• Re: Topoisomerase animation

    From Glenn@21:1/5 to MarkE on Wed Oct 4 23:53:26 2023
    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.

    --- SoupGate-Win32 v1.05
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  • From MarkE@21:1/5 to All on Wed Oct 4 23:35:18 2023
    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.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Athel Cornish-Bowden@21:1/5 to MarkE on Thu Oct 5 09:58:53 2023
    On 2023-10-05 06:35:18 +0000, MarkE said:

    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?

    Hardly. There are plenty of things we don't understand, and won't
    understand for a long time, but preferring a naturalistic
    interpretation over God-did-it has nothing to do with credulity. It has
    do with the fact that naturalistic interpretations of many topics have
    taken us a long way, whereas God-did-it explanations are based on no
    evidence whatsoever and have never led to useful new knowledge.

    In any case, pretty amazing what goes on inside our cells when we're
    not looking.

    Yes, but real scientists do look and try to understand.


    --
    athel cb : Biochemical Evolution, Garland Science, 2016

    --- SoupGate-Win32 v1.05
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  • From jillery@21:1/5 to All on Thu Oct 5 05:55:40 2023
    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.


    <https://youtu.be/ba2h9tqNYAo?t=41>
    ***************************************
    Complexity complexity complexity complexity. Oh look there's a
    pathway. It's very complicated.

    Complexity complexity complexity complexity complexity. And did you
    know that cells are really really complicated. But we're not done.

    Complexity complexity complexity complexity. And you're going to be
    blown away by the bacterial flagellum. It's like a little machine and
    it's really really complicated.

    Complexity complexity complexity complexity. We need more cells.
    They're really complicated. you just get blown away by these things.
    They are so amazingly complicated

    Complexity, therefore design.
    *****************************************
    Thank you, PZ.

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

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From brogers31751@gmail.com@21:1/5 to MarkE on Thu Oct 5 04:05:16 2023
    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.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From RonO@21:1/5 to jillery on Thu Oct 5 06:08:28 2023
    On 10/5/2023 4:55 AM, jillery wrote:
    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.


    <https://youtu.be/ba2h9tqNYAo?t=41>
    ***************************************
    Complexity complexity complexity complexity. Oh look there's a
    pathway. It's very complicated.

    Complexity complexity complexity complexity complexity. And did you
    know that cells are really really complicated. But we're not done.

    Complexity complexity complexity complexity. And you're going to be
    blown away by the bacterial flagellum. It's like a little machine and
    it's really really complicated.

    Complexity complexity complexity complexity. We need more cells.
    They're really complicated. you just get blown away by these things.
    They are so amazingly complicated

    Complexity, therefore design.
    *****************************************
    Thank you, PZ.

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


    Before he quit the ID creationist scam, with his complex specified
    information pseudo science an abject failure, Dembski made the claim
    that natural selection could be the intelligent designer whose work we
    see in nature. Dembski understood that all natural selection has to do
    is to favor change (that could include increased complexity) that does something to increase the ability of a lifeform to survive and
    reproduce. Specification is not needed because anything new has to work
    within the what the lifeform already is. Any changes are selected for
    or against. It doesn't matter what the new function does as long as it
    changes things enough to be more useful than what previously existed.

    It is why Behe started claiming that the irreducible part of IC didn't
    matter, and that it was the order and arrangement of mutations that
    created that IC system that made irreducible systems his type of IC.
    Behe has never found an order and arrangement of mutations that would
    qualify in making a system his type of IC. All that he has found, so
    far, are systems that could have evolved by natural means.

    Ron Okimoto

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  • From Bob Casanova@21:1/5 to All on Thu Oct 5 09:35:40 2023
    On Thu, 5 Oct 2023 04:05:16 -0700 (PDT), the following
    appeared in talk.origins, posted by "broger...@gmail.com" <brogers31751@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?

    --

    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

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Glenn@21:1/5 to Bob Casanova on Thu Oct 5 13:39:57 2023
    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."

    And you're getting you asses kicked hard. The funny thing is that none of you seem to feel anything.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Ron Dean@21:1/5 to Bob Casanova on Thu Oct 5 17:50:09 2023
    TO
    Bob Casanova wrote:
    On Thu, 5 Oct 2023 04:05:16 -0700 (PDT), the following
    appeared in talk.origins, posted by "broger...@gmail.com" <brogers31751@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?

    Audience To is _NOT_ a Goddiditaudience. TOisathereisnogodexceptmeaudence

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From MarkE@21:1/5 to Athel Cornish-Bowden on Thu Oct 5 14:42:59 2023
    On Thursday, October 5, 2023 at 7:00:59 PM UTC+11, Athel Cornish-Bowden wrote:
    On 2023-10-05 06:35:18 +0000, MarkE said:

    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?
    Hardly. There are plenty of things we don't understand, and won't
    understand for a long time, but preferring a naturalistic
    interpretation over God-did-it has nothing to do with credulity. It has
    do with the fact that naturalistic interpretations of many topics have
    taken us a long way, whereas God-did-it explanations are based on no evidence whatsoever and have never led to useful new knowledge.

    In any case, pretty amazing what goes on inside our cells when we're
    not looking.
    Yes, but real scientists do look and try to understand.


    Speaking of understanding, here's a question you might have thought about: would evolution predict the development of topoisomerase early on? Presumably earlier than DNA sequences long enough to require untangling, but what I have in mind is something
    else, as follows.

    The DNA gathering/clamping/snipping/swapping/joining function of topoisomerase in this instance is quite specific. My wondering is, would it therefore require a similarly specific and sustained selection pressure to guide its evolution? And with
    selection acting on the phenotype and not directly on the topoisomerase subfunction, there's an inherent distance between the organism as a whole (subject to "macroselection"), and its various constituent mechanisms under the hood (topoisomerase being
    one example of many molecular machines associated with DNA management). The more complex/developed the organism, more indirect and blunted becomes the reach of NS to internal workings. This attenuation of NS would be a matter of degrees rather than a
    hard cut-off.

    Does this general idea make sense, and if so, what would its implications be?


    --
    athel cb : Biochemical Evolution, Garland Science, 2016

    --- SoupGate-Win32 v1.05
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  • From Ron Dean@21:1/5 to Bob Casanova on Thu Oct 5 19:03:12 2023
    Bob Casanova wrote:
    On Thu, 5 Oct 2023 17:50:09 -0400, the following appeared in
    talk.origins, posted by Ron Dean
    <rondean-noreply@gmail.com>:

    TO
    Bob Casanova wrote:
    On Thu, 5 Oct 2023 04:05:16 -0700 (PDT), the following
    appeared in talk.origins, posted by "broger...@gmail.com"
    <brogers31751@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?

    Audience To is _NOT_ a Goddiditaudience. TOisathereisnogodexceptmeaudence

    WHOOOSH

    A bit slow on analogies?

    And learn to read; I wrote "Goddidtheaudience", not
    "Goddiditaudience". A subtle difference, to be sure.

    No spaces ~ a stupid, idiotic spelling!

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Bob Casanova@21:1/5 to All on Thu Oct 5 15:49:43 2023
    On Thu, 5 Oct 2023 17:50:09 -0400, the following appeared in
    talk.origins, posted by Ron Dean
    <rondean-noreply@gmail.com>:

    TO
    Bob Casanova wrote:
    On Thu, 5 Oct 2023 04:05:16 -0700 (PDT), the following
    appeared in talk.origins, posted by "broger...@gmail.com"
    <brogers31751@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?

    Audience To is _NOT_ a Goddiditaudience. TOisathereisnogodexceptmeaudence

    WHOOOSH

    A bit slow on analogies?

    And learn to read; I wrote "Goddidtheaudience", not
    "Goddiditaudience". A subtle difference, to be sure.

    --

    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

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From MarkE@21:1/5 to jillery on Thu Oct 5 15:51:01 2023
    On Thursday, October 5, 2023 at 8:55:59 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.
    <https://youtu.be/ba2h9tqNYAo?t=41>
    ***************************************
    Complexity complexity complexity complexity. Oh look there's a
    pathway. It's very complicated.

    Complexity complexity complexity complexity complexity. And did you
    know that cells are really really complicated. But we're not done.

    Complexity complexity complexity complexity. And you're going to be
    blown away by the bacterial flagellum. It's like a little machine and
    it's really really complicated.

    Complexity complexity complexity complexity. We need more cells.
    They're really complicated. you just get blown away by these things.
    They are so amazingly complicated

    Complexity, therefore design.
    *****************************************
    Thank you, PZ.

    I watched PZ's video, quite a good effort :) In fact, I share some of his frustration. Creationist material and argument does major on showcasing example after example of complex and amazing features of living things. I'm fine with that, and personally
    find this cumulative data compelling evidence for design. My frustration is along these lines: okay, you've made your point, but can you convert this into a formal hypothesis and a paper that can be peer reviewed, rather than just popular books and talks
    (as good as some of these are IMO)?

    This is partly occurring, for example, Behe has done this with his IC ideas, and more recently with his waiting time analysis for multiple dependent mutations, or Douglas Axe's paper estimating the proportion of function sequences for a protein class
    here: https://pubmed.ncbi.nlm.nih.gov/15321723/

    And there are of course also issues of the different categories of argument and epistemology at play here, and the position of mainstream scientific academia to ID, etc.

    All that being said, I find it interesting that naturalists here seem almost completing unwilling to acknowledge any doubt regarding naturalistic explanations. The following quote cuts both ways, so not intended as an insult, but rather a prompt to us
    all: “The problem with the world is that the intelligent people are full of doubts, while the stupid ones are full of confidence.” (Charles Bukowski)


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

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From brogers31751@gmail.com@21:1/5 to Ron Dean on Thu Oct 5 16:16:26 2023
    On Thursday, October 5, 2023 at 5:50:59 PM UTC-4, Ron Dean wrote:
    TO
    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?

    Audience To is _NOT_ a Goddiditaudience. TOisathereisnogodexceptmeaudence

    I cannot speak fro everyone, but I am a "the truth of evolution and a naturalistic explanation tell you absolutely nothing one way or the other about the existence of God" audience.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From brogers31751@gmail.com@21:1/5 to MarkE on Thu Oct 5 16:14:54 2023
    On Thursday, October 5, 2023 at 6:55:59 PM UTC-4, MarkE wrote:
    On Thursday, October 5, 2023 at 8:55:59 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.
    <https://youtu.be/ba2h9tqNYAo?t=41> ***************************************
    Complexity complexity complexity complexity. Oh look there's a
    pathway. It's very complicated.

    Complexity complexity complexity complexity complexity. And did you
    know that cells are really really complicated. But we're not done.

    Complexity complexity complexity complexity. And you're going to be
    blown away by the bacterial flagellum. It's like a little machine and
    it's really really complicated.

    Complexity complexity complexity complexity. We need more cells.
    They're really complicated. you just get blown away by these things.
    They are so amazingly complicated

    Complexity, therefore design.
    *****************************************
    Thank you, PZ.
    I watched PZ's video, quite a good effort :) In fact, I share some of his frustration. Creationist material and argument does major on showcasing example after example of complex and amazing features of living things. I'm fine with that, and personally
    find this cumulative data compelling evidence for design. My frustration is along these lines: okay, you've made your point, but can you convert this into a formal hypothesis and a paper that can be peer reviewed, rather than just popular books and talks
    (as good as some of these are IMO)?

    This is partly occurring, for example, Behe has done this with his IC ideas, and more recently with his waiting time analysis for multiple dependent mutations, or Douglas Axe's paper estimating the proportion of function sequences for a protein class
    here: https://pubmed.ncbi.nlm.nih.gov/15321723/

    And there are of course also issues of the different categories of argument and epistemology at play here, and the position of mainstream scientific academia to ID, etc.

    All that being said, I find it interesting that naturalists here seem almost completing unwilling to acknowledge any doubt regarding naturalistic explanations. The following quote cuts both ways, so not intended as an insult, but rather a prompt to us
    all: “The problem with the world is that the intelligent people are full of doubts, while the stupid ones are full of confidence.” (Charles Bukowski)

    When you say naturalists are almost completely unwilling to acknowledge doubt regarding naturalistic explanations, I think you have to be clear what you mean. Certainly, naturalists are very willing to doubt specific naturalistic explanations of specific
    things. Scientists are a skeptical bunch. You seem to wish that they would be open to the possibility of simply giving up, when no naturalistic explanation is found after some sufficiently long amount of time. Well, eventually, we might say, "Yeah, that
    problem is just too hard for us, at least for now." But then you want them to be willing to turn to supernatural explanations; the problem is that supernatural explanations (as you have said in the past) are in a different category entirely from
    scientific ones. They make no testable predictions; they need contain no details at all; and they are, or some of them are, perfectly compatible with simultaneous naturalistic explanations. The naturalists here are perhaps unwilling to indulge in
    supernatural explanations because they do not lead anywhere. And some of the religious here are unwilling to indulge in supernatural explanations because of the weaknesses of "god of the gaps" theology that several of us have posted about fairly often.

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

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From MarkE@21:1/5 to Glenn on Thu Oct 5 16:49:16 2023
    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

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From brogers31751@gmail.com@21:1/5 to MarkE on Thu Oct 5 17:36:50 2023
    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.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Bob Casanova@21:1/5 to All on Thu Oct 5 18:12:46 2023
    On Thu, 5 Oct 2023 19:03:12 -0400, the following appeared in
    talk.origins, posted by Ron Dean
    <rondean-noreply@gmail.com>:

    Bob Casanova wrote:
    On Thu, 5 Oct 2023 17:50:09 -0400, the following appeared in
    talk.origins, posted by Ron Dean
    <rondean-noreply@gmail.com>:

    TO
    Bob Casanova wrote:
    On Thu, 5 Oct 2023 04:05:16 -0700 (PDT), the following
    appeared in talk.origins, posted by "broger...@gmail.com"
    <brogers31751@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?

    Audience To is _NOT_ a Goddiditaudience. TOisathereisnogodexceptmeaudence >>>
    WHOOOSH

    A bit slow on analogies?

    And learn to read; I wrote "Goddidtheaudience", not
    "Goddiditaudience". A subtle difference, to be sure.

    No spaces ~ a stupid, idiotic spelling!

    As noted, WHOOOSH.

    Have a nice day.

    --

    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

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Bob Casanova@21:1/5 to All on Thu Oct 5 18:14:43 2023
    On Thu, 5 Oct 2023 16:16:26 -0700 (PDT), the following
    appeared in talk.origins, posted by "broger...@gmail.com" <brogers31751@gmail.com>:

    On Thursday, October 5, 2023 at 5:50:59?PM UTC-4, Ron Dean wrote:
    TO
    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?

    Audience To is _NOT_ a Goddiditaudience. TOisathereisnogodexceptmeaudence

    I cannot speak fro everyone, but I am a "the truth of evolution and a naturalistic explanation tell you absolutely nothing one way or the other about the existence of God" audience.

    Same here; religious belief has nothing to do with science,
    and vice versa. Skew lines in the volume of reality.

    --

    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

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From DB Cates@21:1/5 to broger...@gmail.com on Thu Oct 5 21:20:36 2023
    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> --
    --
    Don Cates ("he's a cunning rascal" PN)

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Ron Dean@21:1/5 to Bob Casanova on Fri Oct 6 00:42:22 2023
    Bob Casanova wrote:
    On Thu, 5 Oct 2023 16:16:26 -0700 (PDT), the following
    appeared in talk.origins, posted by "broger...@gmail.com" <brogers31751@gmail.com>:

    On Thursday, October 5, 2023 at 5:50:59?PM UTC-4, Ron Dean wrote:
    TO
    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?

    Audience To is _NOT_ a Goddiditaudience. TOisathereisnogodexceptmeaudence >>
    I cannot speak fro everyone, but I am a "the truth of evolution and a naturalistic explanation tell you absolutely nothing one way or the other about the existence of God" audience.

    Belief or disbelief in the existence of God is all a matter of faith -
    not evidence!

    Same here; religious belief has nothing to do with science,
    and vice versa. Skew lines in the volume of reality.

    It interesting that many famous scientist were/are religious. Several
    or whom were the fathers of scientific disciplines.

    https://www.famous scientists.org/great-scientists-christians/

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From jillery@21:1/5 to All on Fri Oct 6 04:10:55 2023
    On Thu, 5 Oct 2023 13:39:57 -0700 (PDT), Glenn <GlennSheldon@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.

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

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Ernest Major@21:1/5 to DB Cates on Fri Oct 6 11:01:26 2023
    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.)

    --
    alias Ernest Major

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From brogers31751@gmail.com@21:1/5 to DB Cates on Fri Oct 6 03:00:11 2023
    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.
    --
    --
    Don Cates ("he's a cunning rascal" PN)

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From brogers31751@gmail.com@21:1/5 to Ron Dean on Fri Oct 6 03:03:30 2023
    On Friday, October 6, 2023 at 12:46:00 AM UTC-4, Ron Dean wrote:
    Bob Casanova wrote:
    On Thu, 5 Oct 2023 16:16:26 -0700 (PDT), the following
    appeared in talk.origins, posted by "broger...@gmail.com" <broger...@gmail.com>:

    On Thursday, October 5, 2023 at 5:50:59?PM UTC-4, Ron Dean wrote:
    TO
    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?

    Audience To is _NOT_ a Goddiditaudience. TOisathereisnogodexceptmeaudence

    I cannot speak fro everyone, but I am a "the truth of evolution and a naturalistic explanation tell you absolutely nothing one way or the other about the existence of God" audience.

    Belief or disbelief in the existence of God is all a matter of faith -
    not evidence!

    Exactly. So why do you waste your time looking for evidence? Why do you think that showing flaws in the theory of evolution would be evidence for God? Why do you think evidence supporting the ToE would be evidence against God?

    Same here; religious belief has nothing to do with science,
    and vice versa. Skew lines in the volume of reality.

    It interesting that many famous scientist were/are religious. Several
    or whom were the fathers of scientific disciplines.

    https://www.famous scientists.org/great-scientists-christians/

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Lawyer Daggett@21:1/5 to Ernest Major on Fri Oct 6 03:42:21 2023
    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.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From DB Cates@21:1/5 to broger...@gmail.com on Fri Oct 6 10:57:06 2023
    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)

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From brogers31751@gmail.com@21:1/5 to DB Cates on Fri Oct 6 09:15:04 2023
    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)

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  • From jillery@21:1/5 to All on Sat Oct 7 03:48:33 2023
    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

    --- SoupGate-Win32 v1.05
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  • From MarkE@21:1/5 to jillery on Sat Oct 7 00:59:27 2023
    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

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  • From peter2nyikos@gmail.com@21:1/5 to MarkE on Mon Oct 9 18:32:51 2023
    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

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  • From MarkE@21:1/5 to peter2...@gmail.com on Tue Oct 10 04:26:57 2023
    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

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  • From Mark Isaak@21:1/5 to peter2...@gmail.com on Tue Oct 10 07:45:05 2023
    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

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  • From Martin Harran@21:1/5 to peter2nyikos@gmail.com on Tue Oct 10 15:45:33 2023
    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.

    [...]

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  • From peter2nyikos@gmail.com@21:1/5 to MarkE on Tue Oct 10 09:48:36 2023
    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

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  • From peter2nyikos@gmail.com@21:1/5 to Mark Isaak on Tue Oct 10 10:38:03 2023
    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

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  • From Lawyer Daggett@21:1/5 to peter2...@gmail.com on Tue Oct 10 10:55:04 2023
    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."

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  • From peter2nyikos@gmail.com@21:1/5 to Mark Isaak on Tue Oct 10 11:24:09 2023
    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.

    What say you to that, Mark?

    Why do you ask?? Did you forget to "skip for focus"?

    What's the point of this snarky evasion? I am genuinely interested in the answer. If this
    is the way search engines are to be in the AI-controlled future, it will be the nanny state
    to end all nanny states.

    I thought you were a *professional* computer scientist. Which better talk.origins
    regular to turn to than you?

    Okay. I suggest in the future you signal such changes in topic (e.g., "Drastic subject change coming").

    My apologies for any "mental whiplash" you might have suffered.

    I have never worked with or on AI; I have never (knowingly) used
    ChatGPT; and I have not used Bing in many years. Whereof I cannot
    speak, thereof I must be silent.

    Your candor here is refreshing.


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

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  • From MarkE@21:1/5 to peter2...@gmail.com on Wed Oct 11 04:49:29 2023
    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

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  • From Ernest Major@21:1/5 to MarkE on Wed Oct 11 13:51:24 2023
    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

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  • From brogers31751@gmail.com@21:1/5 to Lawyer Daggett on Wed Oct 11 07:10:10 2023
    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.

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  • From Lawyer Daggett@21:1/5 to Ernest Major on Wed Oct 11 06:25:42 2023
    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.

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  • From Ernest Major@21:1/5 to Lawyer Daggett on Wed Oct 11 15:55:45 2023
    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

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  • From Ernest Major@21:1/5 to broger...@gmail.com on Wed Oct 11 16:28:11 2023
    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

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  • From peter2nyikos@gmail.com@21:1/5 to Lawyer Daggett on Thu Oct 12 12:16:05 2023
    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

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  • From Lawyer Daggett@21:1/5 to peter2...@gmail.com on Thu Oct 12 12:48:52 2023
    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

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  • From peter2nyikos@gmail.com@21:1/5 to MarkE on Thu Oct 12 12:41:46 2023
    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

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  • From Glenn@21:1/5 to jillery on Wed Feb 21 13:18:00 2024
    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.

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