On Friday, October 6, 2023 at 6:06:00 AM UTC-4, Ernest Major wrote:
> On 06/10/2023 03:20, DB Cates wrote:
>
> Piggybacking, since the original hasn't turned up here.
> >> If you want to see some very bizarre RNA editing, have a look at RNA
> >> editing in the mitochondria (also called kinetoplasts) of
> >> kinetoplastid protozoa (responsible for a couple of tropical diseases
> >> - Leishmaniasis and African Sleeping Sickness). A different mechanism
> >> entirely from that in cephalopods.
> RNA editing also occurs in plastids (chloroplasts). I can see the point
> of editing ribozymes, in that incorporating non-canonical bases expands
> or improves the catalytic repertoire, but mRNA editing (rather than just
> have the genome specify the desired mRNA directly) strikes me as
> evidence against design. Unnecessary complexity is not a marker of
> competent design.
> >>
> >> Here's a review of what happens
> >>
> >> https://www.tandfonline.com/doi/pdf/10.4161/rna.7.2.11393
> >>
> >> and here's a short paper on a part of the evolution of the editing system
> >>
> >> https://kdna.net/simpsonlab/Lab%20publications/maslov%20evol%201994.pdf
> >>
> >> Why is anybody still using the phrase "central dogma"? I mean, it
> >> seemed nifty back when transcription and translation were first worked
> >> out, but reverse transcriptase stuck a knife in it, and, outside of
> >> elementary textbooks, most molecular biologists haven't really used
> >> the phrase for decades.
> >>
> > Hmmm. You may want to read this from Larry Moran's blog.
> > <https://sandwalk.blogspot.com/2007/01/central-dogma-of-molecular-biology.html>
> I hadn't thought of mRNA editing as a breach of the central dogma. (Same
> for DNA repair.)

The best candidate for breaking the central dogma (sensu Crick, and Larry)
is RNA editing.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3420917/
I say this as it is protein sequence information going back and changing
nucleotide sequence information in ways that do rely, in some sense, on
a peptide sequence code. You can stretch this a few ways regards
RNA editing such that I'd say the lines of where this claim works and
doesn't become blurred. The paper I'm citing isn't the best to explain
that but I do think it provides some clues about how the editing might
expand to be considered a way to feed sequence information from
protein to nucleotide. The biggest reservations are that the PPR proteins
aren't reverse translating RNA to encode PPR proteins or even limited
Pentatricopeptide Repeat subunits, reservations about if it really counts
if you aren't efficiently getting back to replicating DNA. I wouldn't want
to have to engineer in reverse transcriptase into such an imagined
derivative of RNA editing. But you might write some cheesy SciFi
off of the idea.

And of course strong nitpicking will say that any protein of a specific
sequence that does anything to alter an RNA sequence was already
part way home. That, however, is too trite in my view.

On 2023-10-06 5:00 AM, broger...@gmail.com wrote:
> On Thursday, October 5, 2023 at 10:20:59 PM UTC-4, DB Cates wrote:
>> On 2023-10-05 7:36 PM, broger...@gmail.com wrote:
>>> On Thursday, October 5, 2023 at 7:50:59 PM UTC-4, MarkE wrote:
>>>> On Thursday, October 5, 2023 at 5:55:58 PM UTC+11, Glenn wrote:
>>>>> On Wednesday, October 4, 2023 at 11:35:58 PM UTC-7, MarkE wrote:
>>>>>> https://youtu.be/wQ5oPL0PqYE?si=KTKgIexdoLAuOI0o
>>>>>>
>>>>>> You might dismiss this as another ID argument from incredulity, but in doing do you feel a flicker of uncertainty or momentary wondering that your own belief might be from credulity?
>>>>>>
>>>>>> In any case, pretty amazing what goes on inside our cells when we're not looking.
>>>>> Another amazing topic is the rna editing of some organisms, such as octopi. Apparently brain neurons at lightning speed edit rna for many specific purposes. This is cognition, intelligence. In fact, it appears all life is intelligent, and has some cognitive abilities which provide for adaptation, behavior and purpose, with only a very small percentage having a "brain" as we humans.
>>>>> Slime molds, fungus, plants are also quite interesting in that they communicate, cooperate on an intelligent level, on purpose.
>>>>>
>>>>> Anyone who denies "consciousness", "intelligence", "purpose" in life has to be a few hands short of a deck.
>>>> RNA editing is a surprising extra layer of genetic variability, and an exception to the "central dogma". This article describes RNA editing in humans as well, though a couple of orders of magnitude less than cephalopods: https://www.sciencenews.org/article/octopus-squid-rna-editing-dna-cephalopods
>>>
>>> If you want to see some very bizarre RNA editing, have a look at RNA editing in the mitochondria (also called kinetoplasts) of kinetoplastid protozoa (responsible for a couple of tropical diseases - Leishmaniasis and African Sleeping Sickness). A different mechanism entirely from that in cephalopods.
>>>
>>> Here's a review of what happens
>>>
>>> https://www.tandfonline.com/doi/pdf/10.4161/rna.7.2.11393
>>>
>>> and here's a short paper on a part of the evolution of the editing system
>>>
>>> https://kdna.net/simpsonlab/Lab%20publications/maslov%20evol%201994.pdf
>>>
>>> Why is anybody still using the phrase "central dogma"? I mean, it seemed nifty back when transcription and translation were first worked out, but reverse transcriptase stuck a knife in it, and, outside of elementary textbooks, most molecular biologists haven't really used the phrase for decades.
>>>
>> Hmmm. You may want to read this from Larry Moran's blog.
>> <https://sandwalk.blogspot.com/2007/01/central-dogma-of-molecular-biology.html>
>
> I don't disagree with the blog, I just don't think lots of molecular biologists spend a lot of time thinking about the "central dogma." Sure, people are pretty convinced it's unlikely anyone will discover "reverse translation" ; sufficiently convinced that mostly they don't give it a second thought. Mostly I see the "central dogma" discussed by creationists who want to call science a religion, and are happy to have find a religious sounding phrase about molecular biology.

All true. But... creationists do delight in finding "a religious
sounding phrase about molecular biology" in particular because it is
also FALSE. something that is supported when knowledgeable scientists
use phrases like "reverse transcriptase stuck a knife in it" when they
SHOULD know (and note) that it is a strawman version of the "central
dogma" that is being referred to.

--
--
Don Cates ("he's a cunning rascal" PN)

On Friday, October 6, 2023 at 12:01:01 PM UTC-4, DB Cates wrote:
> On 2023-10-06 5:00 AM, broger...@gmail.com wrote:
> > On Thursday, October 5, 2023 at 10:20:59 PM UTC-4, DB Cates wrote:
> >> On 2023-10-05 7:36 PM, broger...@gmail.com wrote:
> >>> On Thursday, October 5, 2023 at 7:50:59 PM UTC-4, MarkE wrote:
> >>>> On Thursday, October 5, 2023 at 5:55:58 PM UTC+11, Glenn wrote:
> >>>>> On Wednesday, October 4, 2023 at 11:35:58 PM UTC-7, MarkE wrote:
> >>>>>> https://youtu.be/wQ5oPL0PqYE?si=KTKgIexdoLAuOI0o
> >>>>>>
> >>>>>> You might dismiss this as another ID argument from incredulity, but in doing do you feel a flicker of uncertainty or momentary wondering that your own belief might be from credulity?
> >>>>>>
> >>>>>> In any case, pretty amazing what goes on inside our cells when we're not looking.
> >>>>> Another amazing topic is the rna editing of some organisms, such as octopi. Apparently brain neurons at lightning speed edit rna for many specific purposes. This is cognition, intelligence. In fact, it appears all life is intelligent, and has some cognitive abilities which provide for adaptation, behavior and purpose, with only a very small percentage having a "brain" as we humans.
> >>>>> Slime molds, fungus, plants are also quite interesting in that they communicate, cooperate on an intelligent level, on purpose.
> >>>>>
> >>>>> Anyone who denies "consciousness", "intelligence", "purpose" in life has to be a few hands short of a deck.
> >>>> RNA editing is a surprising extra layer of genetic variability, and an exception to the "central dogma". This article describes RNA editing in humans as well, though a couple of orders of magnitude less than cephalopods: https://www.sciencenews.org/article/octopus-squid-rna-editing-dna-cephalopods
> >>>
> >>> If you want to see some very bizarre RNA editing, have a look at RNA editing in the mitochondria (also called kinetoplasts) of kinetoplastid protozoa (responsible for a couple of tropical diseases - Leishmaniasis and African Sleeping Sickness). A different mechanism entirely from that in cephalopods.
> >>>
> >>> Here's a review of what happens
> >>>
> >>> https://www.tandfonline.com/doi/pdf/10.4161/rna.7.2.11393
> >>>
> >>> and here's a short paper on a part of the evolution of the editing system
> >>>
> >>> https://kdna.net/simpsonlab/Lab%20publications/maslov%20evol%201994.pdf
> >>>
> >>> Why is anybody still using the phrase "central dogma"? I mean, it seemed nifty back when transcription and translation were first worked out, but reverse transcriptase stuck a knife in it, and, outside of elementary textbooks, most molecular biologists haven't really used the phrase for decades.
> >>>
> >> Hmmm. You may want to read this from Larry Moran's blog.
> >> <https://sandwalk.blogspot.com/2007/01/central-dogma-of-molecular-biology.html>
> >
> > I don't disagree with the blog, I just don't think lots of molecular biologists spend a lot of time thinking about the "central dogma." Sure, people are pretty convinced it's unlikely anyone will discover "reverse translation" ; sufficiently convinced that mostly they don't give it a second thought. Mostly I see the "central dogma" discussed by creationists who want to call science a religion, and are happy to have find a religious sounding phrase about molecular biology.
> All true. But... creationists do delight in finding "a religious
> sounding phrase about molecular biology" in particular because it is
> also FALSE. something that is supported when knowledgeable scientists
> use phrases like "reverse transcriptase stuck a knife in it" when they
> SHOULD know (and note) that it is a strawman version of the "central
> dogma" that is being referred to.

I'd say "strawman" is a bit much for a version of the central dogma that Watson himself included in his molecular biology text back in the 60's. Crick's version was better and Watson's was indeed FALSE, but 50-60 years later it just doesn't matter anymore. We all know what goes on between DNA, RNA, and protein in much more detail than back then, so it's just puzzling why anyone wastes any thought on whether or not some kind of RNA editing "violates the central dogma."
> --
> --
> Don Cates ("he's a cunning rascal" PN)

On Wed, 4 Oct 2023 23:35:18 -0700 (PDT), MarkE <me22over7@gmail.com>
wrote:

>https://youtu.be/wQ5oPL0PqYE?si=KTKgIexdoLAuOI0o
>
>You might dismiss this as another ID argument from incredulity, but in doing do you feel a flicker of uncertainty or momentary wondering that your own belief might be from credulity?
>
>In any case, pretty amazing what goes on inside our cells when we're not looking.

Here's a link to an article titled "Is the cell really a machine?" by
Daniel Nicholson. It argues persuasively that the machine analogy is
misleading and overly simplistic, that proteins work nothing like the
static shapes animations like the above illustrate:

<https://philpapers.org/archive/NICITC.pdf>

From the abstract:
**************************************************
It has become customary to conceptualize the living cell as an
intricate piece of machinery, different to a man-made machine only in
terms of its superior complexity. This familiar understanding grounds
the conviction that a cell’s organization can be explained
reductionistically, as well as the idea that its molecular pathways
can be construed as deterministic circuits. The machine conception of
the cell owes a great deal of its success to the methods traditionally
used in molecular biology. However, the recent introduction of novel
experimental techniques capable of tracking individual molecules
within cells in real time is leading to the rapid accumulation of data
that are inconsistent with an engineering view of the cell.
*************************************************

--
To know less than we don't know is the nature of most knowledge

On Saturday, October 7, 2023 at 6:51:01 PM UTC+11, jillery wrote:
> On Wed, 4 Oct 2023 23:35:18 -0700 (PDT), MarkE <me22...@gmail.com>
> wrote:
>
> >https://youtu.be/wQ5oPL0PqYE?si=KTKgIexdoLAuOI0o
> >
> >You might dismiss this as another ID argument from incredulity, but in doing do you feel a flicker of uncertainty or momentary wondering that your own belief might be from credulity?
> >
> >In any case, pretty amazing what goes on inside our cells when we're not looking.
> Here's a link to an article titled "Is the cell really a machine?" by
> Daniel Nicholson. It argues persuasively that the machine analogy is
> misleading and overly simplistic, that proteins work nothing like the
> static shapes animations like the above illustrate:
>
> <https://philpapers.org/archive/NICITC.pdf>
>
> From the abstract:
> **************************************************
> It has become customary to conceptualize the living cell as an
> intricate piece of machinery, different to a man-made machine only in
> terms of its superior complexity. This familiar understanding grounds
> the conviction that a cell’s organization can be explained
> reductionistically, as well as the idea that its molecular pathways
> can be construed as deterministic circuits. The machine conception of
> the cell owes a great deal of its success to the methods traditionally
> used in molecular biology. However, the recent introduction of novel
> experimental techniques capable of tracking individual molecules
> within cells in real time is leading to the rapid accumulation of data
> that are inconsistent with an engineering view of the cell.
> *************************************************
> --
> To know less than we don't know is the nature of most knowledge

Or this: https://groups.google.com/g/talk.origins/c/tuZKo8y-AHw

Mark, I'd like to remind you that Martin Harran has responded quite extensively
to a long post by you on another thread. Here is your long post, inquiring about
certain aspects of his religious beliefs:

Re: Tour's 60 day challenge
https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/Z7pICkYjAQAJ
Sep 25, 2023, 8:10:49 AM

Martin gave two replies, the first one addressing all your questions and statements:
https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/rdUrj8czAQAJ
Sep 27, 2023, 12:55:50 PM

The other went deeper into one part of your last question.

https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/eCPXVOd8AQAJ
Sep 28, 2023, 11:15:51 AM

Have you lost track of this thread, or are you unable to wrap your mind
around some of his answers? If the latter is the case, I might be able
to help you out there.

I have a few comments to make below to what you wrote/quoted here.

On Saturday, October 7, 2023 at 4:01:01 AM UTC-4, MarkE wrote:
> On Saturday, October 7, 2023 at 6:51:01 PM UTC+11, jillery wrote:
> > On Wed, 4 Oct 2023 23:35:18 -0700 (PDT), MarkE <me22...@gmail.com>
> > wrote:
> >
> > >https://youtu.be/wQ5oPL0PqYE?si=KTKgIexdoLAuOI0o
> > >
> > >You might dismiss this as another ID argument from incredulity, but in doing do you feel a flicker of uncertainty or momentary wondering that your own belief might be from credulity?
> > >
> > >In any case, pretty amazing what goes on inside our cells when we're not looking.
> > Here's a link to an article titled "Is the cell really a machine?" by
> > Daniel Nicholson. It argues persuasively that the machine analogy is
> > misleading and overly simplistic, that proteins work nothing like the
> > static shapes animations like the above illustrate:
> >
> > <https://philpapers.org/archive/NICITC.pdf>
> >
> > From the abstract:
> > **************************************************
> > It has become customary to conceptualize the living cell as an
> > intricate piece of machinery, different to a man-made machine only in
> > terms of its superior complexity.

This custom is out of place in a forum like talk.origins.
Cells are too big a unit to be successfully compared to a machine,
and participants want something they can wrap their minds around.

On the other hand, the IC structures that Michael Behe deals with in his first book,
_Darwin's Black Box_ *can* be compared to machines --- Behe even compares
the bacterial flagellum to an "outboard motor" although its means of propelling
a bacterium forward are different.

Earlier today, I made similar points in reply to Mark Isaak on that same thread,
Re: Tour's 60 day challenge
https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/F9k6GouRAwAJ

Also, the protein translation machinery seems to work, over and over and over
again, like a factory assembly line. Ribosomes "read off" individual genes from
mRNA, providing places for tRNA molecules with attached amino acids
to latch onto long enough for their attached aminos to transfer to an ever-growing chain of aminos,
linked by peptide bonds. The end result is a polypeptide which is a vital ingredient
in a protein, or is itself a protein.

> > This familiar understanding grounds
> > the conviction that a cell’s organization can be explained
> > reductionistically, as well as the idea that its molecular pathways
> > can be construed as deterministic circuits. The machine conception of
> > the cell owes a great deal of its success to the methods traditionally
> > used in molecular biology. However, the recent introduction of novel
> > experimental techniques capable of tracking individual molecules
> > within cells in real time is leading to the rapid accumulation of data
> > that are inconsistent with an engineering view of the cell.
> > *************************************************
> > --
> > To know less than we don't know is the nature of most knowledge

> Or this: https://groups.google.com/g/talk.origins/c/tuZKo8y-AHw

This is about a single enzyme that is the subject of this thread.
It's about as far from a complete cell as you can get.

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

On Tuesday, October 10, 2023 at 12:36:03 PM UTC+11, peter2...@gmail..com wrote:
> Mark, I'd like to remind you that Martin Harran has responded quite extensively
> to a long post by you on another thread. Here is your long post, inquiring about
> certain aspects of his religious beliefs:
>
> Re: Tour's 60 day challenge
> https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/Z7pICkYjAQAJ
> Sep 25, 2023, 8:10:49 AM
>
> Martin gave two replies, the first one addressing all your questions and statements:
> https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/rdUrj8czAQAJ
> Sep 27, 2023, 12:55:50 PM
>
> The other went deeper into one part of your last question.
>
> https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/eCPXVOd8AQAJ
> Sep 28, 2023, 11:15:51 AM
>
> Have you lost track of this thread, or are you unable to wrap your mind
> around some of his answers? If the latter is the case, I might be able
> to help you out there.

Thank Peter, I had missed those responses from Martin, will consider them.

>
>
> I have a few comments to make below to what you wrote/quoted here.
> On Saturday, October 7, 2023 at 4:01:01 AM UTC-4, MarkE wrote:
> > On Saturday, October 7, 2023 at 6:51:01 PM UTC+11, jillery wrote:
> > > On Wed, 4 Oct 2023 23:35:18 -0700 (PDT), MarkE <me22...@gmail.com>
> > > wrote:
> > >
> > > >https://youtu.be/wQ5oPL0PqYE?si=KTKgIexdoLAuOI0o
> > > >
> > > >You might dismiss this as another ID argument from incredulity, but in doing do you feel a flicker of uncertainty or momentary wondering that your own belief might be from credulity?
> > > >
> > > >In any case, pretty amazing what goes on inside our cells when we're not looking.
> > > Here's a link to an article titled "Is the cell really a machine?" by
> > > Daniel Nicholson. It argues persuasively that the machine analogy is
> > > misleading and overly simplistic, that proteins work nothing like the
> > > static shapes animations like the above illustrate:
> > >
> > > <https://philpapers.org/archive/NICITC.pdf>
> > >
> > > From the abstract:
> > > **************************************************
> > > It has become customary to conceptualize the living cell as an
> > > intricate piece of machinery, different to a man-made machine only in
> > > terms of its superior complexity.
> This custom is out of place in a forum like talk.origins.
> Cells are too big a unit to be successfully compared to a machine,
> and participants want something they can wrap their minds around.
>
> On the other hand, the IC structures that Michael Behe deals with in his first book,
> _Darwin's Black Box_ *can* be compared to machines --- Behe even compares
> the bacterial flagellum to an "outboard motor" although its means of propelling
> a bacterium forward are different.
>
> Earlier today, I made similar points in reply to Mark Isaak on that same thread,
> Re: Tour's 60 day challenge
> https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/F9k6GouRAwAJ
>
>
> Also, the protein translation machinery seems to work, over and over and over
> again, like a factory assembly line. Ribosomes "read off" individual genes from
> mRNA, providing places for tRNA molecules with attached amino acids
> to latch onto long enough for their attached aminos to transfer to an ever-growing chain of aminos,
> linked by peptide bonds. The end result is a polypeptide which is a vital ingredient
> in a protein, or is itself a protein.
> > > This familiar understanding grounds
> > > the conviction that a cell’s organization can be explained
> > > reductionistically, as well as the idea that its molecular pathways
> > > can be construed as deterministic circuits. The machine conception of
> > > the cell owes a great deal of its success to the methods traditionally
> > > used in molecular biology. However, the recent introduction of novel
> > > experimental techniques capable of tracking individual molecules
> > > within cells in real time is leading to the rapid accumulation of data
> > > that are inconsistent with an engineering view of the cell.
> > > *************************************************
> > > --
> > > To know less than we don't know is the nature of most knowledge
>
> > Or this: https://groups.google.com/g/talk.origins/c/tuZKo8y-AHw
> This is about a single enzyme that is the subject of this thread.
> It's about as far from a complete cell as you can get.

Acknowledging the limits of metaphors and analogies, and the finer points of definitions and semantics, would you agree with these approximations:

flagellum = machine
cell = factory
  
I note you use both "machinery" and "factory" in this description: "Also, the protein translation machinery seems to work, over and over and over again, like a factory assembly line."

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

On 10/9/23 6:32 PM, peter2...@gmail.com wrote:
[...]
>
> Earlier today, I made similar points in reply to Mark Isaak on that same thread,
> Re: Tour's 60 day challenge
> https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/F9k6GouRAwAJ

That post has not shown up on my newsreader, and I'm not going to
struggle with Google groups to respond there, so I'll summarize some
thoughts here.

You said it is not the job of anti-evolutionists to "Find a system that
could evolve more easily than the irreducibly complex bacterial
flagellum Minnich researched, and work just as well or better, and which
becomes a bacterial flagellum by losing a bunch of parts." That is
simply not entirely true. What is true is that it is not their job to
*challenge other people* to do work that they refuse to approach
themselves. (Well, maybe that is their job as propagandists, but not as
scientists.) There already exists a perfectly good, if not complete in
every detail, model for how the flagellum could have evolved. That
suffices for Minnich's challenge. If you want more, do it yourself.

You still ignore the fact that there are multiple ways by which IC can
evolve. You and others challenge, "how could such-and-such have
evolved?" You could make that challenge for anything, and for
long-existing systems which don't leave a good fossil record, it will be
nigh impossible to give a detailed answer, except ones that people like
you will immediately dismiss as speculation. What you miss is that IC
HAS ABSOLUTELY NOTHING TO DO WITH IT. IC can evolve from non-IC by
gradual steps. Believe it or not as you will, but Deal With It.

--
Mark Isaak
"Wisdom begins when you discover the difference between 'That
doesn't make sense' and 'I don't understand.'" - Mary Doria Russell

On Mon, 9 Oct 2023 18:32:51 -0700 (PDT), "peter2...@gmail.com"
<peter2nyikos@gmail.com> wrote:

>
>Mark, I'd like to remind you that Martin Harran has responded quite extensively
>to a long post by you on another thread. Here is your long post, inquiring about
>certain aspects of his religious beliefs:
>
>Re: Tour's 60 day challenge
>https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/Z7pICkYjAQAJ
>Sep 25, 2023, 8:10:49?AM
>
>Martin gave two replies, the first one addressing all your questions and statements:
>https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/rdUrj8czAQAJ
>Sep 27, 2023, 12:55:50?PM
>
>The other went deeper into one part of your last question.
>
>https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/eCPXVOd8AQAJ
>Sep 28, 2023, 11:15:51?AM
>
>Have you lost track of this thread, or are you unable to wrap your mind
>around some of his answers? If the latter is the case, I might be able
>to help you out there.

Whilst I disagree with Mark on some issues, he is clearly a highly
intelligent person, far too intelligent, I am sure, to rely on *your*
interpretation of what I mean when I say something to him.

[...]

On Tuesday, October 10, 2023 at 7:31:04 AM UTC-4, MarkE wrote:
> On Tuesday, October 10, 2023 at 12:36:03 PM UTC+11, peter2...@gmail.com wrote:

[snip of issues on a different thread, not relevant here]

> > I have a few comments to make below to what you wrote/quoted here.

> > On Saturday, October 7, 2023 at 4:01:01 AM UTC-4, MarkE wrote:
> > > On Saturday, October 7, 2023 at 6:51:01 PM UTC+11, jillery wrote:
> > > > On Wed, 4 Oct 2023 23:35:18 -0700 (PDT), MarkE <me22...@gmail.com>
> > > > wrote:
> > > >
> > > > >https://youtu.be/wQ5oPL0PqYE?si=KTKgIexdoLAuOI0o
> > > > >
> > > > >You might dismiss this as another ID argument from incredulity, but in doing do you feel a flicker of uncertainty or momentary wondering that your own belief might be from credulity?
> > > > >
> > > > >In any case, pretty amazing what goes on inside our cells when we're not looking.

I was rushed for time when I made my earlier reply to you, Mark,
and did not address the following quote:

> > > > Here's a link to an article titled "Is the cell really a machine?" by
> > > > Daniel Nicholson. It argues persuasively that the machine analogy is
> > > > misleading and overly simplistic, that proteins work nothing like the
> > > > static shapes animations like the above illustrate:
> > > >
> > > > <https://philpapers.org/archive/NICITC.pdf>

"static shapes" is something of a straw man in this context.
The real issue is whether a reductionist attitude towards
whatever the protein molecules do, is adequate to account for what happens.

And "materialistic reductionist" is at the heart of the issue.
It may use the buzz words "emergent properties" or
"a fluid, self-organizing process" [1] but these will
be interpreted as being ultimately reducible to the action of
subatomic particles according to physical laws [2].

[1] See the last paragraph on page 110 of the article.

[2] like Brownian motion, *ibid*. It's usually described
on the molecular level, but the motions of the molecules
are in turn governed ultimately by the protons and electrons and
neutrons that they are made up of.

> > > > From the abstract:
> > > > **************************************************
> > > > It has become customary to conceptualize the living cell as an
> > > > intricate piece of machinery, different to a man-made machine only in
> > > > terms of its superior complexity.

> > This custom is out of place in a forum like talk.origins.
> > Cells are too big a unit to be successfully compared to a machine,
> > and participants want something they can wrap their minds around.
> > On the other hand, the IC structures that Michael Behe deals with in his first book,
> > _Darwin's Black Box_ *can* be compared to machines --- Behe even compares
> > the bacterial flagellum to an "outboard motor" although its means of propelling
> > a bacterium forward are different.
> >
> > Earlier today, I made similar points in reply to Mark Isaak on that same thread,
> > Re: Tour's 60 day challenge
> > https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/F9k6GouRAwAJ
> >
> >
> > Also, the protein translation machinery seems to work, over and over and over
> > again, like a factory assembly line. Ribosomes "read off" individual genes from
> > mRNA, providing places for tRNA molecules with attached amino acids
> > to latch onto long enough for their attached aminos to transfer to an ever-growing chain of aminos,
> > linked by peptide bonds. The end result is a polypeptide which is a vital ingredient
> > in a protein, or is itself a protein.

> > > > This familiar understanding grounds
> > > > the conviction that a cell’s organization can be explained
> > > > reductionistically, as well as the idea that its molecular pathways
> > > > can be construed as deterministic circuits. The machine conception of
> > > > the cell owes a great deal of its success to the methods traditionally
> > > > used in molecular biology.

> > > >However, the recent introduction of novel
> > > > experimental techniques capable of tracking individual molecules
> > > > within cells in real time is leading to the rapid accumulation of data
> > > > that are inconsistent with an engineering view of the cell.
> > > > *************************************************

I think this data is consistent with a deterministic view of the cell
that ignores quantum uncertainty. I don't think we can go further
without the reductionists clamoring in protest.

> > > > To know less than we don't know is the nature of most knowledge
> >
> > > Or this: https://groups.google.com/g/talk.origins/c/tuZKo8y-AHw

> > This is about a single enzyme that is the subject of this thread.
> > It's about as far from a complete cell as you can get.

> Acknowledging the limits of metaphors and analogies, and the finer points of definitions and semantics, would you agree with these approximations:
>
> flagellum = machine
> cell = factory

It's an improvement, that's for sure. But I think "machinery" makes an intermediate
step in the case of the flagellum:

> I note you use both "machinery" and "factory" in this description: "Also, the protein translation machinery seems to work, over and over and over again, like a factory assembly line."

The cell itself might be called a factory, but that seems to fall in line with
the reductionist method. What do you think of the following idea:

cell = nano-biosphere

That is consistent with reductionism, but it also gives full scope to Gaia enthusiasts
and those who talk about "emergent properties," etc.

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

On Tuesday, October 10, 2023 at 10:46:04 AM UTC-4, Mark Isaak wrote:
> On 10/9/23 6:32 PM, peter2...@gmail.com wrote:
> [...]
> >
> > Earlier today, I made similar points in reply to Mark Isaak on that same thread,
> > Re: Tour's 60 day challenge
> > https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/F9k6GouRAwAJ

> That post has not shown up on my newsreader, and I'm not going to
> struggle with Google groups to respond there, so I'll summarize some
> thoughts here.

Your first sentence is way out of line. You use "anti-evolutionists" where
I wrote "anti-ID folks like yourself." Minnich, Behe, and I are no more
opposed to evolution than you are. The difference is in the theories
to which we subscribe. You opt for the reductionist idea of
"natural selection" in current theory being "competition WITHIN
populations of the same species". I see truly epic forms of competition, like between
birds and pterosaurs, as being more faithful to the fossil record.

I started a thread on this theme in sci.bio.paleontology, and it
really took off with the following post.

https://groups.google.com/g/sci.bio.paleontology/c/Q0GRZFRBSjo/m/SJlqZfTRAAAJ
Re: Triassic Mega-Evolution
Sep 28, 2023, 1:52:15 PM

> You said it is not the job of anti-evolutionists to "Find a system that
> could evolve more easily than the irreducibly complex bacterial
> flagellum Minnich researched, and work just as well or better, and which
> becomes a bacterial flagellum by losing a bunch of parts."

I've snipped the rest. It's more productive at this point for me to
re-post the reply that hasn't shown up yet.

Lest your newsreader drop the ball again, I'm piggybacking the repost
on a reply to this same post of yours. That way, you will at least
know that the effort has been made, to within a very high degree of probability.

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

On Tuesday, October 10, 2023 at 1:41:04 PM UTC-4, peter2...@gmail.com wrote:
[focus]
> You opt for the reductionist idea of
> "natural selection" in current theory being "competition WITHIN
> populations of the same species". I see truly epic forms of competition, like between
> birds and pterosaurs, as being more faithful to the fossil record.
It is axiomatic that the greatest competitor an individual organism has is usually
its own siblings. How fossil evidence could even begin to address that is a puzzlement.

Whether an organism is competing to access resources, or avoid predation, it's
pretty clear where the first competition comes from. Respective to the specifics
of the competition to reproduce, it's rather clear. It's an observation from the science
of ecology. Species competition can be a factor in macroevolution per extinction,
but you specifically referenced "natural selection."

Here is my reply that you missed, Mark, from the other thread.

On Tuesday, October 3, 2023 at 11:25:56 AM UTC-4, Mark Isaak wrote:
> On 10/2/23 6:10 PM, peter2...@gmail.com wrote:
> > On Thursday, September 28, 2023 at 12:30:51 PM UTC-4, Mark Isaak wrote:
> >> On 9/27/23 11:11 AM, peter2...@gmail.com wrote:
> >>> On Friday, September 22, 2023 at 10:35:45 PM UTC-4, Mark Isaak wrote:
> >>>> On 9/22/23 2:34 PM, peter2...@gmail.com wrote:
> >>>>> On Thursday, September 21, 2023 at 4:15:44 PM UTC-4, Lawyer Daggett wrote:
> >
> >> [big skip for focus]
> >
> >>>>>>> “Irreducible Complexity” was originally proposed by Herman J. Muller in 1918.
> >>>>>
> >>>>> This is one of the most enduring falsehoods in the anti-ID literature.
> >>>>> Muller only talked about SOME components being essential. Irreducible complexity
> >>>>> says, by definition, that EACH AND EVERY component is essential.
> >>>
> >>> Now you come in, Mark, with a generality and no specific examples, except for
> >>> Behe's teaching aid of a mousetrap.
> >>>
> >>>> Well, in practice, Behe's IC, like Muller's, says that each and every
> >>>> one of the *essential* components is essential.
> >>>
> >>> Wrong. Muller's "interlocking complexity" is applicable to the human body,
> >>> in which the heart is essential but the individual kidney is not essential.
> >>> That's what makes kidney donation such an important part of modern medicine.
> >>> And the individual kidney is far from irreducibly complex: you could lose
> >>> 80% of the parts that make up your kidney, and as long as the rest is working efficiently,
> >>> you will be OK.

> >>> Behe's actual examples are different. Minnich broke down a bacterial flagellum
> >>> into its individual molecules, and found that each and every one of them
> >>> was essential to the basic function of swimming. Take away molecule X,
> >>> it doesn't swim; restore molecule X, it swims.
> >>>
> >>> The individual components of the clotting system and the immune
> >>> system are molecules.
> >>>
> >>>
> >>>> To take an extreme and
> >>>> silly example, your ability to alter the company's logo on a mousetrap
> >>>> does not mean the mousetrap is not IC.
> >>>
> >>> I'm glad you caught on to that much. It spares me from going into
> >>> detail on a satire I did a number of years ago about your use
> >>> (back then) of the word "part."
> >>>
> >>> Anyway, the mousetrap has always been for educational purposes,
> >>> to illustrate the *concept* of irreducible complexity. Smart-alecky
> >>> nitpicks miss that point.
..
..
..
> >>>> And even if Muller's argument
> >>>> does talk about SOME components (actually, to quote him (p. 464), "very
> >>>> numerous different elementary parts or factors"), his argument does not
> >>>> change an iota if ALL components are involved.

Far below, I wrote something which referred specifically to my
being able to find p. 464, thanks to your very complete identification
of where it appeared. If more t.o. regulars were this conscientious,
t.o. would not be a cesspool headed for hellhole status.

> >>> I take it you are referring to loss of components making a formerly
> >>> nonessential component essential [same page]. That still doesn't
> >>> mean that ALL nonessential components suffer the same fate.
> >>> So the gulf between Behe and Muller is still there.
> >
> >> Okay, I accept that Muller's interlocking complexity allows some
> >> non-essential parts. However, it does not *require* them. Thus Behe's
> >> (original) irreducible complexity is a subset of Muller's interlocking
> >> complexity.
> >
> > That's like saying that humans are a subset of Mammalia. Doesn't tell
> > us much about our fellow humans. [Although Jonathan Swift did try
> > in Gulliver's Fourth Voyage.]

> More like saying that insects are a subset of Hexapoda.

Why? Insects are a huge subset of Hexapoda, outnumbering all other
candidates put together on the species level.

OTOH we humans are a single species of Mammalia.

If you are thinking of comparisons of individuals, I do believe
we humans are outnumbered just by the members of Rodentia.
OTOH I believe insects outnumber all other hexapods on an individual
to individual basis. What other hexapod can outnumber the ants alone?

> >> Muller remains significant in that he showed how Behe's IC could evolve
> >> naturally, indeed that such systems might be expected to evolve.
> >
> > By armchair theorists who don't look at such things but speculate in airy rhetorical
> > ways about them, minimizing their difficulty by the same one-size-fits-all generalities
> > that anti-ID zealots use to minimize the difficulty of OOL.
> >
> > Find a system that could evolve more easily than the irreducibly complex
> > bacterial flagellum Minnich researched [see above], and work just as well or better, and which becomes
> > a bacterial flagellum by losing a bunch of parts.

> Minnich never tried to find such a system.

Errmm... it's the job of anti-ID folks like yourself to find such a system.
Try re-reading the paragraph to whose content you are replying.

> Neither have you.

Not my job. Moreover, I haven't the foggiest idea how that could be done.

> Muller at
> least pointed a way past the apparent roadblocks.

If you know about anyone who applied Muller's idea of "a way past"
to ANY of the IC systems that Behe treats in _DBB_, I'd love to know about it.

In fact, Muller's idea is just another "Exaptor of the gaps" argument until someone
provides such a "way past" for those systems.

> >> Of course, he preceded Behe by decades, so he was not directly addressing
> >> Behe's claims, and he did not (as far as I know) mention the other ways
> >> that Behe's IC could evolve gradually.

IC systems can and do evolve without losing their IC status.
The real issue is whether an IC system itself can evolve gradually
from non-IC systems. Exaptationdiddit is not an explanation.

>>> For example, possible ambiguity
> >> in what may be regarded as a "part", which Peter thinks he can ignore
> >> now that he has made up a lampoon about it.
> >
> > Not a lampoon. A challenge for you to fix your thinking about the definition of "part"
> > to where you realize that the relevant parts of Behe's serious examples are MOLECULES.

> How is that relevant?

Keep reading.

> > Do you know enough chemistry to know how different chemical bonds are from physical
> > attachments? Or chemical reactions are from physical ones?

> I'm sure you know that molecules can be created, destroyed, and, most
> importantly, altered, right?

Alteration is a very different thing from *removal* (IOW, destruction), which is what IC is all about.

By the way, is "created" a Freudian slip? I've been suspected of being
a closet creationist for less than that.

>In particular, you know that such changes
> of molecules are *essential* to the life of a cell?

Cells are not IC systems. No one has succeeded in either finding
or "creating" an irreducibly complex cell.

And if someone DID succeed, [s]he could write *finis* to the next thing you wrote:

> To consider molecules as the relevant "parts" is absurd.

Please stick to molecules that are parts of IC systems that Behe wrote about.

Now do you see why it is relevant for the parts to be molecules?
[See where I wrote "Keep reading" way up there.]

> >>>>>>> He called it "interlocking complexity," and showed how it was supporting evolutionary theory. That original paper was, "Genetic Variablity, Twin Hybrids and Constant Hybrids, in a Case of Balanced Lethal Factors", Hermann J. Muller, Genetics, Vol 3, No 5: 422-499, Sept 1918.
> >>>
> >>> Google was my friend, as usual. Bing betrayed me by sending me to a specific
> >>> webpage that was flagged as suspicious by my anti-virus software.
> >>> Bing has started using ChatGPT, so that might account for the difference.

What had happened was that I pasted
"Genetic Variablity, Twin Hybrids and Constant Hybrids, in a Case of Balanced Lethal Factors"
into Bing, then into Google, and Google came through with lots of hits. Not so Bing.

On Wednesday, October 11, 2023 at 3:51:04 AM UTC+11, peter2...@gmail.com wrote:
> On Tuesday, October 10, 2023 at 7:31:04 AM UTC-4, MarkE wrote:
> > On Tuesday, October 10, 2023 at 12:36:03 PM UTC+11, peter2...@gmail.com wrote:
> [snip of issues on a different thread, not relevant here]
> > > I have a few comments to make below to what you wrote/quoted here.
>
> > > On Saturday, October 7, 2023 at 4:01:01 AM UTC-4, MarkE wrote:
> > > > On Saturday, October 7, 2023 at 6:51:01 PM UTC+11, jillery wrote:
> > > > > On Wed, 4 Oct 2023 23:35:18 -0700 (PDT), MarkE <me22...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > >https://youtu.be/wQ5oPL0PqYE?si=KTKgIexdoLAuOI0o
> > > > > >
> > > > > >You might dismiss this as another ID argument from incredulity, but in doing do you feel a flicker of uncertainty or momentary wondering that your own belief might be from credulity?
> > > > > >
> > > > > >In any case, pretty amazing what goes on inside our cells when we're not looking.
> I was rushed for time when I made my earlier reply to you, Mark,
> and did not address the following quote:
> > > > > Here's a link to an article titled "Is the cell really a machine?" by
> > > > > Daniel Nicholson. It argues persuasively that the machine analogy is
> > > > > misleading and overly simplistic, that proteins work nothing like the
> > > > > static shapes animations like the above illustrate:
> > > > >
> > > > > <https://philpapers.org/archive/NICITC.pdf>
> "static shapes" is something of a straw man in this context.
> The real issue is whether a reductionist attitude towards
> whatever the protein molecules do, is adequate to account for what happens.

Note that the article Daniel Nicholson was quoted by jillery (which you may realise).

> And "materialistic reductionist" is at the heart of the issue.
> It may use the buzz words "emergent properties" or
> "a fluid, self-organizing process" [1] but these will
> be interpreted as being ultimately reducible to the action of
> subatomic particles according to physical laws [2].
>
> [1] See the last paragraph on page 110 of the article.
>
> [2] like Brownian motion, *ibid*. It's usually described
> on the molecular level, but the motions of the molecules
> are in turn governed ultimately by the protons and electrons and
> neutrons that they are made up of.

Is "emergent properties" effectively a euphemism for "deterministic behaviour with causality pathways we don't understand"?

> > > > > From the abstract:
> > > > > **************************************************
> > > > > It has become customary to conceptualize the living cell as an
> > > > > intricate piece of machinery, different to a man-made machine only in
> > > > > terms of its superior complexity.
>
> > > This custom is out of place in a forum like talk.origins.
> > > Cells are too big a unit to be successfully compared to a machine,
> > > and participants want something they can wrap their minds around.
>
> > > On the other hand, the IC structures that Michael Behe deals with in his first book,
> > > _Darwin's Black Box_ *can* be compared to machines --- Behe even compares
> > > the bacterial flagellum to an "outboard motor" although its means of propelling
> > > a bacterium forward are different.
> > >
> > > Earlier today, I made similar points in reply to Mark Isaak on that same thread,
> > > Re: Tour's 60 day challenge
> > > https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/F9k6GouRAwAJ
> > >
> > >
> > > Also, the protein translation machinery seems to work, over and over and over
> > > again, like a factory assembly line. Ribosomes "read off" individual genes from
> > > mRNA, providing places for tRNA molecules with attached amino acids
> > > to latch onto long enough for their attached aminos to transfer to an ever-growing chain of aminos,
> > > linked by peptide bonds. The end result is a polypeptide which is a vital ingredient
> > > in a protein, or is itself a protein.
>
> > > > > This familiar understanding grounds
> > > > > the conviction that a cell’s organization can be explained
> > > > > reductionistically, as well as the idea that its molecular pathways
> > > > > can be construed as deterministic circuits. The machine conception of
> > > > > the cell owes a great deal of its success to the methods traditionally
> > > > > used in molecular biology.
>
> > > > >However, the recent introduction of novel
> > > > > experimental techniques capable of tracking individual molecules
> > > > > within cells in real time is leading to the rapid accumulation of data
> > > > > that are inconsistent with an engineering view of the cell.
> > > > > *************************************************
> I think this data is consistent with a deterministic view of the cell
> that ignores quantum uncertainty. I don't think we can go further
> without the reductionists clamoring in protest.
> > > > > To know less than we don't know is the nature of most knowledge
> > >
> > > > Or this: https://groups.google.com/g/talk.origins/c/tuZKo8y-AHw
>
> > > This is about a single enzyme that is the subject of this thread.
> > > It's about as far from a complete cell as you can get.
>
> > Acknowledging the limits of metaphors and analogies, and the finer points of definitions and semantics, would you agree with these approximations:
> >
> > flagellum = machine
> > cell = factory
> It's an improvement, that's for sure. But I think "machinery" makes an intermediate
> step in the case of the flagellum:
> > I note you use both "machinery" and "factory" in this description: "Also, the protein translation machinery seems to work, over and over and over again, like a factory assembly line."
> The cell itself might be called a factory, but that seems to fall in line with
> the reductionist method. What do you think of the following idea:
>
> cell = nano-biosphere
>
> That is consistent with reductionism, but it also gives full scope to Gaia enthusiasts
> and those who talk about "emergent properties," etc.

The cell does function as a busy autonomous enclosed-but-permeable system - nano-biosphere works.

If "factory" can be used to describe a major cellular susbsystem (the protein translation machinery), then by extension is the cell in toto a city? And to further overextend the metaphor, a city with central planning and autonomous but predictable citizens?!

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

On 11/10/2023 12:49, MarkE wrote:
> Is "emergent properties" effectively a euphemism for "deterministic
> behaviour with causality pathways we don't understand"?

I would say no. Water molecules don't have melting points, boiling
points, viscosities, surface tension, and so on, but water does. I would
define an emergent property as something which is a property of a
system, but not of the components (making even temperature and pressure
emergent properties). This definition has no restriction as to whether
we do or don't understand how the behaviour of the components gives rise
to the property. (I'd drop the deterministic since in many cases the
behaviour involved is stochastic.)

Because of our repeated success in accounting for many properties of
systems as emerging from the interactions of the systems' components, it
is a reasonable working hypothesis (and in accordance with Occam's
Razor) that properties of systems of unknown origin are also emergent
properties.

--
alias Ernest Major

On Wednesday, October 11, 2023 at 8:56:04 AM UTC-4, Ernest Major wrote:
> On 11/10/2023 12:49, MarkE wrote:
> > Is "emergent properties" effectively a euphemism for "deterministic
> > behaviour with causality pathways we don't understand"?
> I would say no. Water molecules don't have melting points, boiling
> points, viscosities, surface tension, and so on, but water does. I would
> define an emergent property as something which is a property of a
> system, but not of the components (making even temperature and pressure
> emergent properties). This definition has no restriction as to whether
> we do or don't understand how the behaviour of the components gives rise
> to the property. (I'd drop the deterministic since in many cases the
> behaviour involved is stochastic.)
>
> Because of our repeated success in accounting for many properties of
> systems as emerging from the interactions of the systems' components, it
> is a reasonable working hypothesis (and in accordance with Occam's
> Razor) that properties of systems of unknown origin are also emergent
> properties.
>
> --
> alias Ernest Major

Thank you for that. I was recoiling in horror at the prior comments on Brownian
motion as emergent from the behavior of subatomic particles but anticipated
any corrections devolving into who knows what. My one thought was that if
we took a bunch of bowling balls up into a zero G environment, put then in a
container with some helium, we'd get Brownian motion of the bowling balls.
That's a perfectly predictable stochastic process. It would be rather subtle of
course.

Emergence is a rather touchy subject. Consideration of ensembles helps to
anticipate stochastic properties of collections. I don't think it's teleological at all.
Many things often labeled as emergent are like that.

The most fraught aspect to me seems to be the distinctions between I couldn't
have anticipated, "we" couldn't have anticipated, and it's impossible to anticipate
property X of some form of collection or connection of parts. That could be
about anticipating the boiling point of water from quantum mechanics, or the
folded structure of a protein from its amino acid sequence. Calling it emergent
just because I can't anticipate it is obviously ridiculous. Calling it emergent
because "we" can't do it is arrogance. Calling something emergent because it
is impossible to anticipate it in concept (rather than in practice) seems the most
sensible meaning --- other than the difficulty around knowing what is impossible.
Thus, it is a very fraught concept.

On Wednesday, October 11, 2023 at 9:31:05 AM UTC-4, Lawyer Daggett wrote:
> On Wednesday, October 11, 2023 at 8:56:04 AM UTC-4, Ernest Major wrote:
> > On 11/10/2023 12:49, MarkE wrote:
> > > Is "emergent properties" effectively a euphemism for "deterministic
> > > behaviour with causality pathways we don't understand"?
> > I would say no. Water molecules don't have melting points, boiling
> > points, viscosities, surface tension, and so on, but water does. I would
> > define an emergent property as something which is a property of a
> > system, but not of the components (making even temperature and pressure
> > emergent properties). This definition has no restriction as to whether
> > we do or don't understand how the behaviour of the components gives rise
> > to the property. (I'd drop the deterministic since in many cases the
> > behaviour involved is stochastic.)
> >
> > Because of our repeated success in accounting for many properties of
> > systems as emerging from the interactions of the systems' components, it
> > is a reasonable working hypothesis (and in accordance with Occam's
> > Razor) that properties of systems of unknown origin are also emergent
> > properties.
> >
> > --
> > alias Ernest Major
> Thank you for that. I was recoiling in horror at the prior comments on Brownian
> motion as emergent from the behavior of subatomic particles but anticipated
> any corrections devolving into who knows what. My one thought was that if
> we took a bunch of bowling balls up into a zero G environment, put then in a
> container with some helium, we'd get Brownian motion of the bowling balls..
> That's a perfectly predictable stochastic process. It would be rather subtle of
> course.
>
> Emergence is a rather touchy subject. Consideration of ensembles helps to
> anticipate stochastic properties of collections. I don't think it's teleological at all.
> Many things often labeled as emergent are like that.
>
> The most fraught aspect to me seems to be the distinctions between I couldn't
> have anticipated, "we" couldn't have anticipated, and it's impossible to anticipate
> property X of some form of collection or connection of parts. That could be
> about anticipating the boiling point of water from quantum mechanics, or the
> folded structure of a protein from its amino acid sequence. Calling it emergent
> just because I can't anticipate it is obviously ridiculous. Calling it emergent
> because "we" can't do it is arrogance. Calling something emergent because it
> is impossible to anticipate it in concept (rather than in practice) seems the most
> sensible meaning --- other than the difficulty around knowing what is impossible.
> Thus, it is a very fraught concept.

I agree. I also do not think that saying that some property of a system is "emergent" tells you anything useful about that property. It could mean it's inefficient to try to calculate it from first principles, it could mean we don't know how to calculate it from first principles, it could mean we think we can prove that it is inherently not possible to calculate it from first principles, but whatever it means, it does not tell you anything much new or interesting about the system.

On 11/10/2023 14:25, Lawyer Daggett wrote:
> Thank you for that. I was recoiling in horror at the prior comments on
> Brownian motion as emergent from the behavior of subatomic particles but
> anticipated any corrections devolving into who knows what. My one
> thought was that if we took a bunch of bowling balls up into a zero G
> environment, put then in a container with some helium, we'd get Brownian
> motion of the bowling balls. That's a perfectly predictable stochastic
> process. It would be rather subtle of course.

I'd describe the reference to subatomic particles as greedy
reductionism. Brownian motion, generalised, is an emergent property of
fluids composed of particles of two very different size and masses - to
modify your thought experiment consider a mixture of perfectly elastic
marble and beachball sized spheres shaken up in zero-G.

--
alias Ernest Major

On 11/10/2023 15:10, broger...@gmail.com wrote:
> I agree. I also do not think that saying that some property of a system
> is "emergent" tells you anything useful about that property. It could
> mean it's inefficient to try to calculate it from first principles, it
> could mean we don't know how to calculate it from first principles, it
> could mean we think we can prove that it is inherently not possible to
> calculate it from first principles, but whatever it means, it does not
> tell you anything much new or interesting about the system.

"it could mean we think we can prove that it is inherently not possible
to calculate it from first principles"

Possibly you mean something different (such as "computationally
intractable") from my interpretation, but my position would be that if a
property is not in principle explicable in terms of the nature and
interactions of the parts of the system it is not emergent. Dualists
assert this about consciousness, which is equivalent to denying that
consciousness is an emergent property of brains (or equivalent substrates).

--
alias Ernest Major

On Tuesday, October 10, 2023 at 1:56:04 PM UTC-4, Lawyer Daggett wrote:
> On Tuesday, October 10, 2023 at 1:41:04 PM UTC-4, peter2...@gmail..com wrote:
> [focus]
> > You opt for the reductionist idea of
> > "natural selection" in current theory being "competition WITHIN
> > populations of the same species". I see truly epic forms of competition, like between
> > birds and pterosaurs, as being more faithful to the fossil record.

> It is axiomatic that the greatest competitor an individual organism has is usually
> its own siblings.

That runs up against the theory, if it deserves to be called that, of
the "Selfish Gene" a la Richard Dawkins.

Part of that theory is that, by protecting one's siblings, one is protecting those with the most
alleles in common with them. I dimly recall a "calculus" that postulates
a number N such that saving the lives of N siblings more than makes
up for sacrificing one's own life.

Can you take your thesis and Dawkins's antithesis and arrive at a higher synthesis?

Population geneticists, for the most part, unthinkingly adopt Darwin's 19th century hypothesis,
which is as I stated above. But this hypothesis is no longer entrenched
in the nascent Extended Evolutionary Synthesis, which is trying break out of such
reflexive thinking about competition.

> How fossil evidence could even begin to address that is a puzzlement.

By its one-sidedness. Most data that supports Darwin's hypothesis is not available
to us in the foreseeable future:

"The extreme rarity of transitional forms in the fossil record
persist as the trade secret of paleontology. The evolutionary
trees that adorn our textbooks have data only at the tips and
nodes of their branches; the rest is inference, however reasonable,
not the evidence of fossils."
--Stephen J. Gould - "Evolution's Erratic Pace," _Natural History_,
vol. 86(5) (May 1987): pp. 12-16, at p. 14
Reprinted in _The Panda's Thumb_, pp. 181-182.
http://www.talkorigins.org/faqs/quotes/mine/part3.html#quote3.2

The above quote continued:

"Yet Darwin was so wedded to gradualism that he wagered his entire theory
on a denial of this literal record:
The geological record is extremely imperfect and
this fact will to a large extent explain why we
do not find interminable varieties, connecting
together all the extinct and existing forms of life
by the finest graduated steps. He who rejects these views
on the nature of the geological record, will rightly reject
my whole theory.

"Darwin's argument still persists as the favored escape of most
paleontologists from the embarrassment of a record that seems to show
so little of evolution [directly]. In exposing its cultural and
methodological roots, I wish in no way to impugn the potential
validity of gradualism (for all general views have similar roots).
I only wish to point out that it is never "seen" in the rocks."

Turnabout is fair play: you deleted my link to a sci.bio.paleontology thread where
mega-competition is discussed, and now I delete the rest of your text.

However, I will address it in a later post, should you so wish.

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

On Wednesday, October 11, 2023 at 7:51:05 AM UTC-4, MarkE wrote:
> On Wednesday, October 11, 2023 at 3:51:04 AM UTC+11, peter2...@gmail.com wrote:
> > On Tuesday, October 10, 2023 at 7:31:04 AM UTC-4, MarkE wrote:
> > > On Tuesday, October 10, 2023 at 12:36:03 PM UTC+11, peter2...@gmail.com wrote:
> > [snip of issues on a different thread, not relevant here]
> > > > I have a few comments to make below to what you wrote/quoted here.
> >
> > > > On Saturday, October 7, 2023 at 4:01:01 AM UTC-4, MarkE wrote:
> > > > > On Saturday, October 7, 2023 at 6:51:01 PM UTC+11, jillery wrote:
> > > > > > On Wed, 4 Oct 2023 23:35:18 -0700 (PDT), MarkE <me22...@gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > >https://youtu.be/wQ5oPL0PqYE?si=KTKgIexdoLAuOI0o
> > > > > > >
> > > > > > >You might dismiss this as another ID argument from incredulity, but in doing do you feel a flicker of uncertainty or momentary wondering that your own belief might be from credulity?
> > > > > > >
> > > > > > >In any case, pretty amazing what goes on inside our cells when we're not looking.
> > I was rushed for time when I made my earlier reply to you, Mark,
> > and did not address the following quote:
> > > > > > Here's a link to an article titled "Is the cell really a machine?" by
> > > > > > Daniel Nicholson. It argues persuasively that the machine analogy is
> > > > > > misleading and overly simplistic, that proteins work nothing like the
> > > > > > static shapes animations like the above illustrate:
> > > > > >
> > > > > > <https://philpapers.org/archive/NICITC.pdf>
> > "static shapes" is something of a straw man in this context.
> > The real issue is whether a reductionist attitude towards
> > whatever the protein molecules do, is adequate to account for what happens.

> Note that the article Daniel Nicholson was quoted by jillery (which you may realise).

I did. I do a lot of my posting with the entire readership in mind,
and don't always stop to think about who said what. In the case of
quotes from outside sources, this seems reasonable.

> > And "materialistic reductionist" is at the heart of the issue.
> > It may use the buzz words "emergent properties" or
> > "a fluid, self-organizing process" [1] but these will
> > be interpreted as being ultimately reducible to the action of
> > subatomic particles according to physical laws [2].
> >
> > [1] See the last paragraph on page 110 of the article.
> >
> > [2] like Brownian motion, *ibid*. It's usually described
> > on the molecular level, but the motions of the molecules
> > are in turn governed ultimately by the protons and electrons and
> > neutrons that they are made up of.

> Is "emergent properties" effectively a euphemism for "deterministic behaviour with causality pathways we don't understand"?

I believe it is that, in the eyes of most materialists. Ernest Major even believes that
consciousness is an emergent property of ordinary matter. But there are tenable alternatives,
including the idea that it is a property of dark matter.

tenable = impervious to refutation, given what we know and don't know about dark matter.

> > > > > > From the abstract:
> > > > > > **************************************************
> > > > > > It has become customary to conceptualize the living cell as an
> > > > > > intricate piece of machinery, different to a man-made machine only in
> > > > > > terms of its superior complexity.
> >
> > > > This custom is out of place in a forum like talk.origins.
> > > > Cells are too big a unit to be successfully compared to a machine,
> > > > and participants want something they can wrap their minds around.
> >
> > > > On the other hand, the IC structures that Michael Behe deals with in his first book,
> > > > _Darwin's Black Box_ *can* be compared to machines --- Behe even compares
> > > > the bacterial flagellum to an "outboard motor" although its means of propelling
> > > > a bacterium forward are different.
> > > >
> > > > Earlier today, I made similar points in reply to Mark Isaak on that same thread,
> > > > Re: Tour's 60 day challenge
> > > > https://groups.google.com/g/talk.origins/c/JKnUO3rwKo4/m/F9k6GouRAwAJ
> > > >
> > > >
> > > > Also, the protein translation machinery seems to work, over and over and over
> > > > again, like a factory assembly line. Ribosomes "read off" individual genes from
> > > > mRNA, providing places for tRNA molecules with attached amino acids
> > > > to latch onto long enough for their attached aminos to transfer to an ever-growing chain of aminos,
> > > > linked by peptide bonds. The end result is a polypeptide which is a vital ingredient
> > > > in a protein, or is itself a protein.
> >
> > > > > > This familiar understanding grounds
> > > > > > the conviction that a cell’s organization can be explained
> > > > > > reductionistically, as well as the idea that its molecular pathways
> > > > > > can be construed as deterministic circuits. The machine conception of
> > > > > > the cell owes a great deal of its success to the methods traditionally
> > > > > > used in molecular biology.
> >
> > > > > >However, the recent introduction of novel
> > > > > > experimental techniques capable of tracking individual molecules
> > > > > > within cells in real time is leading to the rapid accumulation of data
> > > > > > that are inconsistent with an engineering view of the cell.
> > > > > > *************************************************
> > I think this data is consistent with a deterministic view of the cell
> > that ignores quantum uncertainty. I don't think we can go further
> > without the reductionists clamoring in protest.

> > > > > > To know less than we don't know is the nature of most knowledge
> > > >
> > > > > Or this: https://groups.google.com/g/talk.origins/c/tuZKo8y-AHw
> >
> > > > This is about a single enzyme that is the subject of this thread.
> > > > It's about as far from a complete cell as you can get.
> >
> > > Acknowledging the limits of metaphors and analogies, and the finer points of definitions and semantics, would you agree with these approximations:
> > >
> > > flagellum = machine
> > > cell = factory
<snip for focus>
> > The cell itself might be called a factory, but that seems to fall in line with
> > the reductionist method. What do you think of the following idea:

flagellum = machine
protein translation = factory
> > cell = nano-biosphere
> >
> > That is consistent with reductionism, but it also gives full scope to Gaia enthusiasts
> > and those who talk about "emergent properties," etc.

> The cell does function as a busy autonomous enclosed-but-permeable system - nano-biosphere works.

"nano- noosphere," in emulation of Teilhard de Chardin, can be substituted by those
who believe that cells have a primitive form of consciousness.

> If "factory" can be used to describe a major cellular susbsystem (the protein translation machinery), then by extension is the cell in toto a city? And to further overextend the metaphor, a city with central planning and autonomous but predictable citizens?!

More food for thought. But not today or tomorrow: too much else on my plate..

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

On Thursday, October 12, 2023 at 3:21:06 PM UTC-4, peter2...@gmail.com wrote:
> On Tuesday, October 10, 2023 at 1:56:04 PM UTC-4, Lawyer Daggett wrote:
> > On Tuesday, October 10, 2023 at 1:41:04 PM UTC-4, peter2...@gmail.com wrote:
> > [focus]
> > > You opt for the reductionist idea of
> > > "natural selection" in current theory being "competition WITHIN
> > > populations of the same species". I see truly epic forms of competition, like between
> > > birds and pterosaurs, as being more faithful to the fossil record.
>
> > It is axiomatic that the greatest competitor an individual organism has is usually
> > its own siblings.
> That runs up against the theory, if it deserves to be called that, of
> the "Selfish Gene" a la Richard Dawkins.
>
> Part of that theory is that, by protecting one's siblings, one is protecting those with the most
> alleles in common with them. I dimly recall a "calculus" that postulates
> a number N such that saving the lives of N siblings more than makes
> up for sacrificing one's own life.
>
> Can you take your thesis and Dawkins's antithesis and arrive at a higher synthesis?
>
> Population geneticists, for the most part, unthinkingly adopt Darwin's 19th century hypothesis,
> which is as I stated above. But this hypothesis is no longer entrenched
> in the nascent Extended Evolutionary Synthesis, which is trying break out of such
> reflexive thinking about competition.

You don't seem to understand the selfish gene or population genetics.
I won't attempt to re-invent the maths, it's already been done. I will point
you to a worthy reference. I have to go a bit indirect to respect the author's
wishes, but start here https://felsenst.github.io/pgbook/pgbook.html
You'll see his disclaimers about fair use. There's a link to his book. You'll
want the chapter on kin selection. I'll suggest you start around page 123.

> > How fossil evidence could even begin to address that is a puzzlement.
> By its one-sidedness. Most data that supports Darwin's hypothesis is not available
> to us in the foreseeable future:
>
> "The extreme rarity of transitional forms in the fossil record
> persist as the trade secret of paleontology. The evolutionary
> trees that adorn our textbooks have data only at the tips and
> nodes of their branches; the rest is inference, however reasonable,
> not the evidence of fossils."
> --Stephen J. Gould - "Evolution's Erratic Pace," _Natural History_,
> vol. 86(5) (May 1987): pp. 12-16, at p. 14
> Reprinted in _The Panda's Thumb_, pp. 181-182.
> http://www.talkorigins.org/faqs/quotes/mine/part3.html#quote3.2
>
> The above quote continued:
>
> "Yet Darwin was so wedded to gradualism that he wagered his entire theory
> on a denial of this literal record:
>
> The geological record is extremely imperfect and
> this fact will to a large extent explain why we
> do not find interminable varieties, connecting
> together all the extinct and existing forms of life
> by the finest graduated steps. He who rejects these views
> on the nature of the geological record, will rightly reject
> my whole theory.
>
> "Darwin's argument still persists as the favored escape of most
> paleontologists from the embarrassment of a record that seems to show
> so little of evolution [directly]. In exposing its cultural and
> methodological roots, I wish in no way to impugn the potential
> validity of gradualism (for all general views have similar roots).
> I only wish to point out that it is never "seen" in the rocks."

You continue to abuse that quote. So, as responded to you before,
". Faced with these facts of evolution and the philosophical bankruptcy
.. of their own position, creationists rely upon distortion and innuendo
.. to buttress their rhetorical claim. If I sound sharp or bitter, indeed I am
.. -- for I have become a major target of these practices.

.. I count myself among the evolutionists who argue for a jerky, or episodic,
.. rather than a smoothly gradual, pace of change. In 1972 my colleague Niles
.. Eldredge and I developed the theory of punctuated equilibrium. We argued
.. that two outstanding facts of the fossil record -- geologically "sudden"
.. origin of new species and failure to change thereafter (stasis) -- reflect
.. the predictions of evolutionary theory, not the imperfections of the fossil
.. record. In most theories, small isolated populations are the source of
.. new species, and the process of speciation takes thousands or tens of
.. thousands of years. This amount of time, so long when measured against
.. our lives, is a geological microsecond . . .

.. Since we proposed punctuated equilibria to explain trends, it is infuriating
.. to be quoted again and again by creationists -- whether through design
.. or stupidity, I do not know -- as admitting that the fossil record includes
.. no transitional forms. Transitional forms are generally lacking at the
.. species level, but they are abundant between larger groups.
- Gould, Stephen Jay 1983. "Evolution as Fact and Theory"
in Hens Teeth and Horse's Toes: Further Reflections in Natural History.

> Turnabout is fair play: you deleted my link to a sci.bio.paleontology thread where
> mega-competition is discussed, and now I delete the rest of your text.
>
> However, I will address it in a later post, should you so wish.
> Peter Nyikos
> Professor, Dept. of Mathematics
> Univ. of South Carolina -- standard disclaimer--
> http://people.math.sc.edu/nyikos

On Friday, October 6, 2023 at 1:16:00 AM UTC-7, jillery wrote:
> On Thu, 5 Oct 2023 13:39:57 -0700 (PDT), Glenn <GlennS...@msn.com>
> wrote:
> >On Thursday, October 5, 2023 at 9:40:59?AM UTC-7, Bob Casanova wrote:
> >> On Thu, 5 Oct 2023 04:05:16 -0700 (PDT), the following
> >> appeared in talk.origins, posted by "broger...@gmail.com"
> >> <broger...@gmail.com>:
> >> >On Thursday, October 5, 2023 at 2:35:58?AM UTC-4, MarkE wrote:
> >> >> https://youtu.be/wQ5oPL0PqYE?si=KTKgIexdoLAuOI0o
> >> >>
> >> >> You might dismiss this as another ID argument from incredulity, but in doing do you feel a flicker of uncertainty or momentary wondering that your own belief might be from credulity?
> >> >>
> >> >> In any case, pretty amazing what goes on inside our cells when we're not looking.
> >> >
> >> >First you made the assumption that lots of us had never thought about God or the supernatural. Now you assume lots of us have no idea that cells are complicated. I'm not sure what you're trying to do, since you say you are not trying to evangelize here, but whatever your goal is, you're more likely to get there if you make an effort to understand your audience.
> >> >
> >> Too complex; the audience can never be understood. Therefore
> >> Goddidtheaudience. See how that works?
> >> >
> >> --
> >You are all very good at making assumptions, even if you have to lie about what you are assuming.
> >
> >"The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection."
> The veracity of the above uncited quote depends very much on the
> criteria used to identify "best explained".
> >And you're getting you asses kicked hard. The funny thing is that none of you seem to feel anything.
> Really? Perhaps that's because the ass-kicking to which you allude is
> a figment of your imagination.

Is that what you mean by "best explained"?
> --
> To know less than we don't know is the nature of most knowledge

If you walk backwards you can't see where you are going.

On Wed, 21 Feb 2024 13:18:00 -0800 (PST), Glenn <GlennSheldon@msn.com>
wrote:

>On Friday, October 6, 2023 at 1:16:00?AM UTC-7, jillery wrote:
>> On Thu, 5 Oct 2023 13:39:57 -0700 (PDT), Glenn <GlennS...@msn.com>
>> wrote:
>> >On Thursday, October 5, 2023 at 9:40:59?AM UTC-7, Bob Casanova wrote:
>> >> On Thu, 5 Oct 2023 04:05:16 -0700 (PDT), the following
>> >> appeared in talk.origins, posted by "broger...@gmail.com"
>> >> <broger...@gmail.com>:
>> >> >On Thursday, October 5, 2023 at 2:35:58?AM UTC-4, MarkE wrote:
>> >> >> https://youtu.be/wQ5oPL0PqYE?si=KTKgIexdoLAuOI0o
>> >> >>
>> >> >> You might dismiss this as another ID argument from incredulity, but in doing do you feel a flicker of uncertainty or momentary wondering that your own belief might be from credulity?
>> >> >>
>> >> >> In any case, pretty amazing what goes on inside our cells when we're not looking.
>> >> >
>> >> >First you made the assumption that lots of us had never thought about God or the supernatural. Now you assume lots of us have no idea that cells are complicated. I'm not sure what you're trying to do, since you say you are not trying to evangelize here, but whatever your goal is, you're more likely to get there if you make an effort to understand your audience.
>> >> >
>> >> Too complex; the audience can never be understood. Therefore
>> >> Goddidtheaudience. See how that works?
>> >> >
>> >> --
>> >You are all very good at making assumptions, even if you have to lie about what you are assuming.
>> >
>> >"The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection."
>> The veracity of the above uncited quote depends very much on the
>> criteria used to identify "best explained".
>> >And you're getting you asses kicked hard. The funny thing is that none of you seem to feel anything.
>> Really? Perhaps that's because the ass-kicking to which you allude is
>> a figment of your imagination.
>
>Is that what you mean by "best explained"?

Either way, what is relevant is what is meant by the one who posted
the uncited quote.

>> --
>> To know less than we don't know is the nature of most knowledge
>
>If you walk backwards you can't see where you are going.

The above sounds like something someone would say who has trouble
chewing gum and walking at the same time, in any direction.

--
To know less than we don't know is the nature of most knowledge