• Peter Nyikos 1946 - 2024?

    From Burkhard@21:1/5 to All on Tue Feb 20 08:24:20 2024
    I just saw this: https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos

    assuming it's genuine (and I have no reason to doubt this) , the details fit, as does his extended absence from posting. He could be a royal pain in the backside, but I do hope he now experiences the type of heaven he always hoped for (with a <10%
    certainty, of course> That the GG version of TO will survive him by barely a week, before getting archived forever, is maybe the most fitting memorial imaginable.

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  • From Ernest Major@21:1/5 to Martin Harran on Tue Feb 20 17:13:37 2024
    On 20/02/2024 17:05, Martin Harran wrote:
    On Tue, 20 Feb 2024 16:49:20 +0000, Martin Harran
    <martinharran@gmail.com> wrote:

    .... I thought it might not be him as it seems strange that he would still >> be employed as a lecturer at 80 years of age.

    Brain fart - 78 years of age.


    77; he would have been 78 next month.

    --
    alias Ernest Major

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  • From *Hemidactylus*@21:1/5 to Burkhard on Tue Feb 20 17:21:57 2024
    Burkhard <b.schafer@ed.ac.uk> wrote:
    I just saw this: https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos

    assuming it's genuine (and I have no reason to doubt this) , the details
    fit, as does his extended absence from posting. He could be a royal pain
    in the backside, but I do hope he now experiences the type of heaven he always hoped for (with a <10% certainty, of course> That the GG version
    of TO will survive him by barely a week, before getting archived
    forever, is maybe the most fitting memorial imaginable.

    The birthdate in the death notice matches his CV: https://sc.edu/study/colleges_schools/artsandsciences/mathematics/our_people/profile_cv/nyikos_peter_cv.pdf

    Ughh! Sad to see him gone. I imagine since his death date was the 18th that
    his absence was due to health issues that had arisen. I can’t recall his
    last posting. Maybe Jan 29th?

    That is going to take some time to process. RIP Peter.

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  • From *Hemidactylus*@21:1/5 to Ernest Major on Tue Feb 20 17:33:03 2024
    Ernest Major <{$to$}@meden.demon.co.uk> wrote:
    On 20/02/2024 17:05, Martin Harran wrote:
    On Tue, 20 Feb 2024 16:49:20 +0000, Martin Harran
    <martinharran@gmail.com> wrote:

    .... I thought it might not be him as it seems strange that he would still >>> be employed as a lecturer at 80 years of age.

    Brain fart - 78 years of age.


    77; he would have been 78 next month.

    He was scrappy and argumentative up til the end. On Jan 25th he said in one
    his preambles: “The preceding three day stretch was the most hectic in the last two years, but things have finally calmed down, and tomorrow I will probably have time to do several posts on t.o. It is only the lateness of
    time that confines me to one today.” from thread *Hard Atheism of John Harshman Contrasted with Agnosticism of Peter Nyikos*

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  • From *Hemidactylus*@21:1/5 to erik simpson on Tue Feb 20 17:58:50 2024
    erik simpson <eastside.erik@gmail.com> wrote:
    On 2/20/24 8:24 AM, Burkhard wrote:
    I just saw this:
    https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos

    assuming it's genuine (and I have no reason to doubt this) , the details
    fit, as does his extended absence from posting. He could be a royal pain
    in the backside, but I do hope he now experiences the type of heaven he
    always hoped for (with a <10% certainty, of course> That the GG version
    of TO will survive him by barely a week, before getting archived
    forever, is maybe the most fitting memorial imaginable.

    I am genuinely unhappy to hear this. Peter and I have had many
    rancorous exchanges over the years, but I have over the last year come
    to the realization that mutual miscommunication was the cause of most of them. I never found it easy to understand what Peter was "getting at"
    in his unique style of writing, but we had many common interests and he
    had strong if sometimes eccentric opinions of all of them. i believe he
    was committed to the truth as he understood it, and I too hope the God
    he wanted to believe in accepts him as he is. I'll miss him.

    You or somebody might want to notify regulars on the paleontology
    newsgroup.

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  • From =?UTF-8?B?w5bDtiBUaWli?=@21:1/5 to Burkhard on Tue Feb 20 11:59:34 2024
    On Tuesday 20 February 2024 at 18:28:16 UTC+2, Burkhard wrote:
    I just saw this: https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos

    assuming it's genuine (and I have no reason to doubt this) , the details fit, as does his extended absence from posting. He could be a royal pain in the backside, but I do hope he now experiences the type of heaven he always hoped for (with a <10%
    certainty, of course> That the GG version of TO will survive him by barely a week, before getting archived forever, is maybe the most fitting memorial imaginable.

    Sad. He was certainly best ID proponent that we had. Unlike others
    he did not run away from opportunity to reason. Hopefully he found
    his bright afterlife.

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  • From Ernest Major@21:1/5 to jillery on Tue Feb 27 13:06:32 2024
    On 27/02/2024 12:29, jillery wrote:
    On Tue, 20 Feb 2024 08:24:20 -0800 (PST), Burkhard
    <b.schafer@ed.ac.uk> wrote:

    I just saw this:
    https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos

    assuming it's genuine (and I have no reason to doubt this) , the details fit, as does his extended absence from posting. He could be a royal pain in the backside, but I do hope he now experiences the type of heaven he always hoped for (with a <10%
    certainty, of course> That the GG version of TO will survive him by barely a week, before getting archived forever, is maybe the most fitting memorial imaginable.


    For anybody who might care about such things, the above post is one of
    a dozen which Eternal September failed to capture.

    It did have it originally, but has since disappeared ("expired"). The
    same happened to a couple of posts from MarkE.


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


    --
    alias Ernest Major

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  • From RonO@21:1/5 to Ernest Major on Tue Feb 27 18:04:38 2024
    On 2/20/2024 11:13 AM, Ernest Major wrote:
    On 20/02/2024 17:05, Martin Harran wrote:
    On Tue, 20 Feb 2024 16:49:20 +0000, Martin Harran
    <martinharran@gmail.com> wrote:

    .... I thought it might not be him as it seems strange that he would
    still
    be employed as a lecturer at 80 years of age.

    Brain fart - 78 years of age.


    77; he would have been 78 next month.


    For some reason my posts are not showing up. I've had trouble just
    getting eternal september to open posts. I was updated, and had to
    reload TO, but nothing has been working. I posted to the Dirt DNA
    thread, but it didn't show up. For the last couple of weeks when I
    click on a post it either opens to a blank page or it goes to a bar at
    the top of the window and ony a partial post is displayed below. It is
    a worthless feature that should have never been implemented. Why would
    anyone want to accumulate partial posts in a bar across the top of the
    window? Once in a while I can open a post and even respond to it like I
    did with the Dirt DNA thread, but it doesn't seem to work.

    So this is sort of a test post.

    Nyikos had to prevaricate and lie about the Phillip Johnson quote where
    Johnson admitted that the ID science didn't exist and that he had given
    up on teaching ID in the public schools after the Dover decision.
    Nyikos would usually just snip and run from the quote, but once he put
    up the lame argument that Johnson could be disregarded because he was
    old. Nyikos, at that time, was older than Phillip Johnson when Johnson
    had made the quote (Johnson had been 65 years old). So Nyikos claimed
    that he was old enough so that his opinions could be disregarded. A
    true TO tale.

    Ron Okimoto

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  • From RonO@21:1/5 to erik simpson on Tue Feb 27 18:34:00 2024
    On 2/27/2024 6:17 PM, erik simpson wrote:
    On 2/27/24 4:04 PM, RonO wrote:
    On 2/20/2024 11:13 AM, Ernest Major wrote:
    On 20/02/2024 17:05, Martin Harran wrote:
    On Tue, 20 Feb 2024 16:49:20 +0000, Martin Harran
    <martinharran@gmail.com> wrote:

    .... I thought it might not be him as it seems strange that he
    would still
    be employed as a lecturer at 80 years of age.

    Brain fart - 78 years of age.


    77; he would have been 78 next month.


    For some reason my posts are not showing up. I've had trouble just
    getting eternal september to open posts.  I was updated, and had to
    reload TO, but nothing has been working.  I posted to the Dirt DNA
    thread, but it didn't show up.  For the last couple of weeks when I
    click on a post it either opens to a blank page or it goes to a bar at
    the top of the window and ony a partial post is displayed below.  It
    is a worthless feature that should have never been implemented.  Why
    would anyone want to accumulate partial posts in a bar across the top
    of the window?  Once in a while I can open a post and even respond to
    it like I did with the Dirt DNA thread, but it doesn't seem to work.

    So this is sort of a test post.

    Nyikos had to prevaricate and lie about the Phillip Johnson quote
    where Johnson admitted that the ID science didn't exist and that he
    had given up on teaching ID in the public schools after the Dover
    decision. Nyikos would usually just snip and run from the quote, but
    once he put up the lame argument that Johnson could be disregarded
    because he was old. Nyikos, at that time, was older than Phillip
    Johnson when Johnson had made the quote (Johnson had been 65 years
    old).  So Nyikos claimed that he was old enough so that his opinions
    could be disregarded.  A true TO tale.

    Ron Okimoto

    Several people have recently had problems with ES.  The paid-for
    newsreaders are probably more reliable.


    Well, it looks like my posts are getting through. My troubles started
    when I donated to the cause, and got some special update. The update
    had multiple issues like I had to keep clicking on posts until they
    opened, and often the posts would go straight to that bar across the top
    of the window and only a partial post would be displayed below. I had
    to keep clicking on a post until it opened normally. I was updated
    again a little over a week ago and have had issues posting. I had to
    reload TO, again, and it would not do the full download even though that
    was an option. Now I click on a post and often get a blank page.
    Things seem to have gotten better. I must have gotten some type of bug fix.

    Ron Okimoto

    Ron Okimoto

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  • From *Hemidactylus*@21:1/5 to erik simpson on Wed Feb 28 01:44:10 2024
    erik simpson <eastside.erik@gmail.com> wrote:
    On 2/27/24 6:54 AM, John Harshman wrote:
    On 2/27/24 5:06 AM, Ernest Major wrote:
    On 27/02/2024 12:29, jillery wrote:
    On Tue, 20 Feb 2024 08:24:20 -0800 (PST), Burkhard
    <b.schafer@ed.ac.uk> wrote:

    I just saw this:
    https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos

    assuming it's genuine (and I have no reason to doubt this) , the
    details fit, as does his extended absence from posting. He could be
    a royal pain in the backside, but I do hope he now experiences the
    type of heaven he always hoped for (with a <10% certainty, of
    course> That  the GG version of TO will survive him by barely a
    week,  before getting archived forever, is maybe the most fitting
    memorial imaginable.


    For anybody who might care about such things, the above post is one of >>>> a dozen which Eternal September failed to capture.

    It did have it originally, but has since disappeared ("expired"). The
    same happened to a couple of posts from MarkE.

    Well, you have to admit that "expired" is appropriate in this case.

    I still see Burkhard's post, as well as MarkE's, but I'm paying for it.

    I have my newsreader set to only keep 30 days worth of posts so still see Burkhard’s. I see a post by MarkE. Weirdly I wasn’t seeing some Daggett posts but saw one clouded which I clicked to download manually. I’ve
    noticed that every once in a while. Not sure what that’s about. Neither Burkhard nor Daggett are probably gonna be active anymore though we could
    have a guess as to who winds up coming back eventually.

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  • From *Hemidactylus*@21:1/5 to John Harshman on Wed Feb 28 01:53:27 2024
    John Harshman <john.harshman@gmail.com> wrote:
    On 2/27/24 5:06 AM, Ernest Major wrote:
    On 27/02/2024 12:29, jillery wrote:
    On Tue, 20 Feb 2024 08:24:20 -0800 (PST), Burkhard
    <b.schafer@ed.ac.uk> wrote:

    I just saw this:
    https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos

    assuming it's genuine (and I have no reason to doubt this) , the
    details fit, as does his extended absence from posting. He could be a
    royal pain in the backside, but I do hope he now experiences the type
    of heaven he always hoped for (with a <10% certainty, of course>
    That  the GG version of TO will survive him by barely a week,  before >>>> getting archived forever, is maybe the most fitting memorial imaginable. >>>

    For anybody who might care about such things, the above post is one of
    a dozen which Eternal September failed to capture.

    It did have it originally, but has since disappeared ("expired"). The
    same happened to a couple of posts from MarkE.

    Well, you have to admit that "expired" is appropriate in this case.

    Still too soon.

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  • From *Hemidactylus*@21:1/5 to erik simpson on Wed Feb 28 02:17:53 2024
    erik simpson <eastside.erik@gmail.com> wrote:
    On 2/20/24 8:24 AM, Burkhard wrote:
    I just saw this:
    https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos

    assuming it's genuine (and I have no reason to doubt this) , the details
    fit, as does his extended absence from posting. He could be a royal pain
    in the backside, but I do hope he now experiences the type of heaven he
    always hoped for (with a <10% certainty, of course> That the GG version
    of TO will survive him by barely a week, before getting archived
    forever, is maybe the most fitting memorial imaginable.

    I am genuinely unhappy to hear this. Peter and I have had many
    rancorous exchanges over the years, but I have over the last year come
    to the realization that mutual miscommunication was the cause of most of them. I never found it easy to understand what Peter was "getting at"
    in his unique style of writing, but we had many common interests and he
    had strong if sometimes eccentric opinions of all of them. i believe he
    was committed to the truth as he understood it, and I too hope the God
    he wanted to believe in accepts him as he is. I'll miss him.

    I kinda envision him giving St Peter an earful about Howard Hershey and
    others. We surely got his more cantankerous and combative side. People who
    knew him personally surely perceived him quite differently. I think I
    managed to get things dialed down with him in the past year or so. If he
    had lived longer he would have probably tackled migrating from Google
    Groups and figured out the reader-server thing.

    I have looked at his obit to see his friends chime in. One mentioned an illness. He was posting so recently so I can only wonder what the onset
    was. At least he was full of life so recently and posted here not that long ago. I got the impression he had a lot on his plate but nothing about
    health issues. It’s still a bit hard to process that someone who had been a constant presence, however hard to get along with, is no longer with us! I
    hope I might live as long as him and be as active and with it that close to
    the end. Again RIP Peter, whatever differences we had over the years.

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  • From J. J. Lodder@21:1/5 to ecphoric@allspamis.invalid on Wed Feb 28 09:31:13 2024
    *Hemidactylus* <ecphoric@allspamis.invalid> wrote:

    Burkhard <b.schafer@ed.ac.uk> wrote:
    I just saw this: https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos

    assuming it's genuine (and I have no reason to doubt this) , the details fit, as does his extended absence from posting. He could be a royal pain
    in the backside, but I do hope he now experiences the type of heaven he always hoped for (with a <10% certainty, of course> That the GG version
    of TO will survive him by barely a week, before getting archived
    forever, is maybe the most fitting memorial imaginable.

    The birthdate in the death notice matches his CV: https://sc.edu/study/colleges_schools/artsandsciences/mathematics/our_people/p
    rofile_cv/nyikos_peter_cv.pdf

    No surprise here:
    He was the kind of mathematician I would have expected.

    Jan

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  • From Richmond@21:1/5 to RonO on Wed Feb 28 11:00:52 2024
    RonO <rokimoto@cox.net> writes:

    opened, and often the posts would go straight to that bar across the
    top of the window and only a partial post would be displayed below. I

    Perhaps you should mention that you are using Thunderbird. Maybe post to alt.comp.software.thunderbird.

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  • From WolfFan@21:1/5 to All on Wed Feb 28 07:19:01 2024
    On Feb 27, 2024, Hemidactylus* wrote
    (in article<2XKdnS5_L_KKD0P4nZ2dnZfqnPqdnZ2d@giganews.com>):

    John Harshman<john.harshman@gmail.com> wrote:
    On 2/27/24 5:06 AM, Ernest Major wrote:
    On 27/02/2024 12:29, jillery wrote:
    On Tue, 20 Feb 2024 08:24:20 -0800 (PST), Burkhard
    <b.schafer@ed.ac.uk> wrote:

    I just saw this: https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos

    assuming it's genuine (and I have no reason to doubt this) , the details fit, as does his extended absence from posting. He could be a royal pain in the backside, but I do hope he now experiences the type of heaven he always hoped for (with a <10% certainty, of course>
    That the GG version of TO will survive him by barely a week, before getting archived forever, is maybe the most fitting memorial imaginable.


    For anybody who might care about such things, the above post is one of a dozen which Eternal September failed to capture.

    It did have it originally, but has since disappeared ("expired"). The same happened to a couple of posts from MarkE.

    Well, you have to admit that "expired" is appropriate in this case.
    Still too soon.

    Oh, Petey the Grate hit his sell-by date at least 20 years ago.

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  • From WolfFan@21:1/5 to RonO on Wed Feb 28 07:25:23 2024
    On Feb 27, 2024, RonO wrote
    (in article <urltam$3fj4a$1@dont-email.me>):

    On 2/20/2024 11:13 AM, Ernest Major wrote:
    On 20/02/2024 17:05, Martin Harran wrote:
    On Tue, 20 Feb 2024 16:49:20 +0000, Martin Harran <martinharran@gmail.com> wrote:

    .... I thought it might not be him as it seems strange that he would still
    be employed as a lecturer at 80 years of age.

    Brain fart - 78 years of age.

    77; he would have been 78 next month.

    For some reason my posts are not showing up. I've had trouble just
    getting eternal september to open posts. I was updated, and had to
    reload TO, but nothing has been working. I posted to the Dirt DNA
    thread, but it didn't show up. For the last couple of weeks when I
    click on a post it either opens to a blank page or it goes to a bar at
    the top of the window and ony a partial post is displayed below. It is
    a worthless feature that should have never been implemented. Why would
    anyone want to accumulate partial posts in a bar across the top of the window? Once in a while I can open a post and even respond to it like I
    did with the Dirt DNA thread, but it doesn't seem to work.

    you seem to be using Thunderbird. Thunderbird is a mail client which can be used to read usenet. Thunderbird has... issues. I would try a dedicated newsreader if I were you.


    So this is sort of a test post.

    Nyikos had to prevaricate and lie about the Phillip Johnson quote where Johnson admitted that the ID science didn't exist and that he had given
    up on teaching ID in the public schools after the Dover decision.
    Nyikos would usually just snip and run from the quote, but once he put
    up the lame argument that Johnson could be disregarded because he was
    old. Nyikos, at that time, was older than Phillip Johnson when Johnson
    had made the quote (Johnson had been 65 years old). So Nyikos claimed
    that he was old enough so that his opinions could be disregarded. A
    true TO tale.

    Ron Okimoto

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  • From *Hemidactylus*@21:1/5 to erik simpson on Wed Feb 28 20:06:57 2024
    erik simpson <eastside.erik@gmail.com> wrote:
    On 2/28/24 4:25 AM, WolfFan wrote:
    On Feb 27, 2024, RonO wrote
    (in article <urltam$3fj4a$1@dont-email.me>):

    On 2/20/2024 11:13 AM, Ernest Major wrote:
    On 20/02/2024 17:05, Martin Harran wrote:
    On Tue, 20 Feb 2024 16:49:20 +0000, Martin Harran
    <martinharran@gmail.com> wrote:

    .... I thought it might not be him as it seems strange that he would >>>>>> still
    be employed as a lecturer at 80 years of age.

    Brain fart - 78 years of age.

    77; he would have been 78 next month.

    For some reason my posts are not showing up. I've had trouble just
    getting eternal september to open posts. I was updated, and had to
    reload TO, but nothing has been working. I posted to the Dirt DNA
    thread, but it didn't show up. For the last couple of weeks when I
    click on a post it either opens to a blank page or it goes to a bar at
    the top of the window and ony a partial post is displayed below. It is
    a worthless feature that should have never been implemented. Why would
    anyone want to accumulate partial posts in a bar across the top of the
    window? Once in a while I can open a post and even respond to it like I
    did with the Dirt DNA thread, but it doesn't seem to work.

    you seem to be using Thunderbird. Thunderbird is a mail client which can be >> used to read usenet. Thunderbird has... issues. I would try a dedicated
    newsreader if I were you.


    So this is sort of a test post.

    Nyikos had to prevaricate and lie about the Phillip Johnson quote where
    Johnson admitted that the ID science didn't exist and that he had given
    up on teaching ID in the public schools after the Dover decision.
    Nyikos would usually just snip and run from the quote, but once he put
    up the lame argument that Johnson could be disregarded because he was
    old. Nyikos, at that time, was older than Phillip Johnson when Johnson
    had made the quote (Johnson had been 65 years old). So Nyikos claimed
    that he was old enough so that his opinions could be disregarded. A
    true TO tale.

    Ron Okimoto


    Any software has some issues, Thunderbird included. It does what it
    does, but it does fine for me. I've been using it for reading email for
    many years.

    T-bird worked fine for me. I kinda liked Pan too. KNode was my fave but was linked to the KDE monstrosity, which I mostly didn’t like.

    --- SoupGate-Win32 v1.05
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  • From J. J. Lodder@21:1/5 to erik simpson on Wed Feb 28 23:11:39 2024
    erik simpson <eastside.erik@gmail.com> wrote:

    On 2/28/24 12:31 AM, J. J. Lodder wrote:
    *Hemidactylus* <ecphoric@allspamis.invalid> wrote:

    Burkhard <b.schafer@ed.ac.uk> wrote:
    I just saw this:
    https://www.templeshalloranfuneralhome.com/obituary/dr-peter-nyikos

    assuming it's genuine (and I have no reason to doubt this) , the details >>> fit, as does his extended absence from posting. He could be a royal pain >>> in the backside, but I do hope he now experiences the type of heaven he >>> always hoped for (with a <10% certainty, of course> That the GG version >>> of TO will survive him by barely a week, before getting archived
    forever, is maybe the most fitting memorial imaginable.

    The birthdate in the death notice matches his CV:
    https://sc.edu/study/colleges_schools/artsandsciences/mathematics/our_peopl
    e/p
    rofile_cv/nyikos_peter_cv.pdf

    No surprise here:
    He was the kind of mathematician I would have expected.

    Jan

    It's a pretty obscure corner of math.

    Yes, completely divorced from any connection with reality.
    I had some discussions with him about fine-tuning,
    and found him to be clueless about the physics of it.
    That said, he was willing and capable to learn.
    (and to forget again)

    A mathematician friend many years
    ago told me that if I ever find myself having doubts about the validity
    of arithmetic, I should consult either a psychiatrist or a point-set topologist. He further suggested that going to the psychiatrist first
    would just save time.

    I think I agree. If faced with it many years ago
    I would have consulted Imre Lakatos,
    and I would have asked him if all this is a typical example
    of 'a degenerating research program' within mathematics.
    By Lakatos' definition a degenerating research program
    doesn't deal with real problems,
    but only with problems generated by the program itself.
    That said, Peter was probaby good at it.

    A real mathematician, like Erdos for example,
    would look down upon it with contempt, I guess,
    as 'much ado about nothing',
    and not contributing to pushing back the SF.

    Jan
    (but what do I know)

    --
    "Ich glaube das er ein Hochstapler ist."
    "Beweisen kan ich es aber nicht."
    "Dazu sollte ich seine Werke lesen, und das fallt mich schwer."
    (Wolfgang Pauli)

    --- SoupGate-Win32 v1.05
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  • From RonO@21:1/5 to jillery on Sun Mar 3 14:11:14 2024
    On 2/28/2024 9:53 PM, jillery wrote:
    On Tue, 27 Feb 2024 18:04:38 -0600, RonO <rokimoto@cox.net> wrote:

    I posted to the Dirt DNA thread, but it didn't show up.


    If you still have a copy of what you posted, I would be very
    interested to read it. Repost?

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


    It was about the limitations of the technology. The paper that you put
    up was using PCR to amplify the DNA before sequencing. You can only
    amplify short pieces because the DNA is degraded, and you need to either
    know the sequence of what you are amplifying or you have to try to find
    some highly conserved sequences in which to amplify, but Highly
    conserved sequence, is highly conserved and you will only be able to
    identify species that are distantly enough related to have a different
    sequence that can be identified using that primer set. You also have to
    deal with the degraded DNA sequence and things like the deamination of cytosines over time.

    Success will be limited to how long the surviving DNA fragments are in
    the soil samples.

    We have tech that will sequence short fragments without PCR
    amplification, but at this time the sequence error rates are high 10 to
    20% can be erroneous calls for nanopore sequencing, so they aren't much
    good at identifying specific short fragments to specific species. What
    we need to develop to make biome sequencing really useful is a highly
    accurate means of sequencing the short fragments that survive in the
    soil samples. It might be possible with current short read technology,
    but they haven't been trying it. You need to ligate sequence tags to
    the ends of the fragments (PCR can be used to do a little amplification)
    and then sequence the mess, but that isn't what they are doing.

    This may be due to the fact that most of the DNA that they find in these
    types of samples is from bacteria and fungi.

    Ron Okimoto

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From RonO@21:1/5 to jillery on Fri Mar 8 17:18:33 2024
    On 3/6/2024 12:07 AM, jillery wrote:
    On Sun, 3 Mar 2024 14:11:14 -0600, RonO <rokimoto@cox.net> wrote:

    On 2/28/2024 9:53 PM, jillery wrote:
    On Tue, 27 Feb 2024 18:04:38 -0600, RonO <rokimoto@cox.net> wrote:

    I posted to the Dirt DNA thread, but it didn't show up.


    If you still have a copy of what you posted, I would be very
    interested to read it. Repost?



    It was about the limitations of the technology. The paper that you put
    up was using PCR to amplify the DNA before sequencing. You can only
    amplify short pieces because the DNA is degraded, and you need to either
    know the sequence of what you are amplifying or you have to try to find
    some highly conserved sequences in which to amplify, but Highly
    conserved sequence, is highly conserved and you will only be able to
    identify species that are distantly enough related to have a different
    sequence that can be identified using that primer set. You also have to
    deal with the degraded DNA sequence and things like the deamination of
    cytosines over time.

    Success will be limited to how long the surviving DNA fragments are in
    the soil samples.

    We have tech that will sequence short fragments without PCR
    amplification, but at this time the sequence error rates are high 10 to
    20% can be erroneous calls for nanopore sequencing, so they aren't much
    good at identifying specific short fragments to specific species. What
    we need to develop to make biome sequencing really useful is a highly
    accurate means of sequencing the short fragments that survive in the
    soil samples. It might be possible with current short read technology,
    but they haven't been trying it. You need to ligate sequence tags to
    the ends of the fragments (PCR can be used to do a little amplification)
    and then sequence the mess, but that isn't what they are doing.

    This may be due to the fact that most of the DNA that they find in these
    types of samples is from bacteria and fungi.

    Ron Okimoto


    IIUC you're saying the paper's claims are false, that their evidence
    doesn't support the claim of identifying biomes full ancient species
    from DNA collected from dirt.

    I did not say that their claims were false. I just stated the
    limitations of what they were doing, and there is a bias in what they
    find. Essentially, they find things that they can look for and
    differentiate from each other, not necessarily everything that was there.

    Ron Okimoto

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


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