Origin of the Flagellum ON TRIAL, Continued

[Steady Eddie]

After several failed attempts to reply to Mark Isaak on the original thread, I think we need to start a fresh one...

Last comment from the original thread:

-quote-
On 7/29/16 8:22 PM, Steady Eddie wrote:
> On Tuesday, 26 July 2016 00:02:57 UTC-6, Mark Isaak wrote:
>> On 7/25/16 6:12 PM, Steady Eddie wrote:
>>> On Wednesday, 20 July 2016 17:08:12 UTC-6, Mark Isaak wrote:
>>>> On 7/20/16 6:15 AM, Steady Eddie wrote:
>>>>> [...]
>>>>> How do you think 'parts having parts' is fatal to Behe's conclusions?
>>>>
>>>> The answer should be obvious, but if there is anyone who:
>>>> a) understands Behe's thesis;
>>>> b) does not see how "parts having parts" is fatal to it, even after
>>>> serious consideration; and
>>>> c) honestly wants to know;
>>>> then such a person I would be happy to answer.
>>>
>>> Do you only teach those who sit submissively at your feet, or do you also defend your assertions before
>>> those who aren't convinced of your infallibility?
>>
>> I do not teach people who choose not to come to class, such as yourself.
>
> Professor, since you (seem to have) brought it up (in your
> cryptic style), can you explain how the existence of the T3SS
> shows that the flagellum will work without all of its parts?

The T3SS works.

The T3SS is essentially a flagellum without all of its parts.

Therefore, a flagellum without all of its parts will work.

Got that?
-end quote-

A flagellum without all of its parts won't work as a flagellum.
Any particular reason you missed that fine point?

[Bill Rogers]

As long as it works as something useful it can be selected for.

[Öö Tiib]

For what that Type III Secretory System worked as useful at time
when flagella supposedly evolved?

Wikipedia says that (right now) bacteria detect the presence of
eukaryotic organisms with it and secrete proteins that help the
bacteria to infect these organisms.

However flagella did supposedly evolve hundreds of millions of
years before eukaryotic organisms. So for what the T3SS was
useful back then?

[Bill Rogers]

The point is simply that if some subset of an allegedly IC structure has a selectable function, then the conclusion that IC = "impossible to evolve" is incorrect.

[jillery]

Nobody missed that fine point. Apparently you missed that nobody
disputes it. OTOH, the fact that a flagellum without all its parts
still has a function, is the final nail in IC's coffin.

If you were capable of following a line of reasoning, you would
understand that Behe's argument for IC rests on his claim that an IC
system lacking a part provides no function at all. Even Behe
understands that if a system provides some functionality, that's all
that evolution needs to adapt and modify its function, and to build
parts of systems over time rather than all at once, as Behe says IC
systems require. That's why Behe argues so strongly, if incoherently,
against Miller's mousetrap tie clips.
--
This space is intentionally not blank.

[jillery]

On Wed, 10 Aug 2016 12:36:33 -0400, jillery <69jp...@gmail.com>
wrote:

In the spirit of accuracy, I correct myself here. There are people
who dispute that a bacterial flagellum without all its parts won't
work as a flagellum:

<https://www.newscientist.com/article/dn13663-evolution-myths-the-bacterial-flagellum-is-irreducibly-complex/>

<http://tinyurl.com/z77q8ej>

My bad.

[Mark Isaak]

It is irrelevant. Evolution does not say new functions are not allowed
to arise. In fact, it says (or at least implies) quite the opposite.

Do you have any reason to consider your statement relevant?

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"The evil that is in the world always comes of ignorance, and good
intentions may do as much harm as malevolence, if they lack
understanding." - Albert Camus, _The Plague_

[Steady Eddie]

Only that this thread is about the origin of the cellular propulsion system known as the flagellum.

[Steady Eddie]

The idea that a flagellum without all its parts still has "A" function in no way disqualifies it from being IC.

> If you were capable of following a line of reasoning, you would
> understand that Behe's argument for IC rests on his claim that an IC
> system lacking a part provides no function at all. Even Behe
> understands that if a system provides some functionality, that's all
> that evolution needs to adapt and modify its function, and to build
> parts of systems over time rather than all at once, as Behe says IC
> systems require. That's why Behe argues so strongly, if incoherently,
> against Miller's mousetrap tie clips.

Behe plainly explains his notion of irreducible complexity in Darwin's Black Box.
Time to go back and re-read it.

I don't need to start another book club, do I?

[Steady Eddie]

This piece was half-comedic, half-story-telling.

He runs headlong into the main issue:

"Either a “designer” created thousands of variants on the flagellum or, contrary to creationist claims, it is possible to make considerable changes to the machinery without mucking it up."

Then he figures he told you so, and the obvious answer is the latter, and fails to weigh the two
possibilities. He just proceeds as though he forgot that perhaps "a “designer” created thousands of
variants on the flagellum".

That's exactly my point - Darwinists are fanatics who don't necessarily use reason.

[jillery]

On Fri, 12 Aug 2016 23:31:37 -0700 (PDT), Steady Eddie

>> <http://tinyurl.com/z77q8ej>
>>
>> My bad.

>
>
>This piece was half-comedic, half-story-telling.

And here's a good example of how you dismiss cites.

>He runs headlong into the main issue:

...which you then completely avoid.

>"Either a “designer” created thousands of variants on the flagellum or, contrary to creationist claims, it is possible to make considerable changes to the machinery without mucking it up."
>
>Then he figures he told you so, and the obvious answer is the latter, and fails to weigh the two
>possibilities. He just proceeds as though he forgot that perhaps "a “designer” created thousands of
>variants on the flagellum".
>
>That's exactly my point - Darwinists are fanatics who don't necessarily use reason.

Apparently you don't understand that the line you quote is a summary
of documented facts. You can stop proving why you're village idiot.

[jillery]

On Fri, 12 Aug 2016 23:10:05 -0700 (PDT), Steady Eddie

Of course it does, as I point out immediately below.

>> If you were capable of following a line of reasoning, you would
>> understand that Behe's argument for IC rests on his claim that an IC
>> system lacking a part provides no function at all. Even Behe
>> understands that if a system provides some functionality, that's all
>> that evolution needs to adapt and modify its function, and to build
>> parts of systems over time rather than all at once, as Behe says IC
>> systems require. That's why Behe argues so strongly, if incoherently,
>> against Miller's mousetrap tie clips.
>
>Behe plainly explains his notion of irreducible complexity in Darwin's Black Box.
>Time to go back and re-read it.

Let us know when you're done. And this time, read it for
comprehension. Don't be insulted that I don't wait for you.

>I don't need to start another book club, do I?

Another? When did you start any?

[Bill Rogers]

.....

> The idea that a flagellum without all its parts still has "A" function in no way disqualifies it from being IC.

No, but it does refute the argument that IC things are automatically impossible to evolve.

[jillery]

Your "no" is valid if one considers only Behe's *definition* of IC,
which is a truism by definition, and so is an incomplete and
misleading statement. If one considers Behe's complete line of
reasoning for IC, there is no "no" here, as you acknowledge in the
second part of your sentence above, and I explain below.

>> > If you were capable of following a line of reasoning, you would
>> > understand that Behe's argument for IC rests on his claim that an IC
>> > system lacking a part provides no function at all. Even Behe
>> > understands that if a system provides some functionality, that's all
>> > that evolution needs to adapt and modify its function, and to build
>> > parts of systems over time rather than all at once, as Behe says IC
>> > systems require. That's why Behe argues so strongly, if incoherently,
>> > against Miller's mousetrap tie clips.
>>
>> Behe plainly explains his notion of irreducible complexity in Darwin's Black Box.
>> Time to go back and re-read it.
>>
>> I don't need to start another book club, do I?

[Steady Eddie]

Oh. Sorry, my mistake.
Please quote the documented facts that can be summarized as:

"Either a “designer” created thousands of variants on the flagellum or, contrary to creationist claims, it is

possible to make considerable changes to the machinery without mucking it up.",

SO, which option do you support? What is your support?

[Steady Eddie]

On Saturday, 13 August 2016 03:26:59 UTC-6, jillery wrote:

Now would have been a great place to quote any redeeming feature of this article.
Just sayin.

> >He runs headlong into the main issue:
>
>
> ...which you then completely avoid.
>
>
> >"Either a “designer” created thousands of variants on the flagellum or, contrary to creationist claims, it is possible to make considerable changes to the machinery without mucking it up."
> >
> >Then he figures he told you so, and the obvious answer is the latter, and fails to weigh the two
> >possibilities. He just proceeds as though he forgot that perhaps "a “designer” created thousands of
> >variants on the flagellum".
> >
> >That's exactly my point - Darwinists are fanatics who don't necessarily use reason.
>
>
> Apparently you don't understand that the line you quote is a summary
> of documented facts. You can stop proving why you're village idiot.

Apparently you have some "documented facts" in mind to show us...
Anything from the article?

[jillery]

On Sun, 14 Aug 2016 13:22:45 -0700 (PDT), Steady Eddie

Since you make the claim that it's half-comedic, half story-telling,
you're the one who's obliged to support your claim. Otherwise your
half-assed comments make you look like a complete asshole.

>> >He runs headlong into the main issue:
>>
>>
>> ...which you then completely avoid.
>>
>>
>> >"Either a “designer” created thousands of variants on the flagellum or, contrary to creationist claims, it is possible to make considerable changes to the machinery without mucking it up."
>> >
>> >Then he figures he told you so, and the obvious answer is the latter, and fails to weigh the two
>> >possibilities. He just proceeds as though he forgot that perhaps "a “designer” created thousands of
>> >variants on the flagellum".
>> >
>> >That's exactly my point - Darwinists are fanatics who don't necessarily use reason.
>>
>>
>> Apparently you don't understand that the line you quote is a summary
>> of documented facts. You can stop proving why you're village idiot.
>
>Apparently you have some "documented facts" in mind to show us...
>Anything from the article?

Second verse, same as the first...

[jillery]

On Sun, 14 Aug 2016 13:19:10 -0700 (PDT), Steady Eddie

The latter of course.


> What is your support?


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

"Three types of flagella have so far been distinguished: bacterial,
archaeal, and eukaryotic."

"Gram-positive organisms have two of these basal body rings, one in
the peptidoglycan layer and one in the plasma membrane. Gram-negative
organisms have four such rings: the L ring associates with the
lipopolysaccharides, the P ring associates with peptidoglycan layer,
the M ring is embedded in the plasma membrane, and the S ring is
directly attached to the plasma membrane. "

"In most bacteria that have been studied, including the Gram negative
Escherichia coli, Salmonella typhimurium, Caulobacter crescentus, and
Vibrio alginolyticus, the filament is made up of eleven protofilaments
approximately parallel to the filament axis. Each protofilament is a
series of tandem protein chains. However, in Campylobacter jejuni,
there are seven protofilaments."

"in Vibrio species there are two kinds of flagella, lateral and polar,
and some are driven by a sodium ion pump rather than a proton pump"

"Different species of bacteria have different numbers and arrangements
of flagella."

"Monotrichous bacteria have a single flagellum (e.g., Vibrio
cholerae)."

"Lophotrichous bacteria have multiple flagella located at the same
spot on the bacteria's surfaces which act in concert to drive the
bacteria in a single direction."

"Amphitrichous bacteria have a single flagellum on each of two
opposite ends (only one flagellum operates at a time, allowing the
bacteria to reverse course rapidly by switching which flagellum is
active)."

"Peritrichous bacteria have flagella projecting in all directions
(e.g., E. coli)."

"In certain large forms of Selenomonas, more than 30 individual
flagella are organized outside the cell body, helically twining about
each other to form a thick structure (easily visible with the light
microscope) called a "fascicle".

"Other bacteria, such as most Spirochetes, have two or more
specialized flagella (endoflagella) arising from opposite poles of the
cell, which together constitute the so-called "axial filament" that is
located within the periplasmic space between the flexible cell wall
and an outer sheath. The rotation of the axial filament relative to
the cell body causes the entire bacterium to move forward in a
corkscrew-like motion, even through material viscous enough to prevent
the passage of normally flagellated bacteria."


Now then, where is your support for a designer? Don't be insulted
that I don't wait for your answer.

[Steady Eddie]

Good, you've established the factual basis for the question: Why are there so many kinds of flagella?

You haven't provided support for your chosen answer that:
"It is possible to [without intelligent design] make considerable changes to the machinery without mucking
it up".

Why do you conclude that?

[jillery]

On Sun, 14 Aug 2016 19:29:58 -0700 (PDT), Steady Eddie

BZZT! No I didn't. I established *that* there are many kinds of
flagella, with different parts, which refutes your claim that they're
IC. That says nothing about "why". And "why" isn't relevant to this
discussion, unless you're just trying to show that you don't know what
talking about. If so, you can stop now; I'm already convinced.

>You haven't provided support for your chosen answer that:
>"It is possible to [without intelligent design] make considerable changes to the machinery without mucking
>it up".
>
>Why do you conclude that?

[Peter Nyikos]

On Saturday, August 13, 2016 at 7:42:01 AM UTC-4, Bill Rogers wrote:
> On Saturday, August 13, 2016 at 2:12:00 AM UTC-4, Steady Eddie wrote:
> > On Wednesday, 10 August 2016 10:37:08 UTC-6, jillery wrote:
> > > On Wed, 10 Aug 2016 07:02:18 -0700 (PDT), Steady Eddie
> > > <1914o...@gmail.com> wrote:
> > >
> > > >After several failed attempts to reply to Mark Isaak on the original thread, I think we need to start a fresh one...
> > > >
> > > >Last comment from the original thread:
> > > >
> > > >-quote-
> > > >On 7/29/16 8:22 PM, Steady Eddie wrote:

<snip for focus>

> > > >> Professor, since you (seem to have) brought it up (in your
> > > >> cryptic style), can you explain how the existence of the T3SS
> > > >> shows that the flagellum will work without all of its parts?
> > > >
> > > >The T3SS works.
> > > >
> > > >The T3SS is essentially a flagellum without all of its parts.
> > > >Therefore, a flagellum without all of its parts will work.
> > > >
> > > >Got that?
> > > >-end quote-
> > > >
> > > >A flagellum without all of its parts won't work as a flagellum.
> > > >Any particular reason you missed that fine point?
>
> > >
> > > Nobody missed that fine point. Apparently you missed that nobody
> > > disputes it. OTOH, the fact that a flagellum without all its parts
> > > still has a function, is the final nail in IC's coffin.
>
>
> .....
> > The idea that a flagellum without all its parts still has "A" function in no way disqualifies it from being IC.

Eddie is correct, but do you know why?

> No, but it does refute the argument that IC things are automatically impossible to evolve.

Since Behe, the top guru on IC, never made that argument and even expressly
disavowed it (see page 40 of _DBB_) your point is moot.

Behe was not completely clear on the preceding page about "the basic function" being an integral part of what makes the system IC. He does however
mention the function in his sentence where he introduces the concept of IC:

By irreducibly complex I mean a single system composed of several
well-matched, interacting parts that contribute to the basic function,
wherein the removal of any one of the parts causes the system to
effectively cease functioning.

He should have written "effectively puts an end to the basic function"
after "parts".

In later writings he did a better job of it. The basic function of the
flagellum which makes at least some flagellae IC is swimming.

The following sentence is therefore knocking down a straw man, not Behe:

> > > If you were capable of following a line of reasoning, you would
> > > understand that Behe's argument for IC rests on his claim that an IC
> > > system lacking a part provides no function at all.

Here is a passage from Minnich's testimony at the Dover trial which
explains that, with the basic flagellar function specified as swimming,
the flagellum on which he and his students experimented was indeed IC:

We have a mutation in a drive shaft protein or the U joint,
and they can't swim. Now, to confirm that that's the only part
that we've affected, you know, is that we can identify this mutation,
clone the gene from the wild type and reintroduce it
by mechanism of genetic complementation. So this is, these cells up
here are derived from this mutant where we have complemented
with a good copy of the gene.

One mutation, one part knock out, it can't swim. Put that single gene
back in we restore motility. Same thing over here. We put, knock out one
part, put a good copy of the gene back in, and they can swim.
By definition the system is irreducibly complex. We've done that
with all 35 components of the flagellum, and we get the same effect.
==================== end of excerpt
from http://www.talkorigins.org/faqs/dover/day20pm2.html

And Steady Eddie is correct in his riposte below, but as is so
maddeningly typical of him, he does not explain what's wrong with
jillery's editorializing:

> > > Even Behe
> > > understands that if a system provides some functionality, that's all
> > > that evolution needs to adapt and modify its function, and to build
> > > parts of systems over time rather than all at once, as Behe says IC
> > > systems require. That's why Behe argues so strongly, if incoherently,
> > > against Miller's mousetrap tie clips.
> >
> > Behe plainly explains his notion of irreducible complexity in Darwin's Black Box.
> > Time to go back and re-read it.
> >
> > I don't need to start another book club, do I?

By the way, Bill, if you can make sense of jillery's reply to this same
post of yours to which I am replying, I'm all ears.

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

[Peter Nyikos]

On Wednesday, August 10, 2016 at 11:27:08 AM UTC-4, Öö Tiib wrote:

I don't think you will ever get an answer to this question.
Bill Rogers, the only one who replied to your post at all,
knocked down a straw man without directly addressing your question.
See my reply to a different post of Bill's a few minutes ago.

Someone on this thread made the point that there are three kinds of
"flagella": the ones found in (1) bacteria (2) archae and (3) eukaryotes.
But these three are so different from each other that the existence
of the other two kinds is irrelevant to the question of whether the
bacterial flagellum evolved without any intelligent intervention.

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

[John Stockwell]

Using what mechanism? Simply saying a "designer did it" doesn't cut it because it doesn't say how the "designer" did it.

>
> Then he figures he told you so, and the obvious answer is the latter, and fails to weigh the two
> possibilities. He just proceeds as though he forgot that perhaps "a “designer” created thousands of
> variants on the flagellum".
>
> That's exactly my point - Darwinists are fanatics who don't necessarily use reason.

The mechanism of evolution is reproduction with variation and natural selection.

The mechanism of "the designer" is unspecified.

Evolution will continue to win, until a "designer mechanism" is delivered.

Can you not get this?

-John

[Peter Nyikos]

On Monday, August 15, 2016 at 1:21:53 PM UTC-4, John Stockwell wrote:
> On Saturday, August 13, 2016 at 12:32:01 AM UTC-6, Steady Eddie wrote:
> > On Wednesday, 10 August 2016 10:57:08 UTC-6, jillery wrote:

> > > In the spirit of accuracy, I correct myself here. There are people
> > > who dispute that a bacterial flagellum without all its parts won't
> > > work as a flagellum:
> > >
> > > <https://www.newscientist.com/article/dn13663-evolution-myths-the-bacterial-flagellum-is-irreducibly-complex/>
> >
> > This piece was half-comedic, half-story-telling.
> >
> > He runs headlong into the main issue:
> >
> > "Either a “designer” created thousands of variants on the flagellum or,
> > contrary to creationist claims, it is possible to make considerable
> > changes to the machinery without mucking it up."
>
> Using what mechanism?

My favorite possible mechanism is: genetic engineering of existing prokaryotes
by a technological species that need not have been more than a few
decades advanced over us. Nobel Laureate Francis Crick alluded to such a
possibility decades ago, and since his death, I'm probably the person most
responsible for promoting the directed panspermia hypothesis that
he and Orgel cooked up.

I'm not claiming the hypothesis is correct, but it is definitely on
the table, and before 2016 is out, I intend to submit my FAQ on the
subject to the Talk.Origins Archive.

> Simply saying a "designer did it" doesn't cut it because it doesn't say how the "designer" did it.

I, however, have said it. I see no reason for bringing in supernatural
designers for such an isolated phenomenon.

> >
> > Then he figures he told you so, and the obvious answer is the latter, and fails to weigh the two
> > possibilities. He just proceeds as though he forgot that perhaps "a “designer” created thousands of
> > variants on the flagellum".

> > That's exactly my point - Darwinists are fanatics who don't necessarily use reason.
>
> The mechanism of evolution is reproduction with variation and natural selection.

> The mechanism of "the designer" is unspecified.

I doubt that Steady Eddie will go along with my specification, but
mine has it all over yours. This is because my mechanism is close to being
in our own hot little hands, while nobody has a real clue as to
the steps by which the Type III mechanism may have evolved, nor how it might
have evolved into a bacterial flagellum by steps favored by natural
selection.

> Evolution will continue to win, until a "designer mechanism" is delivered.
>
> Can you not get this?
>
> -John

The elephant that you are ignoring here has returned to the room after an
absence of about three months. Time to stop ignoring my mechanism.

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

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

[jillery]

On Mon, 15 Aug 2016 09:59:04 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> wrote:

>On Saturday, August 13, 2016 at 7:42:01 AM UTC-4, Bill Rogers wrote:
>> On Saturday, August 13, 2016 at 2:12:00 AM UTC-4, Steady Eddie wrote:
>> > On Wednesday, 10 August 2016 10:37:08 UTC-6, jillery wrote:
>> > > On Wed, 10 Aug 2016 07:02:18 -0700 (PDT), Steady Eddie
>> > > <1914o...@gmail.com> wrote:
>> > >
>> > > >After several failed attempts to reply to Mark Isaak on the original thread, I think we need to start a fresh one...
>> > > >
>> > > >Last comment from the original thread:
>> > > >
>> > > >-quote-
>> > > >On 7/29/16 8:22 PM, Steady Eddie wrote:
>
><snip for focus>

You're so cute when you're unintentionally ironic.

>> > > >> Professor, since you (seem to have) brought it up (in your
>> > > >> cryptic style), can you explain how the existence of the T3SS
>> > > >> shows that the flagellum will work without all of its parts?
>> > > >
>> > > >The T3SS works.
>> > > >
>> > > >The T3SS is essentially a flagellum without all of its parts.
>> > > >Therefore, a flagellum without all of its parts will work.
>> > > >
>> > > >Got that?
>> > > >-end quote-
>> > > >
>> > > >A flagellum without all of its parts won't work as a flagellum.
>> > > >Any particular reason you missed that fine point?
>>
>> > >
>> > > Nobody missed that fine point. Apparently you missed that nobody
>> > > disputes it. OTOH, the fact that a flagellum without all its parts
>> > > still has a function, is the final nail in IC's coffin.
>>
>>
>> .....
>> > The idea that a flagellum without all its parts still has "A" function in no way disqualifies it from being IC.
>
>Eddie is correct, but do you know why?
>
>> No, but it does refute the argument that IC things are automatically impossible to evolve.
>
>Since Behe, the top guru on IC, never made that argument and even expressly
>disavowed it (see page 40 of _DBB_) your point is moot.

Right here would have been a good place for you to quote where Behe
"expressly disavowed it".

>Behe was not completely clear on the preceding page about "the basic function" being an integral part of what makes the system IC. He does however
>mention the function in his sentence where he introduces the concept of IC:
>
> By irreducibly complex I mean a single system composed of several
> well-matched, interacting parts that contribute to the basic function,
> wherein the removal of any one of the parts causes the system to
> effectively cease functioning.
>
>He should have written "effectively puts an end to the basic function"
>after "parts".
>
>In later writings he did a better job of it. The basic function of the
>flagellum which makes at least some flagellae IC is swimming.

Fortunately for all us, proteins don't care what you say their basic
functions are, so your following sentence is a strawman.

>The following sentence is therefore knocking down a straw man, not Behe:
>
>> > > If you were capable of following a line of reasoning, you would
>> > > understand that Behe's argument for IC rests on his claim that an IC
>> > > system lacking a part provides no function at all.
>
>Here is a passage from Minnich's testimony at the Dover trial which
>explains that, with the basic flagellar function specified as swimming,
>the flagellum on which he and his students experimented was indeed IC:
>
> We have a mutation in a drive shaft protein or the U joint,
> and they can't swim. Now, to confirm that that's the only part
> that we've affected, you know, is that we can identify this mutation,
> clone the gene from the wild type and reintroduce it
> by mechanism of genetic complementation. So this is, these cells up
> here are derived from this mutant where we have complemented
> with a good copy of the gene.
>
> One mutation, one part knock out, it can't swim. Put that single gene
> back in we restore motility. Same thing over here. We put, knock out one
> part, put a good copy of the gene back in, and they can swim.
> By definition the system is irreducibly complex. We've done that
> with all 35 components of the flagellum, and we get the same effect.
>==================== end of excerpt
>from http://www.talkorigins.org/faqs/dover/day20pm2.html
>
>And Steady Eddie is correct in his riposte below, but as is so
>maddeningly typical of him, he does not explain what's wrong with
>jillery's editorializing:

And neither do you, but then backing up your asinine assertions was
never your strong suit.

>> > > Even Behe
>> > > understands that if a system provides some functionality, that's all
>> > > that evolution needs to adapt and modify its function, and to build
>> > > parts of systems over time rather than all at once, as Behe says IC
>> > > systems require. That's why Behe argues so strongly, if incoherently,
>> > > against Miller's mousetrap tie clips.
>> >
>> > Behe plainly explains his notion of irreducible complexity in Darwin's Black Box.
>> > Time to go back and re-read it.
>> >
>> > I don't need to start another book club, do I?
>
>By the way, Bill, if you can make sense of jillery's reply to this same
>post of yours to which I am replying, I'm all ears.

Right here would have been a good place for you to say what you don't
understand about my reply. Don't be insulted that I don't wait for
your to do so.

[Öö Tiib]

On Monday, 15 August 2016 21:51:52 UTC+3, jillery wrote:
> On Mon, 15 Aug 2016 09:59:04 -0700 (PDT), Peter Nyikos
> <nyi...@bellsouth.net> wrote:
>
> >On Saturday, August 13, 2016 at 7:42:01 AM UTC-4, Bill Rogers wrote:

<snip>

> >
> >> No, but it does refute the argument that IC things are automatically
> >> impossible to evolve.
> >
> >Since Behe, the top guru on IC, never made that argument and even expressly
> >disavowed it (see page 40 of _DBB_) your point is moot.
>
>
> Right here would have been a good place for you to quote where Behe
> "expressly disavowed it".

I've read it. Behe indeed did weasel out of position that IC can not
evolve:

"Even if a system is irreducibly complex (and thus cannot have been
produced directly), however, one can not definitely rule out the
possibility of an indirect, circuitous route. As the complexity of
an interacting system increases, though, the likelihood of such an
indirect route drops precipitously."

<snip>

[jillery]

On Mon, 15 Aug 2016 14:58:14 -0700 (PDT), 嘱 Tiib <oot...@hot.ee>
wrote:

I've read that, too. I know the previous poster has claimed that
before. If that's what's he's actually referring to now, it's been
pointed out before that his claim doesn't hold water. Even as one
recognizes that Behe doesn't literally exclude absolutely every
possibility of evolution, that pedantically trivial distinction isn't
the basis of Roger's comment or mine, and so it's a pointless argument
to make.

Instead, the substance of the criticism is that Behe claims IC shows
that most biochemical pathways for evolution are highly unlikely, to
the point that he accepts evolution as a likely cause for only the
least complex processes. This is reinforced by Behe's further
argument that IC is strong evidence of an intelligent designer.

Now recall the relevant part of Behe's argument, that if a biochemical
system is IC, that means the parts had to be well-matched, ie they had
to have assembled simultaneously and already performing the functions
they would do as part of the IC system. That's something evolution
can't do, because it requires foresight, and evolution is an unguided
process. So Behe's argument is that if a system is IC, it's almost
certain that evolution didn't make it.

Now recall Behe's test for IC, to remove a part and see if the system
fails. Unfortunately, that test doesn't show any of Behe claims
described above. It doesn't show the parts had to assemble
simultaneously. It doesn't show the parts had to perform the
functions they would do as part of the system. It doesn't show the
parts are well-matched. The only thing Behe's test for IC shows is
that a system meets Behe's test for IC, a pointless truism.

Now recall the question under discussion here, whether an alleged IC
system with a part removed but still has some function qualifies as
IC. Since Behe's definition is a truism, it doesn't even matter here.
Instead, the important part here is if a biological system has a
function, then it necessarily will evolve, which refutes Behe's claim
that IC systems can't... oops... are "precipitously" unlikely.... to
evolve.

[Steady Eddie]

No, I don't get it, John.
Who says one would have to know the design "mechanism" of a designer before one can conclude that
something is the work of an intelligent agent?

[Glenn]

"Steady Eddie" <1914o...@gmail.com> wrote in message news:e68f9fdc-42dc-4900...@googlegroups.com...

I wonder about his comment concerning what will "win".

"The near future is likely to see continued discussion of the implications and limits of this framework for thinking about science and scientific practice."

http://plato.stanford.edu/entries/science-mechanisms/

[jillery]

On Mon, 15 Aug 2016 20:05:04 -0700 (PDT), Steady Eddie

Actually, not just any old intelligent agent, but an unknown, unseen,
undefined one. So, given that you don't know who or what did a
design, and you don't know how it did a design, on what basis do you,
Steady Eddie, identify something as designed, other than "I know it
when I see it"?

[Öö Tiib]

On Tuesday, 16 August 2016 03:26:52 UTC+3, jillery wrote:
> On Mon, 15 Aug 2016 14:58:14 -0700 (PDT), Öö Tiib <oot...@hot.ee>

Yes, but Behe still technically weasels out from "impossible" there.

>
> Instead, the substance of the criticism is that Behe claims IC shows
> that most biochemical pathways for evolution are highly unlikely, to
> the point that he accepts evolution as a likely cause for only the
> least complex processes. This is reinforced by Behe's further
> argument that IC is strong evidence of an intelligent designer.

I think Behe had to explain the source of his "precipitous unlikelihood"
estimations better. My (possibly naive) thinking is that the situation
in nature contains clear selective push towards Behe's IC. System
with fewer parts is usually more robust and cheaper and simpler to
assemble.

Removing components that can be removed without weakening the system
makes the system therefore more efficient. So if evolution follows
that pressure and removes such components then the direct (not circuitous)
result is Behe's IC system from what nothing can be removed.

>
> Now recall the relevant part of Behe's argument, that if a biochemical
> system is IC, that means the parts had to be well-matched, ie they had
> to have assembled simultaneously and already performing the functions
> they would do as part of the IC system. That's something evolution
> can't do, because it requires foresight, and evolution is an unguided
> process. So Behe's argument is that if a system is IC, it's almost
> certain that evolution didn't make it.
>
> Now recall Behe's test for IC, to remove a part and see if the system
> fails. Unfortunately, that test doesn't show any of Behe claims
> described above. It doesn't show the parts had to assemble
> simultaneously. It doesn't show the parts had to perform the
> functions they would do as part of the system. It doesn't show the
> parts are well-matched. The only thing Behe's test for IC shows is
> that a system meets Behe's test for IC, a pointless truism.
>
> Now recall the question under discussion here, whether an alleged IC
> system with a part removed but still has some function qualifies as
> IC. Since Behe's definition is a truism, it doesn't even matter here.
> Instead, the important part here is if a biological system has a
> function, then it necessarily will evolve, which refutes Behe's claim
> that IC systems can't... oops... are "precipitously" unlikely.... to
> evolve.

I do not understand neither side in this discussion. Both sides seem
to implicitly agree that last mutation that resulted with flagellum had
to be one that added some part to it. Eddie demands that predecessor
(without part) had motility for Roger some other function (T3SS) is fine.
To me however that last mutation did not apparently add a part.

[jillery]

On Tue, 16 Aug 2016 05:41:20 -0700 (PDT), 嘱 Tiib <oot...@hot.ee>
wrote:

>On Tuesday, 16 August 2016 03:26:52 UTC+3, jillery wrote:

>> On Mon, 15 Aug 2016 14:58:14 -0700 (PDT), 嘱 Tiib <oot...@hot.ee>

I disagree. Whether Behe meant literally or practically or
effectively impossible or precipitously unlikely, the criticism of his
argument remains valid. The technicality makes a distinction without
a difference. I don't know that Behe himself ever used it himself,
but it's the kind of argument made by those who are more interested in
noise than substance.

>> Instead, the substance of the criticism is that Behe claims IC shows
>> that most biochemical pathways for evolution are highly unlikely, to
>> the point that he accepts evolution as a likely cause for only the
>> least complex processes. This is reinforced by Behe's further
>> argument that IC is strong evidence of an intelligent designer.
>
>I think Behe had to explain the source of his "precipitous unlikelihood"
>estimations better. My (possibly naive) thinking is that the situation
>in nature contains clear selective push towards Behe's IC. System
>with fewer parts is usually more robust and cheaper and simpler to
>assemble.

I agree that Behe should have explained his point better, but I don't
know that he ever did, and it's been 20 years since DBB. Behe's
argumentation is full of circular reasonings and bald assertions,
features common among ID apologists, so it's no surprise to me that
Behe argued this point similarly.

>Removing components that can be removed without weakening the system
>makes the system therefore more efficient. So if evolution follows
>that pressure and removes such components then the direct (not circuitous)
>result is Behe's IC system from what nothing can be removed.

IIUC that would be an argument favoring evolution, which is something
Behe has done only rarely if at all.

It's no surprise that you misunderstand Steadly. The closest he's
come to posting an argument here is to stomp his feet and shout "IS
NOT".

Unlike Steadly, Roger can speak for himself, but my understanding is
he simply states an objection to Behe's argument, one that's been made
practically since DBB's publication.

I don't understand what your point about "that last mutation" has to
do with either side. My understanding is that evolution assumes
mutations continue to happen. Will you elaborate?

[Steady Eddie]

Interesting article. Thanks for that.

[Öö Tiib]

On Tuesday, 16 August 2016 17:06:50 UTC+3, jillery wrote:
> On Tue, 16 Aug 2016 05:41:20 -0700 (PDT), Öö Tiib <oot...@hot.ee>

> wrote:
>
> >On Tuesday, 16 August 2016 03:26:52 UTC+3, jillery wrote:

Snip the first part where we sort of agree to disagree.

I mean that Behe's experiments did show that if to mutate bacteria so
that it causes removal of some part of flagellum then flagellum stops
working and is entirely useless thing. Behe did effectively show that
last mutation (that reached working flagellum) is not opposite to
the mutations he did in those experiments. Otherwise if last mutation
added final missing part to some useless wreck of flagellum then why
that wreck did evolve?

Both sides however seem to discuss exactly that path and qualities of
that wreck. Steady Eddie claims that it does not work as flagellum
and Bill Rogers that it may be did work as T3SS.

[Steady Eddie]

I've recently told you the answer to that.
Again, some identifying features of intelligently designed things are:
-Irreducible complexity.
-High functional (or prescriptive) information content.

[Peter Nyikos]

On Monday, August 15, 2016 at 6:01:52 PM UTC-4, Öö Tiib wrote:
> On Monday, 15 August 2016 21:51:52 UTC+3, jillery wrote:
> > On Mon, 15 Aug 2016 09:59:04 -0700 (PDT), Peter Nyikos
> > <nyi...@bellsouth.net> wrote:
> >
> > >On Saturday, August 13, 2016 at 7:42:01 AM UTC-4, Bill Rogers wrote:
>
> <snip>
>
> > >
> > >> No, but it does refute the argument that IC things are automatically
> > >> impossible to evolve.
> > >
> > >Since Behe, the top guru on IC, never made that argument and even expressly
> > >disavowed it (see page 40 of _DBB_) your point is moot.
> >
> >
> > Right here would have been a good place for you to quote where Behe
> > "expressly disavowed it".
>
> I've read it.

So has jillery. She even posted it at least once, and sneered at
me on one occasion for not having remembered her having done it.

Of course, it clearly constitutes a disavowal, which may be why
jillery didn't repost it herself. Instead she chose a comment that
could plant the seeds of doubt in people, so that some would feel naturally
inclined to use skeptical language:

>Behe indeed did weasel out of position that IC can not
> evolve:

Be careful with your use of "weasel out of", Tiib. This was the first
mature expression of Behe's stand on IC, and nowhere in the book
does he even hint that "IC cannot evolve".

By the way, the expression in quotes is ambiguous: once an IC
system exists, there is nothing to rule out it evolving into
another system.

In fact, this is what probably happened with the bacterial
flagellum. Originating in gram-negative bacteria, it shed two
rings as the bacterium evolved into a gram-positive bacterium,
which had one less outer layer and so did not need the shed rings.

There may have been other changes along such unexceptional lines,
accounting for the unspecified "thousands of variations"
that have been alleged by Steady Eddie.

> "Even if a system is irreducibly complex (and thus cannot have been
> produced directly), however, one can not definitely rule out the
> possibility of an indirect, circuitous route. As the complexity of
> an interacting system increases, though, the likelihood of such an
> indirect route drops precipitously."
>
> <snip>

Indeed. What made you think this paragraph constituted a "weaseling out"?

[Peter Nyikos]

On Thursday, August 11, 2016 at 4:22:06 PM UTC-4, Steady Eddie wrote:
> On Wednesday, 10 August 2016 17:02:07 UTC-6, Mark Isaak wrote:

> > On 8/10/16 7:02 AM, Steady Eddie wrote:
> > > After several failed attempts to reply to Mark Isaak on the original thread, I think we need to start a fresh one...
> > >
> > > Last comment from the original thread:
> > >
> > > -quote-
> > > On 7/29/16 8:22 PM, Steady Eddie wrote:
> > >> On Tuesday, 26 July 2016 00:02:57 UTC-6, Mark Isaak wrote:
> > >>> On 7/25/16 6:12 PM, Steady Eddie wrote:
> > >>>> On Wednesday, 20 July 2016 17:08:12 UTC-6, Mark Isaak wrote:
> > >>>>> On 7/20/16 6:15 AM, Steady Eddie wrote:
> > >>>>>> [...]
> > >>>>>> How do you think 'parts having parts' is fatal to Behe's conclusions?
> > >>>>>
> > >>>>> The answer should be obvious, but if there is anyone who:
> > >>>>> a) understands Behe's thesis;
> > >>>>> b) does not see how "parts having parts" is fatal to it, even after
> > >>>>> serious consideration; and
> > >>>>> c) honestly wants to know;
> > >>>>> then such a person I would be happy to answer.
> > >>>>
> > >>>> Do you only teach those who sit submissively at your feet, or do you also defend your assertions before
> > >>>> those who aren't convinced of your infallibility?
> > >>>
> > >>> I do not teach people who choose not to come to class, such as yourself.
> > >>
> > >> Professor, since you (seem to have) brought it up (in your
> > >> cryptic style),

I hope your use of the word "Professor" was sarcastic. If Isaak were
a real Professor, he would be a disgrace to the teaching profession.

> > >> can you explain how the existence of the T3SS
> > >> shows that the flagellum will work without all of its parts?
> > >
> > > The T3SS works.
> > >
> > > The T3SS is essentially a flagellum without all of its parts.
> > >
> > > Therefore, a flagellum without all of its parts will work.
> > >
> > > Got that?
> > > -end quote-
> > >
> > > A flagellum without all of its parts won't work as a flagellum.

Nice to see you put in the qualifier "as a flagellum" that should
have been there in the first place. Better late than never, eh?

> > > Any particular reason you missed that fine point?

> > It is irrelevant. Evolution does not say new functions are not allowed
> > to arise. In fact, it says (or at least implies) quite the opposite.
> >
> > Do you have any reason to consider your statement relevant?
>
> Only that this thread is about the origin of the cellular propulsion system known as the flagellum.

Good use of the word "propulsion" there, Eddie. I wonder whether
Mark Isaak took your hint that he is way out on a stratospheric height
of generality instead of dealing with the concrete reality of what the
bacterial flagellum is and does.

Perhaps he did, and perhaps that is the main reason he hasn't done any
posts to this thread in addition to the one to which you are replying here.

Did he ever come down from Cloud No. 9 in the earlier thread of
which this is a continuation?

Peter Nyikos
Professor, Dept. of Mathematics

U. of S. Carolina, Columbia -- standard disclaimer--
http://people.math.sc.edu/nyikos/

[Peter Nyikos]

Use of the question-begging "pointed out that" propagandistic
formula noted.

> > Even as one
> > recognizes that Behe doesn't literally exclude absolutely every
> > possibility of evolution, that pedantically trivial distinction isn't
> > the basis of Roger's comment or mine, and so it's a pointless argument
> > to make.
>
> Yes, but Behe still technically weasels out from "impossible" there.

You really seem to be bending over backwards to avoid offending jillery,
Tiib. So far from being a "pedantically trivial distinction," Behe's
statement needs to be seen in the light of the highly complicated
examples that he chose for his book _Darwin's Black Box_. We are not
dealing here with the usual "refutation" involving an arch that owes
its existence to removing one of four parts from a simple assemblage
of building blocks.

Instead we are dealing with an exquisite molecular machine with
35 parts in the version about whose IC-ness Minnich testified at
Dover, quoted in the part of my earlier post that someone snipped.

> >
> > Instead, the substance of the criticism is that Behe claims IC shows
> > that most biochemical pathways for evolution are highly unlikely, to
> > the point that he accepts evolution as a likely cause for only the
> > least complex processes. This is reinforced by Behe's further
> > argument that IC is strong evidence of an intelligent designer.
>
> I think Behe had to explain the source of his "precipitous unlikelihood"
> estimations better. My (possibly naive) thinking is that the situation
> in nature contains clear selective push towards Behe's IC. System
> with fewer parts is usually more robust and cheaper and simpler to
> assemble.

How many parts do you reckon a hypothetical non-IC precursor to the
35 part flagellum might have had? Any clue as to what it might have
looked like, and what role the surplus parts played in the function
of swimming?

Isaak and jillery deal in stratospheric heights of generality without
ever bothering their heads with pesky little questions like the one
I've asked you. Not on this thread, anyway.

> Removing components that can be removed without weakening the system
> makes the system therefore more efficient. So if evolution follows
> that pressure and removes such components then the direct (not circuitous)
> result is Behe's IC system from what nothing can be removed.

Ironically enough, the Miller-Robison argument that the clotting cascade
could have evolved easily using "small, Darwinian steps" does not
work that way at all.

What it does is to start with a small (and probably IC)
system with three or four parts [well below the threshold of
a "precipitous drop"] and then to successively add redundant parts
through gene duplication...

...but then mutates the redundant parts so that they become
indispensible. And so the cascade gradually lengthened to
something like thirteen parts, alternating between IC and non-IC
stages, always in ways favored by natural selection.

But that scenario does not work for a machine-like assemblage of
molecules like the bacterial flagellum. If someone could come up
with an equally clever argument for how the flagellum could have
evolved by "small, Darwinian steps favored by natural selection"
you can be sure that jillery, Isaak, and Stockwell would be
broadcasting it to the high heavens, and I would be just as willing
to acknowledge its finality as I am about the clotting cascade.

<snip blatant propaganda by jillery, to be dealt with in direct reply to her>

> I do not understand neither side in this discussion. Both sides seem
> to implicitly agree that last mutation that resulted with flagellum had
> to be one that added some part to it.

I never went down that path, because "that last mutation" might have
just rendered a previously redundant part indispensible. There are
other alternatives, as you know:

> Eddie demands that predecessor
> (without part) had motility for Roger some other function (T3SS) is fine.
> To me however that last mutation did not apparently add a part.

So you think it removed a part? What might that part have been doing there?

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

nyikos "at" math.sc.edu

[Öö Tiib]

I assume that evolution often reuses or modifies something and
removal of parts or transformation those into something else is
common. About like when human embryo develops something that
resembles gills that then later transform into other structures
in the ear and neck areas of fetus. Is such development "direct route"
or "circuitous route" of building ear and neck area of human?

>
> > "Even if a system is irreducibly complex (and thus cannot have been
> > produced directly), however, one can not definitely rule out the
> > possibility of an indirect, circuitous route. As the complexity of
> > an interacting system increases, though, the likelihood of such an
> > indirect route drops precipitously."
> >
> > <snip>
>
> Indeed. What made you think this paragraph constituted a "weaseling out"?

Reason was the "precipitously dropping likelihood". I read it as that
IC system can evolve but it has major difficulties (of unidentified
reasons and magnitude) with that "circuitous" sequence of mutations.
It sounds like weaseling.

[Glenn]

"Steady Eddie" <1914o...@gmail.com> wrote in message news:46a444c2-d388-4108...@googlegroups.com...

You're welcome.

[jillery]

On Tue, 16 Aug 2016 09:22:47 -0700 (PDT), 嘱 Tiib <oot...@hot.ee>
wrote:

>On Tuesday, 16 August 2016 17:06:50 UTC+3, jillery wrote:

>> On Tue, 16 Aug 2016 05:41:20 -0700 (PDT), 嘱 Tiib <oot...@hot.ee>

>> wrote:
>>
>> >On Tuesday, 16 August 2016 03:26:52 UTC+3, jillery wrote:
>
>Snip the first part where we sort of agree to disagree.

I suppose, in the sense that you agree (I think) that the distinction
made by the previous poster doesn't strengthen Behe's argument, or
weaken Roger's.

Are you referring to Minnich's experiments, the one he testified about
in the Dover trial? If so, please note that all they did was show
that when a part is removed from a bacterial flagellum, it stopped
moving. Big whoop. They did not identify any particular order of
assembly of those parts, or which part was the last part to be
assembled.

How is the order of assembly of a bacterial flagellum relevant to
Behe's claims?

[jillery]

On Tue, 16 Aug 2016 11:38:19 -0700 (PDT), Steady Eddie

>> >> > > <http://tinyurl.com/z77q8ej>

>> >> >
>> >> > This piece was half-comedic, half-story-telling.
>> >> >
>> >> > He runs headlong into the main issue:
>> >> >
>> >> > "Either a “designer” created thousands of variants on the flagellum or, contrary to creationist claims, it is possible to make considerable changes to the machinery without mucking it up."
>> >>
>> >> Using what mechanism? Simply saying a "designer did it" doesn't cut it because it doesn't say how the "designer" did it.
>> >>
>> >> >
>> >> > Then he figures he told you so, and the obvious answer is the latter, and fails to weigh the two
>> >> > possibilities. He just proceeds as though he forgot that perhaps "a “designer” created thousands of
>> >> > variants on the flagellum".
>> >> >
>> >> > That's exactly my point - Darwinists are fanatics who don't necessarily use reason.
>> >>
>> >> The mechanism of evolution is reproduction with variation and natural selection.
>> >>
>> >> The mechanism of "the designer" is unspecified.
>> >>
>> >> Evolution will continue to win, until a "designer mechanism" is delivered.
>> >>
>> >> Can you not get this?
>> >
>> >No, I don't get it, John.
>> >Who says one would have to know the design "mechanism" of a designer before one can conclude that
>> >something is the work of an intelligent agent?
>>
>>
>> Actually, not just any old intelligent agent, but an unknown, unseen,
>> undefined one. So, given that you don't know who or what did a
>> design, and you don't know how it did a design, on what basis do you,
>> Steady Eddie, identify something as designed, other than "I know it
>> when I see it"?
>
>I've recently told you the answer to that.
>Again, some identifying features of intelligently designed things are:
>-Irreducible complexity.
>-High functional (or prescriptive) information content.

More accurately, you baldly asserted an answer. More to the point,
your use of "some" means you know these features are insufficient by
themselves to show design. And since I recently showed you that the
bacterial flagellum doesn't meet Behe's definition of IC, you can't
even use the presence of IC as a means of identifying design.

Try again.

[jillery]

On Tue, 16 Aug 2016 14:46:50 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> wrote blatant propaganda, the following of
which is but a small sample left in for documentation purposes:

>If someone could come up
>with an equally clever argument for how the flagellum could have
>evolved by "small, Darwinian steps favored by natural selection"
>you can be sure that jillery, Isaak, and Stockwell would be
>broadcasting it to the high heavens, and I would be just as willing
>to acknowledge its finality as I am about the clotting cascade.

Your asinine speculation notwithstanding, the effort you describe
above isn't necessary to show the circularity of Behe's argument. The
past 20 years have not been kind to Behe's IC.

><snip blatant propaganda by jillery, to be dealt with in direct reply to her>

You never learn.

[Peter Nyikos]

This is a misconception. The pharyngeal grooves of the human
embryo never become gill slits, contrary to what umpteen popularizations,
copied from each other, have claimed. [1]

More importantly, Behe expressly abandons such macroscopic structures
at the beginning of _Darwin's Black Box_ and even gives a very favorable
account of the usual "Darwinian" scenario for the evolution of the human eye.
He goes down to the level of molecular systems of a far smaller scale,
where the concept of IC really makes sense.

No organism ever encountered is irreducibly complex, even small bacteria.
We humans are progressing towards the development of an irreducibly complex
organism, a prokaryote to which every single one of its genes is essential,
but that is being done by intelligent design, not evolution.

> that then later transform into other structures
> in the ear and neck areas of fetus. Is such development "direct route"
> or "circuitous route" of building ear and neck area of human?

AFAIK it is direct: the pharyngeal grooves become more and more
complex, in a direction quite different from the one taken by
embryonic fish with homologous structures.

Yes, we can make observations that may allow us to deduce
how one direction, one route evolved from the other; and perhaps this
study has progressed beyond the infant stage of describing the externals
of various developments (fish, amphibian, reptile, mammal) and has
pinpointed the genetic changes that made it possible. But that is something
different from what you are talking about.

[1] Similarly: popularizations, and even textbooks, are still reproducing the
discredited pictures of embryos that were perpetrated by Haeckel a century
ago, and were widely discredited something like half a century ago.

> > > "Even if a system is irreducibly complex (and thus cannot have been
> > > produced directly), however, one can not definitely rule out the
> > > possibility of an indirect, circuitous route. As the complexity of
> > > an interacting system increases, though, the likelihood of such an
> > > indirect route drops precipitously."
> > >
> > > <snip>
> >
> > Indeed. What made you think this paragraph constituted a "weaseling out"?
>
> Reason was the "precipitously dropping likelihood". I read it as that
> IC system can evolve but it has major difficulties (of unidentified
> reasons and magnitude) with that "circuitous" sequence of mutations.
> It sounds like weaseling.

It sounds like something you might try to dispute by talking about
the structure of the bacterial flagellum and the very few other IC
systems with which Behe has challenged the believers in undirected
evolution in _DBB_. I have challenged you in a later reply to you today,
and await your response.

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

Univ. of S. Carolina at Columbia
http://people.math.sc.edu/nyikos/

[Steady Eddie]

That's right!

> > > > Any particular reason you missed that fine point?
>
> > > It is irrelevant. Evolution does not say new functions are not allowed
> > > to arise. In fact, it says (or at least implies) quite the opposite.
> > >
> > > Do you have any reason to consider your statement relevant?
> >
> > Only that this thread is about the origin of the cellular propulsion system known as the flagellum.
>
> Good use of the word "propulsion" there, Eddie. I wonder whether
> Mark Isaak took your hint that he is way out on a stratospheric height
> of generality instead of dealing with the concrete reality of what the
> bacterial flagellum is and does.

Thank you, Peter. Nice to hear positive feedback.

> Perhaps he did, and perhaps that is the main reason he hasn't done any
> posts to this thread in addition to the one to which you are replying here.
>
> Did he ever come down from Cloud No. 9 in the earlier thread of
> which this is a continuation?

No, he was waxing poetic as I left him...

[Peter Nyikos]

jillery vented her spleen, having run out of rational arguments
on Tuesday, August 16, 2016 at 7:51:48 PM UTC-4:

> On Tue, 16 Aug 2016 14:46:50 -0700 (PDT), Peter Nyikos
> <nyi...@bellsouth.net> wrote blatant propaganda, the following of
> which is but a small sample left in for documentation purposes:

Would that "blatant propaganda" include my outline of how
Miller and Robison shot down Behe's claim that the clotting cascade
could not have happened in "small, Darwinian steps"?

That is part of what you snipped, and if the answer to my question
is "no," I'd like to see the IC core of what your copycat allegation of
"blatant propaganda" amounts to.

>
> >If someone could come up
> >with an equally clever argument for how the flagellum could have
> >evolved by "small, Darwinian steps favored by natural selection"
> >you can be sure that jillery, Isaak, and Stockwell would be
> >broadcasting it to the high heavens, and I would be just as willing
> >to acknowledge its finality as I am about the clotting cascade.
>
>
> Your asinine speculation notwithstanding,

Calling it names is not the same thing as outright, explicit denial.

Of course, you are far too cagey to actually deny that you would
behave as described, were such a worthwhile project to succeed.

Nor do I expect you to deny that Isaak or Stockwell would behave like that,
despite your pretense of speaking for everyone in this newsgroup when you
wrote the following to Steady Eddie:

Nobody missed that fine point. Apparently you missed that nobody
disputes it.

As matters now stand, that second sentence is as relevant as saying
"Nobody denied that the Jabberwock came wiffling through the tulgey wood."

Eddie's fine point was:

A flagellum without all of its parts won't work as a flagellum.

Since neither you nor Bill Rogers ever explained what meaning,
if any, you attach to the phrase "as a flagellum," your speaking
in the name of everyone in your first sentence was a bunch of
wasted keystrokes.

> the effort you describe
> above isn't necessary to show the circularity of Behe's argument.

And, I take it, you think the transparent propaganda that I promised
to deal with in a separate reply to you is adequate to show that
alleged circularity.

> The
> past 20 years have not been kind to Behe's IC.

People like you have not been kind to Behe, I'll grant that much.

>
> ><snip blatant propaganda by jillery, to be dealt with in direct reply to her>
>
>
> You never learn.

Au contraire, I learned long ago that you will seize the flimsiest
pretexts to run away from arguments you'd rather not deal with.

Your loss, not mine.

Peter Nyikos
Professor of Math. -standard disclaimer-
U. of S. Carolina

[Öö Tiib]

I was not writing that to please (or not to offend) jillery. I honestly
think that Behe weasels there too much and is pointlessly unclear. It
may be he had good reasons for that. I myself prefer to admit ignorance
and to warn that I speculate instead of being unclear.

>
> Instead we are dealing with an exquisite molecular machine with
> 35 parts in the version about whose IC-ness Minnich testified at
> Dover, quoted in the part of my earlier post that someone snipped.
>
> > >
> > > Instead, the substance of the criticism is that Behe claims IC shows
> > > that most biochemical pathways for evolution are highly unlikely, to
> > > the point that he accepts evolution as a likely cause for only the
> > > least complex processes. This is reinforced by Behe's further
> > > argument that IC is strong evidence of an intelligent designer.
> >
> > I think Behe had to explain the source of his "precipitous unlikelihood"
> > estimations better. My (possibly naive) thinking is that the situation
> > in nature contains clear selective push towards Behe's IC. System
> > with fewer parts is usually more robust and cheaper and simpler to
> > assemble.
>
> How many parts do you reckon a hypothetical non-IC precursor to the
> 35 part flagellum might have had? Any clue as to what it might have
> looked like, and what role the surplus parts played in the function
> of swimming?

It may be is likely that (like with animal embryos) the order of assembly
of flagellum tells us somewhat also the story of its evolution. If to
read about how flagellum is assembled and to assume that the last
evolved protein was most likely in part last dealt with during assembly
then perhaps it was in rod of basal body or in hook of flagellum.
My abecedarian reasoning may be totally wrong of course. ;)

>
> Isaak and jillery deal in stratospheric heights of generality without
> ever bothering their heads with pesky little questions like the one
> I've asked you. Not on this thread, anyway.
>
> > Removing components that can be removed without weakening the system
> > makes the system therefore more efficient. So if evolution follows
> > that pressure and removes such components then the direct (not circuitous)
> > result is Behe's IC system from what nothing can be removed.
>
> Ironically enough, the Miller-Robison argument that the clotting cascade
> could have evolved easily using "small, Darwinian steps" does not
> work that way at all.
>
> What it does is to start with a small (and probably IC)
> system with three or four parts [well below the threshold of
> a "precipitous drop"] and then to successively add redundant parts
> through gene duplication...
>
> ...but then mutates the redundant parts so that they become
> indispensible. And so the cascade gradually lengthened to
> something like thirteen parts, alternating between IC and non-IC
> stages, always in ways favored by natural selection.

I trust that every new feature either starts by changing some
existing thing (possibly regulated with lot of genes) or with single
new gene that produces single protein that somewhat performs it
sometimes.

>
> But that scenario does not work for a machine-like assemblage of
> molecules like the bacterial flagellum. If someone could come up
> with an equally clever argument for how the flagellum could have
> evolved by "small, Darwinian steps favored by natural selection"
> you can be sure that jillery, Isaak, and Stockwell would be
> broadcasting it to the high heavens, and I would be just as willing
> to acknowledge its finality as I am about the clotting cascade.

For example it can be so:
* Some gene that produced proteins that did something in cell's membrane
(for example ejected something) did duplicate.
* Then one of duplicates did mutate to produce proteins that also went
to cell's membrane but instead (of ejecting something) caused limited
motility under certain conditions.
* That was revolutionary since it is important to spread and so from
there started selective pressure to make it more efficient.
* Few millions of years later there was fine-tuned complex flagellum
machine regulated with tens of genes and consisting of number of
sophisticated proteins.

>
> <snip blatant propaganda by jillery, to be dealt with in direct reply to her>
>
> > I do not understand neither side in this discussion. Both sides seem
> > to implicitly agree that last mutation that resulted with flagellum had
> > to be one that added some part to it.
>
> I never went down that path, because "that last mutation" might have
> just rendered a previously redundant part indispensible. There are
> other alternatives, as you know:
>
> > Eddie demands that predecessor
> > (without part) had motility for Roger some other function (T3SS) is fine.
> > To me however that last mutation did not apparently add a part.
>
> So you think it removed a part? What might that part have been doing there?

My opinion likely does not matter but about that Salmonella that
Behe investigated I already speculated.

On general case the flagella are quite diverse. Different bacterial
species have documented from 27 to 80 genes that deal with flagellum.
Not all bacteria are well studied because scientists are most interested
in parasites of human and in bacteria used in food industry (for obvious
reasons). Most scientists are also uninterested in that IC and ID. The
few that are interested in do not seemingly do much experiments.

Therefore it can easily be that different species are in different
stages and that some have IC and some have not IC flagella. Since
Salmonella is whole genus it can even be so about different Salmonella.
IOW we lack experimental data there.

[Mark Isaak]

On 8/16/16 11:38 AM, Steady Eddie wrote:
> [...]

> Again, some identifying features of intelligently designed things are:
> -Irreducible complexity.
> -High functional (or prescriptive) information content.

And those are also features of unintelligently evolved things! What a
coincidence! Do you think the match was intelligently designed?

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"The evil that is in the world always comes of ignorance, and good
intentions may do as much harm as malevolence, if they lack
understanding." - Albert Camus, _The Plague_

[jillery]

On Tue, 16 Aug 2016 18:35:56 -0700 (PDT), rockhead
<nyi...@bellsouth.net> continued to drool his asinine speculations:

>jillery vented her spleen, having run out of rational arguments
> on Tuesday, August 16, 2016 at 7:51:48 PM UTC-4:

Of course, it doesn't help to prove your asinine assertions when you
label my rational arguments as blatant propaganda and then snip them
out.

>> Your asinine speculation notwithstanding,
>
>Calling it names is not the same thing as outright, explicit denial.

Calling it what it is fully explains why no denial is required.

>> ><snip blatant propaganda by jillery, to be dealt with in direct reply to her>
>>
>>
>> You never learn.

Thank you for once again proving that point for me.

[jillery]

On Tue, 16 Aug 2016 14:05:01 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> wrote:

>> Only that this thread is about the origin of the cellular propulsion system known as the flagellum.
>
>Good use of the word "propulsion" there, Eddie.

A good example of giving credit where you can. Will you be giving
praise for remembering to breathe any time soon?

[jillery]

On Tue, 16 Aug 2016 17:42:22 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> wrote:

[note to rockhead: this is how to honestly and intelligently snip for
focus. You should try it some time, if only for the novelty of the
experience.]

>On Tuesday, August 16, 2016 at 6:01:49 PM UTC-4, 嘱 Tiib wrote:

[...]

>> I assume that evolution often reuses or modifies something and
>> removal of parts or transformation those into something else is
>> common. About like when human embryo develops something that
>> resembles gills
>
>This is a misconception. The pharyngeal grooves of the human
>embryo never become gill slits, contrary to what umpteen popularizations,
>copied from each other, have claimed.

Your response is a misrepresentation. 嘱 Tiib's comments are not a
misconception. 嘱 Tiib didn't say human embryos developed gill slits.
Instead, 嘱 Tiib is here referring to the fact that the embryological
structures that develop into gills in fish, instead grow into entirely
different organs in tetrapods.

[Glenn]

"jillery" <69jp...@gmail.com> wrote in message news:74p7rbligt91sokg2...@4ax.com...

"All vertebrates begin development looking like embryonic fish because we all descended from a fishlike ancestor with a fishlike embryo. We see strange contortions and disappearances of organs, blood vessels, and gill slits because descendants still carry the genes and developmental programs of ancestors."

https://www.amazon.com/Why-Evolution-True-Jerry-Coyne/dp/0143116649

[Peter Nyikos]

On Wednesday, August 17, 2016 at 12:31:48 AM UTC-4, jillery wrote:
> On Tue, 16 Aug 2016 17:42:22 -0700 (PDT), Peter Nyikos
> <nyi...@bellsouth.net> wrote:
>
> [note to rockhead: this is how to honestly and intelligently snip for
> focus.

I don't think an ethical nihilist like you knows the meaning of the word "honesty." Your hogwash below shows that you certainly aren't adhering
to the real meaning of the word in this post.

> You should try it some time, if only for the novelty of the
> experience.]

The novelty of dishonestly spin-doctoring the words of others, as
you do below, is something I hope never to experience.

> >On Tuesday, August 16, 2016 at 6:01:49 PM UTC-4, 嘱 Tiib wrote:
>
> [...]
>
> >> I assume that evolution often reuses or modifies something and
> >> removal of parts or transformation those into something else is
> >> common. About like when human embryo develops something that
> >> resembles gills
> >
> >This is a misconception. The pharyngeal grooves of the human
> >embryo never become gill slits, contrary to what umpteen popularizations,
> >copied from each other, have claimed.
>
>
> Your response is a misrepresentation.

Prove it if you can.

> 嘱 Tiib's comments are not a
> misconception. 嘱 Tiib didn't say human embryos developed gill slits.

Then what do you think he was referring to with the words,
"something that resembles gills"? Certainly not what you claim next:

> Instead, 嘱 Tiib is here referring to the fact that the embryological
> structures that develop into gills in fish, instead grow into entirely
> different organs in tetrapods.

Hogwash. That was what *I*, *myself*, wrote about [see repost below].
You snipped that with cunning "intelligence", so that you could indulge in
dishonestly spin doctoring "something that resembles gills" into something
that isn't even hinted at by Öö Tiib.

You know damn well (or do you?) that the pharyngeal grooves of
human embryos look nothing like gills.

=========== begin repost of jillery's snip===================

> that then later transform into other structures
> in the ear and neck areas of fetus. Is such development "direct route"
> or "circuitous route" of building ear and neck area of human?

AFAIK it is direct: the pharyngeal grooves become more and more
complex, in a direction quite different from the one taken by
embryonic fish with homologous structures.

Yes, we can make observations that may allow us to deduce
how one direction, one route evolved from the other; and perhaps this
study has progressed beyond the infant stage of describing the externals
of various developments (fish, amphibian, reptile, mammal) and has
pinpointed the genetic changes that made it possible. But that is something
different from what you are talking about.

============== end of repost of relevant part====================

After his initial comment about evolution that you see above,
Öö Tiib talked exclusively about developmental biology, not evolution,
when speaking of the human embryo, as you can see from the repost.

I believe jillery knows that "ontogeny recapitulates phylogeny"
has been tossed into wastebasket of failed biology
(along with such concepts as "protoplasm").
This would already be enough to explain why jillery snipped
the rest of what Öö Tiib wrote.

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

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

[Öö Tiib]

I did not say that there are gills, I said something that resembles those.

>
> More importantly, Behe expressly abandons such macroscopic structures
> at the beginning of _Darwin's Black Box_ and even gives a very favorable
> account of the usual "Darwinian" scenario for the evolution of the human eye.
> He goes down to the level of molecular systems of a far smaller scale,
> where the concept of IC really makes sense.

Yes, but Behe's IC is about if component can be removed. That is simplistic
because things are assembled in certain order and if something is missing
then that can make assembly impossible.

Evolved self-making system's descendant has to reuse the whole process
of its ancestor assembling and can only add little change to it. Now if we
look how something is assembled or manufactured then we see that the
very possibility of latter steps often depends on if the earlier steps were
done correctly. Therefore the more early in assembling process the change
is added the more likely it is that it breaks whole process (IOW is lethal
change). That makes it most likely that successful descendant adds its
little change or fix close to the end of assembling sequence.

Over time such changes accumulate and result is that the story of
evolution of evolved complex thing is almost recorded into its
assembling sequence. That is indeed what Haeckel said but I don't
see anything wrong with his logic.

>
> No organism ever encountered is irreducibly complex, even small bacteria.
> We humans are progressing towards the development of an irreducibly complex
> organism, a prokaryote to which every single one of its genes is essential,
> but that is being done by intelligent design, not evolution.

Totally optimal efficiency is hard to reach in nature. Competition must be
harsh and frequent and fair and clear and one who is slightly worse must
die. That can be set up in artificial evolution but is not the case in wild
nature so the organisms are always little bit wasteful and not optimal.

>
> > that then later transform into other structures
> > in the ear and neck areas of fetus. Is such development "direct route"
> > or "circuitous route" of building ear and neck area of human?
>
> AFAIK it is direct: the pharyngeal grooves become more and more
> complex, in a direction quite different from the one taken by
> embryonic fish with homologous structures.

Most of those pharyngeal arch cartilages indeed evolve into separate
things however the fourth and sixth fuse into larynx. That we
seemingly inherited already from amphibians.

>
> Yes, we can make observations that may allow us to deduce
> how one direction, one route evolved from the other; and perhaps this
> study has progressed beyond the infant stage of describing the externals
> of various developments (fish, amphibian, reptile, mammal) and has
> pinpointed the genetic changes that made it possible. But that is something
> different from what you are talking about.

I am not sure what you expect that I am talking about. I am exactly saying
that process of building up and assembly of components is a rough record
of evolution for reason that evolution has to happen in little steps.

>
> [1] Similarly: popularizations, and even textbooks, are still reproducing the
> discredited pictures of embryos that were perpetrated by Haeckel a century
> ago, and were widely discredited something like half a century ago.

While it has been widely claimed that Haeckel was charged with fraud by
five professors and convicted by a university court at Jena, there does not
appear to be any verifiable sources for this claim. However the controversy
about those pictures was indeed huge, and the "discrediting" was often lead
by Catholic priests.

To me his claim that ontogeny parallels and summarises phylogeny
makes perfect sense.

>
> > > > "Even if a system is irreducibly complex (and thus cannot have been
> > > > produced directly), however, one can not definitely rule out the
> > > > possibility of an indirect, circuitous route. As the complexity of
> > > > an interacting system increases, though, the likelihood of such an
> > > > indirect route drops precipitously."
> > > >
> > > > <snip>
> > >
> > > Indeed. What made you think this paragraph constituted a "weaseling out"?
> >
> > Reason was the "precipitously dropping likelihood". I read it as that
> > IC system can evolve but it has major difficulties (of unidentified
> > reasons and magnitude) with that "circuitous" sequence of mutations.
> > It sounds like weaseling.
>
> It sounds like something you might try to dispute by talking about
> the structure of the bacterial flagellum and the very few other IC
> systems with which Behe has challenged the believers in undirected
> evolution in _DBB_. I have challenged you in a later reply to you today,
> and await your response.

I did reply to it, but I actually can't find anything in writings of Behe
that sheds light into that circuitousness and reasons of difficulties
with likelihood.

[Peter Nyikos]

How do you expect him to explain such a general statement in ten
thousand words or less? Better to wait until it is challenged, and
then deal with the challenges as they come.

IMHO, a highly structured 35-part entity like the bacterial flagellum
needs to have a plausible hypothetical pathway in place before people can
convincingly assert that Behe is wrong in thinking that it was
intelligently designed. We are very far from having such a thing,
in stark contrast to how the clotting cascade has been explained.

> It
> may be he had good reasons for that. I myself prefer to admit ignorance
> and to warn that I speculate instead of being unclear.

Glad to hear that. You have always struck me as someone with an open
mind. In contrast, jillery and Isaak have been long committed to
discrediting Behe by hook or crook. My next new comment is about two of
myriad such actions.

> > Instead we are dealing with an exquisite molecular machine with
> > 35 parts in the version about whose IC-ness Minnich testified at
> > Dover, quoted in the part of my earlier post that someone snipped.
> >
> > > >
> > > > Instead, the substance of the criticism is that Behe claims IC shows
> > > > that most biochemical pathways for evolution are highly unlikely, to
> > > > the point that he accepts evolution as a likely cause for only the
> > > > least complex processes. This is reinforced by Behe's further
> > > > argument that IC is strong evidence of an intelligent designer.

"only the least complex processes" is at best a distortion, and
the ambiguous "IC is strong evidence" could refer to either the whole
body of IC structures of which Behe wrote in detail (correct) or to
any random instance of IC (wildly incorrect).

> > > I think Behe had to explain the source of his "precipitous unlikelihood"
> > > estimations better. My (possibly naive) thinking is that the situation
> > > in nature contains clear selective push towards Behe's IC. System
> > > with fewer parts is usually more robust and cheaper and simpler to
> > > assemble.
> >
> > How many parts do you reckon a hypothetical non-IC precursor to the
> > 35 part flagellum might have had? Any clue as to what it might have
> > looked like, and what role the surplus parts played in the function
> > of swimming?
>
> It may be is likely that (like with animal embryos) the order of assembly
> of flagellum tells us somewhat also the story of its evolution. If to
> read about how flagellum is assembled and to assume that the last
> evolved protein was most likely in part last dealt with during assembly
> then perhaps it was in rod of basal body or in hook of flagellum.
> My abecedarian reasoning may be totally wrong of course. ;)

Your suggestion looks like a good way to proceed, but your "most likely"
is really going out on a limb: the very limited extent to which
"ontogeny recapitulates phylogeny" doesn't allow for confidence about
such specifics.

More relevantly, it gives no clue as to what sort of structure was
the immediate precursor of the flagellum among non-IC structures.
This was your favored evolutionary route, no?

Continued in next reply.

Peter Nyikos

[Greg Guarino]

On 8/16/2016 5:46 PM, Peter Nyikos wrote:

>> I do not understand neither side in this discussion. Both sides seem
>> > to implicitly agree that last mutation that resulted with flagellum had
>> > to be one that added some part to it.


> I never went down that path, because "that last mutation" might have
> just rendered a previously redundant part indispensible. There are
> other alternatives, as you know:

What I have never seen adequately explained is how irreducible
complexity - as demonstrated by "knockout" experiments - presents a
difficulty for standard biology.

If we demonstrate that a "core" function fails to work when any of 35
parts is removed, we have reasonably demonstrated that none of those
34-part "knockout" configurations is likely to have been the "step" that
immediately preceded the current configuration.

But what biologist would think that a likely scenario?

As you say, there are other alternatives, one of which you mention. As
mutation and selection are expected to refine a function over time to be
more effective and efficient, the current configuration may differ
greatly from the first one that performed the function, albeit possibly
poorly. Today's collection of parts may not work with one missing, but
what about a more likely scenario: with one or more parts *altered*?

There are many biological mysteries, but I see no reason that a claim of
irreducible complexity makes that particular puzzle a "problem" that
suggests a non-biological explanation until it is solved.

[Peter Nyikos]

On Tuesday, August 16, 2016 at 10:36:48 PM UTC-4, Mark Isaak wrote:
> On 8/16/16 11:38 AM, Steady Eddie wrote:
> > [...]
> > Again, some identifying features of intelligently designed things are:
> > -Irreducible complexity.
> > -High functional (or prescriptive) information content.
>
> And those are also features of unintelligently evolved things!

Only of a vanishingly small percentage. Do I need to trot out
my satire again about you going to the "parts department" of
an automobile dealership? IOW, will you be posting such garbage as
"IC is refuted by the fact that the real parts of every biological
organism are protons, neutrons, and electrons."?

The part in scare quotes is a mini-satire, not a quote of something
you actually wrote. You are too slippery to let yourself be nailed
down on any specific claim on what the parts of things are, aren't you?
IIRC, you play at nihilism by suggesting that the very concept "a part"
has no place in biology.

> What a
> coincidence! Do you think the match was intelligently designed?

Classic GIGO at work here, folks.

Peter Nyikos
Professor of Mathematics -- standard disclaimer --

[Glenn]

"Peter Nyikos" <nyi...@bellsouth.net> wrote in message news:e2c0dc3f-e4c5-4da9...@googlegroups.com...

> On Tuesday, August 16, 2016 at 10:36:48 PM UTC-4, Mark Isaak wrote:
>> On 8/16/16 11:38 AM, Steady Eddie wrote:
>> > [...]
>> > Again, some identifying features of intelligently designed things are:
>> > -Irreducible complexity.
>> > -High functional (or prescriptive) information content.
>>
>> And those are also features of unintelligently evolved things!
>
> Only of a vanishingly small percentage. Do I need to trot out
> my satire again about you going to the "parts department" of
> an automobile dealership? IOW, will you be posting such garbage as
> "IC is refuted by the fact that the real parts of every biological
> organism are protons, neutrons, and electrons."?
>

Why would you think not?

[Peter Nyikos]

On Wednesday, August 17, 2016 at 11:01:48 AM UTC-4, Greg Guarino wrote:
> On 8/16/2016 5:46 PM, Peter Nyikos wrote:
>
> >> I do not understand neither side in this discussion. Both sides seem
> >> > to implicitly agree that last mutation that resulted with flagellum had
> >> > to be one that added some part to it.
>
>
> > I never went down that path, because "that last mutation" might have
> > just rendered a previously redundant part indispensible. There are
> > other alternatives, as you know:
>
> What I have never seen adequately explained is how irreducible
> complexity - as demonstrated by "knockout" experiments - presents a
> difficulty for standard biology.

That is because you don't see the real roles of IC in these arguments.
And I don't think Behe does either.

I have no dog in this fight, only a desire to see truth win out
over sophistry. IMO, IC is a gimmick that does the following:

1. Focus our attention on structures whose evolution has been,
shall we say, grossly under-explained. The more the parts, and
the better coordinated they are in remarkable patterns, the
more this is true. The bacterial flagellum is a prime example.

2. Give us "more bang for the buck" by forcing the "it evolved
easily within the time it seems to have taken" proponents to explain
the evolution of something with MORE parts.

3. [see below]

> If we demonstrate that a "core" function fails to work when any of 35
> parts is removed, we have reasonably demonstrated that none of those
> 34-part "knockout" configurations is likely to have been the "step" that
> immediately preceded the current configuration.
>
> But what biologist would think that a likely scenario?
>
> As you say, there are other alternatives, one of which you mention. As
> mutation and selection are expected to refine a function over time to be
> more effective and efficient, the current configuration may differ
> greatly from the first one that performed the function, albeit possibly
> poorly.

3. It puts the onus on people like you to give some ideas of
what those objects whose refinement you tout actually looked
like, and what they were doing.

Behe repeatedly complains about vague hand-waving like what you
are doing here. In one case, he even devotes several pages of _DBB_ to
talking about one attempt at doing what 3. prescribes, and shows
the maddening incompleteness of it, concluding that "the universe
cannot wait that long" or words to that effect.

He was describing a now-obsolete scenario provided by the world's
leading expert on clotting of the time, Doolittle. This stung Doolittle
so much that he wrote an article in which he hilariously misread
a paper on clotting in genetically altered mice and incorrectly concluded
that the "wild type" clotting system was not IC. Behe exposed Doolittle's
mistake at Dover in 2005 and has done so many times in public appearances.

> Today's collection of parts may not work with one missing, but
> what about a more likely scenario: with one or more parts *altered*?

Trouble is, nobody has tried to describe such a "more likely scenario"
except with hand-waving much worse even than that done by Doolittle.

> There are many biological mysteries, but I see no reason that a claim of
> irreducible complexity makes that particular puzzle a "problem" that
> suggests a non-biological explanation until it is solved.

It isn't the claim itself so much as points 1., 2., and 3.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --
Univ. of S. Carolina at Columbia

[Glenn]

"Greg Guarino" <gdgu...@gmail.com> wrote in message news:np1tvf$620$1...@dont-email.me...

> As mutation and selection are expected to refine a function over time to be
> more effective and efficient,

Do you think any evolutionist would challenge this claim?

[Glenn]

"John Stockwell" <john.1...@gmail.com> wrote in message news:45182326-3102-44f4...@googlegroups.com...

> On Saturday, August 13, 2016 at 12:32:01 AM UTC-6, Steady Eddie wrote:
>> On Wednesday, 10 August 2016 10:57:08 UTC-6, jillery wrote:
>> > On Wed, 10 Aug 2016 12:36:33 -0400, jillery <69jp...@gmail.com>
>> > wrote:
>> >
>> > >On Wed, 10 Aug 2016 07:02:18 -0700 (PDT), Steady Eddie

>> > ><1914o...@gmail.com> wrote:
>> > >
>> > >>After several failed attempts to reply to Mark Isaak on the original thread, I think we need to start a fresh one...
>> > >>
>> > >>Last comment from the original thread:
>> > >>
>> > >>-quote-
>> > >>On 7/29/16 8:22 PM, Steady Eddie wrote:
>> > >>> On Tuesday, 26 July 2016 00:02:57 UTC-6, Mark Isaak wrote:
>> > >>>> On 7/25/16 6:12 PM, Steady Eddie wrote:
>> > >>>>> On Wednesday, 20 July 2016 17:08:12 UTC-6, Mark Isaak wrote:

>> > >>>>>> On 7/20/16 6:15 AM, Steady Eddie wrote:
>> > >>>>>>> [...]

>> > >>>>>>> How do you think 'parts having parts' is fatal to Behe's conclusions?
>> > >>>>>>
>> > >>>>>> The answer should be obvious, but if there is anyone who:
>> > >>>>>> a) understands Behe's thesis;
>> > >>>>>> b) does not see how "parts having parts" is fatal to it, even after
>> > >>>>>> serious consideration; and
>> > >>>>>> c) honestly wants to know;
>> > >>>>>> then such a person I would be happy to answer.
>> > >>>>>
>> > >>>>> Do you only teach those who sit submissively at your feet, or do you also defend your assertions before
>> > >>>>> those who aren't convinced of your infallibility?
>> > >>>>
>> > >>>> I do not teach people who choose not to come to class, such as yourself.
>> > >>>
>> > >>> Professor, since you (seem to have) brought it up (in your

>> > >>> cryptic style), can you explain how the existence of the T3SS

>> > >>> shows that the flagellum will work without all of its parts?
>> > >>
>> > >>The T3SS works.
>> > >>
>> > >>The T3SS is essentially a flagellum without all of its parts.
>> > >>
>> > >>Therefore, a flagellum without all of its parts will work.
>> > >>
>> > >>Got that?
>> > >>-end quote-
>> > >>

>> > >>A flagellum without all of its parts won't work as a flagellum.

>> > >>Any particular reason you missed that fine point?
>> > >
>> > >

>> > >Nobody missed that fine point. Apparently you missed that nobody

>> > >disputes it. OTOH, the fact that a flagellum without all its parts
>> > >still has a function, is the final nail in IC's coffin.
>> >
>> >
>> > In the spirit of accuracy, I correct myself here. There are people

>> > who dispute that a bacterial flagellum without all its parts won't
>> > work as a flagellum:
>> >
>> > <https://www.newscientist.com/article/dn13663-evolution-myths-the-bacterial-flagellum-is-irreducibly-complex/>

>>
>> This piece was half-comedic, half-story-telling.
>>
>> He runs headlong into the main issue:
>>
>> "Either a “designer” created thousands of variants on the flagellum or, contrary to creationist claims, it is possible to make considerable changes to the machinery without mucking it up."
>
> Using what mechanism? Simply saying a "designer did it" doesn't cut it because it doesn't say how the "designer" did it.
>
>>
>> Then he figures he told you so, and the obvious answer is the latter, and fails to weigh the two
>> possibilities. He just proceeds as though he forgot that perhaps "a “designer” created thousands of
>> variants on the flagellum".
>>
>> That's exactly my point - Darwinists are fanatics who don't necessarily use reason.
>
> The mechanism of evolution is reproduction with variation and natural selection.
>

Reproduction itself is not "the" mechanism of evolution.
Variation in a population is not in itself "the" mechanism of evolution.
"Reproduction with variation" by itself is not a model or "the" mechanism of evolution.
Natural selection has, since Darwin's time, been questioned as to whether it is a mechanism of evolution, or "the" mechanism.

"Skipper and Millstein analyze natural selection and mechanism, concluding that natural selection is not a mechanism in the sense of the new mechanistic philosophy. Barros disagrees and provides his own account of natural selection as a mechanism. This discussion identifies a missing piece of Barros's account, attempts to fill in that piece, and reconsiders the revised account. Two principal objections are developed: one, the account does not characterize natural selection; two, the account is not mechanistic. Extensive and persistent variability causes both of these difficulties, so further attempts to describe natural selection as a mechanism are also unlikely to succeed. "

http://philpapers.org/rec/HAVPFN

[jillery]

On Wed, 17 Aug 2016 08:48:31 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> wrote:

>On Wednesday, August 17, 2016 at 11:01:48 AM UTC-4, Greg Guarino wrote:
>> On 8/16/2016 5:46 PM, Peter Nyikos wrote:
>>
>> >> I do not understand neither side in this discussion. Both sides seem
>> >> > to implicitly agree that last mutation that resulted with flagellum had
>> >> > to be one that added some part to it.
>>
>>
>> > I never went down that path, because "that last mutation" might have
>> > just rendered a previously redundant part indispensible. There are
>> > other alternatives, as you know:
>>
>> What I have never seen adequately explained is how irreducible
>> complexity - as demonstrated by "knockout" experiments - presents a
>> difficulty for standard biology.
>
>That is because you don't see the real roles of IC in these arguments.
>And I don't think Behe does either.
>
>I have no dog in this fight, only a desire to see truth win out
>over sophistry.

Don't forget to mention your quest to preserve Truth, Justice, and the
American Way.

[jillery]

On Wed, 17 Aug 2016 07:45:47 -0700 (PDT), 嘱 Tiib <oot...@hot.ee>
wrote:

[...]

>Yes, but Behe's IC is about if component can be removed. That is simplistic
>because things are assembled in certain order and if something is missing
>then that can make assembly impossible.
>
>Evolved self-making system's descendant has to reuse the whole process
>of its ancestor assembling and can only add little change to it. Now if we
>look how something is assembled or manufactured then we see that the
>very possibility of latter steps often depends on if the earlier steps were
>done correctly. Therefore the more early in assembling process the change
>is added the more likely it is that it breaks whole process (IOW is lethal
>change). That makes it most likely that successful descendant adds its
>little change or fix close to the end of assembling sequence.
>
>Over time such changes accumulate and result is that the story of
>evolution of evolved complex thing is almost recorded into its
>assembling sequence. That is indeed what Haeckel said but I don't
>see anything wrong with his logic.

Now I understand the point you made, and I asked you about, the order
of assembly, that if a system is assembled with a missing step, it
can't be completed. IIUC by analogy, an auto manufacturer can't
install wheels if they haven't previously assembled the axles. And of
course, biological systems which assemble other systems are also
evolved, and so are indeed applicable to Behe's claims.

Haeckel is one of those pointlessly noisy arguments raised by
anti-evolutionists who aren't interested in the substance of his
claims, that ontogeny is conserved within and between species. Don't
be derailed by these injections. Haeckel's errors have been
identified and corrected for decades, and aren't relevant to this
topic.

[jillery]

On Tue, 16 Aug 2016 23:03:36 -0700, "Glenn" <g...@invalid.invalid>
wrote:

And your point is...???

There's a well-understood and sound evolutionary basis for why it's
easier to follow existing developmental programs as far as possible,
rather than modify those developmental plans from the beginning, like
a human designer would typically do.

[jillery]

On Wed, 17 Aug 2016 08:22:16 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> wrote:

>On Tuesday, August 16, 2016 at 10:36:48 PM UTC-4, Mark Isaak wrote:
>> On 8/16/16 11:38 AM, Steady Eddie wrote:
>> > [...]
>> > Again, some identifying features of intelligently designed things are:
>> > -Irreducible complexity.
>> > -High functional (or prescriptive) information content.
>>
>> And those are also features of unintelligently evolved things!
>
>Only of a vanishingly small percentage. Do I need to trot out
>my satire again about you going to the "parts department" of
>an automobile dealership? IOW, will you be posting such garbage as
>"IC is refuted by the fact that the real parts of every biological
>organism are protons, neutrons, and electrons."?
>
>The part in scare quotes is a mini-satire, not a quote of something
>you actually wrote. You are too slippery to let yourself be nailed
>down on any specific claim on what the parts of things are, aren't you?
>IIRC, you play at nihilism by suggesting that the very concept "a part"
>has no place in biology.
>
>> What a
>> coincidence! Do you think the match was intelligently designed?
>
>Classic GIGO at work here, folks.

You described your comments accurately enough. Give yourself a gold
star.

[jillery]

On Wed, 17 Aug 2016 07:26:43 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> was caught washing his hogs:

On Wednesday, August 17, 2016 at 12:31:48 AM UTC-4, jillery wrote:

>> Your response is a misrepresentation. 嘱 Tiib's comments are not a

>> misconception. 嘱 Tiib didn't say human embryos developed gill slits.

>> Instead, 嘱 Tiib is here referring to the fact that the embryological
>> structures that develop into gills in fish, instead grow into entirely
>> different organs in tetrapods.

>Prove it if you can.

Already did, restored above. Perhaps you would have realized that, if
you weren't focused on mangling my comments into incoherence.

>Then what do you think he was referring to with the words,
>"something that resembles gills"?

Only someone with a serious reading comprehension problem, or someone
interested in posting pointless noise, would claim "something that
resembles gills" means the same thing as "developed gill slits". I
leave it as an exercise which better fits you.

[Glenn]

"jillery" <69jp...@gmail.com> wrote in message news:9h89rbtdggd2ev0b7...@4ax.com...

Wow, three question marks!

[Bob Casanova]

On Wed, 17 Aug 2016 11:21:39 -0700, the following appeared
in talk.origins, posted by "Glenn" <g...@invalid.invalid>:

Wow, four words, no answer, and an exclamation point!
--

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 Wednesday, August 17, 2016 at 1:46:46 PM UTC-4, jillery wrote:
> On Wed, 17 Aug 2016 07:26:43 -0700 (PDT), Peter Nyikos

> <nyi...@bellsouth.net> [wrote]:

> On Wednesday, August 17, 2016 at 12:31:48 AM UTC-4, jillery wrote:
>
> >> Your response is a misrepresentation. 嘱 Tiib's comments are not a
> >> misconception. 嘱 Tiib didn't say human embryos developed gill slits.
> >> Instead, 嘱 Tiib is here referring to the fact that the embryological
> >> structures that develop into gills in fish, instead grow into entirely
> >> different organs in tetrapods.
>
> >Prove it if you can.
>
>
> Already did, restored above.

That is not a proof, it is a blatant assertion which I have disputed
with reasoning that you snipped. What's more...

...your use of "restored" is misleading in the context of Usenet, where it
typically refers to reposting (usually with the appropriate number of
attribution marks in the margin) text which was deleted by someone earlier, typically the person to whom one is directly responding.

You did nothing of the sort, you simply left in text that your newsreader
(or should I say netserver?) automatically quoted while indulging in
highly selective and shamelessly self-serving snips of the rest.

Real restorations are an indispensible weapon against highly dishonest
persons like yourself. Right in the post to which you are replying here,
I did a repost [not a restoration in the usual sense above]
to demonstrate how you indulged in a snip to give the readers the
impression that your blatant assertion is plausible.

And you've snipped that demonstration here, in order to continue to
give readers the mistaken impression of plausibility. You are thereby
giving astute readers evidence that you are, indeed, an ethical
nihilist, just as I said you are.

To help astute readers realize this, I will be giving a restoration
(in the usual sense) of what you snipped. I will do that in a separate
post, otherwise I'd be playing into your nefarious hands by
making this post so long that hardly anyone will take the trouble
to read it.

> Perhaps you would have realized that, if
> you weren't focused on mangling my comments into incoherence.

It is you who gave incoherent comments and lent them plausibility
with your highly selective deletia.

>
> >Then what do you think he was referring to with the words,
> >"something that resembles gills"?

You ducked this question. Whatever it was, it wasn't anything
to do with what you have left in at the beginning of this post.

>
> Only someone with a serious reading comprehension problem, or someone
> interested in posting pointless noise, would claim "something that
> resembles gills" means the same thing as "developed gill slits".

Since I did not do that, it is you who are in need of a refresher
in reading comprehension -- or, rather, in not underestimating
your adversaries. You are reading meanings into what I
wrote that simply aren't there.

You are a master at catching others in such reading-meanings-into,
so you should have no trouble catching yourself at it.

> I leave it as an exercise which better fits you.

Neither of the above, as I believe you know already.

Peter Nyikos

[John Stockwell]

IC is always had the same role in science. When we invoke it, this has been more of a statement of our ignorance than a statement
about phenomena. Indeed, if the people who think that "intelligent
design" is "obvious" or is "everywhere" were right, it would be
possible to find ever greater numbers of examples of IC.

The last time that this happened was when Paley wrote his "natural theology" book. It was a collection of things that were not understood in his day, and encompassed a large suite of biology.

Since Darwin, IC has become much harder to find. Now, we are relegated to the shadows of our understanding. But that is what
an argument from ignorance is all about (it's about the ignorance).


-John

[Peter Nyikos]

On Tuesday, August 16, 2016 at 9:46:49 PM UTC-4, Öö Tiib wrote:
> On Wednesday, 17 August 2016 00:51:50 UTC+3, Peter Nyikos wrote:
> > On Tuesday, August 16, 2016 at 8:41:51 AM UTC-4, Öö Tiib wrote:

> > > Removing components that can be removed without weakening the system
> > > makes the system therefore more efficient. So if evolution follows
> > > that pressure and removes such components then the direct (not circuitous)
> > > result is Behe's IC system from what nothing can be removed.
> >
> > Ironically enough, the Miller-Robison argument that the clotting cascade
> > could have evolved easily using "small, Darwinian steps" does not
> > work that way at all.
> >
> > What it does is to start with a small (and probably IC)
> > system with three or four parts [well below the threshold of
> > a "precipitous drop"] and then to successively add redundant parts
> > through gene duplication...
> >
> > ...but then mutates the redundant parts so that they become
> > indispensible. And so the cascade gradually lengthened to
> > something like thirteen parts, alternating between IC and non-IC
> > stages, always in ways favored by natural selection.
>
> I trust that every new feature either starts by changing some
> existing thing (possibly regulated with lot of genes) or with single
> new gene that produces single protein that somewhat performs it
> sometimes.

I won't argue with that. I only note that the claim that the
bacterial flagellum evolved without intelligent (and NOT necessarily
supernatural) design is the very point most in dispute here.

[In re "NOT necessarily" -- have you seen my reply to John Stockwell
earlier this week?]

> >
> > But that scenario does not work for a machine-like assemblage of
> > molecules like the bacterial flagellum. If someone could come up
> > with an equally clever argument for how the flagellum could have
> > evolved by "small, Darwinian steps favored by natural selection"
> > you can be sure that jillery, Isaak, and Stockwell would be
> > broadcasting it to the high heavens, and I would be just as willing
> > to acknowledge its finality as I am about the clotting cascade.

As I put it in the first reply to this post of yours [this being the
second]:

IMHO, a highly structured 35-part entity like the bacterial flagellum
needs to have a plausible hypothetical pathway in place before people can
convincingly assert that Behe is wrong in thinking that it was
intelligently designed. We are very far from having such a thing,
in stark contrast to how the clotting cascade has been explained.

> For example it can be so:
> * Some gene that produced proteins that did something in cell's membrane
> (for example ejected something) did duplicate.
> * Then one of duplicates did mutate to produce proteins that also went
> to cell's membrane but instead (of ejecting something) caused limited
> motility under certain conditions.

How would it do that without ejecting anything? Ejection would cause
some slight motility due to one of Newton's laws of motion, but nothing
like that produced by the parts of the flagellum (hook and long flagellin
strand) not present in your hypothetical precursor.

> * That was revolutionary since it is important to spread and so from
> there started selective pressure to make it more efficient.

The devil is in the details. There is lots of selective pressure to
make elephants fly, but the physical properties of elephants and
of earth gravity make it an impossibility. [1] Just how is that selective
pressure going to produce all the genes necessary to produce the extra
parts that make it possible for bacteria with functioning flagellae to swim?

> * Few millions of years later there was fine-tuned complex flagellum
> machine regulated with tens of genes and consisting of number of
> sophisticated proteins.

Why only a few million? Why not a few billion (or at least a few
milliard, to use EU terminology)?

[1] To make a more realistic analogy, why has no mammal evolved to
replace the dinosaurs who fed on high branches of conifers? The world
is replete with conifers that would be hog heaven for *Diplodocus*
or any number of long-necked sauropods. Giraffes, the closest
thing we have to them, do not feast on pine needles.

What's more, almost all mammals are restricted to 7 vertebrae in their
necks. There is all the selective pressure you could ask for to produce
mammals with lots of neck vertebrae, on the order of what you see in
sauropods. Think of all the broadleaf trees that a number of mammals could
feast on the leaaves of, if only that selective pressure produced that
naturally expected result.

Concluded in next reply to this post, hopefully by some time tomorrow.
I've done more posting already today than I originally intended to do.

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

University of South Carolina

[Mark Isaak]

On 8/17/16 8:22 AM, Peter Nyikos wrote:
> On Tuesday, August 16, 2016 at 10:36:48 PM UTC-4, Mark Isaak wrote:
>> On 8/16/16 11:38 AM, Steady Eddie wrote:
>>> [...]
>>> Again, some identifying features of intelligently designed things are:
>>> -Irreducible complexity.
>>> -High functional (or prescriptive) information content.
>>
>> And those are also features of unintelligently evolved things!
>
> Only of a vanishingly small percentage. Do I need to trot out
> my satire again about you going to the "parts department" of
> an automobile dealership? IOW, will you be posting such garbage as
> "IC is refuted by the fact that the real parts of every biological
> organism are protons, neutrons, and electrons."?

Rather than writing fiction, why don't you try a reality-based argument
on why those things would not be expected to evolve.

> The part in scare quotes is a mini-satire, not a quote of something
> you actually wrote. You are too slippery to let yourself be nailed
> down on any specific claim on what the parts of things are, aren't you?
> IIRC, you play at nihilism by suggesting that the very concept "a part"
> has no place in biology.

What has no place in biology is pretending that parts are always
well-defined and immutable.

[Mark Isaak]

On 8/17/16 7:52 AM, Peter Nyikos wrote:
> [snip a lot]

> IMHO, a highly structured 35-part entity like the bacterial flagellum
> needs to have a plausible hypothetical pathway in place before people can
> convincingly assert that Behe is wrong in thinking that it was
> intelligently designed. We are very far from having such a thing,
> in stark contrast to how the clotting cascade has been explained.

What is special about the flagellum? If a plausible hypothetical
pathway could be found for a different IC system, would that justify
asserting Behe is wrong to think that IC indicates design?

[Bill Rogers]

On Wednesday, August 17, 2016 at 7:21:45 PM UTC-4, Mark Isaak wrote:
> On 8/17/16 7:52 AM, Peter Nyikos wrote:
> > [snip a lot]
> > IMHO, a highly structured 35-part entity like the bacterial flagellum
> > needs to have a plausible hypothetical pathway in place before people can
> > convincingly assert that Behe is wrong in thinking that it was
> > intelligently designed. We are very far from having such a thing,
> > in stark contrast to how the clotting cascade has been explained.
>
> What is special about the flagellum? If a plausible hypothetical
> pathway could be found for a different IC system, would that justify
> asserting Behe is wrong to think that IC indicates design?

And what's waiting in the wings after there's a detailed, plausible pathway for the flagellum?

[jillery]

On Wed, 17 Aug 2016 11:21:39 -0700, "Glenn" <g...@invalid.invalid>

Wow, zero answers. Is anybody surprised?

[jillery]

On Wed, 17 Aug 2016 12:44:44 -0700 (PDT), Peter Nyikos
<nyi...@bellsouth.net> babbled incoherently:

>On Wednesday, August 17, 2016 at 1:46:46 PM UTC-4, jillery wrote:


>> Only someone with a serious reading comprehension problem, or someone
>> interested in posting pointless noise, would claim "something that
>> resembles gills" means the same thing as "developed gill slits".
>
>Since I did not do that,

Perhaps someone spoofed your account. Or perhaps an extraterrestiral
alien took over your mind just at the moment it was posted. Or
perhaps you're denying reality here because you like to post
incoherent noise.

Either way, there is a post stored on numerous news servers around the
world, which contains the text I quoted with that date and time and
your signature, and are irrelevant to the context, 嘱 Tiib's comments,
and this topic.

[Peter Nyikos]

On Wednesday, August 17, 2016 at 7:11:45 PM UTC-4, Mark Isaak wrote:
> On 8/17/16 8:22 AM, Peter Nyikos wrote:
> > On Tuesday, August 16, 2016 at 10:36:48 PM UTC-4, Mark Isaak wrote:
> >> On 8/16/16 11:38 AM, Steady Eddie wrote:
> >>> [...]
> >>> Again, some identifying features of intelligently designed things are:
> >>> -Irreducible complexity.
> >>> -High functional (or prescriptive) information content.
> >>
> >> And those are also features of unintelligently evolved things!
> >
> > Only of a vanishingly small percentage. Do I need to trot out
> > my satire again about you going to the "parts department" of
> > an automobile dealership? IOW, will you be posting such garbage as
> > "IC is refuted by the fact that the real parts of every biological
> > organism are protons, neutrons, and electrons."?
>
> Rather than writing fiction,

It's already been written, and you have no sense of humor when the joke
is on you, do you?

> why don't you try a reality-based argument
> on why those things would not be expected to evolve.

You're addressing the wrong person. Steady Eddie is the one who makes
blanket comments about IC being "not expected to evolve." See my reply to
Greg Guarino if you want to know where I am coming from.

That's a big "if," I know.

> > The part in scare quotes is a mini-satire, not a quote of something
> > you actually wrote. You are too slippery to let yourself be nailed
> > down on any specific claim on what the parts of things are, aren't you?
> > IIRC, you play at nihilism by suggesting that the very concept "a part"
> > has no place in biology.
>
> What has no place in biology is pretending that parts are always
> well-defined and immutable.

No such pretense exists, except perhaps in the mind of Ray Martinez.

Ah, but you think Ray Martinez is on target when he calls the
Inquisitors murderers, don't you? Try arguing him against immutability
of parts with the same amount of respect, and maybe you'll get a coherent
argument from him.

Peter Nyikos

[Peter Nyikos]

Via 1., 2., and 3. above, it is also a statement of the complacency
of most scientists about that ignorance, and indirectly of the eagerness
of some [including the instigators of that public attack on Behe signed by
all his colleagues in his department at Lehigh U.] to play
"shoot the messenger."

> Indeed, if the people who think that "intelligent
> design" is "obvious" or is "everywhere" were right, it would be
> possible to find ever greater numbers of examples of IC.

Don't worry, you will never catch me thinking that way.

> The last time that this happened was when Paley wrote his "natural theology"
> book. It was a collection of things that were not understood in his day,

> encompassed a large suite of biology.

That was then, this is now. In Paley's day there were naturalists who
had a wonderful grasp of the whole of biology known then, and who
were responsible for huge advances in our knowledge. We are now in the
age of commercialization where vertebrate paleontologists, in order
to get published, almost have to have some gimmick connecting their
work with ecology or some other fashionable field, or indulge in
some heavy use of computers which generate grant overhead for their
institutions.

> Since Darwin, IC has become much harder to find.

You mean ID, don't you? Paley never talked about IC, surely.

> Now, we are relegated to the shadows of our understanding. But that is what
> an argument from ignorance is all about (it's about the ignorance).

And the complacency about it, and about the "shoot the messenger"
mentality.

Two decades have elapsed since DBB, and what refutations have
we seen besides the Miller/Robison shooting down of the clotting
cascade as evidence of ID? That came out within a year of DBB,
and Behe's critics actually seem to take pride in not having made
any significant progress on possible scenarios for the bacterial flagellum.

[Glenn]

"jillery" <69jp...@gmail.com> wrote in message news:fn1arb9lv3jc45bc0...@4ax.com...

I doubt anyone is surprised that you have zero answers. Wait for it.

[Steady Eddie]

On Wednesday, 17 August 2016 19:21:45 UTC-6, Peter Nyikos wrote:
> On Wednesday, August 17, 2016 at 7:11:45 PM UTC-4, Mark Isaak wrote:
> > On 8/17/16 8:22 AM, Peter Nyikos wrote:
> > > On Tuesday, August 16, 2016 at 10:36:48 PM UTC-4, Mark Isaak wrote:
> > >> On 8/16/16 11:38 AM, Steady Eddie wrote:
> > >>> [...]
> > >>> Again, some identifying features of intelligently designed things are:
> > >>> -Irreducible complexity.
> > >>> -High functional (or prescriptive) information content.
> > >>
> > >> And those are also features of unintelligently evolved things!
> > >
> > > Only of a vanishingly small percentage. Do I need to trot out
> > > my satire again about you going to the "parts department" of
> > > an automobile dealership? IOW, will you be posting such garbage as
> > > "IC is refuted by the fact that the real parts of every biological
> > > organism are protons, neutrons, and electrons."?
> >
> > Rather than writing fiction,
>
> It's already been written, and you have no sense of humor when the joke
> is on you, do you?
>
> > why don't you try a reality-based argument
> > on why those things would not be expected to evolve.

I endorse the following statement:

> You're addressing the wrong person. Steady Eddie is the one who makes
> blanket comments about IC being "not expected to evolve." See my reply to
> Greg Guarino if you want to know where I am coming from.
>
> That's a big "if," I know.

Thank you, Peter, for the accurate characterization of my position.

[jillery]

Name one poster to T.O. who wouldn't guess that you think IC isn't
expected to evovle.

>> > > The part in scare quotes is a mini-satire, not a quote of something
>> > > you actually wrote. You are too slippery to let yourself be nailed
>> > > down on any specific claim on what the parts of things are, aren't you?
>> > > IIRC, you play at nihilism by suggesting that the very concept "a part"
>> > > has no place in biology.
>> >
>> > What has no place in biology is pretending that parts are always
>> > well-defined and immutable.
>>
>> No such pretense exists, except perhaps in the mind of Ray Martinez.
>>
>> Ah, but you think Ray Martinez is on target when he calls the
>> Inquisitors murderers, don't you? Try arguing him against immutability
>> of parts with the same amount of respect, and maybe you'll get a coherent
>> argument from him.
>>
>> Peter Nyikos

[jillery]

On Wed, 17 Aug 2016 18:53:42 -0700, "Glenn" <g...@invalid.invalid>

You didn't ask any questions, twit.


>Wait for it.


It's almost certain the Universe will suffer heat death before you
post a cogent response.

[jillery]

When the messenger faithfully and honestly executes the role as a
messenger, it would indeed be a travesty of justice to shoot him.

OTOH, when the messenger uses that role as a pretense to advocate for
the message, and/or to assail its opposites, and/or to act as
provocateur and impugn the motives of others for the sake of it, then
shooting the messenger would be a kindness. Figuratively speaking, of
course.

More to the point, to the best of my recollection, I have never heard
of or read where Behe claimed he was acting as a messenger as opposed
to advocating for ID.

So which of your three steps does your compulsive slander apply?

[Peter Nyikos]

It was I who asked one of you [1], in reply to the same spin-doctored
paragraph to which Glenn originally responded [1]. And you
twice ducked the question, playing snip-n-deceive [2]
both times to cover your failure to answer the question.

> >Wait for it.

Perhaps Glenn's "Wait for it" referred to the fact that I
had already confronted you with that question [1] TWICE:

[1] Then what do you think he was referring to with the words,
"something that resembles gills"? Certainly not what you claim next:

> Instead, 嘱 Tiib is here referring to the fact that the embryological
> structures that develop into gills in fish, instead grow into entirely
> different organs in tetrapods.

Recognize your own words from the paragraph to which Glenn replied?
The words I quoted from Tiib were your SOLE basis for them, as
my repost of your snipped text showed.

>
> It's almost certain the Universe will suffer heat death before you
> post a cogent response.

That is a perfect analysis of your repeated ducking of the question [1]
reposted above.


[2] See the following OP for a description of this reprehensible tactic:

https://groups.google.com/d/msg/talk.origins/2nHc4qLCRbo/dUX2oJnfHQAJ
Subject: Dirty Debating Tactics 2: Snip-n-deceive
Date: Wed, 24 Feb 2016 08:41:54 -0800 (PST)

As the persona most addicted to this dirty debating tactic,
you play a prominent role in this OP, and your reply to it revealed
yet other aspects of your mendacious persona.



I expect your reply to this post to be a classic running away
from confronting your irresponsible behavior, something like the following:

================== begin illustrative example==============

> > >I doubt anyone is surprised that you have zero answers.

>
> > You didn't ask any questions, twit.

> It was I who asked one of you

I was addressing Glenn, twit.

--
This space is intentionally not blank.

============ end of illustrative example ================

Peter Nyikos

[Peter Nyikos]

On Wednesday, August 17, 2016 at 7:31:45 PM UTC-4, Bill Rogers wrote:
> On Wednesday, August 17, 2016 at 7:21:45 PM UTC-4, Mark Isaak wrote:
> > On 8/17/16 7:52 AM, Peter Nyikos wrote:
> > > [snip a lot]
> > > IMHO, a highly structured 35-part entity like the bacterial flagellum
> > > needs to have a plausible hypothetical pathway in place before people can
> > > convincingly assert that Behe is wrong in thinking that it was
> > > intelligently designed. We are very far from having such a thing,
> > > in stark contrast to how the clotting cascade has been explained.
> >
> > What is special about the flagellum? If a plausible hypothetical
> > pathway could be found for a different IC system, would that justify
> > asserting Behe is wrong to think that IC indicates design?

"indicates" = "suggests to me"

It does NOT mean "proves."

Moreover, the suggestion can be quickly shelved in cases where
a very few (<< 35) simple parts with no direct function are concerned.
Such is the case trumpeted in one Talk.Origins Archive FAQ pooh-poohing IC:
a four-part stack of brick-shaped stones forms an IC 3-part arch
upon displacement of one of the stones.

Find a plausible precursor of the bacterial flagellum that can
be turned into it in such a simple way, and you may be on to something.

>
> And what's waiting in the wings after there's a detailed,
> plausible pathway for the flagellum?

I'd rather cross that bridge when we come to it, but since I
only can expect to go on living for 2-3 more decades, I'll give
a few:

1. One of the most enduring enigmas in the way of confident assertion
of abiogenesis leading to life as we know it: the protein takeover.
For an introduction to this enigma, see:

Subject: The protein takeover -- a challenge for abiogenesis
https://groups.google.com/forum/#!topic/talk.origins/t5adVev10Ys[1-25]

2. The evolution of the actual biological system for synthesizing
AMP starting with its purine base. This is explained by Behe in
a chapter in _DBB_. It is disqualified from being IC by the
fact that the parts (enzymes) that are responsible for this synthesis
do not all interact with each other, but only with the chains of
molecules that are being built on the purine.

The following website gives a detailed
description of the steps in the synthesis, but without most
of the pictures with which Behe illustrated the steps:

http://library.med.utah.edu/NetBiochem/pupyr/pp.htm#Syn pu

3, ... unexplained IC systems in _Darwin's Black Box_, including
the protein transport mechanism and the eukaryotic cilium.

Maybe 2. and 3., ... will have been explained before my death, but
I have good reasons to believe that enigma 1. will still be around
long afterwards.

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

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

[Peter Nyikos]

On Wednesday, August 17, 2016 at 10:46:48 AM UTC-4, Öö Tiib wrote:
> On Wednesday, 17 August 2016 03:46:49 UTC+3, Peter Nyikos wrote:

> > On Tuesday, August 16, 2016 at 6:01:49 PM UTC-4, Öö Tiib wrote:

> > > I assume that evolution often reuses or modifies something and
> > > removal of parts or transformation those into something else is
> > > common. About like when human embryo develops something that
> > > resembles gills
> >
> > This is a misconception. The pharyngeal grooves of the human
> > embryo never become gill slits, contrary to what umpteen popularizations,

> > copied from each other, have claimed. [1]
>
> I did not say that there are gills, I said something that resembles those.

And what would that "something" be? The pharyngeal grooves of the
human embryo do not look at all like gills, and they bear only the most
superficial resemblance to gill slits, like the resemblance a cave
bears to a tunnel.

> >
> > More importantly, Behe expressly abandons such macroscopic structures
> > at the beginning of _Darwin's Black Box_ and even gives a very favorable
> > account of the usual "Darwinian" scenario for the evolution of the human eye.
> > He goes down to the level of molecular systems of a far smaller scale,
> > where the concept of IC really makes sense.

>
> Yes, but Behe's IC is about if component can be removed.

That is a description, not a prescription for actual formation.

> That is simplistic
> because things are assembled in certain order and if something is missing
> then that can make assembly impossible.

The prescription for assembly in _Darwin's Black Box_ takes on two forms:
"simple, Darwinian steps" [p. 39] that probably do refer to adding components,
and the "indirect, circuitous route" which does not. You don't seem to
be directly talking about either of these prescriptions below.

> Evolved self-making system's descendant has to reuse the whole process
> of its ancestor assembling and can only add little change to it. Now if we
> look how something is assembled or manufactured then we see that the
> very possibility of latter steps often depends on if the earlier steps were
> done correctly. Therefore the more early in assembling process the change
> is added the more likely it is that it breaks whole process (IOW is lethal
> change). That makes it most likely that successful descendant adds its
> little change or fix close to the end of assembling sequence.

As a general rule that seems correct, but there may be exceptions.
I'm not sure, but the woodpecker's tongue may be an exception.

And don't forget, lethality in some individuals may be compensated
for by production of enough others. A significant percentage
of human zygotes become "blighted ova", where the embryonic disc
fails to form or develop, while the trophoblast goes on developing.
The usual result: spontaneous abortion, a.k.a. early miscarriage.

> Over time such changes accumulate and result is that the story of
> evolution of evolved complex thing is almost recorded into its
> assembling sequence.

That does not seem to work for amniotes: the way human embryos develop is
significantly different from the way most eutherian embryos develop,
which in turn is very different from the pattern for egg-laying mammals,
which in turn is very different from the pattern for amphibians.

> That is indeed what Haeckel said but I don't
> see anything wrong with his logic.

Haeckel simply ignored the placenta and umbilical cord, which are integral
parts of the human embryo/fetus, in comparing eutherian embryos/fetuses with
non-eutherian ones. That's over and above the gross inaccuracies
in the pictures he did draw.

Continued in next reply to this post of yours.

Peter Nyikos

[Peter Nyikos]

On Tuesday, August 16, 2016 at 9:46:49 PM UTC-4, Öö Tiib wrote:
> On Wednesday, 17 August 2016 00:51:50 UTC+3, Peter Nyikos wrote:
> > On Tuesday, August 16, 2016 at 8:41:51 AM UTC-4, Öö Tiib wrote:

This is the third and final reply to your thought-provoking post.

> > > I do not understand neither side in this discussion. Both sides seem
> > > to implicitly agree that last mutation that resulted with flagellum had
> > > to be one that added some part to it.
> >
> > I never went down that path, because "that last mutation" might have
> > just rendered a previously redundant part indispensible. There are
> > other alternatives, as you know:
> >

> > > Eddie demands that predecessor
> > > (without part) had motility for Roger some other function (T3SS) is fine.
> > > To me however that last mutation did not apparently add a part.
> >
> > So you think it removed a part? What might that part have been doing there?
>
> My opinion likely does not matter but about that Salmonella that
> Behe investigated I already speculated.

I missed that. Could you give me a synopsis and/or a link?

> On general case the flagella are quite diverse. Different bacterial
> species have documented from 27 to 80 genes that deal with flagellum.

"deal with flagellum" does not mean the same thing as "produce, via
replication and translation, the various component parts of the flagellum."
Did you actually mean the latter statement?

Even if you did, there may be some ambiguity in just "the flagellum"
to account for some variation. I have seen at least one person include,
in "the flagellum," whatever triggers the secretion that causes the
rotor to rotate and thus cause the long strand of flagellin to propel
the bacterium.

Other variations can be accounted for by what I said earlier:

once an IC system exists, there is nothing to rule out it evolving into
another system.

In fact, this is what probably happened with the bacterial
flagellum. Originating in gram-negative bacteria, it shed two
rings as the bacterium evolved into a gram-positive bacterium,
which had one less outer layer and so did not need the shed rings.

There may have been other changes along such unexceptional lines,
accounting for the unspecified "thousands of variations"
that have been alleged by Steady Eddie.

> Not all bacteria are well studied because scientists are most interested
> in parasites of human and in bacteria used in food industry (for obvious
> reasons). Most scientists are also uninterested in that IC and ID. The
> few that are interested in do not seemingly do much experiments.

And yet, you would expect Behe's critics to conduct experiments testing
whether the structures Behe claims to be IC aren't really IC. The only
such experiments of which I know were conducted by Minnich and his students,
and they showed that at least one form of the flagellum is IC.

Why didn't they test more of them? you might ask. The "obvious reasons"
about which you speak include: 1. grant money and 2. publishability.
Those knockout experiments might have been fine for Ph.D. dissertations,
but the source of grant money for Minnich's lab had to do with
parasites, for obvious reasons.


> Therefore it can easily be that different species are in different
> stages and that some have IC and some have not IC flagella.

All the more reason, then, for Behe's critics to conduct further
experiments. Instead, they are taking the path of least
resistance, pretending that the evolution of the flagellum has
been adequately accounted for.

> Since
> Salmonella is whole genus it can even be so about different Salmonella.
> IOW we lack experimental data there.

We have some, and the following excerpt from a webpage on a Nobel Laureate
alludes to one set of them:

Arber's findings have been confirmed by many other scientists,
such as Bullas et al. [5]

[5] Bullas, L. R., C. Colson, and A. Van Pel. 1976. DNA restriction and
modification systems in Salmonella. SQ, a new system derived by
recombination between the SB system of Salmonella typhimurium and
the SP system of Salmonella Potsdam.
Journal of General Microbiology. 95 (1): 166-172.

This being a creationist website, you might find some distortions of
what's in the above article. The webpage then drops a clue as to what
Behe's "precipitous drop" may be about:

The most recent replication is by Lenski et al,
who evaluated the changes in over 30,000 generations of E. coli,
concluding that millions of mutations and trillions of cells
were needed to produce the estimated two to three mutations
required to allow cells to bring citrate into the cell under oxic
conditions. [6] This corresponds with Michael Behe's deductions that
if one mutation is required to confer some advantage to an organism,
this event is likely; if two are required, the likelihood is far
less; but if three or more are required, the probability rapidly
grows exponentially worse, from very improbable to impossible.
Evolution by mutations for this reason has very clear limits. [7]

[6] Blount, Z., C. Borland, and R. Lenski. 2008. Historical Contingency
and the Evolution of a Key Innovation in an Experimental Population
of Escherichia coli.
Proceedings of the National Academy of Science. 105: 7899-7906.
[7] Behe, Michael. 2007. The Edge of Evolution. New York: The Free Press.

http://www.icr.org/article/werner-arber-nobel-laureate-darwin-skeptic/

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

University of South Carolina

[Glenn]

"Peter Nyikos" <nyi...@bellsouth.net> wrote in message news:e79d6669-7deb-48e9...@googlegroups.com...

That, and see below.

>
> [1] Then what do you think he was referring to with the words,
> "something that resembles gills"? Certainly not what you claim next:
>
>> Instead, 嘱 Tiib is here referring to the fact that the embryological
>> structures that develop into gills in fish, instead grow into entirely
>> different organs in tetrapods.
>
> Recognize your own words from the paragraph to which Glenn replied?
> The words I quoted from Tiib were your SOLE basis for them, as
> my repost of your snipped text showed.
>

Zero answers there. Which pertains to sweetie ducking the "answer" to the "we see...gill slits" quote from Jerry Coyne. Coyne is a major player.

[Peter Nyikos]

On Wednesday, August 17, 2016 at 10:46:48 AM UTC-4, Öö Tiib wrote:
> On Wednesday, 17 August 2016 03:46:49 UTC+3, Peter Nyikos wrote:

> > On Tuesday, August 16, 2016 at 6:01:49 PM UTC-4, Öö Tiib wrote:
> > > On Tuesday, 16 August 2016 23:36:49 UTC+3, Peter Nyikos wrote:
> > > > On Monday, August 15, 2016 at 6:01:52 PM UTC-4, Öö Tiib wrote:

This is my second reply to another thought-provoking post by you.

> > No organism ever encountered is irreducibly complex, even small bacteria.
> > We humans are progressing towards the development of an irreducibly complex
> > organism, a prokaryote to which every single one of its genes is essential,
> > but that is being done by intelligent design, not evolution.
>
> Totally optimal efficiency is hard to reach in nature. Competition must be
> harsh and frequent and fair and clear and one who is slightly worse must
> die. That can be set up in artificial evolution but is not the case in wild
> nature so the organisms are always little bit wasteful and not optimal.

Yes, but how do you reconcile this from something you wrote back on the 16th?

Removing components that can be removed without weakening the system
makes the system therefore more efficient. So if evolution follows
that pressure and removes such components then the direct (not circuitous)
result is Behe's IC system from what nothing can be removed.

As Hegel might have said, what is the synthesis you get out of this
thesis and antithesis?

> > > that then later transform into other structures
> > > in the ear and neck areas of fetus. Is such development "direct route"
> > > or "circuitous route" of building ear and neck area of human?
> >
> > AFAIK it is direct: the pharyngeal grooves become more and more
> > complex, in a direction quite different from the one taken by
> > embryonic fish with homologous structures.

I'll have to check my books on developmental biology when I get home:
it seems the real complexity is in the development of the pharyngeal *arches*.

> Most of those pharyngeal arch cartilages indeed evolve into separate
> things however the fourth and sixth fuse into larynx. That we
> seemingly inherited already from amphibians.

The grooves, which look superficially like gill slits,
come between the arches:
https://en.wikipedia.org/wiki/Pharyngeal_arch

Surely you didn't think the pharyngeal *arches* looked
"somewhat like gills"!?


> >
> > Yes, we can make observations that may allow us to deduce
> > how one direction, one route evolved from the other; and perhaps this
> > study has progressed beyond the infant stage of describing the externals
> > of various developments (fish, amphibian, reptile, mammal) and has
> > pinpointed the genetic changes that made it possible. But that is something
> > different from what you are talking about.
>
> I am not sure what you expect that I am talking about. I am exactly saying
> that process of building up and assembly of components is a rough record
> of evolution for reason that evolution has to happen in little steps.

I am skeptical about that "has to happen in little steps": see the
closing excerpt in my third reply, less than an hour ago,
to another thought-provoking post you did a day earlier.

I also question the "rough record" bit. It is of course true that,
inasmuch as the parts of the human body are the result of evolution,
each one's structure can be traced back to earlier precursor structures.
But that is different from saying that these appear in tandem, i.e.,
that each *stage* in embryonic development corresponds to some precursor
*stage* in the development of some ancestor.

Concluded in next reply to this post, hopefully tomorrow.

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

University of South Carolina (Columbia)

[jillery]

On Thu, 18 Aug 2016 08:17:21 -0700 (PDT), Peter Nyikos

>> >>>>>> Your response is a misrepresentation. ? Tiib's comments are not a
>> >>>>>> misconception. ? Tiib didn't say human embryos developed gill slits.
>> >>>>>> Instead, ? Tiib is here referring to the fact that the embryological

>> >>>>>> structures that develop into gills in fish, instead grow into entirely
>> >>>>>> different organs in tetrapods.
>> >>>>>> --
>> >>>>>"All vertebrates begin development looking like embryonic fish because we all descended from a fishlike ancestor with a fishlike embryo. We see strange contortions and disappearances of organs, blood vessels, and gill slits because descendants still carry the genes and developmental programs of ancestors."
>> >>>>>
>> >>>>>https://www.amazon.com/Why-Evolution-True-Jerry-Coyne/dp/0143116649
>> >>>>
>> >>>>
>> >>>> And your point is...???
>> >>>>
>> >>>Wow, three question marks!
>> >>
>> >>
>> >> Wow, zero answers. Is anybody surprised?
>> >> --
>> >I doubt anyone is surprised that you have zero answers.
>
>>
>> You didn't ask any questions, twit.
>

>It was I who asked one of you...


So you and Glenn are twit-tag-teaming me again. Apparently neither of
you are confident enough to deal with me by yourselves.

>I expect your reply to this post to be a classic running away
>from confronting your irresponsible behavior, something like the following:
>
>================== begin illustrative example==============
>
>> > >I doubt anyone is surprised that you have zero answers.
>
>>
>> > You didn't ask any questions, twit.
>
>> It was I who asked one of you
>
>I was addressing Glenn, twit.

Give yourself a gold star for recognizing yourself. It's no surprise
that you conflate my replies with running away and irresponsible
behavior, because that's what you do. Tu quoque back atcha, asshole.

[jillery]

On Thu, 18 Aug 2016 12:24:18 -0700, "Glenn" <g...@invalid.invalid>
wrote:

>>> >>>>>> Your response is a misrepresentation. ? Tiib's comments are not a
>>> >>>>>> misconception. ? Tiib didn't say human embryos developed gill slits.
>>> >>>>>> Instead, ? Tiib is here referring to the fact that the embryological

>>> >>>>>> structures that develop into gills in fish, instead grow into entirely
>>> >>>>>> different organs in tetrapods.
>>> >>>>>> --
>>> >>>>>"All vertebrates begin development looking like embryonic fish because we all descended from a fishlike ancestor with a fishlike embryo. We see strange contortions and disappearances of organs, blood vessels, and gill slits because descendants still carry the genes and developmental programs of ancestors."
>>> >>>>>
>>> >>>>>https://www.amazon.com/Why-Evolution-True-Jerry-Coyne/dp/0143116649
>>> >>>>
>>> >>>>
>>> >>>> And your point is...???
>>> >>>>
>>> >>>Wow, three question marks!
>>> >>
>>> >>
>>> >> Wow, zero answers. Is anybody surprised?
>>> >> --
>>> >I doubt anyone is surprised that you have zero answers.
>>
>>>
>>> You didn't ask any questions, twit.
>>
>> It was I who asked one of you [1], in reply to the same spin-doctored
>> paragraph to which Glenn originally responded [1]. And you
>> twice ducked the question, playing snip-n-deceive [2]
>> both times to cover your failure to answer the question.
>>
>>> >Wait for it.
>>
>> Perhaps Glenn's "Wait for it" referred to the fact that I
>> had already confronted you with that question [1] TWICE:
>
>That, and see below.

So it's your turn in the twit-tag team ring. For someone who avoids
answering questions out of habit, you sure are quick to blame others
for that behavior.

Right here would have been a good place for you to have posted a
coherent and cogent question. Failing that, you show you're just a
troll looking to throw shit for the sake of it, just like your strange
bedfellow. But I have to admit, you and rockhead are so cute when you
get in bed together.

[John Stockwell]

One could argue that we are complacent about the possibility that Phlogiston really exists. Those complacent scientists have failed to see that "dark matter" proves that the phlogiston theory deserves another go.

>
> > Indeed, if the people who think that "intelligent
> > design" is "obvious" or is "everywhere" were right, it would be
> > possible to find ever greater numbers of examples of IC.
>
> Don't worry, you will never catch me thinking that way.

That's the point, IC is not easy to find, yet the world should
be crawling with it if the naive notions of ID held by
ID creationists are true.

>
> > The last time that this happened was when Paley wrote his "natural theology"
> > book. It was a collection of things that were not understood in his day,
> > encompassed a large suite of biology.
>
> That was then, this is now. In Paley's day there were naturalists who
> had a wonderful grasp of the whole of biology known then, and who
> were responsible for huge advances in our knowledge. We are now in the
> age of commercialization where vertebrate paleontologists, in order
> to get published, almost have to have some gimmick connecting their
> work with ecology or some other fashionable field, or indulge in
> some heavy use of computers which generate grant overhead for their
> institutions.

So you are still sore that you were never recognized as the great vertebrate paleontologist that you are PeePee. PeePee NyNy in the academy of science. PeePee NyNy in tails before the King of Sweden.

>
> > Since Darwin, IC has become much harder to find.
>
> You mean ID, don't you? Paley never talked about IC, surely.

ID and IC mean exactly the same thing. No possibility of
there being anything but special creation like the Paley
Watch Company.

>
> > Now, we are relegated to the shadows of our understanding. But that is what
> > an argument from ignorance is all about (it's about the ignorance).
>
> And the complacency about it, and about the "shoot the messenger"
> mentality.
>
> Two decades have elapsed since DBB, and what refutations have
> we seen besides the Miller/Robison shooting down of the clotting
> cascade as evidence of ID? That came out within a year of DBB,
> and Behe's critics actually seem to take pride in not having made
> any significant progress on possible scenarios for the bacterial flagellum.

IC is dead in the water. IC = IGnorance. There is plenty of
biological context in terms of secretory systems for the
flagellum.

Case closed? No. The case is never closed in science.

-John

[Glenn]

"jillery" <69jp...@gmail.com> wrote in message news:no5crbh3h1lp7kuge...@4ax.com...

So is Jerry Coyne full of "shit"?

[rsNorman]

Peter Nyikos <nyi...@bellsouth.net> Wrote in message:

> On Wednesday, August 17, 2016 at 10:46:48 AM UTC-4, 嘱 Tiib wrote:
>> On Wednesday, 17 August 2016 03:46:49 UTC+3, Peter Nyikos wrote:

Peter, you are only partly right in reference to the fact that
humans do not produce "gills" nor "gill slits" nor anything
associated with gills. I admit to having taught that "pharyngeal
slits" are an important characteristic of all chordates including
humans and also to having used Haeckel's drawing in teaching.
Intro teaching means leaving out an enromous amount of details
and trying to create grand stories to help studens understand
general patterns. So we are guilty of taking some shortcuts.
But the essential fact is that human embros _do_ have pharyngeal
pouches which in fish develop into gills but which have been
diverted in tetrapods to different uses. The structural elements
that formed gill support arches are modified by tetrapods,
mammals, and humans for other functions. The same pattern of
blood circulation and of innervation of the pouches which
originally served the gills have been diverted to different
functions in tetrapods and mammals and humans. Oo tib is
basically correct in claiming that evolution takes existing
structures and, through modification, results in very different
functions. The evolution of complex structures is often reflected
in the embryological developmental pattern. I have been out of
teaching for more than a decade but well before I retired we were
rather more careful about describing just what those similarities
are between our own embryos and those of fish and amphibians and
whatever.

Haeckel did take different stages of embryos for his drawing and
did abstract certain features to emphasis parallels and
similarities. What he was trying to illustrate was, in fact,
quite true although his drawing exaggerated or, better,
overemphasized the facts. Yes, he did not include placentas and
embilical cords. Anybody who has ever had any eperience in
drawing diagrams from life to illustrate points knows you have to
crop away irrelevant features. The placenta and umbilical cord
is irrelevant to understand what is happening to the overall
development of those pharyngeal structures, to the
three-component brain (fore- mid- and hind-), to the limb buds,
the tail, the segmented myotomes. Those extremely important
similarities are what are illustrated in the drawing. And they
are quite true.

Incidentally, the placenta and umbilical cord are not so special
as you suggest here and illustrate the point of taking an
existing structure and modifying it for different function.
Eutherians produce exactly the same set of extraembryonic
structures as do all amniotes: amnion, chorion, yolk sac, and
allantois. Chick embryos produce a tubular structure containing
blood vessels originating in the center of the abdomen to the
more peripheral yolk sac and chorion so that the embryo can take
in nutrients and oxygen and give off carbon dioxide and wastes
(not through the blood but into the allantois). The human
embilical cord is just that same structure with blood vessels and
even an allantois so the embryo/fetus can take in nutrients and
oxygen and give off carbon dioxide and wastes. The placenta is
formed from the chorion, the fetal contribution, along with
tissues from the uterus, the maternal contribution. Eutherians
are merely rather specialized amniotes with classic amniote
embryonic structures.

Your claim is true that human development differs from that of all
other animals. That is obvious, we, the result of development,
are different from all other animals. However there is an
enormity of similarly in the most fundamental and earliest
developmental sequences in all triploblastic animals, in all
deuterostomes,in all chordates, vertebrates, tetrapods,
eutherians, primates ...
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[jillery]

On Thu, 18 Aug 2016 14:23:01 -0700, "Glenn" <g...@invalid.invalid>
wrote:

>>>>> >>>>>"All vertebrates begin development looking like embryonic fish because we all descended from a fishlike ancestor with a fishlike embryo. We see strange contortions and disappearances of organs, blood vessels, and gill slits because descendants still carry the genes and developmental programs of ancestors."
>>>>> >>>>>
>>>>> >>>>>https://www.amazon.com/Why-Evolution-True-Jerry-Coyne/dp/0143116649
>>>>> >>>>
>>>>> >>>>
>>>>> >>>> And your point is...???
>>>>> >>>>
>>>>> >>>Wow, three question marks!
>>>>> >>
>>>>> >>
>>>>> >> Wow, zero answers. Is anybody surprised?
>>>>> >> --
>>>>> >I doubt anyone is surprised that you have zero answers.
>>>>
>>>>>
>>>>> You didn't ask any questions, twit.
>

>So is Jerry Coyne full of "shit"?

Since you finally figured out how to ask a question, I will answer it

Almost certainly, as are almost all healthy tetrapods.

And your point is...???

And try not to evade my question this time, if only for the novelty of
the experience.

[Glenn]

"jillery" <69jp...@gmail.com> wrote in message news:9fccrbll1b7k163j2...@4ax.com...

Did you ask one?

[jillery]

You did an excellent job elaborating on Haeckel, gill slits, and
ontogeny, but in the process you didn't explain how any of these
things relate to IC or ID. Not that you should have, since nobody
else has either.

[jillery]

On Thu, 18 Aug 2016 15:16:14 -0700, "Glenn" <g...@invalid.invalid>
wrote:

No, I asked several. Your turn, twit.

[Glenn]

"jillery" <69jp...@gmail.com> wrote in message news:l2dcrbt531gjahh0d...@4ax.com...

Thanks, sweetie.