooting from the hip, rather than
>capitalizing on the way he backpedaled after the "daggett" entity
>supported him in *ad* *hominem* fashion.
>
>Apparently, the entity's support made him stop and think about what he
>had foolishly written.

Actually, "daggett" didn't post anything in this thread about
Harshman's comments above. You're very confused.

>> > Then again, if we're talking about the expected number of beneficial
>> > mutations, doubling the population certainly doubles that.
>
>Perhaps you didn't realize that Harshman is playing dumb here.
>He must know that the standard claim about you is that you
>write about single, targeted mutations, in exactly the way you wrote
>above. So he is still doing damage control here.

Actually, it's you doing damage control for drdr bonzo. drdr bonzo
never wrote anything about single, targeted mutations, but only
"beneficial mutations" as Harshman specified. Not sure why you're so
willing to destroy what little credibility you might have left with
anybody.

>> Does that mean you are finally ready to explain the physics and mathematics of the evolution occurring in the Kishony and Lenski experiments based on your understanding of probability theory? Please do so PhuD evolutionary biologist.
>> >
>> > It's just his canned response to me. You can ignore it.
>
>Ironically enough, the last thing you wrote above is perfectly
>described by this one-liner that Harshman wrote BEFORE it.
>
>I told you once before about Hannibal's general, when you won
>a victory over Ron O. You really ought to take what the general said to heart.

The only place drdr bonzo won a victory over anybody was in his wet
dreams. Perhaps you and he dreamt about it together.

>> Ignore it if you don't want to understand the physics and mathematics of evolution occurring in the Kishony and Lenski experiments and how antimicrobial drug resistance evolves and why cancer treatments fail. Elmer, you really have a contribution to make to society and it is not a good one. Elmer Phud, you really are a blithering and harmful idiot.
>
>Just to make sure YOU aren't describing yourself as missed opportunities
>for contribution to society go, I'd advise you to think seriously about what
>I wrote about Jonathan in my earlier reply to you today. If that "diagnosis"
>had a chance of being correct, an awful lot of Jonathan's flaky behavior would
>fall into place.
>
>Peter Nyikos
>Professor, Dept. of Mathematics
>U. of South Carolina -- standard disclaimer --
>http://people.math.sc.edu/nyikos/

Do you employers know you associate them with your Alzheimer's?

[Alan Kleinman MD PhD]

half a banana hides in her anonymity. Obviously a yellow banana. It is quite understandable though. Who would want people to know how dumb a half a banana you are.

[jillery]

Yet more of your boring and willfully stupid nonsense non-sequiturs
and asinine ad-hominems. They just show you know you have nothing
intelligent to say and are proud of it.

[Alan Kleinman MD PhD]

It fits perfectly with half a banana.

[jillery]

The above is yet another one of your willfully stupid Creationist
PRATTs.

>> > This particular constraint is of course not problematic for systems
>> > far from equilibrium where the flow of energy is relatively large
>> > compared to the temporary reduction in entropy in dissipative structures.
>> >
>> > This is formalized in some treatments of statistical mechanics. It's
>> > standard fair for basic fluid dynamics. And apparently, it's misunderstood
>> > by people whose understanding of probability is limited to introductory
>> > courses.
>> >
>>
>>
>> --
>> "All opinions are not equal. Some are a very great deal more robust,
>> sophisticated and well supported in logic and argument than others." -
>> Douglas Adams
>>
>> https://peradectes.wordpress.com/

[jillery]

On Mon, 16 Mar 2020 11:40:45 -0700 (PDT), Alan Kleinman MD PhD

Could you be more specific? Of course not.

Just as well, the quote above disproves your comment all by itself.

[Alan Kleinman MD PhD]

What's the matter? Half a banana having difficulty with all the math?

[Glenn]

And other lifeforms dead. Oxy often makes such stupid claims.

[Alan Kleinman MD PhD]

What else can you say other than these reptifeatharians are indoctrinated and not well trained in the sciences. What is incredible is how they have managed to get control of the field of biology.

[jillery]

On Mon, 16 Mar 2020 17:13:33 -0700 (PDT), Glenn <GlennS...@msn.com>

Oxyaena didn't make that claim. drdr bonzo made it up.

[Alan Kleinman MD PhD]

Half a banana thinks that all you need is sunlight for life to occur. Half a banana thinking is in the dark.

[Glenn]

On Tuesday, March 17, 2020 at 7:30:03 AM UTC-7, jillery wrote:

What you don't get is that life is not an isolated system.