To Harshman and Carlip----First Dr. Hurd and now Rolf

[T Pagano]

First Dr. Hurd and now Rolf.

The morale among the secular-atheist cheerleaders is waning. Apparently
they haven't see a sustainable argument on the secular-atheist side in a
L O N G while and are tired of going under the bus. Harshman is trying
but he needs some serious help. Carlip doesn't need help, he needs new
theories rather than the frankenstein ones he holds. If Dr. Hurd and
Rolf are getting tired of seeing tire marks on their bodies the others
aren't far behind. That group I get; they're savable.

Okimoto is like the Wile E. Coyote, who keeps chasing some non existent
ID phantom but instead spends most of his time plunging over the cliff
holding an anvil. And Professor Nyikos, who knows what side he's on.
He's playing both sides against the middle.

God is good.

[Öö Tiib]

Lets see the current best ID arguments:

1) There is huge, inaccessible universe.
2) In that universe at least one tiny rock is suitable for life.
3) Reproducing lifeforms contain molecular mechanisms of replication.
4) If to remove some vital protein from alive being then it will be
crippled or even die.
5) Some of the single-cellular organisms have formed into multi-
cellular colonies.
6) Some apes have evolved into humans.

:D These are good arguments for atheism. What is there even to discuss?
I would suspect supernatural intervention far more when some (or all) of
above listed "evidences" of "intelligent design theory" were not so.
How not to be atheist? I like folk stories and fairy tales ... but
to take these as true is superstition.

[Bill Rogers]

Tony, I hear there's a job opening in Iraq; they're looking for someone to replace that Information Minister who disappeared in 2003. You'd be a perfect fit. "There are no American tanks in Baghdad."

[Rolf Aalberg]

"嘱 Tiib" <oot...@hot.ee> wrote in message
news:f8bdc852-d842-4290...@googlegroups.com...

> On Sunday, 4 March 2018 21:35:03 UTC+2, T Pagano wrote:
>> First Dr. Hurd and now Rolf.
>>
>> The morale among the secular-atheist cheerleaders is waning. Apparently
>> they haven't see a sustainable argument on the secular-atheist side in a
>> L O N G while and are tired of going under the bus. Harshman is trying
>> but he needs some serious help. Carlip doesn't need help, he needs new
>> theories rather than the frankenstein ones he holds. If Dr. Hurd and
>> Rolf are getting tired of seeing tire marks on their bodies the others
>> aren't far behind. That group I get; they're savable.
>>
>> Okimoto is like the Wile E. Coyote, who keeps chasing some non existent
>> ID phantom but instead spends most of his time plunging over the cliff
>> holding an anvil. And Professor Nyikos, who knows what side he's on.
>> He's playing both sides against the middle.
>>
>> God is good.
>
> Lets see the current best ID arguments:
>
> 1) There is huge, inaccessible universe.
> 2) In that universe at least one tiny rock is suitable for life.
> 3) Reproducing lifeforms contain molecular mechanisms of replication.
> 4) If to remove some vital protein from alive being then it will be
> crippled or even die.
> 5) Some of the single-cellular organisms have formed into multi-
> cellular colonies.
> 6) Some apes have evolved into humans.

I may be nitpicking, but no ape ever evolved.

Populations evolve.
And humans are apes, along with other ape species like Bonobos, Chimpanzees
or Gorillas.
The human species share a common ancestor with those mentioned above.

[Ron O]

Of course the Discovery Institute is the ID phantom, but their best 6 means that all your Dembski bull pucky is rated lower than the stupid fossil gap argument that failed the scientific creationists over 30 years ago. You ran so why lie about reality like this? I didn't rate the IDiocy, the ID perps that sold you the crap rated it and Dembski's junk nor anything else the Discovery Institute ID perps have come up with in the last 22 years made the grade. All the IDiocy was worse than the abiogenesis and Cambrian explosion junk that failed the scientific creationists over 30 years ago.

Ron Okimoto

[John Harshman]

Descent into entire posts with nothing but trash-talk is a sign of
desperation. Just sayin'.

[jillery]

"Apes" refer to populations. Just sayin'.

>Populations evolve.
>And humans are apes, along with other ape species like Bonobos, Chimpanzees
>or Gorillas.
>The human species share a common ancestor with those mentioned above.

The human species share a common ancestor with all life on Earth, no
matter how often they try to disown us.

>> :D These are good arguments for atheism. What is there even to discuss?
>> I would suspect supernatural intervention far more when some (or all) of
>> above listed "evidences" of "intelligent design theory" were not so.
>> How not to be atheist? I like folk stories and fairy tales ... but
>> to take these as true is superstition.
>>
>

--
I disapprove of what you say, but I will defend to the death your right to say it.

Evelyn Beatrice Hall
Attributed to Voltaire

[Bob Casanova]

On Sun, 04 Mar 2018 13:30:25 -0600, the following appeared
in talk.origins, posted by T Pagano <notmya...@dot.com>:

>...secular-atheist cheerleaders...

>...secular-atheist...

Do those "secular-atheists" include the many Jesuit
scientists, and other scientists who are believers of
various religions, who all accept the evidence for
evolution? I keep asking this, and none of the creationists
seem to want to respond; they just continue repeating their
lies...

>God is good.

How would you know, since you violate His commandment about
the bearing of false witness on a regular basis? His face is
turned from you.
--

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

[Bob Casanova]

On Mon, 05 Mar 2018 00:36:35 -0500, the following appeared
in talk.origins, posted by jillery <69jp...@gmail.com>:

Well,Rolf *did* say he was nitpicking, Tony's statement was
ambiguous, and some idiots *have* claimed that individuals
evolve. Too many bad movies, I guess...

>>Populations evolve.
>>And humans are apes, along with other ape species like Bonobos, Chimpanzees
>>or Gorillas.
>>The human species share a common ancestor with those mentioned above.
>
>
>The human species share a common ancestor with all life on Earth, no
>matter how often they try to disown us.

Yep.

>>> :D These are good arguments for atheism. What is there even to discuss?
>>> I would suspect supernatural intervention far more when some (or all) of
>>> above listed "evidences" of "intelligent design theory" were not so.
>>> How not to be atheist? I like folk stories and fairy tales ... but
>>> to take these as true is superstition.
>>>
>>
--

[Mark Isaak]

On 3/4/18 11:30 AM, T Pagano wrote:

It's not those people you need to argue with. The pesky opponent who
smashes every point you make is known as Reality.

I think it is no accident that reality never gets any mention in your posts.

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"Ignorance, allied with power, is the most ferocious enemy justice can
have." - James Baldwin

[jillery]

On Mon, 05 Mar 2018 10:16:03 -0700, Bob Casanova <nos...@buzz.off>
wrote:

I'm not interested in a pedantic semantic discussion about the meaning
of "nitpicking" or "ambiguous". Apparently your mileage varies.

>>>Populations evolve.
>>>And humans are apes, along with other ape species like Bonobos, Chimpanzees
>>>or Gorillas.
>>>The human species share a common ancestor with those mentioned above.
>>
>>
>>The human species share a common ancestor with all life on Earth, no
>>matter how often they try to disown us.
>
>Yep.
>
>>>> :D These are good arguments for atheism. What is there even to discuss?
>>>> I would suspect supernatural intervention far more when some (or all) of
>>>> above listed "evidences" of "intelligent design theory" were not so.
>>>> How not to be atheist? I like folk stories and fairy tales ... but
>>>> to take these as true is superstition.
>>>>
>>>

--

[Bob Casanova]

On Tue, 06 Mar 2018 00:57:25 -0500, the following appeared

Have A Nice Day.

>>>>Populations evolve.
>>>>And humans are apes, along with other ape species like Bonobos, Chimpanzees
>>>>or Gorillas.
>>>>The human species share a common ancestor with those mentioned above.
>>>
>>>
>>>The human species share a common ancestor with all life on Earth, no
>>>matter how often they try to disown us.
>>
>>Yep.
>>
>>>>> :D These are good arguments for atheism. What is there even to discuss?
>>>>> I would suspect supernatural intervention far more when some (or all) of
>>>>> above listed "evidences" of "intelligent design theory" were not so.
>>>>> How not to be atheist? I like folk stories and fairy tales ... but
>>>>> to take these as true is superstition.
>>>>>
>>>>
--

[Peter Nyikos]

On Sunday, March 4, 2018 at 4:35:04 PM UTC-5, Öö Tiib wrote:
> On Sunday, 4 March 2018 21:35:03 UTC+2, T Pagano wrote:
> > First Dr. Hurd and now Rolf.
> >
> > The morale among the secular-atheist cheerleaders is waning. Apparently
> > they haven't see a sustainable argument on the secular-atheist side in a
> > L O N G while and are tired of going under the bus. Harshman is trying
> > but he needs some serious help. Carlip doesn't need help, he needs new
> > theories rather than the frankenstein ones he holds. If Dr. Hurd and
> > Rolf are getting tired of seeing tire marks on their bodies the others
> > aren't far behind. That group I get; they're savable.
> >
> > Okimoto is like the Wile E. Coyote, who keeps chasing some non existent
> > ID phantom but instead spends most of his time plunging over the cliff
> > holding an anvil. And Professor Nyikos, who knows what side he's on.

I explain my side below.

> > He's playing both sides against the middle.

It's not playing, its working in science far beyond Tony's expertise.


Now we come to you, Tiib. Unfortunately, your list below is incomplete.
You leave out MY arguments for why intelligent design can be a serious
scientific hypothesis. Whether you agree with it -- I'm only proposing
it as something I think is somewhat likely -- is another issue.

>
> Lets see the current best ID arguments:
>
> 1) There is huge, inaccessible universe.
> 2) In that universe at least one tiny rock is suitable for life.
> 3) Reproducing lifeforms contain molecular mechanisms of replication.
> 4) If to remove some vital protein from alive being then it will be
> crippled or even die.
> 5) Some of the single-cellular organisms have formed into multi-
> cellular colonies.
> 6) Some apes have evolved into humans.
>
> :D These are good arguments for atheism.

No, they are good arguments against biblical literalism.
The Roman Catholic denomination is quite open to the idea of
common descent of bodies; John Paul II has even written that
evolution is "more than just a hypothesis".

Perhaps you've been reading too much atheistic propaganda.
Not hard to do in a forum like talk.origins.



> what is there even to discuss?

Abiogenesis, for one. I've written about the enormous hurdles
which scientists still have very little idea how to overcome.
As I wrote to Ernest Major on another thread:

____________________ excerpt___________________

The Achilles' Heel of the
protein translation mechanism is the AA-synthetases that are
responsible for matching the 20 amino acids to about three times
as many kinds of tRNA molecules. If one of these synthetases
were to undergo mutation, it could go haywire and start messing
up proteins of all sorts.

Worse yet, a devastating positive feedback loop could result in which
some amino acids of the synthetase itself can undergo mutation.


Once life as we know it became established in the form of
prokaryotes, the effects would generally be local, leading to a line
of mutants that would self-destruct, so to speak.

But in the early days of the "protein takeover", this kind of
event could have huge repercussions. These are intimately
related to a Catch-22 situation which makes the protein
takeover hugely problematic. A stable genetic code was necessary
for the part of the takeover dealing with these enzymes to
even begin.


> In the context of most genomes these would be defective codes to the
> point of being incompatible with life.
>

Where abiogenesis is the issue, the situation is bad enough
even without any feedback loops. The primordial genetic code
would first have to be stabilized and maintained by non-protein enzymes,
probably RNA based ribozymes. But the early precursors of the
the protein enzymes would necessarily have less fidelity than the
ribozymes themselves. And their clumsy efforts to mimic the
match of amino acid to tRNA would result in protocells that
are unable to compete effectively with protocells where the
process hasn't begun yet. This is the Catch-22 that makes abiogenesis
leading to our form of life such a huge puzzle.

=================== end of excerpt from
https://groups.google.com/d/msg/talk.origins/RmJfq-PdDl0/n-br4IlIBAAJ
Subject: Re: Judge Jones and Plagiarism at the Dover Trial.?
Date: Mon, 5 Mar 2018 07:32:17 -0800 (PST)
Message-ID: <0e3c07e7-2cd5-4349...@googlegroups.com>

Elsewhere on that thread -- with a different Subject: line but
still "directly descended" from the OP of the thread shown,
I give Casanova a non-supernatural scenario that bypasses
this Catch-22. It has to do with "life as we do not know it"
in the form of intelligent beings, designing "life as we know it"
in the form of microscopic organisms with which it seeds earth
from light years away, without ever traveling to earth themselves
-- thus avoiding the pejorative description "space aliens."

Would you like some details?

> I would suspect supernatural intervention far more when some (or all) of
> above listed "evidences" of "intelligent design theory" were not so.

I steer clear of all of them in my ID theory. The earliest beginnings
of life ON EARTH is what all my ID hypotheses talk about.

None of them involve supernatural beings, or even creatures more
intelligent than ourselves.


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

[Peter Nyikos]

On Sunday, March 4, 2018 at 6:15:03 PM UTC-5, Ron O wrote:
> On Sunday, March 4, 2018 at 1:35:03 PM UTC-6, T Pagano wrote:

> > Okimoto is like the Wile E. Coyote, who keeps chasing some non existent
> > ID phantom but instead spends most of his time plunging over the cliff
> > holding an anvil. And Professor Nyikos, who knows what side he's on.
> > He's playing both sides against the middle.
> >
> > God is good.
>
> Of course the Discovery Institute is the ID phantom,

I do believe Tony was not referring to the DI at all. Hopefully,
he'll clarify that comment.

> but their best 6 means that all your Dembski bull pucky is rated lower than the stupid fossil gap argument that failed the scientific creationists over 30 years ago. You ran so why lie about reality like this? I didn't rate the IDiocy, the ID perps that sold you the crap rated it and Dembski's junk nor anything else the Discovery Institute ID perps have come up with in the last 22 years made the grade. All the IDiocy was worse than the abiogenesis and Cambrian explosion junk that failed the scientific creationists over 30 years ago.
>
> Ron Okimoto

Do you still define "creationists" as people who believe in a creator?
specifically, a creator of our universe?

If so, Kenneth Miller is a scientific creationist, except that
he has no truck with the Cambrian explosion, nor with any
intelligent designers behind abiognenesis.


I'm more nuanced. Since I am an agnostic whose confidence level in
a creator of our world is no greater than 10%, I reject the
hypothesis of supernatural involvement in abiogenesis.

The beginning of life on earth, however, is an utterly different
matter. Here, my confidence level in a NON-supernatural designer
of the first prokaryotes, while still less than 50%, is somewhat
higher than the alternative of "Mother Earthdidit". The slack is
taken up by the undirected panspermia hypothesis, various forms
of which are due to Arrhenius, Hoyle, and Wickramasinghe.


For more about non-supernatural designers, see my reply to Mr. Tiib.
Unfortunately for Kenneth Miller, he doesn't have a clue as
to how to overcome the Catch-22 that I mention to Tiib. Neither
does anyone else on earth, not now and not for the foreseeable future.
That is, unless one adopts one of my scenarios, which has it that
the Catch-22 was not overcome without the work of intelligent designers.

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

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

[zencycle]

On Sunday, March 4, 2018 at 5:15:04 PM UTC-5, Bill Rogers wrote:

>
> Tony, I hear there's a job opening in Iraq; they're looking for someone to replace that Information Minister who disappeared in 2003. You'd be a perfect fit. "There are no American tanks in Baghdad."

I still think he'd be an excellent replacement for Sarah Sanders upon her inevitable demise.

"The presidents position is clear and consistent"

"This problem is obviously the fault of the previous administration"

Seems right up his alley.

[John Harshman]

On 3/7/18 11:37 AM, Peter Nyikos wrote:
> The beginning of life on earth, however, is an utterly different
> matter. Here, my confidence level in a NON-supernatural designer
> of the first prokaryotes, while still less than 50%, is somewhat
> higher than the alternative of "Mother Earthdidit".

You have, however, never been able to supply any valid reasons for your
confidence level in either case.

[Peter Nyikos]

On Sunday, March 4, 2018 at 2:35:03 PM UTC-5, T Pagano wrote:

> First Dr. Hurd and now Rolf.

The last I saw of the bumbling Dr. Hurd was on February 24. Replies by
Glenn to that post, and by myself to the one Hurd had done on February 23
evidently sent him packing from the only thread on which I saw him,

Judge Jones and Plagiarism at the Dover Trial.?

Has he fled talk.origins altogether, or has he merely fled to another
thread? New Google Groups no longer displays the posting history
of people without a profile, and Hurd doesn't have one.

> The morale among the secular-atheist cheerleaders is waning.

I can't vouch for that, but I do know that nobody tried to bail out
Gary Hurd after I showed how utterly idiotic his claim about Behe was:

Exactly the stupid "science fiction is the same as ID creationism"
claimed by Mike Behe.

For one thing, Behe wouldn't be caught dead calling ID "creationism".
But even if it weren't for that, the phony quote would be devoid of
reality.

> Apparently
> they haven't see a sustainable argument on the secular-atheist side in a
> L O N G while and are tired of going under the bus.

Well, *I* haven't seen a sustainable argument for abiogenesis. Nor
have I seen anyone competent even to argue against the rather second-rate
arguments for ID that I've seen from Behe. I said in 1976, even before
I saw _Darwin's Black Box_, that if it didn't make a strong statement
about the protein translation mechanism and the problems it poses,
the book isn't worth much. I got my copy at a bargain-basement price,
otherwise I would just be checking it out of the library from time to time.

> Harshman is trying
> but he needs some serious help. Carlip doesn't need help, he needs new
> theories rather than the frankenstein ones he holds. If Dr. Hurd and
> Rolf are getting tired of seeing tire marks on their bodies the others
> aren't far behind. That group I get; they're savable.

You are seriously overestimating Hurd; even Harshman is FAR stronger.
As for Carlip, he is FAR stronger than Harshman, and I'd like to
see you try and demolish his "frankenstein" theory.

Rolf I am not sure of, partly because I do not know whether Rolf Aalberg
is the same person who has posted as simply "Rolf" for many years.

> Okimoto is like the Wile E. Coyote, who keeps chasing some non existent
> ID phantom but instead spends most of his time plunging over the cliff
> holding an anvil. And Professor Nyikos, who knows what side he's on.
> He's playing both sides against the middle.

Not playing at all. See my reply to Mr. Tiib earlier today, to this thread.

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

[Öö Tiib]

On Wednesday, 7 March 2018 20:10:03 UTC+2, Peter Nyikos wrote:
> On Sunday, March 4, 2018 at 4:35:04 PM UTC-5, Öö Tiib wrote:
> > On Sunday, 4 March 2018 21:35:03 UTC+2, T Pagano wrote:
> > > First Dr. Hurd and now Rolf.
> > >
> > > The morale among the secular-atheist cheerleaders is waning. Apparently
> > > they haven't see a sustainable argument on the secular-atheist side in a
> > > L O N G while and are tired of going under the bus. Harshman is trying
> > > but he needs some serious help. Carlip doesn't need help, he needs new
> > > theories rather than the frankenstein ones he holds. If Dr. Hurd and
> > > Rolf are getting tired of seeing tire marks on their bodies the others
> > > aren't far behind. That group I get; they're savable.
> > >
> > > Okimoto is like the Wile E. Coyote, who keeps chasing some non existent
> > > ID phantom but instead spends most of his time plunging over the cliff
> > > holding an anvil. And Professor Nyikos, who knows what side he's on.
>
> I explain my side below.
>
> > > He's playing both sides against the middle.
>
> It's not playing, its working in science far beyond Tony's expertise.
>
>
> Now we come to you, Tiib. Unfortunately, your list below is incomplete.
> You leave out MY arguments for why intelligent design can be a serious
> scientific hypothesis. Whether you agree with it -- I'm only proposing
> it as something I think is somewhat likely -- is another issue.

I used the Discovery Institute's most recently published list.

> >
> > Lets see the current best ID arguments:
> >
> > 1) There is huge, inaccessible universe.
> > 2) In that universe at least one tiny rock is suitable for life.
> > 3) Reproducing lifeforms contain molecular mechanisms of replication.
> > 4) If to remove some vital protein from alive being then it will be
> > crippled or even die.
> > 5) Some of the single-cellular organisms have formed into multi-
> > cellular colonies.
> > 6) Some apes have evolved into humans.
> >
> > :D These are good arguments for atheism.
>
> No, they are good arguments against biblical literalism.
> The Roman Catholic denomination is quite open to the idea of
> common descent of bodies; John Paul II has even written that
> evolution is "more than just a hypothesis".

Ok, I will use scare quoted "atheist" next time to indicate that I
mean Tony's "atheists" that also include Catholic clergy scientists
and lot of other Christians and representatives of other religions.

>
> Perhaps you've been reading too much atheistic propaganda.
> Not hard to do in a forum like talk.origins.

I do not care about most atheistic propaganda despite I am "secular
humanist" myself. Most religious organizations are not source of
evil. On the contrary, they are often nice people. I think vanity
(and waste of resources driven by it), greed (and low quality
production driven by it) and whatever militant radicalism (and
most destruction driven by it) are the sources of majority of evil
we face.

> > what is there even to discuss?
>
> Abiogenesis, for one. I've written about the enormous hurdles
> which scientists still have very little idea how to overcome.

I have read only enough about abiogenesis to realize that it hasn't
been researched enough to decide anything conclusively.
Some proto-life is possible without proteins. How to get even that
far I have no idea and from there are also no clear ways to proteins
and from there to DNA. Probably there are several steps more that we
don't even imagine. Big mystery and since its applicability for
practical purposes is not large, it is not much researched. IOW my
understanding is that we don't know.

> As I wrote to Ernest Major on another thread:
>
> ____________________ excerpt___________________
>
> The Achilles' Heel of the
> protein translation mechanism is the AA-synthetases that are
> responsible for matching the 20 amino acids to about three times
> as many kinds of tRNA molecules. If one of these synthetases
> were to undergo mutation, it could go haywire and start messing
> up proteins of all sorts.
>
> Worse yet, a devastating positive feedback loop could result in which
> some amino acids of the synthetase itself can undergo mutation.
>
>
> Once life as we know it became established in the form of
> prokaryotes, the effects would generally be local, leading to a line
> of mutants that would self-destruct, so to speak.

Malfunction of whatever simple machinery is usually directly damaging
to itself and often non-damaging (or only indirectly damaging) to
others.

> But in the early days of the "protein takeover", this kind of
> event could have huge repercussions. These are intimately
> related to a Catch-22 situation which makes the protein
> takeover hugely problematic. A stable genetic code was necessary
> for the part of the takeover dealing with these enzymes to
> even begin.

Yes, extremely unfortunate backlash or chain reaction would be like
epidemic of today. It would swipe the population that caused it.
However there always are some better defended survivors.
If for early protolife the defenses were weaker and
amount of survivors was very small then there also was lot of time
to regrow back that (better defended) population of it.

>
>
> > In the context of most genomes these would be defective codes to the
> > point of being incompatible with life.
> >
>
> Where abiogenesis is the issue, the situation is bad enough
> even without any feedback loops. The primordial genetic code
> would first have to be stabilized and maintained by non-protein enzymes,
> probably RNA based ribozymes. But the early precursors of the
> the protein enzymes would necessarily have less fidelity than the
> ribozymes themselves. And their clumsy efforts to mimic the
> match of amino acid to tRNA would result in protocells that
> are unable to compete effectively with protocells where the
> process hasn't begun yet. This is the Catch-22 that makes abiogenesis
> leading to our form of life such a huge puzzle.

What I have read is that the likely pull here is bigger stability of
most proteins. We don't have ribozyme-based drugs mostly because
of that. The cell that works only on ribozymes likely needs more resources
and energy to rejuvenate itself than other using (even few, even
primitive) proteins. That seems clear advantage.

>
> =================== end of excerpt from
> https://groups.google.com/d/msg/talk.origins/RmJfq-PdDl0/n-br4IlIBAAJ
> Subject: Re: Judge Jones and Plagiarism at the Dover Trial.?
> Date: Mon, 5 Mar 2018 07:32:17 -0800 (PST)
> Message-ID: <0e3c07e7-2cd5-4349...@googlegroups.com>
>
> Elsewhere on that thread -- with a different Subject: line but
> still "directly descended" from the OP of the thread shown,
> I give Casanova a non-supernatural scenario that bypasses
> this Catch-22. It has to do with "life as we do not know it"
> in the form of intelligent beings, designing "life as we know it"
> in the form of microscopic organisms with which it seeds earth
> from light years away, without ever traveling to earth themselves
> -- thus avoiding the pejorative description "space aliens."
>
> Would you like some details?

It will still only move some of the ribozymes-to-proteins-to-DNA
steps elsewhere. Likelihood of finding facts to support that is
even smaller. It can of course be that the original conditions were
where ribozymes (or some other most simple self-catalyzing
molecules) are more stable. Hard to imagine.
If we didn't waste all computing power to mine worthless bitcoins
then we could run more simulations of abiogenesis scenarios with
more varied conditions.

> > I would suspect supernatural intervention far more when some (or all) of
> > above listed "evidences" of "intelligent design theory" were not so.
>
> I steer clear of all of them in my ID theory. The earliest beginnings
> of life ON EARTH is what all my ID hypotheses talk about.
>
> None of them involve supernatural beings, or even creatures more
> intelligent than ourselves.

I believe that if there is something supernatural then it is clearly
quite passive. Most of our trouble is also clearly anthropogenic and
worsening as such. Until our problems are solvable then it is
irresponsible to even hope for anything paranormal.

[Peter Nyikos]

On Wednesday, March 7, 2018 at 5:35:03 PM UTC-5, Öö Tiib wrote:
> On Wednesday, 7 March 2018 20:10:03 UTC+2, Peter Nyikos wrote:
> > On Sunday, March 4, 2018 at 4:35:04 PM UTC-5, Öö Tiib wrote:
> > > On Sunday, 4 March 2018 21:35:03 UTC+2, T Pagano wrote:
> > > > First Dr. Hurd and now Rolf.
> > > >
> > > > The morale among the secular-atheist cheerleaders is waning. Apparently
> > > > they haven't see a sustainable argument on the secular-atheist side in a
> > > > L O N G while and are tired of going under the bus. Harshman is trying
> > > > but he needs some serious help. Carlip doesn't need help, he needs new
> > > > theories rather than the frankenstein ones he holds. If Dr. Hurd and
> > > > Rolf are getting tired of seeing tire marks on their bodies the others
> > > > aren't far behind. That group I get; they're savable.
> > > >
> > > > Okimoto is like the Wile E. Coyote, who keeps chasing some non existent
> > > > ID phantom but instead spends most of his time plunging over the cliff
> > > > holding an anvil. And Professor Nyikos, who knows what side he's on.
> >
> > I explain my side below.
> >
> > > > He's playing both sides against the middle.
> >
> > It's not playing, its working in science far beyond Tony's expertise.
> >
> >
> > Now we come to you, Tiib. Unfortunately, your list below is incomplete.
> > You leave out MY arguments for why intelligent design can be a serious
> > scientific hypothesis. Whether you agree with it -- I'm only proposing
> > it as something I think is somewhat likely -- is another issue.
>
> I used the Discovery Institute's most recently published list.

The DI isn't aware of my hypotheses. And I doubt that they
would be interested in something that does nothing for their
financial support from creationists.

Like all organizations, they are all too aware of how money
makes the world go around. I have long looked at my university
as a big business, with us faculty as skilled labor. Yesterday
I got a depressing lesson in just HOW far it has come from
a university where professionalism and knowledge are highly valued.
Even research counts for very little if it doesn't rake in BIG
bucks.

I'd rather not go any further into this for a while. Maybe next month.

> > >
> > > Lets see the current best ID arguments:
> > >
> > > 1) There is huge, inaccessible universe.
> > > 2) In that universe at least one tiny rock is suitable for life.
> > > 3) Reproducing lifeforms contain molecular mechanisms of replication.
> > > 4) If to remove some vital protein from alive being then it will be
> > > crippled or even die.
> > > 5) Some of the single-cellular organisms have formed into multi-
> > > cellular colonies.
> > > 6) Some apes have evolved into humans.
> > >
> > > :D These are good arguments for atheism.
> >
> > No, they are good arguments against biblical literalism.
> > The Roman Catholic denomination is quite open to the idea of
> > common descent of bodies; John Paul II has even written that
> > evolution is "more than just a hypothesis".
>
> Ok, I will use scare quoted "atheist" next time to indicate that I
> mean Tony's "atheists" that also include Catholic clergy scientists
> and lot of other Christians and representatives of other religions.

Looks like Tony and Ray have been comparing notes. :-( :-)

Just to be on the safe side, use "Atheists" capitalized and in
scare quotes, to give the devil Ray his due. :-)

> >
> > Perhaps you've been reading too much atheistic propaganda.
> > Not hard to do in a forum like talk.origins.
>
> I do not care about most atheistic propaganda despite I am "secular
> humanist" myself. Most religious organizations are not source of
> evil. On the contrary, they are often nice people. I think vanity
> (and waste of resources driven by it), greed (and low quality
> production driven by it) and whatever militant radicalism (and
> most destruction driven by it) are the sources of majority of evil
> we face.

For greed, see above. The other two are rampant in talk.origins, I
fear. You of course don't strike me as being party to any of these
vices. However, there are several people, including Tony and Ray,
and about a dozen anti-ID fanatics who are quite capable of
hypocritically saying what you just said, and yet be oblivious
to the kind of radicalism they represent.

> > > what is there even to discuss?
> >
> > Abiogenesis, for one. I've written about the enormous hurdles
> > which scientists still have very little idea how to overcome.
>
> I have read only enough about abiogenesis to realize that it hasn't
> been researched enough to decide anything conclusively.

That could become the understatement of the year, at least in
talk.origins.

> Some proto-life is possible without proteins. How to get even that
> far I have no idea and from there are also no clear ways to proteins
> and from there to DNA. Probably there are several steps more that we
> don't even imagine. Big mystery and since its applicability for
> practical purposes is not large, it is not much researched. IOW my
> understanding is that we don't know.

On this, we agree. There is no money right now for that kind of
research. So the people who would be researching it if there WERE
money for it have to tolerate anti-ID fanatics using dirty debating
tactics to hide the fact that we are in no shape to debate those
who claim that God intervened at the beginning to create the first
prokaryotes.

That's fine as far as it goes, but if the Catch-22 is not overcome,
"life as we know it" -- based on protein enzymes -- cannot evolve.

> >
> >
> > > In the context of most genomes these would be defective codes to the
> > > point of being incompatible with life.
> > >
> >
> > Where abiogenesis is the issue, the situation is bad enough
> > even without any feedback loops. The primordial genetic code
> > would first have to be stabilized and maintained by non-protein enzymes,
> > probably RNA based ribozymes. But the early precursors of the
> > the protein enzymes would necessarily have less fidelity than the
> > ribozymes themselves. And their clumsy efforts to mimic the
> > match of amino acid to tRNA would result in protocells that
> > are unable to compete effectively with protocells where the
> > process hasn't begun yet. This is the Catch-22 that makes abiogenesis
> > leading to our form of life such a huge puzzle.
>
> What I have read is that the likely pull here is bigger stability of
> most proteins.

That bigger stability is of big help once fidelity becomes better
than that of the ribozymes that are to be replaced. But until
that point, it could be more of a handicap than an asset.

> We don't have ribozyme-based drugs mostly because
> of that. The cell that works only on ribozymes likely needs more resources
> and energy to rejuvenate itself than other using (even few, even
> primitive) proteins. That seems clear advantage.

Proteins would be present, all right, but the nonproblematic
ones would be the simple, mostly structural proteins. My scenario
envisions a genetic code like ours, which actually does use
a huge ribozyme -- the ribosome. But the AA-synthetases are absolutely
essential to ours as well, and it is them that the Catch-22 hits the
hardest.

>
> >
> > =================== end of excerpt from
> > https://groups.google.com/d/msg/talk.origins/RmJfq-PdDl0/n-br4IlIBAAJ
> > Subject: Re: Judge Jones and Plagiarism at the Dover Trial.?
> > Date: Mon, 5 Mar 2018 07:32:17 -0800 (PST)
> > Message-ID: <0e3c07e7-2cd5-4349...@googlegroups.com>
> >
> > Elsewhere on that thread -- with a different Subject: line but
> > still "directly descended" from the OP of the thread shown,
> > I give Casanova a non-supernatural scenario that bypasses
> > this Catch-22. It has to do with "life as we do not know it"
> > in the form of intelligent beings, designing "life as we know it"
> > in the form of microscopic organisms with which it seeds earth
> > from light years away, without ever traveling to earth themselves
> > -- thus avoiding the pejorative description "space aliens."
> >
> > Would you like some details?
>
> It will still only move some of the ribozymes-to-proteins-to-DNA
> steps elsewhere. Likelihood of finding facts to support that is
> even smaller. It can of course be that the original conditions were
> where ribozymes (or some other most simple self-catalyzing
> molecules) are more stable. Hard to imagine.
> If we didn't waste all computing power to mine worthless bitcoins
> then we could run more simulations of abiogenesis scenarios with
> more varied conditions.

Granted, I have nothing to say about these things right now. What
I had in mind was the way intelligent ribozyme-based beings might
get the idea of manufacturing protein enzymes, and by steps design
the first prokaryotes. I also have ideas about how this scenariro
could be supported or falsified. Would you like to hear them?

> > > I would suspect supernatural intervention far more when some (or all) of
> > > above listed "evidences" of "intelligent design theory" were not so.
> >
> > I steer clear of all of them in my ID theory. The earliest beginnings
> > of life ON EARTH is what all my ID hypotheses talk about.
> >
> > None of them involve supernatural beings, or even creatures more
> > intelligent than ourselves.
>
> I believe that if there is something supernatural then it is clearly
> quite passive. Most of our trouble is also clearly anthropogenic and
> worsening as such. Until our problems are solvable then it is
> irresponsible to even hope for anything paranormal.

But it is responsible to hope that, some day, probes will be sent
to planetary systems circling other stars. Greed might have the
beneficial effect of mining asteroids and increasing many-fold the
gross national product of all countries that do the mining. Then
reaching for the stars might be as fulfilling to the human psyche,
and as easy to sustain, as spectator sports are now.

One can always hope.

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

PS I'll be going on a posting break starting late Friday and extending
until Monday March 19. This coincides with my university's spring break.
So if we don't have much interaction these next two days, I hope you
will still be around on the week of the 19th.

[Peter Nyikos]

On Monday, March 5, 2018 at 7:00:02 PM UTC-5, Mark Isaak wrote:
> On 3/4/18 11:30 AM, T Pagano wrote:
> > First Dr. Hurd and now Rolf.
> >
> > The morale among the secular-atheist cheerleaders is waning. Apparently
> > they haven't see a sustainable argument on the secular-atheist side in a
> > L O N G while and are tired of going under the bus. Harshman is trying
> > but he needs some serious help. Carlip doesn't need help, he needs new
> > theories rather than the frankenstein ones he holds. If Dr. Hurd and
> > Rolf are getting tired of seeing tire marks on their bodies the others
> > aren't far behind. That group I get; they're savable.
> >
> > Okimoto is like the Wile E. Coyote, who keeps chasing some non existent
> > ID phantom but instead spends most of his time plunging over the cliff
> > holding an anvil. And Professor Nyikos, who knows what side he's on.
> > He's playing both sides against the middle.
>
> It's not those people you need to argue with. The pesky opponent who
> smashes every point you make is known as Reality.

It's reality that it takes someone with far more aptitude for science
than yourself to elucidate.

> I think it is no accident that reality never gets any mention in your posts.

I agree, but I would add that you are just a cheerleader for reality
while other people do the heavy lifting.

Martin Harran is in the same boat. Confronted with the complete
inability of even the best minds to figure out an evolutionary
pathway, even a hypothetical one, that could culminate in Hox genes,
all he can do is regurgitate a claim that this is all just an argument
from personal incredulity.

That's the kind of high school level stuff you read in the first few
pages of introductory logic textbooks, about "logical fallacies." In the
hands of a polemicist like Martin, it becomes the most advanced part
of his stock in trade.

Less advanced parts include sneering at anything [1] beginning with an
"if" clause with the retort, "If my aunt had balls, she'd be my uncle."

[1] understood: anything he disagrees with.

In anticipation of the usual reaction, PLEASE DO let Martin know
I am saying this about him. And let him know the reason: I want him
to see that I know that you and he are birds of a feather.

Unless, of course, you think Martin would consider me paranoid
for thinking anyone would talk about me behind my back. That's
the kind of thing Harshman associates with paranoia, even if I
WANT it done.

And Martin sure seems to want to fit in with Harshman and his
fan club -- which includes you, of course.

Oh, and please DO tell Harshman about this post too. He knows I
have nothing to hide, but I'm sure that wouldn't stop him from
spin-doctoring a charge of paranoia when he sees this post.

Peter Nyikos

[erik simpson]

Are you really pinning a "kick me" sign to your own back?

[Mark Isaak]

On 3/8/18 1:42 PM, Peter Nyikos wrote:
[snip all but Peter's actual content]


--

[Peter Nyikos]

Do your worst, Erik, but remember that I have the goods on Harshman
as far as his bizarre attitude towards "paranoia" is concerned.

One of the worst examples is hinted at above: Harshman thought I was
paranoid for suggesting that Hemidactylus might have let him know
that he (Harshman) was being severely criticized on another thread,
from which he was missing. Hemidactylus was his only defender
on that thread, unless you count my telling someone who seemed
to be overdoing it that he shouldn't make such claims without
any evidence. But since I was Harshman's most accurate and telling
critic on that thread, I certainly don't count myself as a defender there.

Harshman is really screwed up if he thinks "paranoia" applies to thinking
Hemidactylus might have done a very laudable and honorable thing.

But hey, you are Harshman's most ardent fan, so I don't expect
you to think any differently about this matter than Harshman did.

Peter Nyikos

[Peter Nyikos]

Nor has anyone been able to supply any valid reasons for any other
confidence level, nor against mine. Least of all you, who deleted
mention of reasons for the relative status of these two alternatives.

I can understand why you don't want people who don't read my posts
(but who do read yours) for deleting all that. But what was the point
of you deleting the third alternative?

It certainly can't undermine your confidence in Mother Earth or some
other part of our solar system didit. Here it is again.

________________________repost___________________

The slack is
taken up by the undirected panspermia hypothesis, various forms
of which are due to Arrhenius, Hoyle, and Wickramasinghe.

For more about non-supernatural designers, see my reply to Mr. Tiib.
Unfortunately for Kenneth Miller, he doesn't have a clue as
to how to overcome the Catch-22 that I mention to Tiib. Neither
does anyone else on earth, not now and not for the foreseeable future.
That is, unless one adopts one of my scenarios, which has it that
the Catch-22 was not overcome without the work of intelligent designers.

===================== end of repost =======================

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

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

PS If you choose to reply to this post, please do leave in the part
about "the rest of the slack" even if you AGAIN delete what I reposted
next (and, of course, this PS).

[John Harshman]

On 3/9/18 5:50 PM, Peter Nyikos wrote:
> On Wednesday, March 7, 2018 at 3:05:02 PM UTC-5, John Harshman wrote:
>> On 3/7/18 11:37 AM, Peter Nyikos wrote:
>>> The beginning of life on earth, however, is an utterly different
>>> matter. Here, my confidence level in a NON-supernatural designer
>>> of the first prokaryotes, while still less than 50%, is somewhat
>>> higher than the alternative of "Mother Earthdidit".
>>
>> You have, however, never been able to supply any valid reasons for your
>> confidence level in either case.
>
> Nor has anyone been able to supply any valid reasons for any other
> confidence level, nor against mine.

That was an invitation to supply a valid reason, which you chose not to
do. Would you like to admit that you have no reasons and are just
pulling those numbers from nowhere?

[Peter Nyikos]

On Friday, March 9, 2018 at 9:20:03 PM UTC-5, John Harshman wrote:
> On 3/9/18 5:50 PM, Peter Nyikos wrote:
> > On Wednesday, March 7, 2018 at 3:05:02 PM UTC-5, John Harshman wrote:
> >> On 3/7/18 11:37 AM, Peter Nyikos wrote:
> >>> The beginning of life on earth, however, is an utterly different
> >>> matter. Here, my confidence level in a NON-supernatural designer
> >>> of the first prokaryotes, while still less than 50%, is somewhat
> >>> higher than the alternative of "Mother Earthdidit".
> >>
> >> You have, however, never been able to supply any valid reasons for your
> >> confidence level in either case.
> >
> > Nor has anyone been able to supply any valid reasons for any other
> > confidence level, nor against mine.
>
> That was an invitation to supply a valid reason, which you chose not to
> do.

I chose to give reasons to Öö Tiib, right on this thread, before you
butted in.

And you chose to TWICE delete the information that I had done so.

If you disagree that those are valid reasons, why are you such
a coward that you not only do not answer THOSE posts, you
even delete the information that they exist? Are you afraid
to admit that you have no valid arguments for Hemidactylus's
fanatical claim that my alternative to Mother Earthdidit
is "nonsense"?

> Would you like to admit that you have no reasons and are just
> pulling those numbers from nowhere?

Would you like to admit that you are a control freak who
asks authoritartian questions like this because they sound
good with the truth of what is going on between us hidden from
people who read your posts but not mine?

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

PS The people referred to in my last paragraph include Burkhard, who is
probably far more respected than you are, because unlike you, he isn't
fond of what Kleinman calls "mud wrestling."

[Öö Tiib]

Why is "God planted life" (none of 6 indicates that) worse than
"God turned life into multi-cellular" (implied by evidence #5)?

> Like all organizations, they are all too aware of how money
> makes the world go around. I have long looked at my university
> as a big business, with us faculty as skilled labor. Yesterday
> I got a depressing lesson in just HOW far it has come from
> a university where professionalism and knowledge are highly valued.
> Even research counts for very little if it doesn't rake in BIG
> bucks.
>
> I'd rather not go any further into this for a while. Maybe next month.

Doing something that benefits world often also results with profit
and other benefits as a side-effect. Trying to squeeze out profit
from some questionable junk usually results with loss of trust and
negative reputation that are later expensive to buy back.

I assume that being arrogant and militant has been tradition
and part of the game here in talk.origins.

I am speculating here but it can be that RNA world evolved AA-ribozymes
first for building first proteins that were simple. Then there can
evolve enough capability to make more complex proteins (for example
AA-synthetases) that gradually replaced RNA ensymes (AA-ribozymes)
by being more efficient.

Yes, how to falsify something that may be happened so long time ago
that all traces of it are likely erased? Anything that can evolve
can be likely manufactured as well.

>
> > > > I would suspect supernatural intervention far more when some (or all) of
> > > > above listed "evidences" of "intelligent design theory" were not so.
> > >
> > > I steer clear of all of them in my ID theory. The earliest beginnings
> > > of life ON EARTH is what all my ID hypotheses talk about.
> > >
> > > None of them involve supernatural beings, or even creatures more
> > > intelligent than ourselves.
> >
> > I believe that if there is something supernatural then it is clearly
> > quite passive. Most of our trouble is also clearly anthropogenic and
> > worsening as such. Until our problems are solvable then it is
> > irresponsible to even hope for anything paranormal.
>
> But it is responsible to hope that, some day, probes will be sent
> to planetary systems circling other stars. Greed might have the
> beneficial effect of mining asteroids and increasing many-fold the
> gross national product of all countries that do the mining. Then
> reaching for the stars might be as fulfilling to the human psyche,
> and as easy to sustain, as spectator sports are now.
>
> One can always hope.

The greed does not work yet there. Transportation to space and
back is expensive. Level of radiation is deadly high. One will get
lethal doze of X-rays with 6 months. Also there are psychological
problems wit work-force since most people have difficulties to stay
happy being in condensed places for extended duration.
So the communication- and observation-satellites are worth their
value, but with mining and such we are not there yet.

> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> University of South Carolina
> http://people.math.sc.edu/nyikos/
>
> PS I'll be going on a posting break starting late Friday and extending
> until Monday March 19. This coincides with my university's spring break.
> So if we don't have much interaction these next two days, I hope you
> will still be around on the week of the 19th.

For me it is fine, I write only couple posts per week anyway.

[John Harshman]

On 3/9/18 6:51 PM, Peter Nyikos wrote:
> On Friday, March 9, 2018 at 9:20:03 PM UTC-5, John Harshman wrote:
>> On 3/9/18 5:50 PM, Peter Nyikos wrote:
>>> On Wednesday, March 7, 2018 at 3:05:02 PM UTC-5, John Harshman wrote:
>>>> On 3/7/18 11:37 AM, Peter Nyikos wrote:
>>>>> The beginning of life on earth, however, is an utterly different
>>>>> matter. Here, my confidence level in a NON-supernatural designer
>>>>> of the first prokaryotes, while still less than 50%, is somewhat
>>>>> higher than the alternative of "Mother Earthdidit".
>>>>
>>>> You have, however, never been able to supply any valid reasons for your
>>>> confidence level in either case.
>>>
>>> Nor has anyone been able to supply any valid reasons for any other
>>> confidence level, nor against mine.
>>
>> That was an invitation to supply a valid reason, which you chose not to
>> do.
>
> I chose to give reasons to Öö Tiib, right on this thread, before you
> butted in.

You gave reasons?

> And you chose to TWICE delete the information that I had done so.
>
> If you disagree that those are valid reasons, why are you such
> a coward that you not only do not answer THOSE posts, you
> even delete the information that they exist? Are you afraid
> to admit that you have no valid arguments for Hemidactylus's
> fanatical claim that my alternative to Mother Earthdidit
> is "nonsense"?
>
>
>> Would you like to admit that you have no reasons and are just
>> pulling those numbers from nowhere?
>
> Would you like to admit that you are a control freak who
> asks authoritartian questions like this because they sound
> good with the truth of what is going on between us hidden from
> people who read your posts but not mine?
>
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> University of South Carolina
> http://people.math.sc.edu/nyikos/
>
> PS The people referred to in my last paragraph include Burkhard, who is
> probably far more respected than you are, because unlike you, he isn't
> fond of what Kleinman calls "mud wrestling."

Must every post refer to 5 other things that happened somewhere else,
long ago?

[Mark Isaak]

On 3/9/18 5:50 PM, Peter Nyikos rewrote:

>
> The slack is
> taken up by the undirected panspermia hypothesis, various forms
> of which are due to Arrhenius, Hoyle, and Wickramasinghe.

You may want to study economics. I think you will find it argues
forcibly against your hypothesis. Organisms do not routinely throw away
large proportions of their resources for nothing. Not on Earth; not,
unless you can suggest reasons otherwise, on other planets.

--

[Peter Nyikos]

On Friday, March 9, 2018 at 10:10:03 PM UTC-5, Öö Tiib wrote:
> On Thursday, 8 March 2018 03:40:03 UTC+2, Peter Nyikos wrote:
> > On Wednesday, March 7, 2018 at 5:35:03 PM UTC-5, Öö Tiib wrote:
> > > On Wednesday, 7 March 2018 20:10:03 UTC+2, Peter Nyikos wrote:
> > > > On Sunday, March 4, 2018 at 4:35:04 PM UTC-5, Öö Tiib wrote:

> > > > Now we come to you, Tiib. Unfortunately, your list below is incomplete.
> > > > You leave out MY arguments for why intelligent design can be a serious
> > > > scientific hypothesis. Whether you agree with it -- I'm only proposing
> > > > it as something I think is somewhat likely -- is another issue.
> > >
> > > I used the Discovery Institute's most recently published list.
> >
> > The DI isn't aware of my hypotheses. And I doubt that they
> > would be interested in something that does nothing for their
> > financial support from creationists.

The following comment by you refers to a list you posted earlier;
it appears further down.

> Why is "God planted life" (none of 6 indicates that) worse than
> "God turned life into multi-cellular" (implied by evidence #5)?

It restricts God to being sufficiently prescient as to what
mutations would lead where, on a planet with such a host of
various selection pressures that could ensue. And it also
makes God a single entity instead of dividing the job of
overseeing Earth among several supernatural beings.

If one is ever to have real competition between ID (Intelligent
Design) people, such possibilities need to be kept open.

Fortunately for all but the most diehard creationists, Genesis 1
speaks of God in the plural: Elohim. Also it says, "let us
make man..." But it would take near-genius PR for the DI to get such
a message across without it adversely affecting their sales. As I
was saying:

> > Like all organizations, they are all too aware of how money
> > makes the world go around. I have long looked at my university
> > as a big business, with us faculty as skilled labor. Yesterday
> > I got a depressing lesson in just HOW far it has come from
> > a university where professionalism and knowledge are highly valued.
> > Even research counts for very little if it doesn't rake in BIG
> > bucks.
> >
> > I'd rather not go any further into this for a while. Maybe next month.
>
> Doing something that benefits world often also results with profit
> and other benefits as a side-effect.

My university isn't into benefiting the world, except as a means
to the end of raking in big bucks. And that means going for the
research that most seems to produce immediate rewards.

> Trying to squeeze out profit
> from some questionable junk usually results with loss of trust and
> negative reputation that are later expensive to buy back.

Unfortunately, the general public is unable to distinguish between
questionable junk and far-sighted research goals. Politicians have
to appeal to their constituents, who are by and large "looking
out for Number 1".

Yes, and the Roman Catholic Church is against all these evils today;
Pope Francis is especially good about pushing the need for people
to be "stewards of the environment." How successful he is in getting
all this across to the rank and file is a different matter. He has
alienated a lot of them with sometimes speculative talk about global
climate change and what needs to be done about it, and how soon.

> > For greed, see above. The other two are rampant in talk.origins, I
> > fear. You of course don't strike me as being party to any of these
> > vices. However, there are several people, including Tony and Ray,
> > and about a dozen anti-ID fanatics who are quite capable of
> > hypocritically saying what you just said, and yet be oblivious
> > to the kind of radicalism they represent.
>
> I assume that being arrogant and militant has been tradition
> and part of the game here in talk.origins.

Yes, talk.origins is a veritable microcosm of the big outside
world. The arrogant and militant minority here are just as
effective as their counterparts in the world at large.

Historians and sociologists and psychologists have a lot of
raw material here in talk.origins if they want insight into
what people are like in the world at large. For instance, many
of the dirty debating tactics used by this vocal minority
in talk.origins also work in the outside world, when suitably
modified for use in politics, rallies, ...

> > > > > what is there even to discuss?
> > > >
> > > > Abiogenesis, for one. I've written about the enormous hurdles
> > > > which scientists still have very little idea how to overcome.
> > >
> > > I have read only enough about abiogenesis to realize that it hasn't
> > > been researched enough to decide anything conclusively.
> >
> > That could become the understatement of the year, at least in
> > talk.origins.

This post has already grown very long, so I am holding off on
the rest until later -- probably until tomorrow.

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

PS the theme of the rest is scientifically oriented, and I will
stick to that in my reply to it.

[Peter Nyikos]

On Friday, March 9, 2018 at 10:10:03 PM UTC-5, Öö Tiib wrote:
> On Thursday, 8 March 2018 03:40:03 UTC+2, Peter Nyikos wrote:
> > On Wednesday, March 7, 2018 at 5:35:03 PM UTC-5, Öö Tiib wrote:
> > > On Wednesday, 7 March 2018 20:10:03 UTC+2, Peter Nyikos wrote:
> > > > On Sunday, March 4, 2018 at 4:35:04 PM UTC-5, Öö Tiib wrote:

[repeating a bit of context from my first reply]

This is true once lateral transfer is at a minimum. It's an interesting
question whether this became true with the first [proto-] cell membranes,
or whether it happened considerably later.

> > > > But in the early days of the "protein takeover", this kind of
> > > > event could have huge repercussions. These are intimately
> > > > related to a Catch-22 situation which makes the protein
> > > > takeover hugely problematic. A stable genetic code was necessary
> > > > for the part of the takeover dealing with these enzymes to
> > > > even begin.
> > >
> > > Yes, extremely unfortunate backlash or chain reaction would be like
> > > epidemic of today. It would swipe the population that caused it.
> > > However there always are some better defended survivors.
> > > If for early protolife the defenses were weaker and
> > > amount of survivors was very small then there also was lot of time
> > > to regrow back that (better defended) population of it.
> >
> > That's fine as far as it goes, but if the Catch-22 is not overcome,
> > "life as we know it" -- based on protein enzymes -- cannot evolve.

This Catch-22 remains to the end of this post, but with some new
features.

> > > >
> > > > > In the context of most genomes these would be defective codes to the
> > > > > point of being incompatible with life.
> > > > >
> > > >
> > > > Where abiogenesis is the issue, the situation is bad enough
> > > > even without any feedback loops. The primordial genetic code
> > > > would first have to be stabilized and maintained by non-protein enzymes,
> > > > probably RNA based ribozymes. But the early precursors of the
> > > > the protein enzymes would necessarily have less fidelity than the
> > > > ribozymes themselves. And their clumsy efforts to mimic the
> > > > match of amino acid to tRNA would result in protocells that
> > > > are unable to compete effectively with protocells where the
> > > > process hasn't begun yet. This is the Catch-22 that makes abiogenesis
> > > > leading to our form of life such a huge puzzle.
> > >
> > > What I have read is that the likely pull here is bigger stability of
> > > most proteins.
> >
> > That bigger stability is of big help once fidelity becomes better
> > than that of the ribozymes that are to be replaced. But until
> > that point, it could be more of a handicap than an asset.

By "fidelity" I meant a completely consistent way of matching amino acids
to codons. The AA-synthetases have to be very exacting for this.

> >
> > > We don't have ribozyme-based drugs mostly because
> > > of that. The cell that works only on ribozymes likely needs more resources
> > > and energy to rejuvenate itself than other using (even few, even
> > > primitive) proteins. That seems clear advantage.
> >
> > Proteins would be present, all right, but the nonproblematic
> > ones would be the simple, mostly structural proteins. My scenario
> > envisions a genetic code like ours, which actually does use
> > a huge ribozyme -- the ribosome. But the AA-synthetases are absolutely
> > essential to ours as well, and it is them that the Catch-22 hits the
> > hardest.
>
> I am speculating here but it can be that RNA world evolved AA-ribozymes
> first for building first proteins that were simple.

Yes, that seems unavoidable.

> Then there can
> evolve enough capability to make more complex proteins (for example
> AA-synthetases) that gradually replaced RNA ensymes (AA-ribozymes)
> by being more efficient.

Eventually they would become more efficient, but only after their
fidelity is about as good as that of the AA-ribozymes. But just to
get to that point requires the overcoming of tremendous odds,
unless somehow the precursors of the protein AA-synthetases
can be gainfully employed doing OTHER things along the early
steps of the way.

I seriously wonder whether anyone ever thought this far enough through to
produce a plausible scenario.

>
> > >
> > > >
> > > > =================== end of excerpt from
> > > > https://groups.google.com/d/msg/talk.origins/RmJfq-PdDl0/n-br4IlIBAAJ
> > > > Subject: Re: Judge Jones and Plagiarism at the Dover Trial.?
> > > > Date: Mon, 5 Mar 2018 07:32:17 -0800 (PST)
> > > > Message-ID: <0e3c07e7-2cd5-4349...@googlegroups.com>
> > > >
> > > > Elsewhere on that thread -- with a different Subject: line but
> > > > still "directly descended" from the OP of the thread shown,
> > > > I give Casanova a non-supernatural scenario that bypasses
> > > > this Catch-22. It has to do with "life as we do not know it"
> > > > in the form of intelligent beings, designing "life as we know it"
> > > > in the form of microscopic organisms with which it seeds earth
> > > > from light years away, without ever traveling to earth themselves
> > > > -- thus avoiding the pejorative description "space aliens."

With this "trailer," I leave off for today, intending to continue
(and perhaps finish) this "bypass" theme tomorrow.


Peter Nyikos
Mathematics Professor
University of South Carolina (in Columbia) -- standard disclaimer--
http://people.math.sc.edu/nyikos/

[Peter Nyikos]

On Friday, March 9, 2018 at 10:10:03 PM UTC-5, Öö Tiib wrote:
> On Thursday, 8 March 2018 03:40:03 UTC+2, Peter Nyikos wrote:
> > On Wednesday, March 7, 2018 at 5:35:03 PM UTC-5, Öö Tiib wrote:
> > > On Wednesday, 7 March 2018 20:10:03 UTC+2, Peter Nyikos wrote:

Repeating some context from the first two replies to this post:

> > > > As I wrote to Ernest Major on another thread:
> > > >
> > > > ____________________ excerpt___________________
> > > >
> > > > The Achilles' Heel of the
> > > > protein translation mechanism is the AA-synthetases that are
> > > > responsible for matching the 20 amino acids to about three times
> > > > as many kinds of tRNA molecules. If one of these synthetases
> > > > were to undergo mutation, it could go haywire and start messing
> > > > up proteins of all sorts.

[...]

> > > > Where abiogenesis is the issue, the situation is bad enough
> > > > even without any feedback loops. The primordial genetic code
> > > > would first have to be stabilized and maintained by non-protein enzymes,
> > > > probably RNA based ribozymes. But the early precursors of the
> > > > the protein enzymes would necessarily have less fidelity than the
> > > > ribozymes themselves. And their clumsy efforts to mimic the
> > > > match of amino acid to tRNA would result in protocells that
> > > > are unable to compete effectively with protocells where the
> > > > process hasn't begun yet. This is the Catch-22 that makes abiogenesis
> > > > leading to our form of life such a huge puzzle.

[...]

> > > > =================== end of excerpt from
> > > > https://groups.google.com/d/msg/talk.origins/RmJfq-PdDl0/n-br4IlIBAAJ
> > > > Subject: Re: Judge Jones and Plagiarism at the Dover Trial.?
> > > > Date: Mon, 5 Mar 2018 07:32:17 -0800 (PST)
> > > > Message-ID: <0e3c07e7-2cd5-4349...@googlegroups.com>
> > > >
> > > > Elsewhere on that thread -- with a different Subject: line but
> > > > still "directly descended" from the OP of the thread shown,
> > > > I give Casanova a non-supernatural scenario that bypasses
> > > > this Catch-22. It has to do with "life as we do not know it"
> > > > in the form of intelligent beings, designing "life as we know it"
> > > > in the form of microscopic organisms with which it seeds earth
> > > > from light years away, without ever traveling to earth themselves
> > > > -- thus avoiding the pejorative description "space aliens."
> > > >
> > > > Would you like some details?
> > >
> > > It will still only move some of the ribozymes-to-proteins-to-DNA
> > > steps elsewhere.

Yes, the most difficult ones. The ribozyme-based translation mechanism
would have a genetic code for churning out some proteins, but key
enzymes are enormously difficult to "evolve" because of the exacting
standards for a catalyst with just ONE function out of literally millions.

So they may well have been confined to some simpler structural proteins,
and the subsequent evolution of this life would depend on cells based
on ribozymes.


By the way, your phrase "proteins-to-DNA" has to refer to an indirect
process. What was needed was some kind of enzyme that converts RNA to
the more stable DNA. The conventional wisdom of biochemists is that
this was a protein enzyme, but I would guess that this was a ribozyme,
even if the firmly held belief of "abiogenesis on earth" is correct.

> > > Likelihood of finding facts to support that is
> > > even smaller. It can of course be that the original conditions were
> > > where ribozymes (or some other most simple self-catalyzing
> > > molecules) are more stable.

Not more stable than protein enzymes, just stable enough to carry
on the work of the protocell -- that is all that was needed.
And ribozymes are far from simple -- look at how huge the ribosome is,
for example.

As for facts: if biochemists had enough financial incentive, they might
be able to reproduce possible steps in the long road to ribozyme-based
protocells. As it is, they are stuck in the very early stages of just
producing RNA itself.

> > > Hard to imagine.
> > > If we didn't waste all computing power to mine worthless bitcoins
> > > then we could run more simulations of abiogenesis scenarios with
> > > more varied conditions.
> >
> > Granted, I have nothing to say about these things right now. What
> > I had in mind was the way intelligent ribozyme-based beings might
> > get the idea of manufacturing protein enzymes, and by steps design
> > the first prokaryotes. I also have ideas about how this scenariro
> > could be supported or falsified. Would you like to hear them?
>
> Yes, how to falsify something that may be happened so long time ago
> that all traces of it are likely erased? Anything that can evolve
> can be likely manufactured as well.

One means of falsification was already posted back in 2013:

B8: Isn't directed panspermia essentially untestable, thereby removing
it from the category of science?

It is eminently testable *in principle*, and may also become testable
in practice if human beings make serious attempts to find out whether
there is life on other worlds. The following is mostly taken from

http://groups.google.com/group/talk.origins/msg/90027d90c58f7b4c


If we send enough probes, whether manned or unmanned, to
investigate the occurrence of life in many likely planets
in our galaxy, a lot of possibilities will be tested and
of the following four, only one will emerge the winner:


(1) We may find life in many stages of "protein takeover", all with
closely similar genetic codes.

That would be a big argument in favor of what I have called "the
Throomian sub-hypothesis." This has it that the panspermia project was
carried out by intelligent creatures that had ribozymes in place of
protein enzymes, and who carried out experiments in which they
replaced ribozymes incrementally with protein enzymes in organisms
over the course of thousands of years. They might have sent "the
latest models" to the planets they were seeding at that time.

On the other hand, if the takeover is in essentially the same stage as
that of earth, and the genetic code is very similar, that would
strongly support the overall hypothesis of directed panspermia while
all but falsifying the Throomian sub-hypothesis.

A third possible outcome is that we encounter lots of life with
genetic codes all very different from ours. That would all but
falsify all three main sub-hypotheses of directed panspermia,.

And finally, if we find no life after searching a million likely
planets, that would falsify the hypothesis that WE are the result of
evolution from unicellular organisms sent here by directed
panspermists, but would still leave my general hypothesis about the
frequency of directed panspermia largely unscathed.

++++++++++++++++++ end of excerpt from
https://groups.google.com/d/msg/talk.origins/bcWYrv-0cI8/KZgmxbWFjHQJ
Subject: Re: FAQ on Directed Panspermia, Sections ABCD
Date: Tue, 15 Jan 2013 12:18:28 -0800 (PST)
Message-ID: <f4b4dc97-45a5-49b1...@k6g2000yqf.googlegroups.com>


Concluded in next reply to your post, to be done soon after
I see that this one has posted.

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

PS Reviewing old correspondence between us, I see that we have
talked about this theme a while ago. See, for instance,

https://groups.google.com/d/msg/talk.origins/O4LVZjK0SkM/6Fxv01_DFAAJ
Message-ID: <df3a3e0b-ecef-4fa6...@googlegroups.com>
Subject: Re: The astonishing language written on microtubules, amazing
evidence of design
Date: Mon, 25 Jan 2016 16:23:42 -0800 (PST)

[Peter Nyikos]

Finally, I reply to the end of your long post, Öö.

Initial outlay will be huge, but it is already taking place and
has been taking place since before 1968, when the first manned circumlunar
flight took place. But once it really gets going, the dividends
can be spectacular.

> Level of radiation is deadly high. One will get
> lethal doze of X-rays with 6 months.

Not if adequately protected. The program may take us into the
next century before it really gets going. The first stage would
be to build a base on the moon, underground. Then spaceships
could be manufactured there, and take off under the far smaller
lunar gravity. So they could be smaller than the Saturn V, with
HALF of it payload, as was the case with the lunar modules (LEMs).

Remember the LEM that saved the lives of the Apollo 13 astronauts?
That was the kind of high drama that I expect to occur from time
to time during the shift to mining asteroids, and to keep up public
interest while it is still in need of taxpayer money.

> Also there are psychological
> problems wit work-force since most people have difficulties to stay
> happy being in condensed places for extended duration.
> So the communication- and observation-satellites are worth their
> value, but with mining and such we are not there yet.

But our grandchildren might live to see the day.


Getting back to the theme of the Catch-22 alternative: what we've
discussed just now would be the first stages of preparation for
the grandest project of all. This is the project of probing
other planetary systems for signs of life, and action in the event that
no life is ever found.

This could be our own project, all of it, unless the hypothesis
that earth life (and life on many other planets) was the result
of directed panspermia (DP). Then only the first half need be our
project, although we may still want to seed many planets that
were formed after the DPists had terminated their project.

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

[the above kept in, in lieu of posting it at the end]

> > PS I'll be going on a posting break starting late Friday and extending
> > until Monday March 19. This coincides with my university's spring break.
> > So if we don't have much interaction these next two days, I hope you
> > will still be around on the week of the 19th.
>
> For me it is fine, I write only couple posts per week anyway.

Well, I do hope you will see these four replies to your post, and
have helpful comments in reply to at least one of them.

I close this series with a link to another thread on which we
discussed DP a while ago:

https://groups.google.com/d/msg/talk.origins/88-9d0VSvG0/nQwkm4ruLAAJ
Message-ID: <58c1dea9-adad-4199...@googlegroups.com>
Subject: Re: Misconceptions about my directed panspermia (DP) hypothesis
Date: Wed, 13 Apr 2016 11:03:22 -0700 (PDT)

[Ernest Major]

On 08/03/2018 21:42, Peter Nyikos wrote:
> Martin Harran is in the same boat. Confronted with the complete
> inability of even the best minds to figure out an evolutionary
> pathway, even a hypothetical one, that could culminate in Hox genes,
> all he can do is regurgitate a claim that this is all just an argument
> from personal incredulity.

I haven't seen any "design" argument about HOX genes that is more than
an argument from incredulity.

However, while we shouldn't expect it to be easy to identify a detailed
evolutionary path to HOX genes - over time evolution erases history, an
outline doesn't seem that difficult.

It is to the advantage of an organism to regulate transcription of its
genome so that it doesn't waste energy producing proteins that have no
use in its current environment. This is especially true of prokaryotes.

Consequently organisms have DNA binding proteins (10% of human genes
produce DNA binding proteins) which regulate metabolism and the cell
cycle. Given the existence of DNA binding proteins they can be exapted
to regulate other stuff, such as development.

There are several families of DNA binding proteins. (Wikipedia lists 14
of these.) One of these is homeobox proteins. Hox proteins are are
subset of these, and both these and the larger enclosing ANTP family
seem to be phylogenetically restricted to animals (apparently
secondarily absent from sponges and Trichoplax), but other homeobox
families are more widely distributed among eukaryotes - the TALE family
is found in animals, fungi and plants, and might well be universal or
nearly so among eukaryotes.

From these observations it is readily hypothesised that as the
ancestors of animals changed from a colonial habit to an early
multicellular habit with cell-type differention existing or newly
created (by recombination or duplication) homeobox proteins were pressed
into service as regulators of development. The protein marks the
position of cells within the organism this enabling the right
development path to be selected - Hox genes specify position on the
anterior-posterior axis, Dlx genes specify position of the
proximal-distal axis of limbs, Pax genes specify, inter alia, the
portion of the face where eyes develop, and so on. Duplication and
neofunctionalisation of these genes over the course of evolution allow
increasing diversely repertoires of cell types and increasingly
elaborate anatomies.

Most animals have HOX genes. Perhap all animals have ParaHOX genes.
(Some animals have the region of the genome were HOX genes are found,
but no HOX genes - Ghost HOX loci.) The HOX and ParaHOX clusters are
believed to have originated from duplication of an ancestral ProtoHOX
cluster, following by differential loss of duplicate non-HOX genes from
the duplicated regions.

The ANTP (super)family of homeobox proteins contains 14 families in
total, of which Hox proteins are one. Apparently 4 of these are
restricted to bilaterians, which suggests duplication events in the
ancestors of bilaterians. And in general all 14 families would be
expected to have arise by gene duplication.

The origin of ANTP seems to where the trail goes cold. Perhaps evolution
has erased its links with some other older class of homeobox proteins.
Perhaps I haven't found the right Google incantation. Perhaps molecular
biologists haven't yet done the work needed to find its homologs.

--
alias Ernest Major

[Peter Nyikos]

You have interesting ways of burying your head in the sand, Mark.

The day you post actual content of relevance to the real issues
of talk.origins, and leave off dirty debating tactics in disparaging
others, will be the day your cranial interment in brackets above
will start to hold water.

Peter Nyikos

[Peter Nyikos]

On Wednesday, March 21, 2018 at 10:35:04 AM UTC-4, Ernest Major wrote:
> On 08/03/2018 21:42, Peter Nyikos wrote:
> > Martin Harran is in the same boat. Confronted with the complete
> > inability of even the best minds to figure out an evolutionary
> > pathway, even a hypothetical one, that could culminate in Hox genes,
> > all he can do is regurgitate a claim that this is all just an argument
> > from personal incredulity.
>
> I haven't seen any "design" argument about HOX genes that is more than
> an argument from incredulity.

That may be because the ID theorists you have read arguments from are
too much in sympathy with classical creationist nonsense, rather
than sophisticated alternatives like that presented by a widely
read agnostic:

Perhaps there also, among rotting fish heads and blue,
night-burning bog lights, moved the eternal mystery,
the careful finger of God. The increase was not much.
It was two bubbles, two thin-walled little balloons at the
end of the Snout's small brain. The cerebral hemispheres
had appeared.
--Loren Eiseley_The Immense Journey_

The idea is that evolutionary change could have been effected
by judicious "creation" of mutations at key places in earth history.
By that I mean mutations that are just a little like "hopeful monsters"
but not so drastic as to be outside the ability of species on our
level of intelligence.

> However, while we shouldn't expect it to be easy to identify a detailed
> evolutionary path to HOX genes - over time evolution erases history, an
> outline doesn't seem that difficult.

You do provide an outline of sorts below, with lots of good information,
much of it new to me.

Was it you whom I praised on another thread for being
more sophisticated in biochemistry than anyone I've seen
since the unfortunate death of "el cid" and the disappearance of
"Roger Shrubber"? That certainly is the case here, if I remember
correctly.

> It is to the advantage of an organism to regulate transcription of its
> genome so that it doesn't waste energy producing proteins that have no
> use in its current environment. This is especially true of prokaryotes.
>
> Consequently organisms have DNA binding proteins (10% of human genes
> produce DNA binding proteins) which regulate metabolism and the cell
> cycle. Given the existence of DNA binding proteins they can be exapted
> to regulate other stuff, such as development.

DNA binding is a very general concept. Are any of the simpler of these
proteins good candidates for "ancestry" of homeobox proteins?

> There are several families of DNA binding proteins. (Wikipedia lists 14
> of these.) One of these is homeobox proteins. Hox proteins are are
> subset of these, and both these and the larger enclosing ANTP family
> seem to be phylogenetically restricted to animals (apparently
> secondarily absent from sponges and Trichoplax), but other homeobox
> families are more widely distributed among eukaryotes - the TALE family
> is found in animals, fungi and plants, and might well be universal or
> nearly so among eukaryotes.
>
> From these observations it is readily hypothesised that as the
> ancestors of animals changed from a colonial habit to an early
> multicellular habit with cell-type differention existing or newly
> created (by recombination or duplication) homeobox proteins were pressed
> into service as regulators of development.

Very plausible, but the devil is in the details. As I told jillery
on another thread:


As Behe never tired of pointing out, the standard technique
for evolutionary theorists is simply to classify the proteins
that are related to the ones in question and to point to similarities
in the sequences as evidence that they evolved. But the how and why
of it, or scenarios for how it might have happened, are events for
which they haven't gotten to the starting blocks.

The only exception I know of is the wretched "scenario"
Doolittle conjured up for the evolution of the clotting sequence.
Behe took it apart in _Darwin's Black Box_, and was so sucessful
that Doolittle felt compelled to retaliate -- with disastrous results,
as recounted by Behe in the Dover trial.

> The protein marks the
> position of cells within the organism this enabling the right
> development path to be selected - Hox genes specify position on the
> anterior-posterior axis, Dlx genes specify position of the
> proximal-distal axis of limbs, Pax genes specify, inter alia, the
> portion of the face where eyes develop, and so on. Duplication and
> neofunctionalisation of these genes over the course of evolution allow
> increasing diversely repertoires of cell types and increasingly
> elaborate anatomies.

This isn't even as detailed as the scenario Doolittle, perhaps THE
greatest expert on blood clotting, wrote about.

But don't get me wrong: there might be clever scenarios somewhere
out there for this evolution of which you speak. Only, "gene duplication
and subsequent divergence" is not going to cut it unless there
is a good reason why the divergent enzymes should take up the
new roles.

It was brilliantly done for the clotting cascade by Kenneth Miller
and/or Keith Robison [1] and so Behe's criticism was partly answered,
though not his criticism of Doolittle's blunder when he sought to
avenge the ignominy of Behe's critique.

[1] In his Talk.origins Archive FAQ on the clotting cascade. Were
you around in 1995-2000, when Robison was probably THE best authority
on biochemistry posting to talk.origins? I miss him very much.
do you remember Robison from 1995-2000?

> Most animals have HOX genes. Perhap all animals have ParaHOX genes.
> (Some animals have the region of the genome were HOX genes are found,
> but no HOX genes - Ghost HOX loci.) The HOX and ParaHOX clusters are
> believed to have originated from duplication of an ancestral ProtoHOX
> cluster, following by differential loss of duplicate non-HOX genes from
> the duplicated regions.

See above. The key in the clotting cascade was autocatalicity of most
of the factors in the cascade. But that's not true of these genes,
is it?

> The ANTP (super)family of homeobox proteins contains 14 families in
> total, of which Hox proteins are one. Apparently 4 of these are
> restricted to bilaterians, which suggests duplication events in the
> ancestors of bilaterians. And in general all 14 families would be
> expected to have arise by gene duplication.

Here too, where's the magic "silver bullet" that autocatalycity [sp?]
provided?

Got to go now. My ride will soon be waiting for me.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

University of South Carolina
http://people.math.sc.edu/nyikos/

[Öö Tiib]

On Tuesday, 20 March 2018 17:20:03 UTC+2, Peter Nyikos wrote:
> On Friday, March 9, 2018 at 10:10:03 PM UTC-5, Öö Tiib wrote:
> > On Thursday, 8 March 2018 03:40:03 UTC+2, Peter Nyikos wrote:
> > > On Wednesday, March 7, 2018 at 5:35:03 PM UTC-5, Öö Tiib wrote:
> > > > On Wednesday, 7 March 2018 20:10:03 UTC+2, Peter Nyikos wrote:
> > > > > On Sunday, March 4, 2018 at 4:35:04 PM UTC-5, Öö Tiib wrote:

Just cutting pasting some things together ...

> > > > > > In the context of most genomes these would be defective codes to the
> > > > > > point of being incompatible with life.
> > > > > >
> > > > >
> > > > > Where abiogenesis is the issue, the situation is bad enough
> > > > > even without any feedback loops. The primordial genetic code
> > > > > would first have to be stabilized and maintained by non-protein enzymes,
> > > > > probably RNA based ribozymes. But the early precursors of the
> > > > > the protein enzymes would necessarily have less fidelity than the
> > > > > ribozymes themselves. And their clumsy efforts to mimic the
> > > > > match of amino acid to tRNA would result in protocells that
> > > > > are unable to compete effectively with protocells where the
> > > > > process hasn't begun yet. This is the Catch-22 that makes abiogenesis
> > > > > leading to our form of life such a huge puzzle.
> > > >
> > > > What I have read is that the likely pull here is bigger stability of
> > > > most proteins.
> > >
> > > That bigger stability is of big help once fidelity becomes better
> > > than that of the ribozymes that are to be replaced. But until
> > > that point, it could be more of a handicap than an asset.
>
> By "fidelity" I meant a completely consistent way of matching amino acids
> to codons. The AA-synthetases have to be very exacting for this.

I am not sure of that initial fidelity requirement. Shorter amino
acid chains (peptides) with more freedom of variance are widely used
in living cells.

>
> > >
> > > > We don't have ribozyme-based drugs mostly because
> > > > of that. The cell that works only on ribozymes likely needs more resources
> > > > and energy to rejuvenate itself than other using (even few, even
> > > > primitive) proteins. That seems clear advantage.
> > >
> > > Proteins would be present, all right, but the nonproblematic
> > > ones would be the simple, mostly structural proteins. My scenario
> > > envisions a genetic code like ours, which actually does use
> > > a huge ribozyme -- the ribosome. But the AA-synthetases are absolutely
> > > essential to ours as well, and it is them that the Catch-22 hits the
> > > hardest.
> >
> > I am speculating here but it can be that RNA world evolved AA-ribozymes
> > first for building first proteins that were simple.
>
> Yes, that seems unavoidable.
>
>
> > Then there can
> > evolve enough capability to make more complex proteins (for example
> > AA-synthetases) that gradually replaced RNA ensymes (AA-ribozymes)
> > by being more efficient.
>
> Eventually they would become more efficient, but only after their
> fidelity is about as good as that of the AA-ribozymes. But just to
> get to that point requires the overcoming of tremendous odds,
> unless somehow the precursors of the protein AA-synthetases
> can be gainfully employed doing OTHER things along the early
> steps of the way.

I thought that evolution is based on fact that most things are useful
for several purposes and situations. When something is too sub-optimal
for some situation then it splits and specializes until good enough.
It may even lose usefulness for original situation but may gain slight
potential for entirely new situation. So as result it gradually
spreads everywhere and in spontaneous cooperation with others forms
there complex biomes after a while.

> I seriously wonder whether anyone ever thought this far enough through to
> produce a plausible scenario.

It is impossible to figure it out from evidence that we have because
all current AA-ribozymes are synthetic.
LUCA clearly lived long after AA-ribozymes or whatever other
alternatives there were. We only know that there had to be
alternatives otherwise it is chicken and egg issue.

> > > > > Elsewhere on that thread -- with a different Subject: line but
> > > > > still "directly descended" from the OP of the thread shown,
> > > > > I give Casanova a non-supernatural scenario that bypasses
> > > > > this Catch-22. It has to do with "life as we do not know it"
> > > > > in the form of intelligent beings, designing "life as we know it"
> > > > > in the form of microscopic organisms with which it seeds earth
> > > > > from light years away, without ever traveling to earth themselves
> > > > > -- thus avoiding the pejorative description "space aliens."
> > > > >

> > > > > Would you like some details?
> > > >
> > > > It will still only move some of the ribozymes-to-proteins-to-DNA
> > > > steps elsewhere.
>

> Yes, the most difficult ones. The ribozyme-based translation mechanism
> would have a genetic code for churning out some proteins, but key
> enzymes are enormously difficult to "evolve" because of the exacting
> standards for a catalyst with just ONE function out of literally millions.
>
> So they may well have been confined to some simpler structural proteins,
> and the subsequent evolution of this life would depend on cells based
> on ribozymes.

AFAIK lot of proteins can work in more than one role. There is gene
duplication and specialization but if something happens then there is
often some other backup. Most efficient enzymes can catalyze the
reactions in both directions.

> By the way, your phrase "proteins-to-DNA" has to refer to an indirect
> process. What was needed was some kind of enzyme that converts RNA to
> the more stable DNA. The conventional wisdom of biochemists is that
> this was a protein enzyme, but I would guess that this was a ribozyme,
> even if the firmly held belief of "abiogenesis on earth" is correct.

There is likely long chain of steps that we do not know of. The life
could be was simpler than procaryotes for long time on Earth as
well. For example scientists suggest that they have cyanobacteria
fossils that are 3.5 billions years old. Stromatolites do form from
other bacteria and algae now so it could be these formed from something
simpler than cyanobacteria before.

> > > > Likelihood of finding facts to support that is
> > > > even smaller. It can of course be that the original conditions were
> > > > where ribozymes (or some other most simple self-catalyzing
> > > > molecules) are more stable.
>

> Not more stable than protein enzymes, just stable enough to carry
> on the work of the protocell -- that is all that was needed.
> And ribozymes are far from simple -- look at how huge the ribosome is,
> for example.
>
> As for facts: if biochemists had enough financial incentive, they might
> be able to reproduce possible steps in the long road to ribozyme-based
> protocells. As it is, they are stuck in the very early stages of just
> producing RNA itself.

That likely depends on if there will be indications of some practical
applications for processes in such stages. For example if there ever
were biogenic AA-ribozymes then apparently those became obsolete for
earthly life. That does not mean that such can't be of some economic
value in chemistry or the like. If someone finds such potential then
there will be investments too.

> > > > Hard to imagine.
> > > > If we didn't waste all computing power to mine worthless bitcoins
> > > > then we could run more simulations of abiogenesis scenarios with
> > > > more varied conditions.
> > >
> > > Granted, I have nothing to say about these things right now. What
> > > I had in mind was the way intelligent ribozyme-based beings might
> > > get the idea of manufacturing protein enzymes, and by steps design
> > > the first prokaryotes. I also have ideas about how this scenariro
> > > could be supported or falsified. Would you like to hear them?
> >
> > Yes, how to falsify something that may be happened so long time ago
> > that all traces of it are likely erased? Anything that can evolve
> > can be likely manufactured as well.
>

> One means of falsification was already posted back in 2013:
>
> B8: Isn't directed panspermia essentially untestable, thereby removing
> it from the category of science?
>
> It is eminently testable *in principle*, and may also become testable
> in practice if human beings make serious attempts to find out whether
> there is life on other worlds.

We are may be someday capable to make decent search on Mars and
Enceladus, Callisto, Ganymede, Europa, Titan and Venus. Building
colonies on those feels cheaper project than manned trip to
Alpha-Centauri for example and we can find way to use those places
for something or to turn these to more useful.

If we find something that is close enough to our life there then that
would indicate panspermia (still not sure if directed).
However if we find nothing or something too different then that would
not falsify panspermia since that nothing may mean that the conditions
were too harsh for seeds to self-sustain or that panspermists targeted
only few best candidates. Large difference may mean that the panspermists
used seeds of different build for different conditions. Tricky
problem, and currently we have just no knowledge at all.

> http://groups.google.com/group/talk.origins/msg/90027d90c58f7b4c

> > > > > > I would suspect supernatural intervention far more when some (or all) of
> > > > > > above listed "evidences" of "intelligent design theory" were not so.
> > > > >
> > > > > I steer clear of all of them in my ID theory. The earliest beginnings
> > > > > of life ON EARTH is what all my ID hypotheses talk about.
> > > > >
> > > > > None of them involve supernatural beings, or even creatures more
> > > > > intelligent than ourselves.
> > > >
> > > > I believe that if there is something supernatural then it is clearly
> > > > quite passive. Most of our trouble is also clearly anthropogenic and
> > > > worsening as such. Until our problems are solvable then it is
> > > > irresponsible to even hope for anything paranormal.
> > >
> > > But it is responsible to hope that, some day, probes will be sent
> > > to planetary systems circling other stars. Greed might have the
> > > beneficial effect of mining asteroids and increasing many-fold the
> > > gross national product of all countries that do the mining. Then
> > > reaching for the stars might be as fulfilling to the human psyche,
> > > and as easy to sustain, as spectator sports are now.
> > >
> > > One can always hope.
> >
> > The greed does not work yet there. Transportation to space and
> > back is expensive.
>

> Initial outlay will be huge, but it is already taking place and
> has been taking place since before 1968, when the first manned circumlunar
> flight took place. But once it really gets going, the dividends
> can be spectacular.

All it can be. The race for space was mostly ideologically and politically
feed. As of economic usage ... so far we use less hospitable
parts of surface of our planet (oceans, deserts and arctic regions)
next for nothing. Such can be are cheaper to put into beneficial use
than moon is.

> > Level of radiation is deadly high. One will get
> > lethal doze of X-rays with 6 months.
>

> Not if adequately protected. The program may take us into the
> next century before it really gets going. The first stage would
> be to build a base on the moon, underground. Then spaceships
> could be manufactured there, and take off under the far smaller
> lunar gravity. So they could be smaller than the Saturn V, with
> HALF of it payload, as was the case with the lunar modules (LEMs).
>
> Remember the LEM that saved the lives of the Apollo 13 astronauts?
> That was the kind of high drama that I expect to occur from time
> to time during the shift to mining asteroids, and to keep up public
> interest while it is still in need of taxpayer money.

Yes, protection from radiation can be achieved with thick walls.
Thick walls also make the ships big and heavy. It still likely
has lot of entertainment and political value and I myself like
all such efforts. However if economic situation worsens (and it
possibly will quite soon) then the people will oppose it.

> > Also there are psychological
> > problems wit work-force since most people have difficulties to stay
> > happy being in condensed places for extended duration.
> > So the communication- and observation-satellites are worth their
> > value, but with mining and such we are not there yet.
>

> But our grandchildren might live to see the day.
>
> Getting back to the theme of the Catch-22 alternative: what we've
> discussed just now would be the first stages of preparation for
> the grandest project of all. This is the project of probing
> other planetary systems for signs of life, and action in the event that
> no life is ever found.

My opinion is that exploring our solar system and trying to use it
is likely worth doing on any case even if we do not find out origins
of life. It happened very long time ago.

>
> This could be our own project, all of it, unless the hypothesis
> that earth life (and life on many other planets) was the result
> of directed panspermia (DP). Then only the first half need be our
> project, although we may still want to seed many planets that
> were formed after the DPists had terminated their project.

When we see it then we see it. :)
Right now it is likely easier to find people who volunteer to one way
trip to Mars than to find people who volunteer to work in some
underground moon factory of flinging cyanobacteria to other stars.

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

> [the above kept in, in lieu of posting it at the end]
>

> > > PS I'll be going on a posting break starting late Friday and extending
> > > until Monday March 19. This coincides with my university's spring break.
> > > So if we don't have much interaction these next two days, I hope you
> > > will still be around on the week of the 19th.
> >
> > For me it is fine, I write only couple posts per week anyway.
>

[Peter Nyikos]

On Wednesday, March 21, 2018 at 7:40:03 PM UTC-4, Öö Tiib wrote:
> On Tuesday, 20 March 2018 17:20:03 UTC+2, Peter Nyikos wrote:
> > On Friday, March 9, 2018 at 10:10:03 PM UTC-5, Öö Tiib wrote:
> > > On Thursday, 8 March 2018 03:40:03 UTC+2, Peter Nyikos wrote:
> > > > On Wednesday, March 7, 2018 at 5:35:03 PM UTC-5, Öö Tiib wrote:
> > > > > On Wednesday, 7 March 2018 20:10:03 UTC+2, Peter Nyikos wrote:
> > > > > > On Sunday, March 4, 2018 at 4:35:04 PM UTC-5, Öö Tiib wrote:
>
> Just cutting pasting some things together ...

Well done, too. I only have time to reply to one little bit today,
but I'm sure you don't mind waiting for comments on the rest,
spaced out over a week or more.

> > > > > > > In the context of most genomes these would be defective codes to the
> > > > > > > point of being incompatible with life.
> > > > > > >
> > > > > >
> > > > > > Where abiogenesis is the issue, the situation is bad enough
> > > > > > even without any feedback loops. The primordial genetic code
> > > > > > would first have to be stabilized and maintained by non-protein enzymes,
> > > > > > probably RNA based ribozymes. But the early precursors of the
> > > > > > the protein enzymes would necessarily have less fidelity than the
> > > > > > ribozymes themselves. And their clumsy efforts to mimic the
> > > > > > match of amino acid to tRNA would result in protocells that
> > > > > > are unable to compete effectively with protocells where the
> > > > > > process hasn't begun yet. This is the Catch-22 that makes abiogenesis
> > > > > > leading to our form of life such a huge puzzle.
> > > > >
> > > > > What I have read is that the likely pull here is bigger stability of
> > > > > most proteins.
> > > >
> > > > That bigger stability is of big help once fidelity becomes better
> > > > than that of the ribozymes that are to be replaced. But until
> > > > that point, it could be more of a handicap than an asset.
> >
> > By "fidelity" I meant a completely consistent way of matching amino acids
> > to codons. The AA-synthetases have to be very exacting for this.
>
> I am not sure of that initial fidelity requirement. Shorter amino
> acid chains (peptides) with more freedom of variance are widely used
> in living cells.

Initially, the requirements are minimal, because that is the
only way a genetic code could even get going. But once it does,
high fidelity is a *sine qua non*.


<snip of much to be dealt with later>

> > By the way, your phrase "proteins-to-DNA" has to refer to an indirect
> > process. What was needed was some kind of enzyme that converts RNA to
> > the more stable DNA. The conventional wisdom of biochemists is that
> > this was a protein enzyme, but I would guess that this was a ribozyme,
> > even if the firmly held belief of "abiogenesis on earth" is correct.
>
> There is likely long chain of steps that we do not know of. The life
> could be was simpler than procaryotes for long time on Earth as
> well. For example scientists suggest that they have cyanobacteria
> fossils that are 3.5 billions years old.

That may be the conventional wisdom among biologists. FWIW.

> Stromatolites do form from
> other bacteria and algae now so it could be these formed from something
> simpler than cyanobacteria before.

Yes, and I see no reason why these might not have been ribozyme-based
"protocells" able to carry on photosynthesis.

Here is a possible scenario that occurred to me just in the last day.
There may have been an intelligent species of ribozyme-based
creatures living in a globular cluster. As various stars drifted
within less than half a light year of their home planet, they
were able to establish colonies on some of the planets orbiting them,
and so the process multipllied until they were spread throughout
the inhabitable planets of the cluster.

A directed panspermia project, using their analogue of cyanobacteria
at first and then designed protein-based photosynthesizers, could
have been started after the first few colonizations. These
could easily have gone all through the cluster, in anticipation
of the future spreading via chance close encounters.

Thus, in the later stages of the process, millions of years later,
the terraforming might have advanced to the point where the colonizers
could set up protective domes and collect the oxygen easily,
replenishing the supply within each dome from outside.


Now, globular clusters orbit outside the plane of the galaxy,
with passages though the disk on the order of once every 100
thousand years. In each such passage, they might have
sent out directed panspermia probes to not-too-distant planets,
say on the order of 100 light years or less. On one such
passage, roughly 1 gigayear ago, they might have seeded earth
with prokaryotes and primitive eukaryotes that quickly took over
the planet from their own protocells.

Then, perhaps around 600 million years ago, there may have
been a "closer encounter" in which they were able to send
primitive animals with homeobox genes along with other advanced life
forms. The first successful ones among these were the Vendobionta
and other enigmatic Ediacaran organisms. These died out as
predatory animals took over and evolved to the point of the
great Cambrian explosion.


<snip long remainder, to be dealt with next week>

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

[erik simpson]

On Friday, March 23, 2018 at 7:40:04 AM UTC-7, Peter Nyikos wrote:
> <...>

Planetary systems in globular clusters are quite problematic. The very high
density of stars in the centers of these systems would perturb planetary orbits
to such a degree that the orbits would be unstable on the order of 10^8 years.
The generally low "metallicity" in most halo objects might also be a barrier
to any technological advancement, for lack of raw materials, even if the orbital
problems could be alleviated.

Imaginative scifi, but probably not imaginative enough.

[John Harshman]

On 3/21/18 3:00 PM, Peter Nyikos wrote:
> On Wednesday, March 21, 2018 at 10:35:04 AM UTC-4, Ernest Major wrote:
>> On 08/03/2018 21:42, Peter Nyikos wrote:
>>> Martin Harran is in the same boat. Confronted with the complete
>>> inability of even the best minds to figure out an evolutionary
>>> pathway, even a hypothetical one, that could culminate in Hox genes,
>>> all he can do is regurgitate a claim that this is all just an argument
>>> from personal incredulity.
>>
>> I haven't seen any "design" argument about HOX genes that is more than
>> an argument from incredulity.
>
> That may be because the ID theorists you have read arguments from are
> too much in sympathy with classical creationist nonsense, rather
> than sophisticated alternatives like that presented by a widely
> read agnostic:
>
> Perhaps there also, among rotting fish heads and blue,
> night-burning bog lights, moved the eternal mystery,
> the careful finger of God. The increase was not much.
> It was two bubbles, two thin-walled little balloons at the
> end of the Snout's small brain. The cerebral hemispheres
> had appeared.
> --Loren Eiseley_The Immense Journey_

That's a sophisticated alternative? That's a single tossed-off sentence
that explains nothing and leads nowhere. Not only that, you're only 10%
willing to believe that such a thing would even be possible.

> The idea is that evolutionary change could have been effected
> by judicious "creation" of mutations at key places in earth history.
> By that I mean mutations that are just a little like "hopeful monsters"
> but not so drastic as to be outside the ability of species on our
> level of intelligence.

Yes, that's one of Behe's notions. But a sufficiently sophisticated
careful finger is indistinguishable from random mutation and selection,
so how could this ever be tested?

I suppose a somewhat less sophisticated careful finger could be
testable, i.e. if you could find a set of simultaneous mutations that
are outside the bounds of probability for random mutation. But can you
find any such thing in Hox evolution?

>> However, while we shouldn't expect it to be easy to identify a detailed
>> evolutionary path to HOX genes - over time evolution erases history, an
>> outline doesn't seem that difficult.
>
> You do provide an outline of sorts below, with lots of good information,
> much of it new to me.
>
> Was it you whom I praised on another thread for being
> more sophisticated in biochemistry than anyone I've seen
> since the unfortunate death of "el cid" and the disappearance of
> "Roger Shrubber"? That certainly is the case here, if I remember
> correctly.
>
>
>> It is to the advantage of an organism to regulate transcription of its
>> genome so that it doesn't waste energy producing proteins that have no
>> use in its current environment. This is especially true of prokaryotes.
>>
>> Consequently organisms have DNA binding proteins (10% of human genes
>> produce DNA binding proteins) which regulate metabolism and the cell
>> cycle. Given the existence of DNA binding proteins they can be exapted
>> to regulate other stuff, such as development.
>
> DNA binding is a very general concept. Are any of the simpler of these
> proteins good candidates for "ancestry" of homeobox proteins?

It's not simpler proteins you need to look for; there's no reason to
suppose that the ancestor of the Hox cluster was any simpler. The
complexity of Hox lies in its many divergent copies. And of course no
current protein is the ancestor of any other; all homologous proteins
are equally old. But the ancestral condition can be inferred using a
tree of homologous sequences.

>> There are several families of DNA binding proteins. (Wikipedia lists 14
>> of these.) One of these is homeobox proteins. Hox proteins are are
>> subset of these, and both these and the larger enclosing ANTP family
>> seem to be phylogenetically restricted to animals (apparently
>> secondarily absent from sponges and Trichoplax), but other homeobox
>> families are more widely distributed among eukaryotes - the TALE family
>> is found in animals, fungi and plants, and might well be universal or
>> nearly so among eukaryotes.
>>
>> From these observations it is readily hypothesised that as the
>> ancestors of animals changed from a colonial habit to an early
>> multicellular habit with cell-type differention existing or newly
>> created (by recombination or duplication) homeobox proteins were pressed
>> into service as regulators of development.
>
> Very plausible, but the devil is in the details. As I told jillery
> on another thread:
>
>
> As Behe never tired of pointing out, the standard technique
> for evolutionary theorists is simply to classify the proteins
> that are related to the ones in question and to point to similarities
> in the sequences as evidence that they evolved. But the how and why
> of it, or scenarios for how it might have happened, are events for
> which they haven't gotten to the starting blocks.

Time for you to get specific. The how and why of what events, exactly,
in the long history and prehistory of Hox genes? And are you attempting
to discount phylogenetic evidence here, as Behe would seem to be doing?

> The only exception I know of is the wretched "scenario"
> Doolittle conjured up for the evolution of the clotting sequence.
> Behe took it apart in _Darwin's Black Box_, and was so sucessful
> that Doolittle felt compelled to retaliate -- with disastrous results,
> as recounted by Behe in the Dover trial.

Let's ignore the digression into clotting factors for now, shall we?

>> The protein marks the
>> position of cells within the organism this enabling the right
>> development path to be selected - Hox genes specify position on the
>> anterior-posterior axis, Dlx genes specify position of the
>> proximal-distal axis of limbs, Pax genes specify, inter alia, the
>> portion of the face where eyes develop, and so on. Duplication and
>> neofunctionalisation of these genes over the course of evolution allow
>> increasing diversely repertoires of cell types and increasingly
>> elaborate anatomies.
>
> This isn't even as detailed as the scenario Doolittle, perhaps THE
> greatest expert on blood clotting, wrote about.

Please stop trying to introduce blood clotting.

> But don't get me wrong: there might be clever scenarios somewhere
> out there for this evolution of which you speak. Only, "gene duplication
> and subsequent divergence" is not going to cut it unless there
> is a good reason why the divergent enzymes should take up the
> new roles.

First off, they aren't enzymes; they catalyze no reactions. They're
transcription factors. Now which divergent transcription factors are you
referring to? One can't come up with more than a general statement about
the whole system, which you reject. You need to pick a few specific events.

> It was brilliantly done for the clotting cascade by Kenneth Miller
> and/or Keith Robison [1] and so Behe's criticism was partly answered,
> though not his criticism of Doolittle's blunder when he sought to
> avenge the ignominy of Behe's critique.
>
> [1] In his Talk.origins Archive FAQ on the clotting cascade. Were
> you around in 1995-2000, when Robison was probably THE best authority
> on biochemistry posting to talk.origins? I miss him very much.
> do you remember Robison from 1995-2000?

Again, reference to the clotting cascade is a pointless digression,
which you should resist.

>> Most animals have HOX genes. Perhap all animals have ParaHOX genes.
>> (Some animals have the region of the genome were HOX genes are found,
>> but no HOX genes - Ghost HOX loci.) The HOX and ParaHOX clusters are
>> believed to have originated from duplication of an ancestral ProtoHOX
>> cluster, following by differential loss of duplicate non-HOX genes from
>> the duplicated regions.
>
> See above. The key in the clotting cascade was autocatalicity of most
> of the factors in the cascade. But that's not true of these genes,
> is it?

Correct. Forget the clotting cascade.

>> The ANTP (super)family of homeobox proteins contains 14 families in
>> total, of which Hox proteins are one. Apparently 4 of these are
>> restricted to bilaterians, which suggests duplication events in the
>> ancestors of bilaterians. And in general all 14 families would be
>> expected to have arise by gene duplication.
>
> Here too, where's the magic "silver bullet" that autocatalycity [sp?]
> provided?

Trying to figure out what you mean by "magic silver bullet". Not
succeeding. I can't tell what you're asking for, unless it's an account
of the exact list of mutations required for every step in the evolution
of the human (presumably) Hox genes, their reasons for happening, and
their selective advantages at the time. Is that it?

[Peter Nyikos]

John Harshman finally ceases his importunities to be spoon-fed,
and makes a stab at the deep conversations I've had with others
on this threads.

Unfortunately, his thinking is rusty from long near-disuse.

On Friday, March 23, 2018 at 1:20:03 PM UTC-4, John Harshman wrote:
> On 3/21/18 3:00 PM, Peter Nyikos wrote:
> > On Wednesday, March 21, 2018 at 10:35:04 AM UTC-4, Ernest Major wrote:
> >> On 08/03/2018 21:42, Peter Nyikos wrote:
> >>> Martin Harran is in the same boat. Confronted with the complete
> >>> inability of even the best minds to figure out an evolutionary
> >>> pathway, even a hypothetical one, that could culminate in Hox genes,
> >>> all he can do is regurgitate a claim that this is all just an argument
> >>> from personal incredulity.
> >>
> >> I haven't seen any "design" argument about HOX genes that is more than
> >> an argument from incredulity.
> >
> > That may be because the ID theorists you have read arguments from are
> > too much in sympathy with classical creationist nonsense, rather
> > than sophisticated alternatives like that presented by a widely
> > read agnostic:
> >
> > Perhaps there also, among rotting fish heads and blue,
> > night-burning bog lights, moved the eternal mystery,
> > the careful finger of God. The increase was not much.
> > It was two bubbles, two thin-walled little balloons at the
> > end of the Snout's small brain. The cerebral hemispheres
> > had appeared.
> > --Loren Eiseley_The Immense Journey_
>
> That's a sophisticated alternative?

Yes, when compared to the usual ID-creationist [that's NOT redundant]
suggestion that every new animal was poofed into existence. It's too
bad that this suggestion is what keeps the rank and file creationists
[not too different from the rank and file anti-ID types who are
in the talk.origins majority] happy and contributing.

>That's a single tossed-off sentence
> that explains nothing and leads nowhere.

That "leads nowhere" is your philistine attitude towards a book
that you SHOULD have read in your youth, had you as interested
in the history of life on earth as I was in my youth.

Had you read it, you might have appreciated what Eiseley wrote
just before the passage above, right in the same paragraph,
underscoring the monumental difference those "little bubbles"
may have made:

Mammalian insects perhaps we should have been -- solid-brained,
our neurones wired for mechanical responses, our lives running
out with the perfection of beautiful, intricate, and mindless clocks.
-- page 52 of 1957 edition, Vintage books.

Hmmm... that last description closely fits some of the polemicists
to whom you have shackled yourself in talk.origins.

> Not only that, you're only 10%
> willing to believe that such a thing would even be possible.

Need I remind you of the many times you've showered me with
contempt for thinking that anyone is interested in what *I*
think about this or that?

> > The idea is that evolutionary change could have been effected
> > by judicious "creation" of mutations at key places in earth history.
> > By that I mean mutations that are just a little like "hopeful monsters"
> > but not so drastic as to be outside the ability of species on our
> > level of intelligence.
>
> Yes, that's one of Behe's notions. But a sufficiently sophisticated
> careful finger is indistinguishable from random mutation and selection,

That is as superficial a sentence as "a sufficiently advanced
technology is indistinguishable from magic" -- which, interestingly
enough, works in the opposite direction from yours. YOURS is saying,
"the workings of a sufficiently advanced technology are indistinguishable
from mindless mutations, working in sequence." in a way to gladden the heart
of Alan Kleinman, rather than working so powerfully as to defeat 100-drug
cocktails.

> so how could this ever be tested?

To do you credit, you start groping for an answer, "rediscovering"
something I told you on the other thread:

> I suppose a somewhat less sophisticated careful finger could be
> testable, i.e. if you could find a set of simultaneous mutations that
> are outside the bounds of probability for random mutation. But can you
> find any such thing in Hox evolution?

The real question is: can you AVOID running into such an obstacle
in Hox evolution? So far, nobody has any hint of a path to a
YES answer.

These aren't just ordinary proteins, or run of the mill enzymes,
you know.

> >> However, while we shouldn't expect it to be easy to identify a detailed
> >> evolutionary path to HOX genes - over time evolution erases history, an
> >> outline doesn't seem that difficult.
> >
> > You do provide an outline of sorts below, with lots of good information,
> > much of it new to me.
> >
> > Was it you whom I praised on another thread for being
> > more sophisticated in biochemistry than anyone I've seen
> > since the unfortunate death of "el cid" and the disappearance of
> > "Roger Shrubber"? That certainly is the case here, if I remember
> > correctly.
> >
> >
> >> It is to the advantage of an organism to regulate transcription of its
> >> genome so that it doesn't waste energy producing proteins that have no
> >> use in its current environment. This is especially true of prokaryotes.
> >>
> >> Consequently organisms have DNA binding proteins (10% of human genes
> >> produce DNA binding proteins) which regulate metabolism and the cell
> >> cycle. Given the existence of DNA binding proteins they can be exapted
> >> to regulate other stuff, such as development.
> >
> > DNA binding is a very general concept. Are any of the simpler of these
> > proteins good candidates for "ancestry" of homeobox proteins?
>
> It's not simpler proteins you need to look for; there's no reason to
> suppose that the ancestor of the Hox cluster was any simpler.

And so, you kick the can further down the road in a particularly
inept way.

> The
> complexity of Hox lies in its many divergent copies.

Alleles of the same gene.

Really, John, you HAVE to get back to simpler proteins or you are in
the same boat as someone "explaining" anthropoid evolution leading
to humans by focusing on the step from *Homo sapiens neanderthalensis*
to *Homo sapiens sapiens.*

> And of course no
> current protein is the ancestor of any other; all homologous proteins
> are equally old. But the ancestral condition can be inferred using a
> tree of homologous sequences.

The ancestral gene of all those alleles.

OK, let's throw in the Denisovians and those "hobbits" of Java
and the owner of that Swanscombe skullcap.
Do you reckon their common ancestor with the Neanderthalers
is still *Homo sapiens* or only *Homo erectus*.


Really, John, you need to shuck off this tunnel vision
and the mental laziness that comes from years of being spoon-fed.
You need to go back to thinking like an intelligent professional
biologist.


Remainder deleted, to be replied to on Monday, if time permits.


Peter Nyikos
Professor of Mathematics -- standard disclaimer--

[John Harshman]

On 3/23/18 5:32 PM, Peter Nyikos wrote:
> John Harshman finally ceases his importunities to be spoon-fed,
> and makes a stab at the deep conversations I've had with others
> on this threads.
>
> Unfortunately, his thinking is rusty from long near-disuse.

Ask yourself: was that particular introductory bit of trash talk
necessary? When you have to declare the situation up front, perhaps it
isn't as evident as you suppose.

Again, more gratuitous trash talk. I don't see the sophistication,
except that it's calculated to be less falsifiable.

>> That's a single tossed-off sentence
>> that explains nothing and leads nowhere.
>
> That "leads nowhere" is your philistine attitude towards a book
> that you SHOULD have read in your youth, had you as interested
> in the history of life on earth as I was in my youth.

Not talking about the book. I'm talking about the single tossed-off
sentence.

> Had you read it, you might have appreciated what Eiseley wrote
> just before the passage above, right in the same paragraph,
> underscoring the monumental difference those "little bubbles"
> may have made:
>
> Mammalian insects perhaps we should have been -- solid-brained,
> our neurones wired for mechanical responses, our lives running
> out with the perfection of beautiful, intricate, and mindless clocks.
> -- page 52 of 1957 edition, Vintage books.
>
> Hmmm... that last description closely fits some of the polemicists
> to whom you have shackled yourself in talk.origins.

So all that was just a setup for more trash talk? Predictable,
unfortunately. Are you trying to convince me not to keep trying to have
a discussion with you?

>> Not only that, you're only 10%
>> willing to believe that such a thing would even be possible.
>
> Need I remind you of the many times you've showered me with
> contempt for thinking that anyone is interested in what *I*
> think about this or that?

There you go again, bringing up past wrongs.

>>> The idea is that evolutionary change could have been effected
>>> by judicious "creation" of mutations at key places in earth history.
>>> By that I mean mutations that are just a little like "hopeful monsters"
>>> but not so drastic as to be outside the ability of species on our
>>> level of intelligence.
>>
>> Yes, that's one of Behe's notions. But a sufficiently sophisticated
>> careful finger is indistinguishable from random mutation and selection,
>
> That is as superficial a sentence as "a sufficiently advanced
> technology is indistinguishable from magic" -- which, interestingly
> enough, works in the opposite direction from yours. YOURS is saying,
> "the workings of a sufficiently advanced technology are indistinguishable
> from mindless mutations, working in sequence." in a way to gladden the heart
> of Alan Kleinman, rather than working so powerfully as to defeat 100-drug
> cocktails.

About ready to give up on this.

>> so how could this ever be tested?
>
> To do you credit, you start groping for an answer, "rediscovering"
> something I told you on the other thread:
>
>> I suppose a somewhat less sophisticated careful finger could be
>> testable, i.e. if you could find a set of simultaneous mutations that
>> are outside the bounds of probability for random mutation. But can you
>> find any such thing in Hox evolution?
>
> The real question is: can you AVOID running into such an obstacle
> in Hox evolution? So far, nobody has any hint of a path to a
> YES answer.
>
> These aren't just ordinary proteins, or run of the mill enzymes,
> you know.

They aren't enzymes at all. But in what way are they not ordinary proteins?

>>>> However, while we shouldn't expect it to be easy to identify a detailed
>>>> evolutionary path to HOX genes - over time evolution erases history, an
>>>> outline doesn't seem that difficult.
>>>
>>> You do provide an outline of sorts below, with lots of good information,
>>> much of it new to me.
>>>
>>> Was it you whom I praised on another thread for being
>>> more sophisticated in biochemistry than anyone I've seen
>>> since the unfortunate death of "el cid" and the disappearance of
>>> "Roger Shrubber"? That certainly is the case here, if I remember
>>> correctly.
>>>
>>>
>>>> It is to the advantage of an organism to regulate transcription of its
>>>> genome so that it doesn't waste energy producing proteins that have no
>>>> use in its current environment. This is especially true of prokaryotes.
>>>>
>>>> Consequently organisms have DNA binding proteins (10% of human genes
>>>> produce DNA binding proteins) which regulate metabolism and the cell
>>>> cycle. Given the existence of DNA binding proteins they can be exapted
>>>> to regulate other stuff, such as development.
>>>
>>> DNA binding is a very general concept. Are any of the simpler of these
>>> proteins good candidates for "ancestry" of homeobox proteins?
>>
>> It's not simpler proteins you need to look for; there's no reason to
>> suppose that the ancestor of the Hox cluster was any simpler.
>
> And so, you kick the can further down the road in a particularly
> inept way.

The question is what bit of evolution you think we're talking about
here? The ancestor of all Hox genes? The ancestor of all homeobox genes?
How far back are we talking about?

>> The
>> complexity of Hox lies in its many divergent copies.
>
> Alleles of the same gene.

No, no, no. Apparently you know nothing about the subject. They're
separate loci. Several loci in a cluster, several clusters in (some)
genomes. While I'm sure there is allelic variation in Hox genes, that
isn't at all what we're talking about.

> Really, John, you HAVE to get back to simpler proteins or you are in
> the same boat as someone "explaining" anthropoid evolution leading
> to humans by focusing on the step from *Homo sapiens neanderthalensis*
> to *Homo sapiens sapiens.*

Again, you need to clarify what step in Hox evolution you want to talk
about. But apparently you don't know enough about Hox genes to know what
steps there are to be discussed.

>> And of course no
>> current protein is the ancestor of any other; all homologous proteins
>> are equally old. But the ancestral condition can be inferred using a
>> tree of homologous sequences.
>
> The ancestral gene of all those alleles.

Again, not alleles. Separate loci. You will note that, according to
Ernest, Hox genes are nested within the AntP family. One could
reconstruct that ancestral gene. It would not be simpler than a Hox
gene. These are all just transcription factors. Their operation is
fairly simple. The complexity is in the network.

> OK, let's throw in the Denisovians and those "hobbits" of Java
> and the owner of that Swanscombe skullcap.
> Do you reckon their common ancestor with the Neanderthalers
> is still *Homo sapiens* or only *Homo erectus*.

I refuse to participate in an irrelevant digression.

> Really, John, you need to shuck off this tunnel vision
> and the mental laziness that comes from years of being spoon-fed.
> You need to go back to thinking like an intelligent professional
> biologist.

More trash talk, and in fact most of your post was trash talk with very
little substantive content. Keep this up and I'll probably stop
responding to you.

[Ernest Major]

I don't know what meaning Eiseley intended - a cursory google didn't
turn up a copy of the source. For all I know he, like Dawkins, was
cursed with a gift for metaphor. For all I know he was no more a
creationist than Einstein. But I don't see on what criteria you identify
this as more sophisticated. In some senses ID is more sophisticated - it
says that the designer isn't necessarily God, nudge, nudge, wink, wink.

But you present the interpretation that is on the cusp between theistic
evolutionism and progressive creationism. You don't come out and say
that natural processes couldn't have produced the same mutations - the
creationst end of theistic evolution says that evolution could have
produced a biota of equivalent complexity, but God intervened to select
a particular path among the stochastic choices, while theistic
evolutionist end of progressive creationism claims that natural
processes are incapable of producing the observed results.

I don't know how to describe the former (an argument from credulity? -
"God could have done it"), but is unfalsifiable and a religious rather
than a scientific position. I would appeal to Occam's Razor to discount
it. (When I included interuniversal transfer among a list of imaginable
origins of life of earth you commented that was going too far, so you do
accept that principle that we don't need to consider all ideas
seriously.) The latter is in principle testable - it predicts a bias in
mutations - but in practice it can be made resistant to falsification by
making the bias vanishingly small, or by banishing it to the past (now
we have the pinnacle of creation it's not needed any more), but it's
just as much an argument from incredulity as the appeal to Hox genes as
evidence of design.

In either case, one wonders why God didn't choose to or was unable to
create an evolutionary process that didn't require intervention.

(Note that as a species we're probably better at producing gross changes
than subtle ones. For example we could knock out a plant homeobox gene
to produce a flower with a grossly different structure. What we do more
often is move traits from one species to another - for example replacing
a crop 5-enolpyruvoyl-shikimate-3-phosphate synthetase with one from
Agrobacterium - or introducing insulin synthesis into a bacterium, or
extending a plant secondary metabolite chain to produce a new pigment.)

>
>> However, while we shouldn't expect it to be easy to identify a detailed
>> evolutionary path to HOX genes - over time evolution erases history, an
>> outline doesn't seem that difficult.
>
> You do provide an outline of sorts below, with lots of good information,
> much of it new to me.
>
> Was it you whom I praised on another thread for being
> more sophisticated in biochemistry than anyone I've seen
> since the unfortunate death of "el cid" and the disappearance of
> "Roger Shrubber"? That certainly is the case here, if I remember
> correctly.
>

I'd guess Bill Rogers knows more than I do. My knowledge of biochemistry
is sketchy, especially on the metabolic side.

>
>> It is to the advantage of an organism to regulate transcription of its
>> genome so that it doesn't waste energy producing proteins that have no
>> use in its current environment. This is especially true of prokaryotes.
>>
>> Consequently organisms have DNA binding proteins (10% of human genes
>> produce DNA binding proteins) which regulate metabolism and the cell
>> cycle. Given the existence of DNA binding proteins they can be exapted
>> to regulate other stuff, such as development.
>
> DNA binding is a very general concept. Are any of the simpler of these
> proteins good candidates for "ancestry" of homeobox proteins?

I don't know. I don't even know that homeobox proteins are more complex
than other transcription factors. Homeobox proteins vary greatly in size
- at least from 73 (mouse Hopx) to 3703 (human ZFHX3) amino acid
residues. HOX proteins are towards the lower end of this range - 200 to
400 amino acids. If I understand correctly they lack signal sensing
domains, which makes them simpler in some ways that some other
transcription factors.

>
>
>> There are several families of DNA binding proteins. (Wikipedia lists 14
>> of these.) One of these is homeobox proteins. Hox proteins are are
>> subset of these, and both these and the larger enclosing ANTP family
>> seem to be phylogenetically restricted to animals (apparently
>> secondarily absent from sponges and Trichoplax), but other homeobox
>> families are more widely distributed among eukaryotes - the TALE family
>> is found in animals, fungi and plants, and might well be universal or
>> nearly so among eukaryotes.
>>
>> From these observations it is readily hypothesised that as the
>> ancestors of animals changed from a colonial habit to an early
>> multicellular habit with cell-type differention existing or newly
>> created (by recombination or duplication) homeobox proteins were pressed
>> into service as regulators of development.
>
> Very plausible, but the devil is in the details. As I told jillery
> on another thread:
>
>
> As Behe never tired of pointing out, the standard technique
> for evolutionary theorists is simply to classify the proteins
> that are related to the ones in question and to point to similarities
> in the sequences as evidence that they evolved. But the how and why
> of it, or scenarios for how it might have happened, are events for
> which they haven't gotten to the starting blocks.
>

That's an argument from ignorance. Creationists have a bad habit of
ignoring the evidence that we have in favour of the evidence that we
don't have and shouldn't expect to have - given sufficient time
evolution erases its tracks and we can't expect to have the evidence to
provide a blow by blow account of the origin of ancient features of the
genome. Why are you arguing like a creationist?

> The only exception I know of is the wretched "scenario"
> Doolittle conjured up for the evolution of the clotting sequence.
> Behe took it apart in _Darwin's Black Box_, and was so sucessful
> that Doolittle felt compelled to retaliate -- with disastrous results,
> as recounted by Behe in the Dover trial.
>
>
>> The protein marks the
>> position of cells within the organism this enabling the right
>> development path to be selected - Hox genes specify position on the
>> anterior-posterior axis, Dlx genes specify position of the
>> proximal-distal axis of limbs, Pax genes specify, inter alia, the
>> portion of the face where eyes develop, and so on. Duplication and
>> neofunctionalisation of these genes over the course of evolution allow
>> increasing diversely repertoires of cell types and increasingly
>> elaborate anatomies.
>
> This isn't even as detailed as the scenario Doolittle, perhaps THE
> greatest expert on blood clotting, wrote about.
>
> But don't get me wrong: there might be clever scenarios somewhere
> out there for this evolution of which you speak. Only, "gene duplication
> and subsequent divergence" is not going to cut it unless there
> is a good reason why the divergent enzymes should take up the
> new roles.

Put those goalposts down. Your original claim was "the complete

inability of even the best minds to figure out an evolutionary

pathway, even a hypothetical one, that could culminate in Hox genes".

Gene duplication is a known process.

There are 4 possible fates for duplicate genes - deletion,
pseudogenisation (and eventual deletion), subfunctionalisation and
neofunctionalisation. All of these are known processes. I'm most familar
with the literature on tetraploid cottons - cottons as an economically
important crop are extensively studied - but there's plenty of papers on
the topic elsewhere.

In the context of homeobox genes a hypothetical example of
subfunctionalisation would be duplication of a gene expressed in feet,
and specialisation so that one copy was expressed in the forefeet and
the other in the hindfeet. This potentiates adaptive divergence in the
structure of forefeet and hindfeet (eventually hands and feet).

An hypothetical example of neofunctionalisation would be duplication of
a gene expressed in the tail, and the use of one copy to control
development of a thagomiser.

>
> It was brilliantly done for the clotting cascade by Kenneth Miller
> and/or Keith Robison [1] and so Behe's criticism was partly answered,
> though not his criticism of Doolittle's blunder when he sought to
> avenge the ignominy of Behe's critique.
>
> [1] In his Talk.origins Archive FAQ on the clotting cascade. Were
> you around in 1995-2000, when Robison was probably THE best authority

> on biochemistry posting to talk.origins? I miss him very much.7

> do you remember Robison from 1995-2000?
>
>
>> Most animals have HOX genes. Perhap all animals have ParaHOX genes.
>> (Some animals have the region of the genome were HOX genes are found,
>> but no HOX genes - Ghost HOX loci.) The HOX and ParaHOX clusters are
>> believed to have originated from duplication of an ancestral ProtoHOX
>> cluster, following by differential loss of duplicate non-HOX genes from
>> the duplicated regions.
>
> See above. The key in the clotting cascade was autocatalicity of most
> of the factors in the cascade. But that's not true of these genes,
> is it?
>

That's a red herring.

Clotting factors are enzymes - they catalyze chemical reactions. But not
all proteins are enzymes. Some are structural proteins (conceived
broadly) such as crystallins and flagellins, some are chemical
messengers (e.g. insulin), some are transporters (e.g. haemoglobin), and
others are transcription factors*. Transcription factors bind to DNA and
control which genes are active (transcribed). Differences between which
genes are active in a cell determine cell types, and positional control
on where cell types are produced and interactions between them result in
tissue types and anatomical structure. Much of the functionality of the
system is bound up not in the sequence of the transcription factors, but
in the relationship of the binding sites to genes encoding structural
and metabolic proteins. Developmentally active transcription factors
don't directly specify anatomy - they specify a location with the
organism, and it's the action of the downstream genes that build a
particular anatomy. As a generality the richer the set of
developmentally active transcription factors the greater the variety of
cell types and anatomical structures that can be generated - which is
seen in the expansion of (different) homeobox gene families in
(different) multicellular clades.

* this is not an exhaustive classification of protein functions.

>
>> The ANTP (super)family of homeobox proteins contains 14 families in
>> total, of which Hox proteins are one. Apparently 4 of these are
>> restricted to bilaterians, which suggests duplication events in the
>> ancestors of bilaterians. And in general all 14 families would be
>> expected to have arise by gene duplication.
>
> Here too, where's the magic "silver bullet" that autocatalycity [sp?]
> provided?
>
> Got to go now. My ride will soon be waiting for me.
>
> Peter Nyikos
> Professor, Department of Math. -- standard disclaimer --
> University of South Carolina
> http://people.math.sc.edu/nyikos/
>
>
>> The origin of ANTP seems to where the trail goes cold. Perhaps evolution
>> has erased its links with some other older class of homeobox proteins.
>> Perhaps I haven't found the right Google incantation. Perhaps molecular
>> biologists haven't yet done the work needed to find its homologs.
>>
>> --
>> alias Ernest Major
>

--
alias Ernest Major

[Bob Casanova]

On Fri, 23 Mar 2018 18:27:27 -0700, the following appeared
in talk.origins, posted by John Harshman
<jhar...@pacbell.net>:

>On 3/23/18 5:32 PM, Peter Nyikos wrote:
>> John Harshman finally ceases his importunities to be spoon-fed,
>> and makes a stab at the deep conversations I've had with others
>> on this threads.
>>
>> Unfortunately, his thinking is rusty from long near-disuse.
>
>Ask yourself: was that particular introductory bit of trash talk
>necessary? When you have to declare the situation up front, perhaps it
>isn't as evident as you suppose.

Apparently he's been taking the same classes as Tony and
Allie, and personal attacks and ad hominems are all they
teach.

--

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

[Peter Nyikos]

On Saturday, March 24, 2018 at 2:05:03 PM UTC-4, Bob Casanova wrote:
> On Fri, 23 Mar 2018 18:27:27 -0700, the following appeared
> in talk.origins, posted by John Harshman
> <jhar...@pacbell.net>:
>
> >On 3/23/18 5:32 PM, Peter Nyikos wrote:
> >> John Harshman finally ceases his importunities to be spoon-fed,
> >> and makes a stab at the deep conversations I've had with others
> >> on this threads.
> >>
> >> Unfortunately, his thinking is rusty from long near-disuse.
> >
> >Ask yourself: was that particular introductory bit of trash talk
> >necessary? When you have to declare the situation up front, perhaps it
> >isn't as evident as you suppose.
>
> Apparently he's been taking the same classes as Tony and
> Allie, and personal attacks and ad hominems are all they
> teach.

If you were to actually READ what I wrote, and what Harshman
puts emphasis on below, you would know that you are describing
John, not me. John and Tony [who's "Allie"?] probably
did learn their tricks from the "ancestral garbage taxon" of
polemical internet forums.

And that applies to you too. You are evidently too incompetent
to argue against what I wrote, and are reduced to behaving
like a mere camp follower of, and cheerleader for, Harshman.

> 'Eureka!' but [nothing that I, Bob Casanova,
> have ever uttered].

Fixed it for you. By the way, your frequent benefactee
jillery pretended that this well-known Usenet convention
"fixed it for you" was a dishonest forgery on my part,
and I expect you to maintain a "see no evil, hear no evil,
speak no evil" attitude towards this insincere crap by
jillery as long as you both shall post.

The hypocrisy of that expected inaction would be made evident by the
fact that in times past, you indulged in that convention
from time to time, even rubbing it in at least once
with "You're welcome." But jillery is the greater hypocrite,
by pretending these uses by you never existed.

Peter Nyikos

[Peter Nyikos]

I think it is pretty well established that he was an agnostic.
Not that it really matters. The quotation stands on its own
merits -- an eloquent alternative to both mindless evolution
and poofing animals into existence. The latter practically
defines "creationist" in the way it is used by the vast
majority in talk.origins, AFAIK. Of course that includes
both OECs and YECs and near-YECs like Martinez who seems
amenable to a 100 million year old earth, but not much more.

> But I don't see on what criteria you identify
> this as more sophisticated. In some senses ID is more sophisticated - it
> says that the designer isn't necessarily God, nudge, nudge, wink, wink.

Sorry, I don't indulge in "nudge, nudge, wink, wink." My ID comes
in two very explicit forms: (1) purely naturalistic in the case of
directed panspermia (DP) with a confidence approaching 50% in that
hypothesis, and (2) exemplified by that quote from Eiseley with a
confidence less than 10%. IOW, (2) a possibility, but not one
into which I put much stock.

> But you present the interpretation that is on the cusp between theistic
> evolutionism and progressive creationism.

Yes, "theistic" evolutionism is more aptly named "neo-deistic"
evolutionism: the attitude that God created the universe
and then had a hands-off policy until historical Biblical
times. ["Historical" means roughly the time of Abraham, as
opposed to prehistorical events like whatever the Noahide flood
actually referred to originally.]

And your word "present" is very well chosen. I am laying the
hypothesis out for consideration, without having much confidence
in its truth. But I am passionately interested in the truth,
and so I try to cover all reasonable bases.

> You don't come out and say
> that natural processes couldn't have produced the same mutations - the
> creationst end of theistic evolution says that evolution could have
> produced a biota of equivalent complexity, but God intervened to select
> a particular path among the stochastic choices, while theistic
> evolutionist end of progressive creationism claims that natural
> processes are incapable of producing the observed results.

I think like a scientist *qua* scientist about these things, and hence am
in suspended judgment about them. I do not confuse the currently
accepted methodology of science with the thinking of flesh
and blood scientists.

> I don't know how to describe the former (an argument from credulity? -
> "God could have done it"), but is unfalsifiable and a religious rather
> than a scientific position.

So is something that seems to be the be-all and end-all of the
majority of anti-ID participants:

Darwin of the Gaps

This is the default, one-size-fits-all, totally unfalsifiable
naturalistic explanation for any and all biological phenomena:

"Well, it's natural selection, y'know. The __________ that did/could/
are __________ had a survival advantage over the ones that didn't/
couldn't/weren't and so they are the ones we see today."

Fortunately, you yourself have a lot more going for you than this
analogue of "god of the gaps."

> I would appeal to Occam's Razor to discount
> it. (When I included interuniversal transfer among a list of imaginable
> origins of life of earth you commented that was going too far, so you do
> accept that principle that we don't need to consider all ideas
> seriously.)

I try to stay within the bounds of our current understanding
of physics. Even the "careful finger of God" could be mimicked
by extraterrestrials on a level of intelligence comparable
to ours, but the possibilities are just too speculative.

I tried to do the best I could in my latest reply to Öö Tiib,
but my imaginative scenario turned out to be another case of
a "beautiful theory killed by a brutal gang of cold facts"
about globular clusters. I found that out over the weekend
by reading Chapter 14 in a great book by planetary scientist
John L. Lewis, _Worlds_Without_End.

> The latter is in principle testable - it predicts a bias in
> mutations - but in practice it can be made resistant to falsification by
> making the bias vanishingly small, or by banishing it to the past (now
> we have the pinnacle of creation it's not needed any more), but it's
> just as much an argument from incredulity as the appeal to Hox genes as
> evidence of design.

Whereas Darwin of the Gaps is an argument from personal credulity.

> In either case, one wonders why God didn't choose to or was unable to
> create an evolutionary process that didn't require intervention.

Because a God of that magnitude strains even the possibilities
of a multiverse with infinitely many physical universes. I could
never arrive at a 10% confidence -- or even a 0.01% confidence --
in a hypothesis that rested in such a God. The various
forms of the Ontological Argument for an infinite God are just
too fallacious.

> (Note that as a species we're probably better at producing gross changes
> than subtle ones. For example we could knock out a plant homeobox gene
> to produce a flower with a grossly different structure.

Plants are one thing, animals are another. Scroll down to the
bottom of the following blog, and read the last few posts,
about the difficulties of tampering with the geomes of mice
to give them the ability to fly with bat-like wings.

http://scienceblogs.com/tetrapodzoology/2011/03/05/visualising-protobats/

> What we do more
> often is move traits from one species to another - for example replacing
> a crop 5-enolpyruvoyl-shikimate-3-phosphate synthetase with one from
> Agrobacterium - or introducing insulin synthesis into a bacterium, or
> extending a plant secondary metabolite chain to produce a new pigment.)

Child's play compared to a mice-to-batlike-rodents change.


Remainder deleted, to be replied to later, perhaps only tomorrow.
I have back-to-back classes to teach in less than an hour.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

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

[Bob Casanova]

On Mon, 26 Mar 2018 06:36:16 -0700 (PDT), the following
appeared in talk.origins, posted by Peter Nyikos
<nyi...@bellsouth.net>:

>On Saturday, March 24, 2018 at 2:05:03 PM UTC-4, Bob Casanova wrote:
>> On Fri, 23 Mar 2018 18:27:27 -0700, the following appeared
>> in talk.origins, posted by John Harshman
>> <jhar...@pacbell.net>:
>>
>> >On 3/23/18 5:32 PM, Peter Nyikos wrote:
>> >> John Harshman finally ceases his importunities to be spoon-fed,
>> >> and makes a stab at the deep conversations I've had with others
>> >> on this threads.
>> >>
>> >> Unfortunately, his thinking is rusty from long near-disuse.
>> >
>> >Ask yourself: was that particular introductory bit of trash talk
>> >necessary? When you have to declare the situation up front, perhaps it
>> >isn't as evident as you suppose.
>>
>> Apparently he's been taking the same classes as Tony and
>> Allie, and personal attacks and ad hominems are all they
>> teach.
>
>If you were to actually READ what I wrote, and what Harshman
>puts emphasis on below, you would know that you are describing
>John, not me.

I did; I commented on part of its content, shown above. And
I disagree with your self-serving assessment of the balance.

> John and Tony [who's "Allie"?] probably
>did learn their tricks from the "ancestral garbage taxon" of
>polemical internet forums.
>
>And that applies to you too. You are evidently too incompetent
>to argue against what I wrote, and are reduced to behaving
>like a mere camp follower of, and cheerleader for, Harshman.

See what I wrote above about the classes you've taken?
Thanks for confirming.

And "Allie" is The Good DrDr.

<snip to yet another idiotic comment on my sig...>

>> Bob C.
>>
>> "The most exciting phrase to hear in science,
>> the one that heralds new discoveries, is not
>> 'Eureka!' but [nothing that I, Bob Casanova,
>> have ever uttered].
>
>Fixed it for you.

Tell Asimov; I'm sure he'd agree with you. Not.

> By the way, your frequent benefactee
>jillery pretended that this well-known Usenet convention
>"fixed it for you" was a dishonest forgery on my part,
>and I expect you to maintain a "see no evil, hear no evil,
>speak no evil" attitude towards this insincere crap by
>jillery as long as you both shall post.
>
>The hypocrisy of that expected inaction would be made evident by the
>fact that in times past, you indulged in that convention
>from time to time, even rubbing it in at least once
>with "You're welcome." But jillery is the greater hypocrite,
>by pretending these uses by you never existed.

Thanks for the additional confirmation, even though it's
redundant. HTH, and HAND.

--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not

[jillery]

On Mon, 26 Mar 2018 06:36:16 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> continued to ejaculate his repetitive
irrelevant spew from his puckered sphincter:

Is anybody surprised.

<snip your irrelevant spew>

>Fixed it for you. By the way, your frequent benefactee
>jillery pretended that this well-known Usenet convention
>"fixed it for you" was a dishonest forgery on my part,
>and I expect you to maintain a "see no evil, hear no evil,
>speak no evil" attitude towards this insincere crap by
>jillery as long as you both shall post.

Of course, you don't cite where Jillery did any such thing. It's
almost certain you never will, because if you did, it would show the
context, that Jillery used it as an example to refute your lying spam,
that Jillery forged other posters' replies.

Your comments above are just another example of your Big Lies against
me, and shows your dishonesty and insincere crap you ejaculate from
your puckered sphincter.

--
I disapprove of what you say, but I will defend to the death your right to say it.

Evelyn Beatrice Hall
Attributed to Voltaire

[Peter Nyikos]

On Friday, March 23, 2018 at 9:30:02 PM UTC-4, John Harshman wrote:
> On 3/23/18 5:32 PM, Peter Nyikos wrote:
> > John Harshman finally ceases his importunities to be spoon-fed,
> > and makes a stab at the deep conversations I've had with others
> > on this threads.
> >
> > Unfortunately, his thinking is rusty from long near-disuse.

For really deep thinking, you are substituting polemic, beginning with
the following schoolmarmish comment:

> Ask yourself: was that particular introductory bit of trash talk
> necessary?

"trash talk" is your Martinez-style term for personal comments
made by *myself*.

On the other hand, all your perennial innuendo [1] about me being a closet
creationist, your Martinez-style definition of paranoia in
your frequent, perennial, never credibly supported accusations of paranoia,
and your paying lip service to a definition of paranoid/paranoia
which NEVER supports your accusations, are NOT "trash talk" in your
self-righteous mind, are they?

[1] Your "see no evil, hear no evil, speak no evil"
behavior in the wake of Hemidactylus becoming relentlessly
explicit in accusing me of creationism, speaks volumes.

> When you have to declare the situation up front, perhaps it
> isn't as evident as you suppose.

Hackneyed polemic, with its gratuitous use of "have to".

You are referring to the bracketed part, I presume; you are quite happy with
what I wrote about creationists, aren't you? After all, you are quite
happy with Hemidactylus ripping into me with trumped-up charges of
me being a creationist.

> I don't see the sophistication,
> except that it's calculated to be less falsifiable.

There is nothing "calculated" about it in that sense,
but I don't expect YOU to acknowledge that, even with
my reply to Ernest Major earlier today to look at.

After all, the innuendo that I am a closet creationist is just
too juicy for you to give up.

> >> That's a single tossed-off sentence
> >> that explains nothing and leads nowhere.
> >
> > That "leads nowhere" is your philistine attitude towards a book
> > that you SHOULD have read in your youth, had you as interested
> > in the history of life on earth as I was in my youth.
>
> Not talking about the book. I'm talking about the single tossed-off
> sentence.

Now that I've given you a bit of the context below, why are you not
revising your assessment?

> > Had you read it, you might have appreciated what Eiseley wrote
> > just before the passage above, right in the same paragraph,
> > underscoring the monumental difference those "little bubbles"
> > may have made:
> >
> > Mammalian insects perhaps we should have been -- solid-brained,
> > our neurones wired for mechanical responses, our lives running
> > out with the perfection of beautiful, intricate, and mindless clocks.
> > -- page 52 of 1957 edition, Vintage books.
> >
> > Hmmm... that last description closely fits some of the polemicists
> > to whom you have shackled yourself in talk.origins.
>
> So all that was just a setup for more trash talk?

You'd love it if that were so, wouldn't you? That way,
you could justify ignoring the solidly on-topic passage that
you disdainfully dismiss with "all that was just...?"


> Predictable,
> unfortunately.

It is your reaction, letting the meaty stuff that demolishes your
"leads nowhere" go like water off a duck's back,
that is the really predictable thing going on here.

> Are you trying to convince me not to keep trying to have
> a discussion with you?

No, I'm giving you a dose of your own medicine that you have
been feeding me for 7+ years, replacing adult give-and-take
with flamebait like

That's a single tossed-off sentence
that explains nothing and leads nowhere.

The "leads nowhere" is you goading me to do 500+ line posts
in which I reveal huge quantities of what an open ended
theme like the Eiseley quote could lead to.

Either that, or you lied when you claimed you weren't
talking about the book. Normal adult give-and-take would
have you realize that the book may well have lots more to say
that is relevant, thus keeping you from going off half-cocked with
crap like "leads nowhere."

> >> Not only that, you're only 10%
> >> willing to believe that such a thing would even be possible.
> >
> > Need I remind you of the many times you've showered me with
> > contempt for thinking that anyone is interested in what *I*
> > think about this or that?
>
> There you go again, bringing up past wrongs.

...which you are too self-righteous to think of as "wrongs,"
aren't you?

My point was that I am interested in the truth, and your
"Not only that" suggests that you aren't interested
in the truth, but only in what *I* think is *most* likely.

If you want to know my attitude towards that 10%, read
my reply to Ernest Major this morning.

> >>> The idea is that evolutionary change could have been effected
> >>> by judicious "creation" of mutations at key places in earth history.
> >>> By that I mean mutations that are just a little like "hopeful monsters"
> >>> but not so drastic as to be outside the ability of species on our
> >>> level of intelligence.
> >>
> >> Yes, that's one of Behe's notions. But a sufficiently sophisticated
> >> careful finger is indistinguishable from random mutation and selection,
> >
> > That is as superficial a sentence as "a sufficiently advanced
> > technology is indistinguishable from magic" -- which, interestingly
> > enough, works in the opposite direction from yours. YOURS is saying,
> > "the workings of a sufficiently advanced technology are indistinguishable
> > from mindless mutations, working in sequence." in a way to gladden the heart
> > of Alan Kleinman, rather than working so powerfully as to defeat 100-drug
> > cocktails.
>
> About ready to give up on this.

You are seizing on my mention of someone as an excuse to ignore
the point I am making about your highly superficial comment.

That comment was grasping at the straw of an extreme to which I
am NOT going. You are too rusty, it seems, to deal with
what I have actually written.

> >> so how could this ever be tested?
> >
> > To do you credit, you start groping for an answer, "rediscovering"
> > something I told you on the other thread:
> >
> >> I suppose a somewhat less sophisticated careful finger could be
> >> testable, i.e. if you could find a set of simultaneous mutations that
> >> are outside the bounds of probability for random mutation. But can you
> >> find any such thing in Hox evolution?
> >
> > The real question is: can you AVOID running into such an obstacle
> > in Hox evolution? So far, nobody has any hint of a path to a
> > YES answer.
> >
> > These aren't just ordinary proteins, or run of the mill enzymes,
> > you know.
>
> They aren't enzymes at all.

They catalyze more general events than single chemical reactions, agreed.

> But in what way are they not ordinary proteins?

By the tremendous impact they have on the anatomy of organisms.

And you've ducked the question. You are stalling, as usual, not just
here but in the rest of your post, ignoring the need for something
a little closer to a REAL explanation of HOW such immensely
powerful control genes could have come from humble beginnings.

The REAL explanation would be something that nobody can be expected
to come up with in centuries: a path that relies only on
changes of alleles within populations. Fortunately for you,
not even Behe is asking for THAT detailed a scenario.

But you aren't even looking for anything like a scenario
at all.


Remainder deleted, to be replied to tomorrow or later.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

U. of South Carolina in Columbia
http://www.math.sc.edu/~nyikos/

[John Harshman]

On 3/26/18 12:22 PM, Peter Nyikos wrote:
> On Friday, March 23, 2018 at 9:30:02 PM UTC-4, John Harshman wrote:
>> On 3/23/18 5:32 PM, Peter Nyikos wrote:
>>> John Harshman finally ceases his importunities to be spoon-fed,
>>> and makes a stab at the deep conversations I've had with others
>>> on this threads.
>>>
>>> Unfortunately, his thinking is rusty from long near-disuse.
>
>
> For really deep thinking, you are substituting polemic, beginning with
> the following schoolmarmish comment:
>
>> Ask yourself: was that particular introductory bit of trash talk
>> necessary?
>
> "trash talk" is your Martinez-style term for personal comments
> made by *myself*.

No, it's my term for trash talk.

> On the other hand, all your perennial innuendo [1] about me being a closet
> creationist, your Martinez-style definition of paranoia in
> your frequent, perennial, never credibly supported accusations of paranoia,
> and your paying lip service to a definition of paranoid/paranoia
> which NEVER supports your accusations, are NOT "trash talk" in your
> self-righteous mind, are they?

I think you are confusing me with someone else in the first case, but I
do accuse you of paranoia. I'm not the only one, though. Do you think
there's a conspiracy to accuse you of paranoia?

> [1] Your "see no evil, hear no evil, speak no evil"
> behavior in the wake of Hemidactylus becoming relentlessly
> explicit in accusing me of creationism, speaks volumes.

What, because I don't get in the way of your fights with him?

>> When you have to declare the situation up front, perhaps it
>> isn't as evident as you suppose.
>
> Hackneyed polemic, with its gratuitous use of "have to".

I think you may not be able to help yourself, so that's one sense. The
other sense is that nobody would come to the "correct" conclusion
without your guidance.

Well, it's true about creationists, isn't it? It's one of their defining
characteristics.

> After all, you are quite
> happy with Hemidactylus ripping into me with trumped-up charges of
> me being a creationist.

I have no interest one way or another in Hemidactylus ripping into you.

>> I don't see the sophistication,
>> except that it's calculated to be less falsifiable.
>
> There is nothing "calculated" about it in that sense,
> but I don't expect YOU to acknowledge that, even with
> my reply to Ernest Major earlier today to look at.
>
> After all, the innuendo that I am a closet creationist is just
> too juicy for you to give up.

Again, you seem to be confusing me with someone else.

>>>> That's a single tossed-off sentence
>>>> that explains nothing and leads nowhere.
>>>
>>> That "leads nowhere" is your philistine attitude towards a book
>>> that you SHOULD have read in your youth, had you as interested
>>> in the history of life on earth as I was in my youth.
>>
>> Not talking about the book. I'm talking about the single tossed-off
>> sentence.
>
> Now that I've given you a bit of the context below, why are you not
> revising your assessment?

No. I don't see anything relevant there.

>>> Had you read it, you might have appreciated what Eiseley wrote
>>> just before the passage above, right in the same paragraph,
>>> underscoring the monumental difference those "little bubbles"
>>> may have made:
>>>
>>> Mammalian insects perhaps we should have been -- solid-brained,
>>> our neurones wired for mechanical responses, our lives running
>>> out with the perfection of beautiful, intricate, and mindless clocks.
>>> -- page 52 of 1957 edition, Vintage books.
>>>
>>> Hmmm... that last description closely fits some of the polemicists
>>> to whom you have shackled yourself in talk.origins.
>>
>> So all that was just a setup for more trash talk?
>
> You'd love it if that were so, wouldn't you? That way,
> you could justify ignoring the solidly on-topic passage that
> you disdainfully dismiss with "all that was just...?"

You must explain what is relevant about that solidly on-topic passage.
Perhaps your point would be clearer if you explained it rather than
ending with trash talk.

>> Predictable,
>> unfortunately.
>
> It is your reaction, letting the meaty stuff that demolishes your
> "leads nowhere" go like water off a duck's back,
> that is the really predictable thing going on here.

What meaty stuff are you referring to? I truly do not know.

>> Are you trying to convince me not to keep trying to have
>> a discussion with you?
>
> No, I'm giving you a dose of your own medicine that you have
> been feeding me for 7+ years, replacing adult give-and-take
> with flamebait like
>
> That's a single tossed-off sentence
> that explains nothing and leads nowhere.
>
> The "leads nowhere" is you goading me to do 500+ line posts
> in which I reveal huge quantities of what an open ended
> theme like the Eiseley quote could lead to.

Truly, I am not attempting to goad you into anything. This is another
example of paranoia, attributing ulterior motives without evidence. I
expressed my opinion of your quote. You don't like that opnion. Why?

> Either that, or you lied when you claimed you weren't
> talking about the book. Normal adult give-and-take would
> have you realize that the book may well have lots more to say
> that is relevant, thus keeping you from going off half-cocked with
> crap like "leads nowhere."

It might, and you could easily show me if it did. So far, not.

>>>> Not only that, you're only 10%
>>>> willing to believe that such a thing would even be possible.
>>>
>>> Need I remind you of the many times you've showered me with
>>> contempt for thinking that anyone is interested in what *I*
>>> think about this or that?
>>
>> There you go again, bringing up past wrongs.
>
> ...which you are too self-righteous to think of as "wrongs,"
> aren't you?

Well, I don't think of them as wrongs, but I don't accept your
characterizations.

> My point was that I am interested in the truth, and your
> "Not only that" suggests that you aren't interested
> in the truth, but only in what *I* think is *most* likely.

That's a lot to get from three words that, on the surface, seem to say
no such thing.

> If you want to know my attitude towards that 10%, read
> my reply to Ernest Major this morning.

It seems I am always doomed never to get a direct reply; I always have
to read something you wrote to someone else, somewhere else.

>>>>> The idea is that evolutionary change could have been effected
>>>>> by judicious "creation" of mutations at key places in earth history.
>>>>> By that I mean mutations that are just a little like "hopeful monsters"
>>>>> but not so drastic as to be outside the ability of species on our
>>>>> level of intelligence.
>>>>
>>>> Yes, that's one of Behe's notions. But a sufficiently sophisticated
>>>> careful finger is indistinguishable from random mutation and selection,
>>>
>>> That is as superficial a sentence as "a sufficiently advanced
>>> technology is indistinguishable from magic" -- which, interestingly
>>> enough, works in the opposite direction from yours. YOURS is saying,
>>> "the workings of a sufficiently advanced technology are indistinguishable
>>> from mindless mutations, working in sequence." in a way to gladden the heart
>>> of Alan Kleinman, rather than working so powerfully as to defeat 100-drug
>>> cocktails.
>>
>> About ready to give up on this.
>
> You are seizing on my mention of someone as an excuse to ignore
> the point I am making about your highly superficial comment.
>
> That comment was grasping at the straw of an extreme to which I
> am NOT going. You are too rusty, it seems, to deal with
> what I have actually written.

Perhaps if you tried making your points directly, by argument and
evidence, it would be harder to miss them. What was your point? As far
as I can tell, it was merely an attack on my sentence because it
resembled another sentence once said by somebody else (Arthur C. Clarke,
as it happens).

>>>> so how could this ever be tested?
>>>
>>> To do you credit, you start groping for an answer, "rediscovering"
>>> something I told you on the other thread:
>>>
>>>> I suppose a somewhat less sophisticated careful finger could be
>>>> testable, i.e. if you could find a set of simultaneous mutations that
>>>> are outside the bounds of probability for random mutation. But can you
>>>> find any such thing in Hox evolution?
>>>
>>> The real question is: can you AVOID running into such an obstacle
>>> in Hox evolution? So far, nobody has any hint of a path to a
>>> YES answer.
>>>
>>> These aren't just ordinary proteins, or run of the mill enzymes,
>>> you know.
>>
>> They aren't enzymes at all.
>
> They catalyze more general events than single chemical reactions, agreed.

They don't catalyze anything. Stop digging. Do you know what catalysis is?

>> But in what way are they not ordinary proteins?
>
> By the tremendous impact they have on the anatomy of organisms.

How does that prevent them from being ordinary proteins?

> And you've ducked the question. You are stalling, as usual, not just
> here but in the rest of your post, ignoring the need for something
> a little closer to a REAL explanation of HOW such immensely
> powerful control genes could have come from humble beginnings.

I'm not ducking any questions. I don't understand what you're trying to
ask. Why should there be a need for multiple simultaneous mutations in
Hox evolution? What part of Hox evolution are we even discussing here?

> The REAL explanation would be something that nobody can be expected
> to come up with in centuries: a path that relies only on
> changes of alleles within populations. Fortunately for you,
> not even Behe is asking for THAT detailed a scenario.

Why bring it up?

> But you aren't even looking for anything like a scenario
> at all.

How do you know what I'm looking for? What are you looking for? Have you
ever in fact looked at any of the literature on Hox evolution?

[erik simpson]

On Monday, March 26, 2018 at 12:25:04 PM UTC-7, Peter Nyikos wrote:
> On Friday, March 23, 2018 at 9:30:02 PM UTC-4, John Harshman wrote:
> > On 3/23/18 5:32 PM, Peter Nyikos wrote:

> <snip bickering complaints>

Nothing seems to get your goat more than being accused of "closet creationism".
It would help if you didn't spend so much time and bile on details that you
think are quite unlikely (~10%), yet you demand be seriously considered as
"sophisticated" challenges to "woefully inadequate" evolutionary explanations.
"Goddidit" or "aliensdidit" aren't clearly different in their level of
sophistication, and the poetic pronoucements of The Agnostic Loren Eisley aren't
really pertinent either.

[*Hemidactylus*]

erik simpson <eastsi...@gmail.com> wrote:
> On Monday, March 26, 2018 at 12:25:04 PM UTC-7, Peter Nyikos wrote:
>> On Friday, March 23, 2018 at 9:30:02 PM UTC-4, John Harshman wrote:
>>> On 3/23/18 5:32 PM, Peter Nyikos wrote:
>> <snip bickering complaints>
>
> Nothing seems to get your goat more than being accused of "closet creationism".
> It would help if you didn't spend so much time and bile on details that you
> think are quite unlikely (~10%), yet you demand be seriously considered as
> "sophisticated" challenges to "woefully inadequate" evolutionary explanations.
> "Goddidit" or "aliensdidit" aren't clearly different in their level of
> sophistication, and the poetic pronoucements of The Agnostic Loren Eisley aren't
> really pertinent either.
>

Keeps him from actually making any detailed factual point about how the
scientific understanding of homeodomain evolution is falling short in his
reputable estimation. We couldn’t have that sort of expectation now could
we. So bickering works wonders to cloud the issue.

[Peter Nyikos]

On Monday, March 26, 2018 at 2:30:03 PM UTC-4, jillery posted
her usual dishonest mangling of the attribution line to me:

> On Mon, 26 Mar 2018 06:36:16 -0700 (PDT), Peter Nyikos
> <nyi...@bellsouth.net> continued to ejaculate his repetitive
> irrelevant spew from his puckered sphincter:
>
> Is anybody surprised.
>
> <snip your irrelevant spew>

The above crap by you is a sure sign that we have entered the
equivalent of what is called "garbage time" in basketball.

This is when the team that is behind does deliberate fouls in
the hope that the fouled opponent misses one of the free throws
[preferably the first] and the fouling team gets the rebound.

>
> >Fixed it for you. By the way, your frequent benefactee
> >jillery pretended that this well-known Usenet convention
> >"fixed it for you" was a dishonest forgery on my part,
> >and I expect you to maintain a "see no evil, hear no evil,
> >speak no evil" attitude towards this insincere crap by
> >jillery as long as you both shall post.

Casanova made a typically amoral comment in reply to the
above. He loves to act as though dishonest and hypocrisy
and cowardice were mere trifles compared to my rudeness
in pointing out behavior that exemplifies these things.

You, on the other hand, make a pretense of caring about
dishonesty below.

>
> Of course, you don't cite where Jillery did any such thing.

Of course, I don't document everything I say on the spot.
Neither do you; in fact, I believe that I document
several times as many things on the spot as you do --
or indeed anyone else in talk.origins does -- in reply to me,
and to others against whom you get into tiffs [recent example
recounted below].

> It's
> almost certain you never will, because if you did, it would show the
> context, that Jillery used it as an example to refute your lying spam,

"to refute your" should be replaced by "to post TbBA [Truth by Blatant
Assertion] that you are guilty of". And if you keep digging yourself
in deeper, I will document the WHOLE context, not just the
context in the isolated post where you used "forgery" without
scare quotes.

> that Jillery forged other posters' replies.

Like Erik Simpson, you dishonestly place the apostrophe
after the s instead of before it.

I dropped that word long ago, except in scare quotes ("forgery")
while posting accurate descriptions of what a dishonest thing
you had done to Martin Harran [2].

And it never was a lie, because I am not a stickler for
using the word "forgery" in an exclusively legal context [3].
But several people [was your benefactor Casanova one of them?]
were such sticklers that I decided I might as well
compromise as described above -- the truth is damning enough.

[2] I see you and Martin were engaged in a typical tiff of
yours over the weekend, but both of you were confining
yourselves to generic insults without either one producing
any justification for them. Very much like your behavior here.

[3] Similarly, I refer to lots of false allegations about me
as "libel" even though they aren't legally actionable
due to the nature of talk.origins.

> Your comments above are just another example of your Big Lies

You implicitly admitted that you had accused me of forgery,
without scare quotes. So "Big Lies" in your vocabulary
apparently mean "Inconvenient Truths About Jillery."

> against
> me, and shows your dishonesty and insincere crap you ejaculate from
> your puckered sphincter.

The dishonesty and insincere crap you ejaculate from your puckered
sphincter would disqualify you from complaining about my alleged
crap, were you not addicted to pathological double standards about
alleged "disqualifications."

Peter Nyikos

[Bob Casanova]

On Tue, 27 Mar 2018 09:28:07 -0700 (PDT), the following
appeared in talk.origins, posted by Peter Nyikos
<nyi...@bellsouth.net>:

>On Monday, March 26, 2018 at 2:30:03 PM UTC-4, jillery posted
>her usual dishonest mangling of the attribution line to me:
>
>> On Mon, 26 Mar 2018 06:36:16 -0700 (PDT), Peter Nyikos
>> <nyi...@bellsouth.net> continued to ejaculate his repetitive
>> irrelevant spew from his puckered sphincter:
>>
>> Is anybody surprised.
>>
>> <snip your irrelevant spew>
>
>The above crap by you is a sure sign that we have entered the
>equivalent of what is called "garbage time" in basketball.
>
>This is when the team that is behind does deliberate fouls in
>the hope that the fouled opponent misses one of the free throws
>[preferably the first] and the fouling team gets the rebound.
>
>
>>
>> >Fixed it for you. By the way, your frequent benefactee
>> >jillery pretended that this well-known Usenet convention
>> >"fixed it for you" was a dishonest forgery on my part,
>> >and I expect you to maintain a "see no evil, hear no evil,
>> >speak no evil" attitude towards this insincere crap by
>> >jillery as long as you both shall post.
>
>Casanova made a typically amoral comment in reply to the
>above.

Was it "Tell Asimov; I'm sure he'd agree with you. Not.",
which was my sole comment in response to your idiotic
revision of my sig? Exactly how is that "immoral"; just the
fact that I refused to bow down to the Great and Wonderful
OZ (aka Peter)?

If not, it should be no problem for you to quote that
"typically amoral comment". Do it here:

[Balance (unbalance?) of Peter's rant left intact as
evidence that my original comment...

"Apparently he's been taking the same classes as Tony and
Allie, and personal attacks and ad hominems are all they
teach."

....was pretty close to the mark. And I probably should have
added something about "developing paranoia"]

--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not

[John Harshman]

"Developing"?

[Peter Nyikos]

On Monday, March 26, 2018 at 6:55:02 PM UTC-4, *Hemidactylus* wrote:
> erik simpson <eastsi...@gmail.com> wrote:
> > On Monday, March 26, 2018 at 12:25:04 PM UTC-7, Peter Nyikos wrote:
> >> On Friday, March 23, 2018 at 9:30:02 PM UTC-4, John Harshman wrote:
> >>> On 3/23/18 5:32 PM, Peter Nyikos wrote:
> >> <snip bickering complaints>
> >
> > Nothing seems to get your goat more than being accused of "closet creationism".

Not even being accused of being habitually dishonest, insincere,
cowardly and hypocritical, is anywhere near as potentially
devastating to one's reputation here in talk.origins as
THAT accusation. Hemidactylus and Simpson both know that,
so the former keeps on making it, while the latter is indulging
in sleazy innuendo to that effect:

> > It would help if you didn't spend so much time and bile on details that you
> > think are quite unlikely (~10%), yet you demand be seriously considered as
> > "sophisticated" challenges to "woefully inadequate" evolutionary explanations.
> > "Goddidit" or "aliensdidit" aren't clearly different in their level of
> > sophistication, and the poetic pronoucements of The Agnostic Loren Eisley aren't
> > really pertinent either.

Typically, Hemi, you ignore the fact that these things are
quite plausible to someone who actually believes in a creator
(except for the sleazily worded "aliensdidit"), and so it is only
Simpson's militant atheism that allows him to indulge in
such trash talk.

But then, you are even more militantly atheistic than Simpson,
so what he wrote must seem completely natural to you.

> Keeps him from actually making any detailed factual point about how the
> scientific understanding of homeodomain evolution is falling short in his
> reputable estimation.

No details are needed in addition to the fact that nobody,
even the experts, have no incentive to even *begin* the
mapping out of an evolutionary scenario of how homeodomain
evolution got started from simple beginnings.

I made that point before on this thread, and you are such
an inept coward, you need the buffering of a post by
Simpson to even broach the subject -- a post where Simpson
snipped the latest of the places where I made the point.

> We couldn’t have that sort of expectation now could
> we.

Since I've already made the point, you are only clouding
the issue with this sneakily obsolete comment.

> So bickering works wonders to cloud the issue.

You took the words out of my mouth, you miscreant. ;-)

Peter Nyikos

[Öö Tiib]

That ribozyme-based intelligent life is interesting hypothesis.
Some of it can be falsifiable. For example if it can be possible?
Is so low mutation rate as in DNA world possible to show in RNA world?
Very low mutation rate is crucial otherwise most of organisms would
die because of damage from mutations during embryonic development. So no
trillion-cell multi-cellularities and so no intelligent lifeforms in
principle.

> As various stars drifted
> within less than half a light year of their home planet, they
> were able to establish colonies on some of the planets orbiting them,
> and so the process multipllied until they were spread throughout
> the inhabitable planets of the cluster.

That is fiction ... how to falsify? Half a light year is 4.7 trillions of
kilometers. For example it is bit less than the number of liters of
crude oil that we consume in one year with whole planet. I would be
super happy if someone proved to me that we survive at least
until single other self-sustainable manned colony on single other rock
within our own plentifully rich solar system has been built.

> A directed panspermia project, using their analogue of cyanobacteria
> at first and then designed protein-based photosynthesizers, could
> have been started after the first few colonizations. These
> could easily have gone all through the cluster, in anticipation
> of the future spreading via chance close encounters.
>
> Thus, in the later stages of the process, millions of years later,
> the terraforming might have advanced to the point where the colonizers
> could set up protective domes and collect the oxygen easily,
> replenishing the supply within each dome from outside.
>
>
> Now, globular clusters orbit outside the plane of the galaxy,
> with passages though the disk on the order of once every 100
> thousand years. In each such passage, they might have
> sent out directed panspermia probes to not-too-distant planets,
> say on the order of 100 light years or less. On one such
> passage, roughly 1 gigayear ago, they might have seeded earth
> with prokaryotes and primitive eukaryotes that quickly took over
> the planet from their own protocells.
>
> Then, perhaps around 600 million years ago, there may have
> been a "closer encounter" in which they were able to send
> primitive animals with homeobox genes along with other advanced life
> forms. The first successful ones among these were the Vendobionta
> and other enigmatic Ediacaran organisms. These died out as
> predatory animals took over and evolved to the point of the
> great Cambrian explosion.

Civilizations that last million of years are also fiction that is hard to
falsify. We have as lot of evidence of such as of magnetic monomers.
Aren't only Japanese managed to keep their empire for more than
thousand years? AFAIK all others have quit being anything as far
younger. Also, we have never before had so high skills in so lot of
so lethal ways of ruining it for whole planet.

[Peter Nyikos]

On Saturday, March 24, 2018 at 9:55:03 AM UTC-4, Ernest Major wrote:
> On 21/03/2018 22:00, Peter Nyikos wrote:
> > On Wednesday, March 21, 2018 at 10:35:04 AM UTC-4, Ernest Major wrote:

Picking up where I left off in reply to this post yesterday:

> >
> >> However, while we shouldn't expect it to be easy to identify a detailed
> >> evolutionary path to HOX genes - over time evolution erases history, an
> >> outline doesn't seem that difficult.
> >
> > You do provide an outline of sorts below, with lots of good information,
> > much of it new to me.
> >
> > Was it you whom I praised on another thread for being
> > more sophisticated in biochemistry than anyone I've seen
> > since the unfortunate death of "el cid" and the disappearance of
> > "Roger Shrubber"? That certainly is the case here, if I remember
> > correctly.
> >
>
> I'd guess Bill Rogers knows more than I do. My knowledge of biochemistry
> is sketchy, especially on the metabolic side.

Thanks for that modest reply. I do believe now that it was Bill Rogers
whom I praised. But you do a good job with what you know.

> >
> >> It is to the advantage of an organism to regulate transcription of its
> >> genome so that it doesn't waste energy producing proteins that have no
> >> use in its current environment. This is especially true of prokaryotes.
> >>
> >> Consequently organisms have DNA binding proteins (10% of human genes
> >> produce DNA binding proteins) which regulate metabolism and the cell
> >> cycle. Given the existence of DNA binding proteins they can be exapted
> >> to regulate other stuff, such as development.
> >
> > DNA binding is a very general concept. Are any of the simpler of these
> > proteins good candidates for "ancestry" of homeobox proteins?
>
> I don't know. I don't even know that homeobox proteins are more complex
> than other transcription factors.

What makes some homeobox genes so special is that they bind a number of
key proteins that are responsible for major parts of bodies.
Do any of the ones in bacteria bind several proteins?

What you say next seems to indicate that sheer size of the
gene does not necessarily correlate with grandioseness of
its effects. Do you know how many aminos the HOM-C gene
has, the one for which mutations have such a comical effect
on fruit flies? There is nothing about that in:

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

> Homeobox proteins vary greatly in size
> - at least from 73 (mouse Hopx) to 3703 (human ZFHX3) amino acid
> residues. HOX proteins are towards the lower end of this range - 200 to
> 400 amino acids. If I understand correctly they lack signal sensing
> domains, which makes them simpler in some ways that some other
> transcription factors.
> >
> >
> >> There are several families of DNA binding proteins. (Wikipedia lists 14
> >> of these.) One of these is homeobox proteins. Hox proteins are are
> >> subset of these, and both these and the larger enclosing ANTP family
> >> seem to be phylogenetically restricted to animals (apparently
> >> secondarily absent from sponges and Trichoplax), but other homeobox
> >> families are more widely distributed among eukaryotes - the TALE family
> >> is found in animals, fungi and plants, and might well be universal or
> >> nearly so among eukaryotes.

How complicated are the functions of the TALE family genes?

HOM-C is identified only as an ANTP gene in the Wiki entry above.
Do you know anything more specific about it? The Wiki entry
does list some related ANTP genes of similar interest.

> >> From these observations it is readily hypothesised that as the
> >> ancestors of animals changed from a colonial habit to an early
> >> multicellular habit with cell-type differention existing or newly
> >> created (by recombination or duplication) homeobox proteins were pressed
> >> into service as regulators of development.
> >
> > Very plausible, but the devil is in the details. As I told jillery
> > on another thread:
> >
> >
> > As Behe never tired of pointing out, the standard technique
> > for evolutionary theorists is simply to classify the proteins
> > that are related to the ones in question and to point to similarities
> > in the sequences as evidence that they evolved. But the how and why
> > of it, or scenarios for how it might have happened, are events for
> > which they haven't gotten to the starting blocks.
> >
>
> That's an argument from ignorance.

So is the argument that there MUST be an undirected evolutionary path
even though none has been identified. Knee-jerk atheists aside
[several of them are on this thread], one cannot completely
discount the possibility of supernatural intervention, albeit
of a relatively modest sort that is within human capabilities.

> Creationists have a bad habit of
> ignoring the evidence that we have in favour of the evidence that we
> don't have and shouldn't expect to have - given sufficient time
> evolution erases its tracks and we can't expect to have the evidence to
> provide a blow by blow account of the origin of ancient features of the
> genome. Why are you arguing like a creationist?

I am not. I am not asking for a reconstruction of the path
actually taken. I would be quite happy with one that looks
plausible, no matter how far it may be from the actual one.

Have you been around long enough to remember Julie Thomas? She
posted ca. 1996 -1998. She may have been even better at biochemistry
than "el cid" and earned grudging respect from Laurence A. Moran,
with whom she could pretty much hold her own despite supporting
ID theory, especially the Behe variety.

The reason I mention her is that she kept holding out for
*actual* evolutionary paths. I reminded her after a while that
none of her critics had the foggiest idea of even plausible
hypothetical scenarios. IOW, she had been pulling her punches.


I'll pick up here, with a bit repeated for context, in tomorrow's
reply to this post.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

U. of South Carolina
http://www.math.sc.edu/~nyikos/

[John Harshman]

Homeobox genes don't bind proteins. Hox proteins don't bind proteins, or
at least that isn't their main function. They bind transcription factor
binding sites in the genome. Just about every transcription factor binds
to several sites in the promoter regions of several proteins. Hox genes
are not at all unusual in this way.

> What you say next seems to indicate that sheer size of the
> gene does not necessarily correlate with grandioseness of
> its effects. Do you know how many aminos the HOM-C gene
> has, the one for which mutations have such a comical effect
> on fruit flies? There is nothing about that in:

I know it's easy to fall into sloppy language, but genes don't have
amino acids. You mean the HOM-C protein. And actually, the term HOM-C
refers not to a gene but to the entire Hox cluster.

> https://en.wikipedia.org/wiki/Antennapedia

378.

>> Homeobox proteins vary greatly in size
>> - at least from 73 (mouse Hopx) to 3703 (human ZFHX3) amino acid
>> residues. HOX proteins are towards the lower end of this range - 200 to
>> 400 amino acids. If I understand correctly they lack signal sensing
>> domains, which makes them simpler in some ways that some other
>> transcription factors.
>>>
>>>
>>>> There are several families of DNA binding proteins. (Wikipedia lists 14
>>>> of these.) One of these is homeobox proteins. Hox proteins are are
>>>> subset of these, and both these and the larger enclosing ANTP family
>>>> seem to be phylogenetically restricted to animals (apparently
>>>> secondarily absent from sponges and Trichoplax), but other homeobox
>>>> families are more widely distributed among eukaryotes - the TALE family
>>>> is found in animals, fungi and plants, and might well be universal or
>>>> nearly so among eukaryotes.
>
> How complicated are the functions of the TALE family genes?

The functions of all transcription factors are pretty much the same:
bind to particular sequences of DNA. The rest is various ways in which
the transcription factors are regulated to bind or not bind.

> HOM-C is identified only as an ANTP gene in the Wiki entry above.
> Do you know anything more specific about it? The Wiki entry
> does list some related ANTP genes of similar interest.

You have that backwards, ANTP is a HOM-C gene belongong to the ANTP
family. The ANTP gene is one member of the ANTP family. HOM-C is the
name for the single Hox cluster in Drosophila (and I think the name is
used with most invertebrates).

>>>> From these observations it is readily hypothesised that as the
>>>> ancestors of animals changed from a colonial habit to an early
>>>> multicellular habit with cell-type differention existing or newly
>>>> created (by recombination or duplication) homeobox proteins were pressed
>>>> into service as regulators of development.
>>>
>>> Very plausible, but the devil is in the details. As I told jillery
>>> on another thread:
>>>
>>>
>>> As Behe never tired of pointing out, the standard technique
>>> for evolutionary theorists is simply to classify the proteins
>>> that are related to the ones in question and to point to similarities
>>> in the sequences as evidence that they evolved. But the how and why
>>> of it, or scenarios for how it might have happened, are events for
>>> which they haven't gotten to the starting blocks.
>>>
>>
>> That's an argument from ignorance.
>
> So is the argument that there MUST be an undirected evolutionary path
> even though none has been identified. Knee-jerk atheists aside
> [several of them are on this thread], one cannot completely
> discount the possibility of supernatural intervention, albeit
> of a relatively modest sort that is within human capabilities.

One can never completely discount the possibility of supernatural
intervention. That doesn't make it a plausible alternative. The
differences we see among homologous genes are the sort that commonly
happen by mutation. Does that tell you anything?

>> Creationists have a bad habit of
>> ignoring the evidence that we have in favour of the evidence that we
>> don't have and shouldn't expect to have - given sufficient time
>> evolution erases its tracks and we can't expect to have the evidence to
>> provide a blow by blow account of the origin of ancient features of the
>> genome. Why are you arguing like a creationist?
>
> I am not. I am not asking for a reconstruction of the path
> actually taken. I would be quite happy with one that looks
> plausible, no matter how far it may be from the actual one.

It isn't clear what you're asking for, possibly because you don't know
enough about Hox genes to ask. There are many evolutionary steps in Hox
evolution. Are you asking about every single one of them, or what?

> Have you been around long enough to remember Julie Thomas? She
> posted ca. 1996 -1998. She may have been even better at biochemistry
> than "el cid" and earned grudging respect from Laurence A. Moran,
> with whom she could pretty much hold her own despite supporting
> ID theory, especially the Behe variety.
>
> The reason I mention her is that she kept holding out for
> *actual* evolutionary paths. I reminded her after a while that
> none of her critics had the foggiest idea of even plausible
> hypothetical scenarios. IOW, she had been pulling her punches.

What do you mean by "actual evolutionary paths", and how would we
recognize them?

[Mark Isaak]

On 3/27/18 2:51 PM, Peter Nyikos wrote:

> On Saturday, March 24, 2018 at 9:55:03 AM UTC-4, Ernest Major wrote:

>> [...]

>> That's an argument from ignorance.
>
> So is the argument that there MUST be an undirected evolutionary path
> even though none has been identified. Knee-jerk atheists aside
> [several of them are on this thread], one cannot completely
> discount the possibility of supernatural intervention, albeit
> of a relatively modest sort that is within human capabilities.

For someone who claims not be a creationist, you sure are trying hard to
mimic a creationist.

What does "supernatural intervention" mean? Either it means something
natural but unknown (like, at one time, the cause of frost), in which
case it is already included in the bin marked "unknown" which you
disparage so much; or it means something outside not just normal
experience, but any possible repeated experience, in which case it only
makes sense that it be completely discounted as unknowable and therefore
profitless to contemplate.

[jillery]

On Tue, 27 Mar 2018 09:28:07 -0700 (PDT), Peter Nyikos

<nyi...@bellsouth.net> continued to ejaculate his repetitive
>> irrelevant spew from his puckered sphincter:
>>
>> Is anybody surprised.

<snip your irrelevant spew>

>You, on the other hand, make a pretense of caring about
>dishonesty below.

Your pretensions of caring about dishonesty disqualify you from
complaining about my alleged pretensions. Tu quoque back atcha,
asshole.

[jillery]

On Tue, 27 Mar 2018 14:51:27 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> wrote:

>> That's an argument from ignorance.
>
>So is the argument that there MUST be an undirected evolutionary path
>even though none has been identified. Knee-jerk atheists aside
>[several of them are on this thread], one cannot completely
>discount the possibility of supernatural intervention, albeit
>of a relatively modest sort that is within human capabilities.

Of course, no authoritative person makes an argument that there MUST
be an evolutionary pathway. That's a Creationist PRATT. What is
actually argued is that undirected evolutionary pathways are the kind
of thing science can test for. The possibility of supernatural
intervention can never be disproved in principle, and its
characteristics can never be specified in principle, and so it's not
possible for science to look for it.

Your last sentence is incoherent; anything within human capabilities
isn't supernatural by definition.

[Bob Casanova]

On Tue, 27 Mar 2018 11:07:50 -0700, the following appeared
in talk.origins, posted by John Harshman
<jhar...@pacbell.net>:

Benefit of the doubt, even though that doubt has become
minuscule.

[Peter Nyikos]

On Wednesday, March 28, 2018 at 12:35:02 AM UTC-4, Mark Isaak wrote:
> On 3/27/18 2:51 PM, Peter Nyikos wrote:
> > On Saturday, March 24, 2018 at 9:55:03 AM UTC-4, Ernest Major wrote:
> >> [...]
> >> That's an argument from ignorance.
> >
> > So is the argument that there MUST be an undirected evolutionary path
> > even though none has been identified. Knee-jerk atheists aside
> > [several of them are on this thread], one cannot completely
> > discount the possibility of supernatural intervention, albeit
> > of a relatively modest sort that is within human capabilities.
>
> For someone who claims not be a creationist, you sure are trying hard to
> mimic a creationist.

Bullshit. I'd like to see you try to NAME any creationist
whom I am supposedly mimicking.


Do you consider yourself to be anything but a militant atheist,
by the way? If so, you have some tall explaining to do about
the sophistic sleight of hand you indulge in below. Methinks
it would gladden the hears of the militant atheists Harshman,
Hemidactylus, and jillery.

> What does "supernatural intervention" mean? Either it means something
> natural but unknown (like, at one time, the cause of frost),

Sloppy thinking. The cause may have been thought to be supernatural,
but the key clause is "thought to be." So you are shedding NO
light on what "supernatural intervention" means.

> in which
> case it is already included in the bin marked "unknown" which you
> disparage so much;

HUH? Where do you think I ever disparaged the unknown?

> or it means something outside not just normal
> experience, but any possible repeated experience,

You are using the word "supernatural" in almost the same question-begging
way that Hume used the word "miracle." He simply claimed that
the universal experience of mankind was that no miracles ever
took place, and thus defined miracles out of existence.

You don't quite do that, you smuggle in the word "repeated"
and thus define the word "supernatural" in
a way no one who believes Jesus rose from the dead would
think of using it.

>in which case it only
> makes sense that it be completely discounted as unknowable and therefore
> profitless to contemplate.

Don't you just wish the Apostle Paul had thought the way you do and
never wrote 1 Corinthians 15?

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

Univ. of South Carolina at Columbia
http://www.math.sc.edu/~nyikos/

[Peter Nyikos]

Stop playing dumb. Your response to the actual content
was:

Thanks for the additional confirmation, even though it's
redundant.

And the "confirmation" referred to the insulting
and indefensble comment,

>> Apparently he's been taking the same classes as Tony and
>> Allie, and personal attacks and ad hominems are all they
>> teach.

"personal attacks and ad hominems" is typically amoral,
even aside from the "informal *sensu* Casanova" literal
falsehood "all they teach."

When I make the "personal attack and ad hominem" that
the dictator of North Korea is a tyrant, or that the
shooter of the students in that Florida high school
is a murderer, only an amoral person would think
there is something WRONG with me saying that. Don't you
agree?


But now, apply that to all but the first sentence
of the paragraph to which you responded with that typically
amoral comment, and tell me straight out what, if anything,
is WRONG with what I wrote there, according to you.

> If not, it should be no problem for you to quote that
> "typically amoral comment". Do it here:

Sorry, I do the quoting where it suits me, not where
it suits you.

> [Balance (unbalance?) of Peter's rant

Read: comments which neither you nor jillery
can undermine the validity of.

IOW, an exposition of inconvenient truths.

> left intact as
> evidence that my original comment...
>
> "Apparently he's been taking the same classes as Tony and
> Allie, and personal attacks and ad hominems are all they
> teach."
>
> ....was pretty close to the mark. And I probably should have
> added something about "developing paranoia"]

I'd love to see you try to explain what even HINTS of paranoia
about what I wrote below.

> > He loves to act as though dishonest and hypocrisy
> >and cowardice were mere trifles compared to my rudeness
> >in pointing out behavior that exemplifies these things.

You made that love pretty clear in your enthusiastic reactions
to the bitty passages cherry-picked by Hemidactylus out
of a reply I did to Harshman. You never read the actual
post Hemidactylus was quote-mining, did you?

THAT was where I pointed out behavior by Harshman that
exemplifies these things, in detail that no one, least
of all Harshman himself, has dared to touch with
a ten foot pole.

However, I quoted some of it to you about an hour ago, in:

https://groups.google.com/d/msg/talk.origins/RmJfq-PdDl0/VH1IsU9DAAAJ
Subject: Re: Judge Jones and Plagiarism at the Dover Trial.?
Date: Wed, 28 Mar 2018 12:18:48 -0700 (PDT)
Message-ID: <9bdeb5ca-6ac7-47e8...@googlegroups.com>

It will be interesting to see just how much of it you dare
to touch with a ten foot pole, figuratively speaking.

Will you be using jillery as a role model in your reply?
All that she dared to touch with a ten foot pole, out
of everything you see below, were the first two lines:

By the way... have you ever personally attacked creationists
with the ad hominem charge of "cherry picking" and "quote mining"?

Peter Nyikos

[John Harshman]

On 3/28/18 1:55 PM, Peter Nyikos wrote:

Yeah, he's not obsessive. Surely that lengthy post proves it.

<snip>

[Peter Nyikos]

On Saturday, March 24, 2018 at 9:55:03 AM UTC-4, Ernest Major wrote:
> On 21/03/2018 22:00, Peter Nyikos wrote:
> > On Wednesday, March 21, 2018 at 10:35:04 AM UTC-4, Ernest Major wrote:

Picking up where I left off yesterday, except for a bit of context.

> >>
> >> From these observations it is readily hypothesised that as the
> >> ancestors of animals changed from a colonial habit to an early
> >> multicellular habit with cell-type differention existing or newly
> >> created (by recombination or duplication) homeobox proteins were pressed
> >> into service as regulators of development.
> >
> > Very plausible, but the devil is in the details. As I told jillery
> > on another thread:
> >
> >
> > As Behe never tired of pointing out, the standard technique
> > for evolutionary theorists is simply to classify the proteins
> > that are related to the ones in question and to point to similarities
> > in the sequences as evidence that they evolved. But the how and why
> > of it, or scenarios for how it might have happened, are events for
> > which they haven't gotten to the starting blocks.

<snip to get to the new material>

Yes, and it was utterly useless for explaining the clotting
cascade until the "silver bullet" of autocatalycity made it
easy. Behe's stinging critique of Doolittle's earlier
very detailed attempt at a scenario made that clear.

What we lack is anything like a "silver bullet" to pave the
way for an explanation for the evolutionary
pathway from simple genes to highly specifically-acting
factors that include homeobox genes.

>
> There are 4 possible fates for duplicate genes - deletion,
> pseudogenisation (and eventual deletion), subfunctionalisation and
> neofunctionalisation. All of these are known processes. I'm most familar
> with the literature on tetraploid cottons - cottons as an economically
> important crop are extensively studied - but there's plenty of papers on
> the topic elsewhere.
>
> In the context of homeobox genes a hypothetical example of
> subfunctionalisation would be duplication of a gene expressed in feet,
> and specialisation so that one copy was expressed in the forefeet and
> the other in the hindfeet. This potentiates adaptive divergence in the
> structure of forefeet and hindfeet (eventually hands and feet).

This is like talking about the evolution of primates from the earliest
chordates by concentrating on their evolution from the LCA of
the earliest primates, or worse.

> An hypothetical example of neofunctionalisation would be duplication of
> a gene expressed in the tail, and the use of one copy to control
> development of a thagomiser.
>
> >
> > It was brilliantly done for the clotting cascade by Kenneth Miller
> > and/or Keith Robison [1] and so Behe's criticism was partly answered,
> > though not his criticism of Doolittle's blunder when he sought to
> > avenge the ignominy of Behe's critique.
> >
> > [1] In his Talk.origins Archive FAQ on the clotting cascade. Were
> > you around in 1995-2000, when Robison was probably THE best authority
> > on biochemistry posting to talk.origins? I miss him very much.7
> > do you remember Robison from 1995-2000?
> >
> >
> >> Most animals have HOX genes. Perhap all animals have ParaHOX genes.
> >> (Some animals have the region of the genome were HOX genes are found,
> >> but no HOX genes - Ghost HOX loci.) The HOX and ParaHOX clusters are
> >> believed to have originated from duplication of an ancestral ProtoHOX
> >> cluster, following by differential loss of duplicate non-HOX genes from
> >> the duplicated regions.
> >
> > See above. The key in the clotting cascade was autocatalicity of most
> > of the factors in the cascade. But that's not true of these genes,
> > is it?
> >
>
> That's a red herring.

Except for the way it illuminates how sorely we are lacking -- and
will probably never have -- an easy explanation for how all
these amazingly potent carriers of specificity came about.


Concluded in tomorrow's reply.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

Univ. of South Carolina in Columbia
http://www.math.sc.edu/~nyikos/

[John Harshman]

I think you don't know what Hox genes do or how they do it. I think you
have some false conception, but you haven't articulated it. It's
difficult to discuss the subject under such conditions.

And it seems you won't talk about it with me, though you are happy to
discuss Captain Queeg bullshit. I think you prefer the Captain Queeg
bullshit.

[Mark Isaak]

On 3/28/18 12:52 PM, Peter Nyikos wrote:
> On Wednesday, March 28, 2018 at 12:35:02 AM UTC-4, Mark Isaak wrote:
>> On 3/27/18 2:51 PM, Peter Nyikos wrote:
>>> On Saturday, March 24, 2018 at 9:55:03 AM UTC-4, Ernest Major wrote:
>>>> [...]
>>>> That's an argument from ignorance.
>>>
>>> So is the argument that there MUST be an undirected evolutionary path
>>> even though none has been identified. Knee-jerk atheists aside
>>> [several of them are on this thread], one cannot completely
>>> discount the possibility of supernatural intervention, albeit
>>> of a relatively modest sort that is within human capabilities.
>>
>> For someone who claims not be a creationist, you sure are trying hard to
>> mimic a creationist.
>
> Bullshit. I'd like to see you try to NAME any creationist
> whom I am supposedly mimicking.

All of them.

> Do you consider yourself to be anything but a militant atheist,
> by the way?

I am not an atheist at all.

>> What does "supernatural intervention" mean? Either it means something
>> natural but unknown (like, at one time, the cause of frost),
>
> Sloppy thinking. The cause may have been thought to be supernatural,
> but the key clause is "thought to be." So you are shedding NO
> light on what "supernatural intervention" means.

That is the sense in which the word is most frequently used, so I had to
mention it.

>> in which

>> case it is already included in the bin marked "unknown" which you
>> disparage so much;
>
> HUH? Where do you think I ever disparaged the unknown?

Every time you defended Behe, among other places.

>> or it means something outside not just normal
>> experience, but any possible repeated experience,
>
> You are using the word "supernatural" in almost the same question-begging
> way that Hume used the word "miracle." He simply claimed that
> the universal experience of mankind was that no miracles ever
> took place, and thus defined miracles out of existence.
>
> You don't quite do that, you smuggle in the word "repeated"
> and thus define the word "supernatural" in
> a way no one who believes Jesus rose from the dead would
> think of using it.

You never answered the question. Why would you say that Jesus rising
from the dead was supernatural, and not a very rare natural occurrence?
Just because a book said it was? How do you know that something from
outside the universe was responsible? How *could* you know?

>> in which case it only
>> makes sense that it be completely discounted as unknowable and therefore
>> profitless to contemplate.
>
> Don't you just wish the Apostle Paul had thought the way you do and
> never wrote 1 Corinthians 15?

Don't even try, Peter. You're not good at religion.

[jillery]

On Wed, 28 Mar 2018 13:55:14 -0700 (PDT), Peter Nyikos

<nyi...@bellsouth.net> continued to ejaculate his repetitive
irrelevant spew from his puckered sphincter:

Is anybody surprised.

<snip your irrelevant spew>

>> [Balance (unbalance?) of Peter's rant
>
>Read: comments which neither you nor jillery
>can undermine the validity of.
>
>IOW, an exposition of inconvenient truths.

Only in your wet dreams. Your rants are PRATTs and so don't need any
additional undermining.

[jillery]

On Wed, 28 Mar 2018 12:52:49 -0700 (PDT), Peter Nyikos

<nyi...@bellsouth.net> continued to ejaculate his repetitive
irrelevant spew from his puckered sphincter:

Is anybody surprised.

<snip your irrelevant spew>

>> For someone who claims not be a creationist, you sure are trying hard to
>> mimic a creationist.
>
>Bullshit. I'd like to see you try to NAME any creationist
>whom I am supposedly mimicking.

Of course, as with ID's creative Agent, a specific name isn't the
issue, but instead merely some of the distinguishing characteristics.

>Do you consider yourself to be anything but a militant atheist,
>by the way? If so, you have some tall explaining to do about
>the sophistic sleight of hand you indulge in below. Methinks
>it would gladden the hears of the militant atheists Harshman,
>Hemidactylus, and jillery.

Methinks you should stop imagining what other people thinks. Just
sayin'.

[Peter Nyikos]

On Wednesday, March 28, 2018 at 10:35:02 PM UTC-4, Mark Isaak wrote:
> On 3/28/18 12:52 PM, Peter Nyikos wrote:
> > On Wednesday, March 28, 2018 at 12:35:02 AM UTC-4, Mark Isaak wrote:
> >> On 3/27/18 2:51 PM, Peter Nyikos wrote:
> >>> On Saturday, March 24, 2018 at 9:55:03 AM UTC-4, Ernest Major wrote:
> >>>> [...]
> >>>> That's an argument from ignorance.
> >>>
> >>> So is the argument that there MUST be an undirected evolutionary path
> >>> even though none has been identified. Knee-jerk atheists aside
> >>> [several of them are on this thread], one cannot completely
> >>> discount the possibility of supernatural intervention, albeit
> >>> of a relatively modest sort that is within human capabilities.
> >>
> >> For someone who claims not be a creationist, you sure are trying hard to
> >> mimic a creationist.
> >
> > Bullshit. I'd like to see you try to NAME any creationist
> > whom I am supposedly mimicking.
>
> All of them.
>

Have you gone bananas? NONE of the ones I know about has
written anything like the paragraph you are supposedly talking
about. I'd like to see you come up with anything any of them
wrote that is even remotely like it.

Notice how easy I am being on you. It's not like I'm asking
you to come up with one from Ray Martinez or Tony Pagano
or indeed any self-proclaimed creationist posting to talk.origins.

I'm giving you the benefit of the doubt, assuming that you are using
the word "All" in a way that would get the stamp of approval
from Bob Casanova or jillery but from hardly anyone
else posting to talk.origins.

[1] Bob thinks such uses of "All of them" fall comfortably
within the range of accepted talk.origins hyperbole,
whereby it could easily mean "about 10% of them". This
is the kind of range he had in mind by his cunningly
worded statement that t.o. is an "informal venue."

[2] Jillery's take is very different. According to her logic,
"All of them" could even mean "none of them." This is because
she claims that "Of course" the naming of a specific person
is "not the issue" and so -- by the logic used --
people who make such claims shoudn't ever have to name ANY of them.

Jillery's use of "Of course" is similar to Martinez's use
of "Imagine that": a red flag should go up so that the reader
is alerted to scrutinize carefully what follows.

> > Do you consider yourself to be anything but a militant atheist,
> > by the way?
>
> I am not an atheist at all.

[repost of unmarked snip by you:]

If so, you have some tall explaining to do about
the sophistic sleight of hand you indulge in below. Methinks
it would gladden the hears of the militant atheists Harshman,
Hemidactylus, and jillery.

[end of repost]

That was cowardly, evading the point of my question.

Are you familiar with the saying, "As ye judge, so too shall
ye be judged?"

>
>
> >> What does "supernatural intervention" mean? Either it means something
> >> natural but unknown (like, at one time, the cause of frost),
> >
> > Sloppy thinking. The cause may have been thought to be supernatural,
> > but the key clause is "thought to be." So you are shedding NO
> > light on what "supernatural intervention" means.
>
> That is the sense in which the word is most frequently used,

...by atheists. The more you keep sounding like them, the
more you reveal what double standards you have.

To theists, the most frequent use is some insignificant
variation on "not being bound by the physical laws of
this little 13-14 gyo universe."

> so I had to mention it.

But not to substitute "That is the sense" for "That is the context".
Had you used the latter, you would not have sounded like an atheist.


Concluded in next reply, to be done shortly after I've seen
that this one has posted.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

Univ. of South Carolina in Columbia
http://www.math.sc.edu/~nyikos/

[Peter Nyikos]

On Wednesday, March 28, 2018 at 10:35:02 PM UTC-4, Mark Isaak wrote:
> On 3/28/18 12:52 PM, Peter Nyikos wrote:
> > On Wednesday, March 28, 2018 at 12:35:02 AM UTC-4, Mark Isaak wrote:
> >> On 3/27/18 2:51 PM, Peter Nyikos wrote:

Picking up where I left off, except for a bit of context.

> >>> Knee-jerk atheists aside
> >>> [several of them are on this thread], one cannot completely
> >>> discount the possibility of supernatural intervention, albeit
> >>> of a relatively modest sort that is within human capabilities.

[...]

> >> What does "supernatural intervention" mean?

Intervention by a supernatural entity, an entity which is
"not bound by the physical laws of this little 13-14 gyo
universe," as I put it. ALSO, an intervention by effecting
something that is unattainable within the constraints
of these physical laws.

Jillery confused these two senses when she ignorantly
claimed that I had been incoherent in the first paragraph
that I've kept in above. As you can see, I had used the word
in the first sense but NOT in the second sense.


Now, on to the part that I didn't get around to in my first reply.

> >> in which
> >> case it is already included in the bin marked "unknown" which you
> >> disparage so much;
> >
> > HUH? Where do you think I ever disparaged the unknown?
>
> Every time you defended Behe, among other places.

How cryptic can you get? Harshman and Simpson would have
a field day criticizing you for being "unclear," were they
not even more addicted to double standards than you are.

By the way, I only defend Behe against misrepresentations.
I don't think very highly of his take on ID.

> >> or it means something outside not just normal
> >> experience, but any possible repeated experience,
> >
> > You are using the word "supernatural" in almost the same question-begging
> > way that Hume used the word "miracle." He simply claimed that
> > the universal experience of mankind was that no miracles ever
> > took place, and thus defined miracles out of existence.
> >
> > You don't quite do that, you smuggle in the word "repeated"
> > and thus define the word "supernatural" in
> > a way no one who believes Jesus rose from the dead would
> > think of using it.
>
> You never answered the question.

I did now, in spades.

> Why would you say that Jesus rising
> from the dead was supernatural, and not a very rare natural occurrence?

Because I don't say it, I say how someone who believes it
would use "supernatural". [See above for hints as to
probable usage.] Knowledgeable Christians know that there
is nothing in the Bible that constrains God from raising
other people from the dead LONG before "the Last Judgment."

Hence the stupidity of your "any possible repeated experience."
You got it from an atheistic source, didn't you? [Caution:
"atheistic" can mean "from demythologizing liberal `Protestant'
theology."]

> Just because a book said it was? How do you know that something from
> outside the universe was responsible? How *could* you know?

Don't ever try to apply for a job with law enforcement
as an interrogator. The testers would have a hard time
keeping from laughing, or stopping if they do start laughing.

> >> in which case it only
> >> makes sense that it be completely discounted as unknowable and therefore
> >> profitless to contemplate.
> >
> > Don't you just wish the Apostle Paul had thought the way you do and
> > never wrote 1 Corinthians 15?
>
> Don't even try, Peter. You're not good at religion.

Transparent bluff, using the word "religion" in place
of "liberal theology." [See above.]

I LIVED the Christian religion until I was 21, and
have done extensive reading in it. You are like the
liberal theologian who once said to John Warwick Montgomery [1],
who actually believes that Jesus rose from the dead,
"I didn't know there were still people like you around."

[1] https://en.wikipedia.org/wiki/John_Warwick_Montgomery


And you never answered the question.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --
Univ. of South Carolina

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

[Bob Casanova]

On Wed, 28 Mar 2018 13:55:14 -0700 (PDT), the following

>By the way... have you ever personally attacked creationists
>with the ad hominem charge of "cherry picking" and "quote mining"?

Those aren't ad hominems, as anyone with even half a brain
knows; they're accusations of a particular dishonest
activity, not personal attacks Of the sort "You're a
[creationist, IDist, DPist, etc], therefore everything you
say is wrong".

As for the rest of your whining rant, most of which wasn't
even about me (as is typical of your whining rants), HAND.

[Mark Isaak]

On 3/29/18 5:24 AM, Peter Nyikos wrote:

[To other readers: There's nothing of substance here.]

> On Wednesday, March 28, 2018 at 10:35:02 PM UTC-4, Mark Isaak wrote:
>> On 3/28/18 12:52 PM, Peter Nyikos wrote:
>>> On Wednesday, March 28, 2018 at 12:35:02 AM UTC-4, Mark Isaak wrote:
>>>> On 3/27/18 2:51 PM, Peter Nyikos wrote:
>>>>> On Saturday, March 24, 2018 at 9:55:03 AM UTC-4, Ernest Major wrote:
>>>>>> [...]
>>>>>> That's an argument from ignorance.
>>>>>
>>>>> So is the argument that there MUST be an undirected evolutionary path
>>>>> even though none has been identified. Knee-jerk atheists aside
>>>>> [several of them are on this thread], one cannot completely
>>>>> discount the possibility of supernatural intervention, albeit
>>>>> of a relatively modest sort that is within human capabilities.
>>>>
>>>> For someone who claims not be a creationist, you sure are trying hard to
>>>> mimic a creationist.
>>>
>>> Bullshit. I'd like to see you try to NAME any creationist
>>> whom I am supposedly mimicking.
>>
>> All of them.
>
> Have you gone bananas? NONE of the ones I know about has
> written anything like the paragraph you are supposedly talking
> about. I'd like to see you come up with anything any of them
> wrote that is even remotely like it.
>

> [snip further raving and bullying]

All creationists which I have encountered (and had more than trivial
conversations with) use the God of the Gaps argument: There's no known
explanation, therefore supernatural. You do that too.

>>> Do you consider yourself to be anything but a militant atheist,
>>> by the way?
>>
>> I am not an atheist at all.
>
> [repost of unmarked snip by you:]
> If so, you have some tall explaining to do about
> the sophistic sleight of hand you indulge in below. Methinks
> it would gladden the hears of the militant atheists Harshman,
> Hemidactylus, and jillery.
> [end of repost]
>
> That was cowardly, evading the point of my question.

Since the point of your question was to bully me and others, I did you a
favor by cutting it. But if you insist on emphasizing your immorality
to the world, so be it.

> Are you familiar with the saying, "As ye judge, so too shall
> ye be judged?"

Please stop abusing my irony meter.

>>
>>>> What does "supernatural intervention" mean? Either it means something
>>>> natural but unknown (like, at one time, the cause of frost),
>>>
>>> Sloppy thinking. The cause may have been thought to be supernatural,
>>> but the key clause is "thought to be." So you are shedding NO
>>> light on what "supernatural intervention" means.
>>
>> That is the sense in which the word is most frequently used,
>
> ...by atheists.

By everyone.

> To theists, the most frequent use is some insignificant
> variation on "not being bound by the physical laws of
> this little 13-14 gyo universe."

Meaning, in practice, by the known physical laws.

[Mark Isaak]

On 3/29/18 6:09 AM, Peter Nyikos wrote:
> On Wednesday, March 28, 2018 at 10:35:02 PM UTC-4, Mark Isaak wrote:
>> On 3/28/18 12:52 PM, Peter Nyikos wrote:
>>> On Wednesday, March 28, 2018 at 12:35:02 AM UTC-4, Mark Isaak wrote:
>>>> On 3/27/18 2:51 PM, Peter Nyikos wrote:
>
> Picking up where I left off, except for a bit of context.
>
>>>>> Knee-jerk atheists aside
>>>>> [several of them are on this thread], one cannot completely
>>>>> discount the possibility of supernatural intervention, albeit
>>>>> of a relatively modest sort that is within human capabilities.
>
> [...]
>
>>>> What does "supernatural intervention" mean?
>
> Intervention by a supernatural entity, an entity which is
> "not bound by the physical laws of this little 13-14 gyo
> universe," as I put it. ALSO, an intervention by effecting
> something that is unattainable within the constraints
> of these physical laws.

Thank you. Now, how would it be possible to tell whether or not
something is supernatural? If, for example, a being is able to fly
without wings, talk with beings 100 miles away, and heal illnesses
caused by other spirits, would that make it supernatural?

"Supernatural" is a label for something found in fantasy. Like many
fantasies, people want to think that it appears in reality. But there
is a huge difference between the concept and the reality.

Consider two candidates for the supernatural. Case 1: A 10-cm-long
humanoid with wings, glowing with a yellowish light, flies up to your
children and drops some dust on them. Your children slowly rise into
the air and, with some practice, are able to fly in a controlled manner.

Is that supernatural? No, it is merely unexplained. Any scientist
would jump at the chance to find out *how* the dust enables such easy
flight. And since the effect is repeatable, they should have
opportunities to do so. Maybe they succeed; certainly they will not
succeed immediately. Their lack of an explanation, however, does not
mean the explanation is supernatural.


Case 2: When the earth became filled with immorality, there came a
drought of seven years; seven suns appeared and dried up all the water.
A fire came which penetrated even to the netherworld. Then the clouds
released their waters and flooded the entire surface of the earth; rain
fell for twelve years. One long-lived sage, Markandeya, survived alone.
As he became fatigued upon the waters, he saw a child seated in a bed
upon a vast banyan. The child bade Markandeya to enter his body and
rest. When he went into the child's mouth, Markandeya saw the entire
universe. A gust of wind later expelled him, the child-deity told a bit
about who and what he was, and creation began again.

Of course, one problem with calling those events supernatural is that
there is no evidence that they happened. We have only a story, with no
way to replicate any part of it.

But even if we grant that the events actually happened, was any of that
supernatural? Certainly it was outside normal experience. But it was
not, apparently, outside all nature. The Deity admits to not knowing
everything, and events such as that are reputed to happen every yuga.
By my reading, the whole point of the myth is that there *is* a nature
of which humans are unaware. That conclusion can apply to any fantastic
story. Even the highest gods exist in some sense of a universe.


[snipping the rest, since this is the point I am interested in]

[Peter Nyikos]

<snip to get to more recent discussion>

> > Here is a possible scenario that occurred to me just in the last day.
> > There may have been an intelligent species of ribozyme-based
> > creatures living in a globular cluster.

Alas, as I told Ernest Major earlier this week, this turned out
to be a case where a "beautiful theory killed by a brutal gang
of cold facts" about globular clusters. I found that out over the weekend
by reading Chapter 14 in a great book by planetary scientist
John L. Lewis, _Worlds_Without_End.

In addition to the difficulties that Erik Simpson pointed out,
the passage through the galactic plane is sometimes

through regions thick in gas and dust at its
relative speed of about 240 kilometers per second.
At that speed a dust grain would have a kinetic energy
over one hundred times its weight of TNT. The entire cluster
is swept clear of any gas, and every planet in the
cluster is bombarded with hydrogen gas. A hydrogen atom
traveling at 240 kilometers per second has an effective
temperature of 4 million degrees K, high enough
to drive some low-energy nuclear reactions. The impact
of these atoms would generate a flood of deadly X-rays.
-- *ibid*, pp. 168-169

There's much more in that "brutal gang," too.

> That ribozyme-based intelligent life is interesting hypothesis.
> Some of it can be falsifiable.

Yes, and I gave some ways that depend on being able to
investigate life on other planetary systems. But there
are ways it could be falsified by progress in understanding
what kinds of cells are possible.

> For example if it can be possible?
> Is so low mutation rate as in DNA world possible to show in RNA world?

I was only talking about ribozymes making the big difference,
and these creatures would probably have DNA genomes. Of course,
that increases the range of ribozymes needed, but that still
avoids the Catch-22 of protein takeover.

> Very low mutation rate is crucial otherwise most of organisms would
> die because of damage from mutations during embryonic development. So no
> trillion-cell multi-cellularities and so no intelligent lifeforms in
> principle.

The falsification would have to come from elsewhere. Beyond the
need for a genetic code, there is a requirement for structural
proteins to line the pores in cell membranes.

I was told back around 1999 by a short term t.o. particpant
with the interesting name of Wolfram Dachs that RNA is
not suitable for this purpose because of some biochemical
reason, perhaps the wrong Ph.


<merciful snip of "murdered theory">

> Civilizations that last million of years are also fiction that is hard to
> falsify. We have as lot of evidence of such as of magnetic monomers.
> Aren't only Japanese managed to keep their empire for more than
> thousand years? AFAIK all others have quit being anything as far
> younger. Also, we have never before had so high skills in so lot of
> so lethal ways of ruining it for whole planet.

This is a very tough issue. Ironically enough, I conceived the
global cluster hypothesis under the impetus of a challenge John Harshman
made after I claimed that a civilization is very unlikely to last for
gigayears, for obvious common sense reasons.

Harshman then posed a question challenging me to prove that it is
highly unlikely. So like a good scientist, I first tried to
come up with something that would prove me wrong, and thought
I had succeeded with my globular cluster hypothesis, whereby
colonization of the whole cluster could take a hundred million
years or more.

But now I think I can challenge John to give me a realistic
scenario for a civilization that can last that long.

[John Harshman]

For the record, I don't recall that challenge, or why I would have made
such a challenge, especially a request to "prove" anything. Proof is
something that happens in mathematics, not the real world.

It does seem to me more likely than not that a civilization wouldn't
last for millions of years, much less billions. And if it did last that
long, it would be unrecognizable.

[jillery]

On Thu, 29 Mar 2018 05:24:15 -0700 (PDT), Peter Nyikos

<nyi...@bellsouth.net>continued to ejaculate his repetitive
irrelevant spew from his puckered sphincter:

Is anybody surprised.

<snip your irrelevant spew>

>[2] Jillery's take is very different. According to her logic,
>"All of them" could even mean "none of them." This is because
>she claims that "Of course" the naming of a specific person
>is "not the issue" and so -- by the logic used --
>people who make such claims shoudn't ever have to name ANY of them.
>
>Jillery's use of "Of course" is similar to Martinez's use
>of "Imagine that": a red flag should go up so that the reader
>is alerted to scrutinize carefully what follows.

Of course, you show nothing which supports your characterization of
what Jillery wrote. And it's almost certain you never will. This is
just another example of your Big Lie. It's what you do.

Of course, your Martinez-style postings disqualify you from
complaining about Jillery's alleged use of same. Tu quoque back
atcha, asshole.

[jillery]

On Thu, 29 Mar 2018 06:09:59 -0700 (PDT), Peter Nyikos

<nyi...@bellsouth.net> continued to ejaculate his repetitive
irrelevant spew from his puckered sphincter:

Is anybody surprised.

<snip your irrelevant spew>

>> >>> Knee-jerk atheists aside
>> >>> [several of them are on this thread], one cannot completely
>> >>> discount the possibility of supernatural intervention, albeit
>> >>> of a relatively modest sort that is within human capabilities.
>
>[...]
>
>> >> What does "supernatural intervention" mean?
>
>Intervention by a supernatural entity, an entity which is
> "not bound by the physical laws of this little 13-14 gyo
>universe," as I put it. ALSO, an intervention by effecting
>something that is unattainable within the constraints
>of these physical laws.
>
>Jillery confused these two senses when she ignorantly
>claimed that I had been incoherent in the first paragraph
>that I've kept in above. As you can see, I had used the word
>in the first sense but NOT in the second sense.

Of course, Jillery confused no such thing, ignorantly or otherwise. As
shown by the quoted text above, you claim human capabilities can be
supernatural, and also admit that supernatural intervention is
unattainable within the constraints of these physical laws. So unless
you think humans can intervene beyond the constraints of physical
laws, your understanding of "supernatural" is a Martinez-style
incoherence.

Of course, it's almost certain you will never admit you're wrong.

Click... click... click...

[Peter Nyikos]

On Saturday, March 24, 2018 at 9:55:03 AM UTC-4, Ernest Major wrote:

> On 21/03/2018 22:00, Peter Nyikos wrote:
> > On Wednesday, March 21, 2018 at 10:35:04 AM UTC-4, Ernest Major wrote:

In this concluding reply, I pick up exactly where I left off
in the preceding one.

> Clotting factors are enzymes - they catalyze chemical reactions. But not
> all proteins are enzymes. Some are structural proteins (conceived
> broadly) such as crystallins and flagellins, some are chemical
> messengers (e.g. insulin), some are transporters (e.g. haemoglobin), and
> others are transcription factors*. Transcription factors bind to DNA and
> control which genes are active (transcribed).

Yes, and the specificity of these factors -- the ones which control
the expression of a very select group of genes and no others -- is
where the riddle of their evolution is to be found.

This specificity is not in the homeodomain itself. This fragment
of a given transcription factor can bind to any part of DNA,
according to the textbook used here to teach beginning biology
majors, _Biology_, by Campbell, Reese et.al. Rather, it is the
other parts of the factor that account for the remarkable specificity.


> Differences between which
> genes are active in a cell determine cell types, and positional control
> on where cell types are produced and interactions between them result in
> tissue types and anatomical structure. Much of the functionality of the
> system is bound up not in the sequence of the transcription factors, but
> in the relationship of the binding sites to genes encoding structural
> and metabolic proteins. Developmentally active transcription factors
> don't directly specify anatomy - they specify a location with the
> organism, and it's the action of the downstream genes that build a
> particular anatomy. As a generality the richer the set of
> developmentally active transcription factors the greater the variety of
> cell types and anatomical structures that can be generated - which is
> seen in the expansion of (different) homeobox gene families in
> (different) multicellular clades.

The big question here is how far the families I write about above
are from proteins that do not have such high specificity and do not
control the transcription of so many downstream genes.

It is impossible to quantify such things, but very roughly, to
what shall we compare this distance to the distance from some group
of eukaryotes to prokaryotes? Shall the group be something like the
order Primates, or the phylum Chordates, or the whole animal kingdom?

The subdivisions of whatever group best applies would be compared to
the various homeobox gene families. Which comparison would work best,
I wonder?


> * this is not an exhaustive classification of protein functions.
> >
> >> The ANTP (super)family of homeobox proteins contains 14 families in
> >> total, of which Hox proteins are one. Apparently 4 of these are
> >> restricted to bilaterians, which suggests duplication events in the
> >> ancestors of bilaterians. And in general all 14 families would be
> >> expected to have arise by gene duplication.
> >
> > Here too, where's the magic "silver bullet" that autocatalycity [sp?]
> > provided?
> >
> > Got to go now. My ride will soon be waiting for me.

> >
> > Peter Nyikos
> > Professor, Department of Math. -- standard disclaimer --

> > University of South Carolina
> > http://people.math.sc.edu/nyikos/
> >
> >
> >> The origin of ANTP seems to where the trail goes cold. Perhaps evolution
> >> has erased its links with some other older class of homeobox proteins.
> >> Perhaps I haven't found the right Google incantation. Perhaps molecular
> >> biologists haven't yet done the work needed to find its homologs.

Finding homologs is very different from even conjecturing a plausible [1]
evolutionary path.

[1] By "plausible" I mean one whose individual steps
do not markedly reduce fitness.

Analogy: We have some rough idea of the "homologs" of Chiroptera (bats).
It used to be believed that its sister group was in the clade
{Primates, Dermoptera, Scandentia} but now it appears that their
closest homolog is Fereuungulata, with the combined clade named
Scrotifera.

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

But this sister group is not the right place to try and
plot an evolutionary path from; the best place to look for
something like an ancestor is the sister group of Scrotifera,
which consists of most of the familiar insectivores: shrews,
moles, hedgehogs, etc.

But there is a huge problem in even guessing at a
plausible evolutionary path from an completely wingless
insectivore to the most primitive fossil bat known.
This was discussed in the blog I told you about in another
reply:

http://scienceblogs.com/tetrapodzoology/2011/03/05/visualising-protobats/

I was a participant. For a long time, the comments section was
"temporarily closed" but now it is simply "closed." Perhaps
I will start a thread in talk.origins "reopening" the discussion
of this fascinating enigma.

[Peter Nyikos]

On Thursday, March 29, 2018 at 2:15:03 PM UTC-4, Mark Isaak wrote:
> On 3/29/18 6:09 AM, Peter Nyikos wrote:
> > On Wednesday, March 28, 2018 at 10:35:02 PM UTC-4, Mark Isaak wrote:
> >> On 3/28/18 12:52 PM, Peter Nyikos wrote:
> >>> On Wednesday, March 28, 2018 at 12:35:02 AM UTC-4, Mark Isaak wrote:
> >>>> On 3/27/18 2:51 PM, Peter Nyikos wrote:
> >
> > Picking up where I left off, except for a bit of context.
> >
> >>>>> Knee-jerk atheists aside
> >>>>> [several of them are on this thread], one cannot completely
> >>>>> discount the possibility of supernatural intervention, albeit
> >>>>> of a relatively modest sort that is within human capabilities.
> >
> > [...]
> >
> >>>> What does "supernatural intervention" mean?
> >
> > Intervention by a supernatural entity, an entity which is
> > "not bound by the physical laws of this little 13-14 gyo
> > universe," as I put it. ALSO, an intervention by effecting
> > something that is unattainable within the constraints
> > of these physical laws.
>
> Thank you. Now, how would it be possible to tell whether or not
> something is supernatural?

I spent a lot of time in the latter half of last year
discussing this theme with Robert Campa, including
one one hypothetical example and one "real" example--
the "dance of the sun" at Fatima as interpreted by
scientifically naive observers.

I'll see whether I can dig it up. I am too pressed
for time to do so now.

>
If, for example, a being is able to fly
> without wings, talk with beings 100 miles away, and heal illnesses
> caused by other spirits, would that make it supernatural?
>
> "Supernatural" is a label for something found in fantasy.

You are already starting to ignore my definition.

> Like many
> fantasies, people want to think that it appears in reality. But there
> is a huge difference between the concept and the reality.
>
> Consider two candidates for the supernatural. Case 1: A 10-cm-long
> humanoid with wings, glowing with a yellowish light, flies up to your
> children and drops some dust on them. Your children slowly rise into
> the air and, with some practice, are able to fly in a controlled manner.
>
> Is that supernatural? No, it is merely unexplained.

Begging the question.

> Any scientist
> would jump at the chance to find out *how* the dust enables such easy
> flight.


> And since the effect is repeatable, they should have
> opportunities to do so. Maybe they succeed; certainly they will not
> succeed immediately. Their lack of an explanation, however, does not
> mean the explanation is supernatural.

Backpedal from your question-begging "No" noted.

>
> Case 2: When the earth became filled with immorality, there came a
> drought of seven years; seven suns appeared and dried up all the water.
> A fire came which penetrated even to the netherworld. Then the clouds
> released their waters and flooded the entire surface of the earth; rain
> fell for twelve years. One long-lived sage, Markandeya, survived alone.
> As he became fatigued upon the waters, he saw a child seated in a bed
> upon a vast banyan. The child bade Markandeya to enter his body and
> rest. When he went into the child's mouth, Markandeya saw the entire
> universe. A gust of wind later expelled him, the child-deity told a bit
> about who and what he was, and creation began again.
>
> Of course, one problem with calling those events supernatural is that
> there is no evidence that they happened. We have only a story, with no
> way to replicate any part of it.
>
> But even if we grant that the events actually happened, was any of that
> supernatural? Certainly it was outside normal experience. But it was
> not, apparently, outside all nature. The Deity admits to not knowing
> everything,

And the God of the Bible never claimed to be all-knowing
in an absolute sense of the word, the one with which
Aquinas hamstrung theistic theology by putting everything
except nonsensical (including self-contradictory) under it.

> and events such as that are reputed to happen every yuga.
> By my reading, the whole point of the myth is that there *is* a nature
> of which humans are unaware. That conclusion can apply to any fantastic
> story. Even the highest gods exist in some sense of a universe.

I cannot make head nor tail of your last sentence.

>
> [snipping the rest, since this is the point I am interested in]

Not so fast, bub. You are snipping everything we said
about the Resurrection. Can I take this to mean
that you are ashamed of your loaded questions
of the "have you stopped beating your wife yet?" genre?
Or that I have successfully demolished your self-satisfied
but highly deluded closing taunt?

____________________reposted excerpt__________________

++++++++++++++++ end of repost ++++++++++++++++++

Have you fled into "Peter Pan" and Hindu and Mesopotamian myths
in order to escape the issues posed by the Resurrection
account in the NT?

Peter Nyikos

[John Harshman]

On 3/30/18 1:44 PM, Peter Nyikos wrote:
> On Saturday, March 24, 2018 at 9:55:03 AM UTC-4, Ernest Major wrote:
>> On 21/03/2018 22:00, Peter Nyikos wrote:
>>> On Wednesday, March 21, 2018 at 10:35:04 AM UTC-4, Ernest Major wrote:
>
> In this concluding reply, I pick up exactly where I left off
> in the preceding one.
>
>> Clotting factors are enzymes - they catalyze chemical reactions. But not
>> all proteins are enzymes. Some are structural proteins (conceived
>> broadly) such as crystallins and flagellins, some are chemical
>> messengers (e.g. insulin), some are transporters (e.g. haemoglobin), and
>> others are transcription factors*. Transcription factors bind to DNA and
>> control which genes are active (transcribed).
>
> Yes, and the specificity of these factors -- the ones which control
> the expression of a very select group of genes and no others -- is
> where the riddle of their evolution is to be found.

Not much of a riddle. The specificity is in three places: the upstream
cascade that controls where and when the homeobox protein is expressed,
various factors that control whether sequences are unwound enough to be
accessible to binding, and the presence of binding sites in the promoter
regions of target genes.

> This specificity is not in the homeodomain itself. This fragment
> of a given transcription factor can bind to any part of DNA,
> according to the textbook used here to teach beginning biology
> majors, _Biology_, by Campbell, Reese et.al. Rather, it is the
> other parts of the factor that account for the remarkable specificity.

You must be reading that incorrectly. Are you quite sure? And why is
that specificity remarkable? Transcription factors have particular short
sequences (well, binding sites are actually quite flexible and can vary
in binding strength due to small changes in sequence) that they bind to,
and the homeodomain is where the binding happens.

>> Differences between which
>> genes are active in a cell determine cell types, and positional control
>> on where cell types are produced and interactions between them result in
>> tissue types and anatomical structure. Much of the functionality of the
>> system is bound up not in the sequence of the transcription factors, but
>> in the relationship of the binding sites to genes encoding structural
>> and metabolic proteins. Developmentally active transcription factors
>> don't directly specify anatomy - they specify a location with the
>> organism, and it's the action of the downstream genes that build a
>> particular anatomy. As a generality the richer the set of
>> developmentally active transcription factors the greater the variety of
>> cell types and anatomical structures that can be generated - which is
>> seen in the expansion of (different) homeobox gene families in
>> (different) multicellular clades.
>
> The big question here is how far the families I write about above
> are from proteins that do not have such high specificity and do not
> control the transcription of so many downstream genes.

I think you are confused about the sources of specificity.

> It is impossible to quantify such things, but very roughly, to
> what shall we compare this distance to the distance from some group
> of eukaryotes to prokaryotes? Shall the group be something like the
> order Primates, or the phylum Chordates, or the whole animal kingdom?
>
> The subdivisions of whatever group best applies would be compared to
> the various homeobox gene families. Which comparison would work best,
> I wonder?

I do not understand the question.

>> * this is not an exhaustive classification of protein functions.
>>>
>>>> The ANTP (super)family of homeobox proteins contains 14 families in
>>>> total, of which Hox proteins are one. Apparently 4 of these are
>>>> restricted to bilaterians, which suggests duplication events in the
>>>> ancestors of bilaterians. And in general all 14 families would be
>>>> expected to have arise by gene duplication.
>>>
>>> Here too, where's the magic "silver bullet" that autocatalycity [sp?]
>>> provided?
>>>
>>> Got to go now. My ride will soon be waiting for me.
>>>
>>> Peter Nyikos
>>> Professor, Department of Math. -- standard disclaimer --
>>> University of South Carolina
>>> http://people.math.sc.edu/nyikos/
>>>
>>>
>>>> The origin of ANTP seems to where the trail goes cold. Perhaps evolution
>>>> has erased its links with some other older class of homeobox proteins.
>>>> Perhaps I haven't found the right Google incantation. Perhaps molecular
>>>> biologists haven't yet done the work needed to find its homologs.
>
> Finding homologs is very different from even conjecturing a plausible [1]
> evolutionary path.

The best tool we have for determining evolutionary paths is mapping
characters onto phylogenetic trees. That too may not be good enough to
answer the questions you have, but it's the best tool there is.

> [1] By "plausible" I mean one whose individual steps
> do not markedly reduce fitness.
>
> Analogy: We have some rough idea of the "homologs" of Chiroptera (bats).
> It used to be believed that its sister group was in the clade
> {Primates, Dermoptera, Scandentia} but now it appears that their
> closest homolog is Fereuungulata, with the combined clade named
> Scrotifera.
>
> https://en.wikipedia.org/wiki/Scrotifera
>
> But this sister group is not the right place to try and
> plot an evolutionary path from; the best place to look for
> something like an ancestor is the sister group of Scrotifera,
> which consists of most of the familiar insectivores: shrews,
> moles, hedgehogs, etc.
>
> But there is a huge problem in even guessing at a
> plausible evolutionary path from an completely wingless
> insectivore to the most primitive fossil bat known.
> This was discussed in the blog I told you about in another
> reply:
>
> http://scienceblogs.com/tetrapodzoology/2011/03/05/visualising-protobats/
>
> I was a participant. For a long time, the comments section was
> "temporarily closed" but now it is simply "closed." Perhaps
> I will start a thread in talk.origins "reopening" the discussion
> of this fascinating enigma.

You understand that Tetrapod Zoology hasn't been on scienceblogs.com for
a long time, and I believe that the site is now out of business. TetZoo
is at Scientific American currently.

[Mark Isaak]

On 3/30/18 2:47 PM, Peter Nyikos wrote:
> On Thursday, March 29, 2018 at 2:15:03 PM UTC-4, Mark Isaak wrote:

[snip no content of real consequence]

>> [snipping the rest, since this is the point I am interested in]
>
> Not so fast, bub. You are snipping everything we said
> about the Resurrection. Can I take this to mean
> that you are ashamed of your loaded questions
> of the "have you stopped beating your wife yet?" genre?
> Or that I have successfully demolished your self-satisfied
> but highly deluded closing taunt?

Get over yourself.

[Earle Jones]

On 2018-03-31 02:41:35 +0000, Mark Isaak said:

> On 3/30/18 2:47 PM, Peter Nyikos wrote:
>> On Thursday, March 29, 2018 at 2:15:03 PM UTC-4, Mark Isaak wrote:
> [snip no content of real consequence]
>
>>> [snipping the rest, since this is the point I am interested in]
>>
>> Not so fast, bub. You are snipping everything we said
>> about the Resurrection. Can I take this to mean
>> that you are ashamed of your loaded questions
>> of the "have you stopped beating your wife yet?" genre?
>> Or that I have successfully demolished your self-satisfied
>> but highly deluded closing taunt?

*

Easter Joke:

Eight-year-old: The only thing I remember about the resurrection is
this: If it lasts more than four hours, you should call the Doctor.

earle
*

[Ernest Major]

On 26/03/2018 16:11, Peter Nyikos wrote:
> On Saturday, March 24, 2018 at 9:55:03 AM UTC-4, Ernest Major wrote:
>> On 21/03/2018 22:00, Peter Nyikos wrote:
>>> On Wednesday, March 21, 2018 at 10:35:04 AM UTC-4, Ernest Major wrote:

>>>> On 08/03/2018 21:42, Peter Nyikos wrote:
>>>>> Martin Harran is in the same boat. Confronted with the complete

>>>>> inability of even the best minds to figure out an evolutionary

>>>>> pathway, even a hypothetical one, that could culminate in Hox genes,
>>>>> all he can do is regurgitate a claim that this is all just an argument
>>>>> from personal incredulity.
>>>>
>>>> I haven't seen any "design" argument about HOX genes that is more than
>>>> an argument from incredulity.
>>>
>>> That may be because the ID theorists you have read arguments from are
>>> too much in sympathy with classical creationist nonsense, rather
>>> than sophisticated alternatives like that presented by a widely
>>> read agnostic:
>>>
>>> Perhaps there also, among rotting fish heads and blue,
>>> night-burning bog lights, moved the eternal mystery,
>>> the careful finger of God. The increase was not much.
>>> It was two bubbles, two thin-walled little balloons at the
>>> end of the Snout's small brain. The cerebral hemispheres
>>> had appeared.
>>> --Loren Eiseley_The Immense Journey_
>>>
>>> The idea is that evolutionary change could have been effected
>>> by judicious "creation" of mutations at key places in earth history.
>>> By that I mean mutations that are just a little like "hopeful monsters"
>>> but not so drastic as to be outside the ability of species on our
>>> level of intelligence.
>>>
>>
>> I don't know what meaning Eiseley intended - a cursory google didn't
>> turn up a copy of the source. For all I know he, like Dawkins, was
>> cursed with a gift for metaphor. For all I know he was no more a
>> creationist than Einstein.
>
> I think it is pretty well established that he was an agnostic.
> Not that it really matters. The quotation stands on its own
> merits -- an eloquent alternative to both mindless evolution
> and poofing animals into existence. The latter practically
> defines "creationist" in the way it is used by the vast
> majority in talk.origins, AFAIK. Of course that includes
> both OECs and YECs and near-YECs like Martinez who seems
> amenable to a 100 million year old earth, but not much more.

I define creationism as "the religiously motivated rejection of the
substantial proportion of the scientific consensus, especially as it
relates to biology, geology, and cosmology, or the promotion thereof".

That last clause avoids the problem of telling whether someone is a
sincere believer - it captures people who believe, people who are in it
for the money, people with think creationism is a useful instrument of
social control, and people whose motivations are a combination of those
and other motives.

The definition includes Tony Pagano's geocentrism - whether or not he
realises it (he's currently arguing against Newton's Laws of Motion) he
throws away most of physics. It includes Vedic Creationism, even though
it's very different from Abrahamic Creationism. It doesn't include the
rejection of a particular carbon date (such as that of the Turin Shroud,
becauses that's not a substantial proportion of the scientific consensus.)

I could have added "with deliberate intent" to that definition, but that
gets us back to reading people's minds. It is conceivable that someone
could accidently promote creationism from a combination of
Dunning-Kruger syndrome, reflective contrarianism, and bothsidesism - if
one is ignorant of evolutionary biology it easier to treat creationism
with more credibility that it deserves.

Eloquence doesn't entail sophistication. From the viewpoint of
philosophy of science poofing a new allele or a new gene into existence
is no different from poofing a new animal into existence.

And it may not be as far from Ray's beliefs as you think. Ray has stated
that his "created from a clay-like ground" was metaphor. Ray has claimed
that there are "no natural processes" - this would make him an
occasionalist, or possible a Manichaean occasionalist. Since he's coy
about what he thinks actually happened for all I know he could be an
occasionalist-evolutionist (everything happened as science thinks it
did, but God did it). Or if you note his inconsistency about the
existence of natural processes he could be a omphalic progressive
creationist of some form, with God created new species with the
appearance of having evolved. This could be poofing new animals into
existence, but it could be a case of poofing new embryos into existence,
so that for example, a lion gives birth to a tiger, or just changing the
genomes of embryos, by which point the difference from Eiseley is that
Ray would have happening often, and Eiseley rarely. Or it might be that
Ray has no coherent concept of creation, other than evolution is
athiestic and wrong, and trying to infer his beliefs is a fool's errand.

>
>
>> But I don't see on what criteria you identify
>> this as more sophisticated. In some senses ID is more sophisticated - it
>> says that the designer isn't necessarily God, nudge, nudge, wink, wink.
>
> Sorry, I don't indulge in "nudge, nudge, wink, wink." My ID comes
> in two very explicit forms: (1) purely naturalistic in the case of
> directed panspermia (DP) with a confidence approaching 50% in that
> hypothesis, and (2) exemplified by that quote from Eiseley with a
> confidence less than 10%. IOW, (2) a possibility, but not one
> into which I put much stock.
>

Directed panspermia, among other hypotheses, is an alternative to
spontaneous abiogenesis in situ as an origin for life on earth. But it
is not ID. Your models also seem to include directed abiogenesis ex
situ, which would fit the etymology of intelligent design, but for some
reason you deemphasise the directed abiogenesis parts of the model.

Perhaps I shouldn't complain, with my expansive definition of
creationism above, but I don't care for expansive definitions of
Intelligent Design - it refers to a particular movement, and adding
other things that fit the etymology (such as roundup resistant soya or
JCVI-syn3.0) is helpful.
>
>> But you present the interpretation that is on the cusp between theistic
>> evolutionism and progressive creationism.
>
> Yes, "theistic" evolutionism is more aptly named "neo-deistic"
> evolutionism: the attitude that God created the universe
> and then had a hands-off policy until historical Biblical
> times. ["Historical" means roughly the time of Abraham, as
> opposed to prehistorical events like whatever the Noahide flood
> actually referred to originally.]
>
> And your word "present" is very well chosen. I am laying the
> hypothesis out for consideration, without having much confidence
> in its truth. But I am passionately interested in the truth,
> and so I try to cover all reasonable bases.

Ah, but's what's reasonable? Omphalism? Occasionalism? Simulationism?
Individual or Social Solipsism?
>
>
>> You don't come out and say
>> that natural processes couldn't have produced the same mutations - the
>> creationst end of theistic evolution says that evolution could have
>> produced a biota of equivalent complexity, but God intervened to select
>> a particular path among the stochastic choices, while theistic
>> evolutionist end of progressive creationism claims that natural
>> processes are incapable of producing the observed results.
>
> I think like a scientist *qua* scientist about these things, and hence am
> in suspended judgment about them. I do not confuse the currently
> accepted methodology of science with the thinking of flesh
> and blood scientists.
>
>
>> I don't know how to describe the former (an argument from credulity? -
>> "God could have done it"), but is unfalsifiable and a religious rather
>> than a scientific position.
>
> So is something that seems to be the be-all and end-all of the
> majority of anti-ID participants:
>
> Darwin of the Gaps
>
> This is the default, one-size-fits-all, totally unfalsifiable
> naturalistic explanation for any and all biological phenomena:
>
> "Well, it's natural selection, y'know. The __________ that did/could/
> are __________ had a survival advantage over the ones that didn't/
> couldn't/weren't and so they are the ones we see today."
>
> Fortunately, you yourself have a lot more going for you than this
> analogue of "god of the gaps."
>
I think that is a false equivalence. God of the gaps refers to the
argument that we don't know how something happens, therefore God did it,
therefore God totally exists. Note that God is the conclusion.

What you disparage as "Darwin of the gaps" is that we know that
evolutionary processes exist, and we know of no reason why they couldn't
have achieved the observed results, so we provisionally infer that they
did achieve them. Occam's Razor applies. Note that no-one is using this
as an argument for the existence of natural selection - we have more
direct evidence.

You've also managed to repeat a couple of mistakes that creationists
often make. Firstly evolutionary processes are not restricted to
mutation and natural selection. The precise number of processes is open
to terminological issues - is allopolyploidy mutation or gene flow or
something else? is recombination included in mutation? is sexual
selection different from natural selection? is population isolation an
evolutionary process? Secondly it's reproductive advantage, not survival
advantage.
>
>
>> I would appeal to Occam's Razor to discount
>> it. (When I included interuniversal transfer among a list of imaginable
>> origins of life of earth you commented that was going too far, so you do
>> accept that principle that we don't need to consider all ideas
>> seriously.)
>
> I try to stay within the bounds of our current understanding
> of physics. Even the "careful finger of God" could be mimicked
> by extraterrestrials on a level of intelligence comparable
> to ours, but the possibilities are just too speculative.
>
> I tried to do the best I could in my latest reply to Öö Tiib,
> but my imaginative scenario turned out to be another case of

> a "beautiful theory killed by a brutal gang of cold facts"
> about globular clusters. I found that out over the weekend
> by reading Chapter 14 in a great book by planetary scientist
> John L. Lewis, _Worlds_Without_End.
>
>

>> The latter is in principle testable - it predicts a bias in
>> mutations - but in practice it can be made resistant to falsification by
>> making the bias vanishingly small, or by banishing it to the past (now
>> we have the pinnacle of creation it's not needed any more), but it's
>> just as much an argument from incredulity as the appeal to Hox genes as
>> evidence of design.
>
> Whereas Darwin of the Gaps is an argument from personal credulity.
>
>
>> In either case, one wonders why God didn't choose to or was unable to
>> create an evolutionary process that didn't require intervention.
>
> Because a God of that magnitude strains even the possibilities
> of a multiverse with infinitely many physical universes. I could
> never arrive at a 10% confidence -- or even a 0.01% confidence --
> in a hypothesis that rested in such a God. The various
> forms of the Ontological Argument for an infinite God are just
> too fallacious.

Cosmological Argument?
>
>
>> (Note that as a species we're probably better at producing gross changes
>> than subtle ones. For example we could knock out a plant homeobox gene
>> to produce a flower with a grossly different structure.
>
> Plants are one thing, animals are another. Scroll down to the
> bottom of the following blog, and read the last few posts,
> about the difficulties of tampering with the geomes of mice
> to give them the ability to fly with bat-like wings.
>
> http://scienceblogs.com/tetrapodzoology/2011/03/05/visualising-protobats/
>
>
>> What we do more
>> often is move traits from one species to another - for example replacing
>> a crop 5-enolpyruvoyl-shikimate-3-phosphate synthetase with one from
>> Agrobacterium - or introducing insulin synthesis into a bacterium, or
>> extending a plant secondary metabolite chain to produce a new pigment.)
>
> Child's play compared to a mice-to-batlike-rodents change.
>

I thought that Eiseley was proposing subtle changes - small swellings in
the brain which eventually became the cerebral hemispheres. If you're
suggesting saltational change instead your "sophisticated" alternative
looks more like creationism.
>
> Remainder deleted, to be replied to later, perhaps only tomorrow.
> I have back-to-back classes to teach in less than an hour.

>
>
> Peter Nyikos
> Professor, Department of Math. -- standard disclaimer --

> U. of South Carolina at Columbia
> http://www.math.sc.edu/~nyikos/
>


--
alias Ernest Major

[Ernest Major]

On 01/04/2018 22:25, Ernest Major wrote:
>
> You've also managed to repeat a couple of mistakes that creationists
> often make. Firstly evolutionary processes are not restricted to
> mutation and natural selection. The precise number of processes is open
> to terminological issues - is allopolyploidy mutation or gene flow or
> something else? is recombination included in mutation? is sexual
> selection different from natural selection? is population isolation an
> evolutionary process? Secondly it's reproductive advantage, not survival
> advantage.

Postscript: And do you count emergent processses such as
subfunctionalisation or neofunctionalisation separately?

--
alias Ernest Major

[Peter Nyikos]

On Saturday, March 31, 2018 at 8:50:02 PM UTC-4, Earle Jones wrote:
> On 2018-03-31 02:41:35 +0000, Mark Isaak said:
>
> > On 3/30/18 2:47 PM, Peter Nyikos wrote:
> >> On Thursday, March 29, 2018 at 2:15:03 PM UTC-4, Mark Isaak wrote:

<snip of a snip-n-snark by Isaak here>

> >>> [snipping the rest, since this is the point I am interested in]
> >>
> >> Not so fast, bub. You are snipping everything we said
> >> about the Resurrection. Can I take this to mean
> >> that you are ashamed of your loaded questions
> >> of the "have you stopped beating your wife yet?" genre?
> >> Or that I have successfully demolished your self-satisfied
> >> but highly deluded closing taunt?
>
> *
>
> Easter Joke:

And very timely, since you posted it the day before this
year's Easter Sunday. [That is, according to the Roman
Catholic calendar; the Orthodox usually have it later.]

> Eight-year-old: The only thing I remember about the resurrection is
> this: If it lasts more than four hours, you should call the Doctor.
>

Funny, I was expecting a "zombie" style punch line -- doctors
are not supposed to have some extra ways of dealing with
the zombies of fiction, are they?

Could it be that zombies are now more popular among atheists
than Jesus or people who literally believe in the Resurrection?

Is your attitude towards the latter kind of people similar
to that of Mark Isaak in a passage that he has twice snipped?
Here is that passage, with names added in brackets and
deletia denoted by [...]:

____________________ re-repost _______________________

[Mark:}

> Why would you say that Jesus rising
> from the dead was supernatural, and not a very rare natural occurrence?

[Peter:]

Because I don't say it, I say how someone who believes it
would use "supernatural". [See above for hints as to
probable usage.] Knowledgeable Christians know that there
is nothing in the Bible that constrains God from raising
other people from the dead LONG before "the Last Judgment."

[...]

[Caution:
"atheistic" can mean "from demythologizing liberal `Protestant'
theology."]

[...]

[Mark:]
> >> in which case it only makes sense that [supernatural
> >> events] be completely discounted as unknowable and therefore
> >> profitless to contemplate.

[Peter:]

> > Don't you just wish the Apostle Paul had thought the way you do and
> > never wrote 1 Corinthians 15?
>
> Don't even try, Peter. You're not good at religion.

Transparent bluff, using the word "religion" in place
of "liberal theology." [See above.]

I LIVED the Christian religion until I was 21, and
have done extensive reading in it. You are like the
liberal theologian who once said to John Warwick Montgomery [1],
who actually believes that Jesus rose from the dead,
"I didn't know there were still people like you around."

[1] https://en.wikipedia.org/wiki/John_Warwick_Montgomery

+++++++++++++++++++++ end of excerpts +++++++++++++++++++++

You may be surprised too, Earle, if you read the
Wikipedia entry, to know that there are still theologians
like Montgomery around. He's had quite a distinguished
career, from the looks of it.

Peter Nyikos

[Peter Nyikos]

On Friday, March 30, 2018 at 10:45:02 PM UTC-4, Mark Isaak wrote:
> On 3/30/18 2:47 PM, Peter Nyikos wrote:
> > On Thursday, March 29, 2018 at 2:15:03 PM UTC-4, Mark Isaak wrote:
> [snip no content of real consequence]

... yours, along with a few comments by me exposing
the fallaciousness of one of them, your backpedal from that
question-begging fallacy, and the incomprehensibility
of a closing sentence by you.

Yes, your comments about Tinker Bell and a hero of
a farfetched myth ARE of no real consequence, except
as a cover for your failure to follow through on
an aggressive bluff about the Resurrection after
I called that bluff.

> >> [snipping the rest, since this is the point I am interested in]
> >
> > Not so fast, bub. You are snipping everything we said
> > about the Resurrection. Can I take this to mean
> > that you are ashamed of your loaded questions
> > of the "have you stopped beating your wife yet?" genre?
> > Or that I have successfully demolished your self-satisfied
> > but highly deluded closing taunt?

Secure in the power with which you are allied [see closing
remarks by me below], you jeered:

> Get over yourself.
>

Translation: "You need to stop being so uppity."

This refers to something I wrote to a person of
power in t.o. with whom your ignorance about
non-liberal theology is allied. It was
Hemidactylus, to whom I wrote the following this afternoon:

____________________ excerpt _________________

The scorn which you have heaped on me since exactly four years before
yesterday is very similar to the scorn that white supremacists of the
old Jim Crow South heaped on people they called "Good N_____s."
While these people of the underdog race were fair game for all kinds
of jeers and condescending remarks, one could also expect
some white man who commanded some respect from the hotheads
to smooth things over if one of these non-whites were threatened
with lynching or even with just being tarred and feathered.


Similarly, if someone were to announce in t.o. that he would subject me
to physical violence, I do believe you would step in and say something
like the following:

While I agree that Peter Nyikos can sound very
[put equivalent of "uppity" here],
he is also capable of behaving like a model
[put equivalent of "good n_____" here]
towards his betters. Give me some time to knock
some good sense into him, and I'm sure he will
treat you with the respect that you deserve,
or else not talk about or to you at all.

================== end of excerpt from
https://groups.google.com/d/msg/talk.origins/RmJfq-PdDl0/3XdSfjbMAQAJ

Subject: Re: Judge Jones and Plagiarism at the Dover Trial.?

Date: Mon, 2 Apr 2018 12:17:57 -0700 (PDT)
Message-ID: <f52b76f1-ad19-4174...@googlegroups.com>


Can I count on you to also make such statements, befitting
the lofty station to which you think you belong, if someone
were to claim on t.o. that he would subject me to violence?

> --
> Mark Isaak eciton (at) curioustaxonomy (dot) net
> "Ignorance, allied with power, is the most ferocious enemy justice can
> have." - James Baldwin

You are allied with power in talk.origins, in the form
of Hemidactylus and eight other people like you and him,
so you can safely ignore such comments as the one you
snipped at the end:

Have you fled into "Peter Pan" and Hindu ... myths

in order to escape the issues posed by the Resurrection
account in the NT?

You are quite comfortable with silly stories no one
takes seriously, but when it comes to something which close
to a billion ordinary people believe, along with some
formidable theologians like John Warwick Montgomery,
you keep snipping the things I say about them.

But you are in good company. The mainstream media,
and innumerable books on philosophy have a way
of ignoring such inconvenient data and
focus instead on secular philosophers like John Dewey [1]
and the "titans" of 20th century theology,
like the demonstrably atheistic Paul Tillich and
the nebulous [2] Hans Küng [3].

[1] But not William James, who had a healthy respect
for theism, as opposed to atheism masquerading as
liberal Protestantism.

[2] At least, in his reasons for believing in what he calls God.

[3] Still active at the age of 94.

Peter Nyikos

[Peter Nyikos]

On Monday, April 2, 2018 at 6:00:04 PM UTC-4, Peter Nyikos wrote:
> The mainstream media,
> and innumerable books on philosophy have a way
> of ignoring such inconvenient data and
> focus instead on secular philosophers like John Dewey [1]
> and the "titans" of 20th century theology,
> like the demonstrably atheistic Paul Tillich and
> the nebulous [2] Hans Küng [3].
>
> [1] But not William James, who had a healthy respect
> for theism, as opposed to atheism masquerading as
> liberal Protestantism.
>
> [2] At least, in his reasons for believing in what he calls God.
>
> [3] Still active at the age of 94.

Correction: age 90. He was born on February 19, 1928.

[*Hemidactylus*]

No just get over yourself. Stop the vindictive vice.

This is weird. You are casting us as a lynch mob as seen in movies such as
Rosewood that show true injustice and racism at root worst. Are you really
trying to sell that horrid distortion and calumny against Mark, me, and
others? That aspersion sickens me to the core. Apologize.

Let’s flip the script to a factual emphasis with recent relevance. Tell me
yes or no. Should the confederate flag and southern heritage monuments be
removed from public spaces? If not why? What does such symbolism promote?
Well being of black citizens? I am concerned with the true victims of
racist white privilege, not the ruffled feathers of snowflake Ole Pete.

>
>> --
>> Mark Isaak eciton (at) curioustaxonomy (dot) net
>> "Ignorance, allied with power, is the most ferocious enemy justice can
>> have." - James Baldwin
>
> You are allied with power in talk.origins, in the form
> of Hemidactylus and eight other people like you and him,
>

That you are now casting as a lynch mob with no real concern expressed for
people who really suffered such fates. Otherwise you would not be cynically
be metaphorizing in that sickening direction. If you are morally consistent
you will fight confederate heritage expression tooth and nail everywhere
you see it. Good luck with that in South Carolina.

>
> so you can safely ignore such comments as the one you
> snipped at the end:
>
> Have you fled into "Peter Pan" and Hindu ... myths
> in order to escape the issues posed by the Resurrection
> account in the NT?
>
> You are quite comfortable with silly stories no one
> takes seriously, but when it comes to something which close
> to a billion ordinary people believe, along with some
> formidable theologians like John Warwick Montgomery,
> you keep snipping the things I say about them.
>
> But you are in good company. The mainstream media,
> and innumerable books on philosophy have a way
> of ignoring such inconvenient data and
> focus instead on secular philosophers like John Dewey [1]
> and the "titans" of 20th century theology,
> like the demonstrably atheistic Paul Tillich and
> the nebulous [2] Hans Küng [3].
>

Are you accurately portraying Tillich? What was the deal then with ultimate
concern? Sounds similar to Jung’s soul searching.

>
> [1] But not William James, who had a healthy respect
> for theism, as opposed to atheism masquerading as
> liberal Protestantism.
>

Is that a Catholic bash on heresy?

[Mark Isaak]

On 4/2/18 2:57 PM, Peter Nyikos wrote:
> On Friday, March 30, 2018 at 10:45:02 PM UTC-4, Mark Isaak wrote:

> [...]
>> Get over yourself.
>
> [snip epic fail]

I am interested in the subject of what "supernatural" really (no pun
intended) means. You obviously are not. Apparently, the subject
detracts from your overriding obsession to lambaste anyone who so much
as hints that your moral judgment is less than godlike.

[Peter Nyikos]

On Thursday, March 29, 2018 at 11:50:02 PM UTC-4, jillery wrote her usual mangling of the attribution line to me, preparatory
as usual to travesty-filled behavior by her.

> On Thu, 29 Mar 2018 06:09:59 -0700 (PDT), Peter Nyikos
> <nyi...@bellsouth.net> continued to ejaculate his repetitive
> irrelevant spew from his puckered sphincter:
>
> Is anybody surprised.
>
> <snip your irrelevant spew>
>
>
> >> >>> Knee-jerk atheists aside
> >> >>> [several of them are on this thread], one cannot completely
> >> >>> discount the possibility of supernatural intervention, albeit
> >> >>> of a relatively modest sort that is within human capabilities.
> >
> >[...]
> >
> >> >> What does "supernatural intervention" mean?
> >
> >Intervention by a supernatural entity, an entity which is
> > "not bound by the physical laws of this little 13-14 gyo
> >universe," as I put it. ALSO, an intervention by effecting
> >something that is unattainable within the constraints
> >of these physical laws.
> >
> >Jillery confused these two senses when she ignorantly
> >claimed that I had been incoherent in the first paragraph
> >that I've kept in above. As you can see, I had used the word
> >in the first sense but NOT in the second sense.
>
>
> Of course,

Thanks for providing the documentation you were confident
I would never provide, of you using "Of course" in the
same dishonest way Martinez habitually uses "Imagine that!"

> Jillery confused no such thing, ignorantly or otherwise. As
> shown by the quoted text above, you claim human capabilities can be
> supernatural,

Sneaky "can be supernatural" substitution of "can be shared
by supernatural beings," noted.

> and also admit that supernatural intervention is
> unattainable within the constraints of these physical laws.

Your convoluted language hides the plain meaning
of what I wrote: that it is the supernatural BEINGS
that are not constrained by these physical laws [1]
and that *some* of their "effects" also violate these laws [2].

This was a *supplement* to what I had written earlier, [3]
indicating that some of their *other* effects could be within
human capabilities, including the producing of mutations
in organisms.

[1] See first definition.

[2] See second definition, beginning with "ALSO"

[3] See the first paragraph of earlier text that
was preserved in this post.

> So unless
> you think humans can intervene beyond the constraints of physical
> laws, your understanding of "supernatural" is a Martinez-style
> incoherence.

Plato probably had extensive experience with sophists like
yourself. He could hardly have composed the Socratic dialogue
"Euthydemus" otherwise.

http://classics.mit.edu/Plato/euthydemus.1b.txt

> Of course, it's almost certain you will never admit you're wrong.

There you go again. But this time, you will have to
show people WHY I am supposedly wrong before your
statement becomes an insult rather than a compliment
to my fortitude in refuting you in detail.

I've snipped a one-liner by you whose words I
have woven into a take-off on the song, "Click Go the Shears".
The latest version of that weaving can be found here:



https://groups.google.com/d/msg/talk.origins/RmJfq-PdDl0/DokoNFYVAgAJ

Subject: Re: Judge Jones and Plagiarism at the Dover Trial.?

Date: Tue, 3 Apr 2018 10:39:09 -0700 (PDT)
Message-ID: <fb1a7297-734f-41ac...@googlegroups.com>


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

University of South Carolina
http://people.math.sc.edu/nyikos/

PS Plato's "Euthydemus" is profoundly insightful in some places
and hilariously funny in others, but I expect an
amoral philistine like yourself to miss out on
both of these aspects.

[Peter Nyikos]

I'll try to remember that long definition, but since I
never encountered it before, please bear with me if I
don't recall it accurately.

I do have one problem with it: what do you mean by "religiously
motivanted"? There are any number of people who have creationist
views that simply accept the many arguments [1] that
people with whom they are familiar give, without having a chance
to see the evidence of science.


[1] Some are a lot more clever than the ones that self-identified
creationists in talk.origins make. Ray Martinez almost never
makes any, but instead harps on this or that person being
an "Atheist."

> That last clause avoids the problem of telling whether someone is a
> sincere believer - it captures people who believe, people who are in it
> for the money, people with think creationism is a useful instrument of
> social control, and people whose motivations are a combination of those
> and other motives.

On the other side of the ledger, many if not most of the
non-creationists posting here seem to have a motivation that
is political rather than scientific. They've read many
read provocative denunciations of the shenanigans of
creationists and want to have something to do about it.

Also, I believe most of the non-creationists posting here are not sufficiently well versed in science to do anything but repeat
little sound bites that they have seen over the years in
very elementary popularizations of what evolution is like.

> The definition includes Tony Pagano's geocentrism - whether or not he
> realises it (he's currently arguing against Newton's Laws of Motion) he
> throws away most of physics.

I haven't seen much of that, only of him using frames of reference
to argue for a modern modification of Tycho Brahe's
heliocentric-but-for-earth-and-moon-system which recognizes the
existence of parallax. If Tycho had known about the parallax
that we can observe with our powerful telescopes, my guess
is that he would have gone over to the Copernican hypothesis.


Continued in next reply to this post, soon after I see that
this one has posted.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

U. of So. Carolina at Columbia
http://www.math.sc.edu/~nyikos/

[Peter Nyikos]

On Sunday, April 1, 2018 at 5:30:05 PM UTC-4, Ernest Major wrote:
> On 26/03/2018 16:11, Peter Nyikos wrote:
> > On Saturday, March 24, 2018 at 9:55:03 AM UTC-4, Ernest Major wrote:
> >> On 21/03/2018 22:00, Peter Nyikos wrote:

> >>> The idea is that evolutionary change could have been effected
> >>> by judicious "creation" of mutations at key places in earth history.
> >>> By that I mean mutations that are just a little like "hopeful monsters"
> >>> but not so drastic as to be outside the ability of species on our
> >>> level of intelligence.

<snip to get closer to new material; the following paragraph was
addressed in my first reply to this post, but is included for context>

> I define creationism as "the religiously motivated rejection of the
> substantial proportion of the scientific consensus, especially as it
> relates to biology, geology, and cosmology, or the promotion thereof".
>
> That last clause avoids the problem of telling whether someone is a
> sincere believer - it captures people who believe, people who are in it
> for the money, people with think creationism is a useful instrument of
> social control, and people whose motivations are a combination of those
> and other motives.
>
> The definition includes Tony Pagano's geocentrism - whether or not he
> realises it (he's currently arguing against Newton's Laws of Motion) he
> throws away most of physics.

Do you know what Pagano means when he calls himself a creationist?

> It includes Vedic Creationism, even though
> it's very different from Abrahamic Creationism.

IIRC Kalkidas endorses this. Anyone else active in t.o. that
you know of?

> It doesn't include the
> rejection of a particular carbon date (such as that of the Turin Shroud,
> becauses that's not a substantial proportion of the scientific consensus.)

And there is some controversy over whether the part tested
for Carbon-14 is from the original shroud or from a portion that
replaced a fire-damaged corner and had been skillfully
rewoven into the rest.

>
> I could have added "with deliberate intent" to that definition, but that
> gets us back to reading people's minds. It is conceivable that someone
> could accidently promote creationism from a combination of
> Dunning-Kruger syndrome, reflective contrarianism, and bothsidesism - if
> one is ignorant of evolutionary biology it easier to treat creationism
> with more credibility that it deserves.

Not to mention that some creationist tracts make a big show
of presenting parts of the scientific evidence (or distortions
thereof) and cleverly "refuting" it (or in the latter case, actually
refuting it sometimes). What's someone with average knowledge
of science [i.e., very low knowledge] supposed to think?

> Eloquence doesn't entail sophistication. From the viewpoint of
> philosophy of science poofing a new allele or a new gene into existence
> is no different from poofing a new animal into existence.

Come on now! We can create new alleles of existing genes
easily, and the day may not be far off when we successfully
incorporate whole genes.

In fact, I vaguely recall an award-winning science experiment
in which a student put a strand of DNA with a coded message
into a microorganism, and it was found in its descendants.
Mayhap it even coded for a polypeptide.

> And it may not be as far from Ray's beliefs as you think. Ray has stated
> that his "created from a clay-like ground" was metaphor. Ray has claimed
> that there are "no natural processes" - this would make him an
> occasionalist, or possible a Manichaean occasionalist. Since he's coy
> about what he thinks actually happened for all I know he could be an
> occasionalist-evolutionist (everything happened as science thinks it
> did, but God did it). Or if you note his inconsistency about the
> existence of natural processes he could be a omphalic progressive
> creationist of some form, with God created new species with the
> appearance of having evolved. This could be poofing new animals into
> existence, but it could be a case of poofing new embryos into existence,
> so that for example, a lion gives birth to a tiger, or just changing the
> genomes of embryos, by which point the difference from Eiseley is that
> Ray would have happening often, and Eiseley rarely. Or it might be that
> Ray has no coherent concept of creation, other than evolution is
> athiestic and wrong, and trying to infer his beliefs is a fool's errand.

Thanks for illustrating just how evasive Ray is about his beliefs.
Ron Okimoto is, if anything, even more evasive. He calls himself
a creationist because he claims to believe in a "creator" but has
very carefully avoided saying anything about that alleged creator
to which he could be pinned down.

> >
> >
> >> But I don't see on what criteria you identify
> >> this as more sophisticated. In some senses ID is more sophisticated - it
> >> says that the designer isn't necessarily God, nudge, nudge, wink, wink.
> >
> > Sorry, I don't indulge in "nudge, nudge, wink, wink." My ID comes
> > in two very explicit forms: (1) purely naturalistic in the case of
> > directed panspermia (DP) with a confidence approaching 50% in that
> > hypothesis, and (2) exemplified by that quote from Eiseley with a
> > confidence less than 10%. IOW, (2) a possibility, but not one
> > into which I put much stock.
> >
>
> Directed panspermia, among other hypotheses, is an alternative to
> spontaneous abiogenesis in situ as an origin for life on earth. But it
> is not ID.

It does, however, open the door wide to ID. I have been expounding
on a hypothesis of a very big ID project in reply to Öö Tiib,
but even if the panspermists shared our biochemistry, there
is still room for a bit of ID:

The senders could well have developed wholly new strains of
microorganisms, specially designed to cope with prebiotic
conditions, though whether it would have been better to try to
combine all the desirable properties within one single type
of organism or to send many different organisms is not
completely clear.
--Nobel Laureate Francis Crick, _Life Itself_
Simon and Schuster, 1981, p. 137

The "senders" to which Crick refers are hypothetical directed
panspermists: intelligent creatures of almost 4 billion years
ago who sent microorganisms to earth, which according to the
hypothesis had an ocean rich in amino acids and various
other organic materials but no living things as yet.

> Your models also seem to include directed abiogenesis ex
> situ, which would fit the etymology of intelligent design, but for some
> reason you deemphasise the directed abiogenesis parts of the model.

That's because there are many possibilities for the "senders".
They might just have indulged in genetic engineering of the sort
which we should be able to carry out before the end of the
21st century.

>
> Perhaps I shouldn't complain, with my expansive definition of
> creationism above, but I don't care for expansive definitions of
> Intelligent Design - it refers to a particular movement, and adding
> other things that fit the etymology (such as roundup resistant soya or
> JCVI-syn3.0) is helpful.

However, the best of the ID theorists, including Behe, avoid
restricting the scope of ID in their *methodology*. It is no
different than an atheist restricting methodology to the
form accepted by NAS -- the atheism of the person is irrelevant
to the validity of the methodology.

> >> But you present the interpretation that is on the cusp between theistic
> >> evolutionism and progressive creationism.
> >
> > Yes, "theistic" evolutionism is more aptly named "neo-deistic"
> > evolutionism: the attitude that God created the universe
> > and then had a hands-off policy until historical Biblical
> > times. ["Historical" means roughly the time of Abraham, as
> > opposed to prehistorical events like whatever the Noahide flood
> > actually referred to originally.]
> >
> > And your word "present" is very well chosen. I am laying the
> > hypothesis out for consideration, without having much confidence
> > in its truth. But I am passionately interested in the truth,
> > and so I try to cover all reasonable bases.
>
> Ah, but's what's reasonable? Omphalism? Occasionalism? Simulationism?
> Individual or Social Solipsism?

No to all of the above. My idea of a reasonable basis is one
that proceeds by considering the best that cosmology has to
offer, and working within that.

And purely materialistic evolution is the conclusion of people
endorsing "Darwin of the Gaps." One sees it in an unequivocal
statement by Mark Isaak:

_________________ excerpt from reply to Mark__________________

> Consider two candidates for the supernatural. Case 1: A 10-cm-long
> humanoid with wings, glowing with a yellowish light, flies up to your
> children and drops some dust on them. Your children slowly rise into
> the air and, with some practice, are able to fly in a controlled manner.
>
> Is that supernatural? No, it is merely unexplained.

Begging the question.

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

I'll leave it to you to guess whether Mark deleted everything
you see above from his reply, and whether he deleted my
calling attention to it in the next round.

> What you disparage as "Darwin of the gaps" is that we know that
> evolutionary processes exist, and we know of no reason why they couldn't
> have achieved the observed results,

Nor do we know of a reason why natural selection might have
favored any number of them. Consider the example I gave
at the end.


<snip of many things to be dealt with later this week>

> >> (Note that as a species we're probably better at producing gross changes
> >> than subtle ones. For example we could knock out a plant homeobox gene
> >> to produce a flower with a grossly different structure.
> >
> > Plants are one thing, animals are another. Scroll down to the
> > bottom of the following blog, and read the last few posts,
> > about the difficulties of tampering with the geomes of mice
> > to give them the ability to fly with bat-like wings.
> >
> > http://scienceblogs.com/tetrapodzoology/2011/03/05/visualising-protobats/
> >
> >
> >> What we do more
> >> often is move traits from one species to another - for example replacing
> >> a crop 5-enolpyruvoyl-shikimate-3-phosphate synthetase with one from
> >> Agrobacterium - or introducing insulin synthesis into a bacterium, or
> >> extending a plant secondary metabolite chain to produce a new pigment.)
> >
> > Child's play compared to a mice-to-batlike-rodents change.
> >
>
> I thought that Eiseley was proposing subtle changes - small swellings in
> the brain which eventually became the cerebral hemispheres. If you're
> suggesting saltational change instead

No, I am staying completely within the mainstream evolutionary theory.
It proposes even more subtle changes than Eiseley's, not less.

> your "sophisticated" alternative
> looks more like creationism.

Sorry, you misunderstood: here I was no longer proposing alternatives
to the existing paradigm with the example of bats. Instead,
I am illustrating how far "Darwin of the Gaps" is from something
that evolutionary theory can handle at our present state of
knowledge.

Back around 1998 I proposed sexual selection to get around
the difficulty of visualizing protobats that were ALL clearly
not much less fit as their immediate ancestors. The people
who responded would have none of it, because they didn't
think that there were any cases of sexual selection which
drastically changed the anatomy of both sexes.

One of them was the militant atheist PZ Myers, by the way.
So he actually did his cause a disservice by making me
go back to the drawing board. There I've stayed ever
since, with my contribution to the tetrapodzoology confined
to pointing out gaps in the proposed scenarios.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

U. of So. Carolina at Columbia
http://www.math.sc.edu/~nyikos/

[jillery]

On Tue, 3 Apr 2018 10:53:01 -0700 (PDT), Peter Nyikos

<nyi...@bellsouth.net> continued to ejaculate his repetitive
irrelevant spew from his puckered sphincter:

Is anybody surprised.

<snip your irrelevant spew>


>> >> >>> Knee-jerk atheists aside
>> >> >>> [several of them are on this thread], one cannot completely
>> >> >>> discount the possibility of supernatural intervention, albeit
>> >> >>> of a relatively modest sort that is within human capabilities.
>> >
>> >[...]
>> >
>> >> >> What does "supernatural intervention" mean?
>> >
>> >Intervention by a supernatural entity, an entity which is
>> > "not bound by the physical laws of this little 13-14 gyo
>> >universe," as I put it. ALSO, an intervention by effecting
>> >something that is unattainable within the constraints
>> >of these physical laws.
>> >
>> >Jillery confused these two senses when she ignorantly
>> >claimed that I had been incoherent in the first paragraph
>> >that I've kept in above. As you can see, I had used the word
>> >in the first sense but NOT in the second sense.
>>
>>

>> Of course, Jillery confused no such thing, ignorantly or otherwise. As

>> shown by the quoted text above, you claim human capabilities can be
>> supernatural,
>
>Sneaky "can be supernatural" substitution of "can be shared
>by supernatural beings," noted.

Of course, you merely assert "sneaky" without even identifying how
anything I wrote qualifies.

>> and also admit that supernatural intervention is
>> unattainable within the constraints of these physical laws.
>
>Your convoluted language

Your convoluted language disqualifies you from complaining about my
alleged convoluted language. Tu quoque back atcha, asshole.

>hides the plain meaning
>of what I wrote: that it is the supernatural BEINGS
>that are not constrained by these physical laws [1]
>and that *some* of their "effects" also violate these laws [2].

Of course, my point stands whether your "supernatural" refers to
BEINGS or their "effects". Of course, you don't have the personal
integrity to reply to the post where I made my point.

>This was a *supplement* to what I had written earlier, [3]
>indicating that some of their *other* effects could be within
>human capabilities, including the producing of mutations
>in organisms.
>
>[1] See first definition.
>
>[2] See second definition, beginning with "ALSO"
>
>[3] See the first paragraph of earlier text that
>was preserved in this post.
>
>
>> So unless
>> you think humans can intervene beyond the constraints of physical
>> laws, your understanding of "supernatural" is a Martinez-style
>> incoherence.
>
>Plato probably had extensive experience with sophists like
>yourself. He could hardly have composed the Socratic dialogue
>"Euthydemus" otherwise.

Your sophistry disqualifies you from complaining about my alleged
sophistry. Tu quoque back atcha, asshole.

<snip your remaining repetitive spew>

[Mark Isaak]

On 4/3/18 2:24 PM, Peter Nyikos wrote:
> [...]

> On the other side of the ledger, many if not most of the
> non-creationists posting here seem to have a motivation that
> is political rather than scientific.

What do you mean by "political"? I have, from time to time, heard
humans described as political animals, which would make everyone
(excepting possibly bots) political automatically. Do you have in mind
a narrower definition?

[Peter Nyikos]

On Wednesday, April 4, 2018 at 12:50:03 AM UTC-4, Mark Isaak wrote:
> On 4/3/18 2:24 PM, Peter Nyikos wrote:
> > [...]
> > On the other side of the ledger, many if not most of the
> > non-creationists posting here seem to have a motivation that
> > is political rather than scientific.
>
> What do you mean by "political"?

You are heavily in tune with the politics of ID vs. undirected
evolution, but have little interest in the scientific side of things.

And all the evidence I've seen over the years suggests that your
are also incompetent at the scientific side, and compensate with
a vast repertoire of dirty debating tactics, including some
you've indulged in this week and the previous one.


I am referring to your lack of interest in, and of competence in
dealing with, one of the theological sides in the case of
Jesus's alleged Resurrection dispute. You prefer to act as though
the whole dispute were between the evasive nuances of some leading
liberal theologians [1], and those who proudly display their
atheistic allegiance.


[1] I'll have more to say about that "titan" of liberal theology,
Paul Tillich, in reply to your fellow outspoken radical
leftist Hemidactylus.

The outspokenness, radicalism, and leftism were especially
evident on the day after the November election. The two
of you even feigned paranoia about the outcome.

> I have, from time to time, heard
> humans described as political animals, which would make everyone
> (excepting possibly bots) political automatically. Do you have in mind
> a narrower definition?

Yes, see above.

Will you now ignore the substantive issues, and pretend
to be ONLY interested in a definition of "political animal"?
That was what you dishonestly claimed to be wrt "supernatural
intervention," [2] when you tried to deflect attention from
your fallacy of begging the question on an issue that had
NOTHING to do with the definition* of "supernatural intervention."
but only with what counts as overwhelming evidence for supernatural occurrences.

[2] To better fool readers, you did a snip-n-snark on your
entire debacle, and took refuge in equivocation: you never
spelled out whether you were looking for a definition
that you could forever after insist was the ONLY correct one,
or whether you were compiling a list of all definitions that
have ever been used in t.o., including some of yours.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --
U. of So. Carolina

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

[*Hemidactylus*]

Peter Nyikos <nyi...@bellsouth.net> wrote:
> On Wednesday, April 4, 2018 at 12:50:03 AM UTC-4, Mark Isaak wrote:
>> On 4/3/18 2:24 PM, Peter Nyikos wrote:
>>> [...]
>>> On the other side of the ledger, many if not most of the
>>> non-creationists posting here seem to have a motivation that
>>> is political rather than scientific.
>>
>> What do you mean by "political"?
>
> You are heavily in tune with the politics of ID vs. undirected
> evolution, but have little interest in the scientific side of things.
>
> And all the evidence I've seen over the years suggests that your
> are also incompetent at the scientific side, and compensate with
> a vast repertoire of dirty debating tactics, including some
> you've indulged in this week and the previous one.
>
>
> I am referring to your lack of interest in, and of competence in
> dealing with, one of the theological sides in the case of
> Jesus's alleged Resurrection dispute. You prefer to act as though
> the whole dispute were between the evasive nuances of some leading
> liberal theologians [1], and those who proudly display their
> atheistic allegiance.
>
>
> [1] I'll have more to say about that "titan" of liberal theology,
> Paul Tillich, in reply to your fellow outspoken radical
> leftist Hemidactylus.
>

This Paul Tillich is sounding better and better. And in what way am I a
radical leftist? Could you be so tilted to the right that your judgment is
clouded?

>
> The outspokenness, radicalism, and leftism were especially
> evident on the day after the November election. The two
> of you even feigned paranoia about the outcome.
>

Yeah, um...George Will bolted the GOP because Trump and you would be hard
pressed to cast him as a radical leftist.

>
>> I have, from time to time, heard
>> humans described as political animals, which would make everyone
>> (excepting possibly bots) political automatically. Do you have in mind
>> a narrower definition?
>
> Yes, see above.
>
> Will you now ignore the substantive issues, and pretend
> to be ONLY interested in a definition of "political animal"?
>

What is so bad about being a political animal? You seem to be punning it in
the negative connotation of machination and manipulation, but how did
Aristotle employ it originally? Was it that humans need a societal milieu
within which to flourish? That’s my take. The opposite of political animal
would be antisocial hermit. Is that your preferred mode? That would explain
much of your behavior here.

[snip rest]

[Peter Nyikos]

On Thursday, March 29, 2018 at 1:05:03 PM UTC-4, Mark Isaak wrote:
> On 3/29/18 5:24 AM, Peter Nyikos wrote:
>
> [To other readers: There's nothing of substance here.]

Do you consider an out and out lie by you this time around
to be "nothing of substance?"

Be that as it may, you are being very cunning in persuading
people to avoid reading just how epic your fail below already
was, and how it is getting worse this time around.

Saul Alinsky should have added the following to his
Rules for Radicals:

14. There is no need to refute people if you can persuade
others not to listen to them.

I'm sure an outspoken radical leftist like you is familiar
with the original 13, but just in case someone less radical
than you is reading this, the list can be found here:

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

> > On Wednesday, March 28, 2018 at 10:35:02 PM UTC-4, Mark Isaak wrote:
> >> On 3/28/18 12:52 PM, Peter Nyikos wrote:
> >>> On Wednesday, March 28, 2018 at 12:35:02 AM UTC-4, Mark Isaak wrote:
> >>>> On 3/27/18 2:51 PM, Peter Nyikos wrote:
> >>>>> On Saturday, March 24, 2018 at 9:55:03 AM UTC-4, Ernest Major wrote:
> >>>>>> [...]
> >>>>>> That's an argument from ignorance.
> >>>>>
> >>>>> So is the argument that there MUST be an undirected evolutionary path
> >>>>> even though none has been identified. Knee-jerk atheists aside
> >>>>> [several of them are on this thread], one cannot completely
> >>>>> discount the possibility of supernatural intervention, albeit
> >>>>> of a relatively modest sort that is within human capabilities.
> >>>>
> >>>> For someone who claims not be a creationist, you sure are trying hard to
> >>>> mimic a creationist.
> >>>
> >>> Bullshit. I'd like to see you try to NAME any creationist
> >>> whom I am supposedly mimicking.
> >>
> >> All of them.
> >
> > Have you gone bananas? NONE of the ones I know about has
> > written anything like the paragraph you are supposedly talking
> > about. I'd like to see you come up with anything any of them
> > wrote that is even remotely like it.
> >
> > [snip further raving and bullying]

Poor baby. You actually believe that the paragraph
you are commenting on with "further" is an example of
raving and bullying. :-)

Actually, you are really a poor baby if you
think your readers are so naive that they believe
this crap about "raving and bullying."

> All creationists which I have encountered (and had more than trivial
> conversations with) use the God of the Gaps argument: There's no known
> explanation, therefore supernatural. You do that too.

I'd like to see you spin-doctor your way about having
posted an out and out lie here. I categorically deny
ever having done this.

In fact, I'd like to see you spin-doctor your way
out of projecting your own brand of "reasoning" onto me.

YOUR brand seems to say, "It is merely unexplained, therefore
it is not supernatural." This is the way you put it, with my
comment about which you are in deep denial:

__________________ excerpt __________________

> Consider two candidates for the supernatural. Case 1: A 10-cm-long
> humanoid with wings, glowing with a yellowish light, flies up to your
> children and drops some dust on them. Your children slowly rise into
> the air and, with some practice, are able to fly in a controlled manner.
>
> Is that supernatural? No, it is merely unexplained.

Begging the question.

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


Concluded in next reply, to be done shortly after I've seen

that this one has posted.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

Univ. of South Carolina at Columbia
http://www.math.sc.edu/~nyikos/