Claim CB901: “No case of macro-evolution has ever been documented.”

[dthe...@gmail.com]

This response does a lousy job of representing what those who object to the unscientific notion of Macro-evolution actually believe. Please read my reply to these responses to get a better understanding of our position. And yes I like may others, reject the unscientific notion that unique life forms can and have evolved into utterly different life forms.

Source:
Morris, Henry M., 2000 (Jan.). Strong Delusion. Back to Genesis 133: a.
Brown, Walt, 1995. In the Beginning: Compelling evidence for creation and the Flood. Phoenix, AZ: Center for Scientific Creation, p. 6.

Response:
1. We would not expect to observe large changes directly. Evolution consists mainly of the accumulation of small changes over large periods of time. If we saw something like a fish turning into a frog in just a couple generations, we would have good evidence against evolution.

My reply: Not what Creationists are even suggesting at all.


2. The evidence for evolution does not depend, even a little, on observing macroevolution directly. There is a very great deal of other evidence (Theobald 2004; see also evolution proof).

My reply: This is an obvious departure from the actual Scientific Method (Observational Science) and an appeal to “historical’ Science that is based on mere opinion not scientific evidence.


3. As biologists use the term, macroevolution means evolution at or above the species level. Speciation has been observed and documented.

My reply: These same scientists dogmatically assert that all life forms evolved from a single life form which is far beyond “speciation”.


4. Microevolution has been observed and is taken for granted even by creationists. False assertion. And because there is no known barrier to large change and because we can expect small changes to accumulate into large changes, microevolution implies macroevolution. Small changes to developmental genes or their regulation can cause relatively large changes in the adult organism (Shapiro et al. 2004).

My reply: This is a logically fallacious conclusion. It's based on a gigantic assumption without any scientific impetus whatsoever for drawing such conclusions. In other words these conclusions are not based in scientific evidence but rather mere assumptions made on mere opinion.


5. There are many transitional forms that show that macroevolution has occurred.

My reply: Hog wash! You never see scientific proof of one unique life form transforming into another completely different life form. A bird is still a bird, a fish a fish, a plant a plant, etc. etc.



References:
1. Shapiro M. D., M. E. Marks, C. L. Peichel, B. K. Blackman, K. S. Nereng, B. Jónsson, D. Schluter and D. M. Kingsley, 2004. Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature 428: 717-723. See also: Shubin, N. H. and R. D. Dahn, 2004. Evolutionary biology: Lost and found. Nature 428: 703.
2. Theobald, Douglas, 2004. 29+ Evidences for macroevolution: The scientific case for common descent. http://www.talkorigins.org/faqs/comdesc/

[Burkhard]

dthe...@gmail.com wrote:
> This response does a lousy job of representing what those who object to the unscientific notion of Macro-evolution actually believe. Please read my reply to these responses to get a better understanding of our position. And yes I like may others, reject the unscientific notion that unique life forms can and have evolved into utterly different life forms.
>
> Source:
> Morris, Henry M., 2000 (Jan.). Strong Delusion. Back to Genesis 133: a.
> Brown, Walt, 1995. In the Beginning: Compelling evidence for creation and the Flood. Phoenix, AZ: Center for Scientific Creation, p. 6.
>
> Response:
> 1. We would not expect to observe large changes directly. Evolution consists mainly of the accumulation of small changes over large periods of time. If we saw something like a fish turning into a frog in just a couple generations, we would have good evidence against evolution.
>
> My reply: Not what Creationists are even suggesting at all.

Quite a number do. You as well, below at 4

>
>
> 2. The evidence for evolution does not depend, even a little, on observing macroevolution directly. There is a very great deal of other evidence (Theobald 2004; see also evolution proof).
>
> My reply: This is an obvious departure from the actual Scientific Method (Observational Science) and an appeal to “historical’ Science that is based on mere opinion not scientific evidence.

Firstly, wrong on its own terms, as these "other forms of evidence" are
of course observations. Science frequently postulates entities and
processes that can only indirectly be observed (otherwise, you would
really not need science, just a list of things you see)

Second, it makes an arbitrary and ultimately meaningless distinction
between historical sciences and other scientific disciplines. Forensic
sciences are an obvious example where we use scientific methods to form
reliable theories about singular past events - maybe you suggest we
should empty our prisons and only convict if there were several
eyewitnesses?

>
>
> 3. As biologists use the term, macroevolution means evolution at or above the species level. Speciation has been observed and documented.
>
> My reply: These same scientists dogmatically assert that all life forms evolved from a single life form which is far beyond “speciation”.

If it goes beyond "speciation", then it is "above" species level, just
as the answer you quote says. You seem to have problems here parsing the
sentence.

>
>
> 4. Microevolution has been observed and is taken for granted even by creationists. False assertion. And because there is no known barrier to large change and because we can expect small changes to accumulate into large changes, microevolution implies macroevolution. Small changes to developmental genes or their regulation can cause relatively large changes in the adult organism (Shapiro et al. 2004).
>
> My reply: This is a logically fallacious conclusion. It's based on a gigantic assumption without any scientific impetus whatsoever for drawing such conclusions. In other words these conclusions are not based in scientific evidence but rather mere assumptions made on mere opinion.

Of course they aren't, just simple logic. If you observe a process, you
need to discover a reason why it would stop at a given point. Burden of
proof is whith whoever stipulates such a barrier or mechanism

>
>
> 5. There are many transitional forms that show that macroevolution has occurred.
>
> My reply: Hog wash! You never see scientific proof of one unique life form transforming into another completely different life form.

And above, you claim that creationists would not make this silly arguer...

[Glenn]

On Friday, February 8, 2019 at 12:00:08 PM UTC-7, Burkhard wrote:
> dthe...@gmail.com wrote:
> > This response does a lousy job of representing what those who object to the unscientific notion of Macro-evolution actually believe. Please read my reply to these responses to get a better understanding of our position. And yes I like may others, reject the unscientific notion that unique life forms can and have evolved into utterly different life forms.
> >
> > Source:
> > Morris, Henry M., 2000 (Jan.). Strong Delusion. Back to Genesis 133: a.
> > Brown, Walt, 1995. In the Beginning: Compelling evidence for creation and the Flood. Phoenix, AZ: Center for Scientific Creation, p. 6.
> >
> > Response:
> > 1. We would not expect to observe large changes directly. Evolution consists mainly of the accumulation of small changes over large periods of time. If we saw something like a fish turning into a frog in just a couple generations, we would have good evidence against evolution.
> >
> > My reply: Not what Creationists are even suggesting at all.
>
> Quite a number do. You as well, below at 4
>
>
> >
> >
> > 2. The evidence for evolution does not depend, even a little, on observing macroevolution directly. There is a very great deal of other evidence (Theobald 2004; see also evolution proof).
> >
> > My reply: This is an obvious departure from the actual Scientific Method (Observational Science) and an appeal to “historical’ Science that is based on mere opinion not scientific evidence.
>
> Firstly, wrong on its own terms, as these "other forms of evidence" are
> of course observations. Science frequently postulates entities and
> processes that can only indirectly be observed (otherwise, you would
> really not need science, just a list of things you see)
>
> Second, it makes an arbitrary and ultimately meaningless distinction
> between historical sciences and other scientific disciplines. Forensic
> sciences are an obvious example where we use scientific methods to form
> reliable theories about singular past events - maybe you suggest we
> should empty our prisons and only convict if there were several
> eyewitnesses?
>

Hmmmmmm, reliable, eh.

"In 2009, the National Academy of Sciences evaluated the state of forensic science and, shockingly, concluded that many of the techniques used in court actually have no scientific validity. This means that the science used to convict the accused is neither reliable, nor robust and cannot be trusted in a court of law."

https://blogs.scientificamerican.com/observations/we-must-strengthen-the-science-in-forensic-science/

Thanks for comparing evolution to forensics.

[Alan Kleinman MD PhD]

There is no mathematical reason for macroevolution to stop but there is a mathematical reason why it is limited. That reason is that microevolutionary changes are random events because mutations are random events. Therefore, the joint probability of these microevolutionary steps are not added, they are multiplied. Now there is some egghead at the University of Edinburgh Law School that is teaching their students that mutations are not random events but deterministic which gives a reason that the sun has set on the British Empire.

[August Rode]

Once upon a time, over in alt.talk.creationism, there was a guy that proposed the existence of something called the "phenotypic shield," the function of which was to "preserve species integrity." He postulated that this was achieved by the existence of a genetic template that identified which alleles were valid for any specific locus, and which would be used during genetic recombination to weed out alleles which weren't "valid" for that species. He seemed certain that the template was located in the DNA. He seemed not to understand that the template would necessarily be larger than the coding part of the DNA and he had no explanation for why the template itself wouldn't be subject to mutations during genetic recombination. It had been clear to me from the start that his was an argument based on confirmation bias: he believed that species were fixed and that macroevolution wasn't a thing and he tried his damnedest to find an argument that would arrive at that conclusion.

[Glenn]

On Friday, February 8, 2019 at 12:00:08 PM UTC-7, Burkhard wrote:

The burden of proof is on the "you" who would describe and explain the "process" "you" observe.

The onus of "proof" is on you to provide a limit to microevolution, as well as "proving" that macroevolution is just gobs of microevolution.

[Ernest Major]

On 08/02/2019 18:44, dthe...@gmail.com wrote:
> This response does a lousy job of representing what those who object to the unscientific notion of Macro-evolution actually believe. Please read my reply to these responses to get a better understanding of our position. And yes I like may others, reject the unscientific notion that unique life forms can and have evolved into utterly different life forms.
>
> Source:
> Morris, Henry M., 2000 (Jan.). Strong Delusion. Back to Genesis 133: a.
> Brown, Walt, 1995. In the Beginning: Compelling evidence for creation and the Flood. Phoenix, AZ: Center for Scientific Creation, p. 6.
>
> Response:
> 1. We would not expect to observe large changes directly. Evolution consists mainly of the accumulation of small changes over large periods of time. If we saw something like a fish turning into a frog in just a couple generations, we would have good evidence against evolution.
>
> My reply: Not what Creationists are even suggesting at all.

We recently had Dale asking why we haven't seen a dog giving birth to a
cat "in written history"? He even entitled the thread "macro-evolution".

Whenever a creationist argues that the absence of change above a certain
magnitude within the last few hundred years is evidence against
evolution they are implicitly suggesting just that.

>
>
> 2. The evidence for evolution does not depend, even a little, on observing macroevolution directly. There is a very great deal of other evidence (Theobald 2004; see also evolution proof).
>
> My reply: This is an obvious departure from the actual Scientific Method (Observational Science) and an appeal to “historical’ Science that is based on mere opinion not scientific evidence.

What's "historical" about DNA sequencing?

>
>
> 3. As biologists use the term, macroevolution means evolution at or above the species level. Speciation has been observed and documented.
>
> My reply: These same scientists dogmatically assert that all life forms evolved from a single life form which is far beyond “speciation”.

That's not an argument for "No case of macro-evolution has ever been
documented."

>
>
> 4. Microevolution has been observed and is taken for granted even by creationists. False assertion. And because there is no known barrier to large change and because we can expect small changes to accumulate into large changes, microevolution implies macroevolution. Small changes to developmental genes or their regulation can cause relatively large changes in the adult organism (Shapiro et al. 2004).
>
> My reply: This is a logically fallacious conclusion. It's based on a gigantic assumption without any scientific impetus whatsoever for drawing such conclusions. In other words these conclusions are not based in scientific evidence but rather mere assumptions made on mere opinion.

Are you denying the observation of homeotic mutations? Are you claiming
that cabbages, cauliflowers, brussel sprouts, broccoli, etc. don't exist?

>
>
> 5. There are many transitional forms that show that macroevolution has occurred.
>
> My reply: Hog wash! You never see scientific proof of one unique life form transforming into another completely different life form. A bird is still a bird, a fish a fish, a plant a plant, etc. etc.
>

Is Helacyton still a human?

>
>
> References:
> 1. Shapiro M. D., M. E. Marks, C. L. Peichel, B. K. Blackman, K. S. Nereng, B. Jónsson, D. Schluter and D. M. Kingsley, 2004. Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature 428: 717-723. See also: Shubin, N. H. and R. D. Dahn, 2004. Evolutionary biology: Lost and found. Nature 428: 703.
> 2. Theobald, Douglas, 2004. 29+ Evidences for macroevolution: The scientific case for common descent. http://www.talkorigins.org/faqs/comdesc/
>

--
alias Ernest Major

[dale]

On 2/8/2019 4:12 PM, Ernest Major wrote:
> On 08/02/2019 18:44, dthe...@gmail.com wrote:
>> This response does a lousy job of representing what those who object
>> to the unscientific notion of Macro-evolution actually believe. Please
>> read my reply to these responses to get a better understanding of our
>> position. And yes I like may others, reject the unscientific notion
>> that unique life forms can and have evolved into utterly different
>> life forms.
>>
>> Source:
>> Morris, Henry M., 2000 (Jan.). Strong Delusion. Back to Genesis 133: a.
>> Brown, Walt, 1995. In the Beginning: Compelling evidence for creation
>> and the Flood. Phoenix, AZ: Center for Scientific Creation, p. 6.
>>
>> Response:
>> 1.    We would not expect to observe large changes directly. Evolution
>> consists mainly of the accumulation of small changes over large
>> periods of time. If we saw something like a fish turning into a frog
>> in just a couple generations, we would have good evidence against
>> evolution.
>>
>> My reply: Not what Creationists are even suggesting at all.
>
> We recently had Dale asking why we haven't seen a dog giving birth to a
> cat "in written history"? He even entitled the thread "macro-evolution".
>
> Whenever a creationist argues that the absence of change above a certain
> magnitude within the last few hundred years is evidence against
> evolution they are implicitly suggesting just that.

how about this? might I be an evolutionist if everything evolves in the
consciousness of God? might there be a creation and ending but
overriding evolution?

here is something I have found ...

https://en.wikipedia.org/wiki/Ānanda_(Hindu_philosophy)

<https://en.wikipedia.org/wiki/Ānanda_(Hindu_philosophy)>

--
dale - https://www.dalekelly.org/
Not a professional opinion unless specified.

[Glenn]

On Friday, February 8, 2019 at 2:15:13 PM UTC-7, Ernest Major wrote:
> On 08/02/2019 18:44, dthe...@gmail.com wrote:

snip

> > 5. There are many transitional forms that show that macroevolution has occurred.
> >
> > My reply: Hog wash! You never see scientific proof of one unique life form transforming into another completely different life form. A bird is still a bird, a fish a fish, a plant a plant, etc. etc.
> >
>
> Is Helacyton still a human?

Was it ever?
> >

[Someone]

On Friday, February 8, 2019 at 6:25:07 PM UTC-5, Glenn wrote:
<snip>
> Was it ever?
> > >

https://www.cell.com/cell/fulltext/S0092-8674(08)01191-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867408011914%3Fshowall%3Dtrue

[zencycle]

It's always so cute when you pretend you know what you're taliking about, glenn. Of course, a good analogy for your debating skills is that a broken clock is right twice a day. Burkhard may not have chosen the best analogy, but as usual with half-wits like you and slowstan, you don't bother to read past a headline. Guess where this snippet came from:

"Forensic techniques such as fingerprints and firearms analysis were developed by law enforcement to help solve crimes. Unlike DNA analysis, these practices were not borne of science, and evolved in a legal system that is binary, adversarial and absolute, requiring verdicts of guilty or not guilty. In contrast, mainstream science functions with an acceptance that all knowledge is provisional and certainty is described by probability. These two approaches create tremendous tension between the ways scientists and legal practitioners perceive evidence."

thanks for playing.....

[Burkhard]

Glenn linked to the NAS report on forensic science? Now that's funny
:o). My team contributed to it, and my then co-director and collaborator
Colin Aitken is cited several times. We've done more direct work for our
UK review.

And no, the report does not say that forensic science is unreliable -
Glenn is of course welcome to commit a crime, leave his DNA and
fingerprints all over the place, and then submit the report in his
defense- should be fun. Or as the report says:

"For decades, the forensic science disciplines have produced valuable
evidence that has contributed to the successful prosecution and
conviction of criminals as well as to the exoneration of innocent
people. Over the last two decades, advances in some forensic science
disciplines, especially the use of DNA technology, have demonstrated
that some areas of forensic science have great additional potential to
help law enforcement identify criminals. Many crimes that may have gone
unsolved are now being solved because forensic science is helping to
identify the perpetrators."

If you look at the Innocence project for instance, the pretty consistent
pattern is people getting exonerated through forensic (mainly DNA)
evidence for convictions based on flawed eyewitness evidence (including
false confessions, if you consider the suspect as eyewitness)

Are there problems in the way forensic science is sometimes practices,
especially in the US? Of course. Unrealistic expectations in jurors and
lawyers caused by TV programs, an increasing workload with stagnating
funding )especially for defense work), an increasing breadth of
techniques that cause tension between the need to specialize and still
to keep an overview of the entire investigation etc etc.

The problem in most of the areas of improvement is not the science, but
the forensic laboratory infrastructure. This includes lack of mandatory
and robust certification standards for labs, mandatory training pathways
into the profession, and also investment in things like modern equipment
and comprehensive data sets. Or as the report put it right at the beginning:

"There are scores of talented and dedicated people in the forensic
science community, and the work that they perform is vitally important.
They are often strapped in their work, however, for lack of adequate
resources, sound policies, and national support".

So what is needed is more money, and more public sector structures -
both unfortunately anathema to the current US government, which promptly
closed down the the National Commission on Forensic Science. I mean, why
spend money on criminal justice if "thoughts and prayers" are so much
cheaper

There have been some forensic disciplines where the problem is more
fundamental, bitemark evidence probably the most dramatic case. There
the self-regulatory mechanisms of scientific practice were
systematically sidelined. The report makes a couple of recommendations
on how to rectify this.

So yes, there is always room for improvement, but the report makes it
clear that this is improvement of something that has already
dramatically changed the accuracy and reliability of trial decision
making for the better. To read it as Glenn does is just your average
quote mine.

[Alan Kleinman MD PhD]

Am I quote mining you when you claim that mutations are deterministic?

[Glenn]

As - its getting better all the time.

> To read it as Glenn does is just your average quote mine.

I read it the way it was printed. That's better than whitewashing it.

Another "quotemine":

"Historically, forensic science has had a huge impact on identifying and confirming suspects in the courtroom, and on the judicial system more generally. And yet, a 2009 report from the U.S. National Academy of Sciences (NAS) identified numerous shortcomings in the field, including an absence of a scientific basis for most forms of forensic evidence, a lack of uniform standards and the need for independence from law enforcement. In short, the report called for nothing less than major reform. "

https://www.livescience.com/49929-faulty-forensic-science-failing-united-states-court-system.html



Burkhard "DNA OK"?

DNA tests in forensic science can't be separated from "Forensic Science".

"Analysts are picking up DNA transferred from one person to another by way of an object that both of them have touched, or from one piece of evidence to another by crime scene investigators, lab techs—or when two items jostled against each other in an evidence bag."

Read more at

http://www.sciencemag.org/news/2016/03/forensics-gone-wrong-when-dna-snares-innocent

[Ron Dean]

[Ron Dean]

On 2/11/2019 10:55 AM, Glenn wrote:

I think we are missing a golden opportunity by ignoring the recently
discovered homeobox genes.

[Burkhard]

You might want to rethink this. Isn't your claim that they are highly
conserved? That makes them pretty useless to differentiate between
possible perpetrators, don't you think?

[Ernest Major]

I thought perhaps he was changing the subject away from forensic
science, but tens of thousands of papers (Google Scholar gives 177,000
results for homeobox) is hardly ignoring them.

--
alias Ernest Major

[Someone]

Is that how much you weigh in grams?

[Burkhard]

Nor are they that recent - 35 years or so. but sure, I tried to come up
with forensic uses though. f you are an investigating officer, and your
only suspects are Mr Smith or athis chap
https://mrstoma.files.wordpress.com/2013/06/animated-mushroom.gif?w=640,
looking if there are hox genes on the traces on the knife could help you
to eliminate one of the suspects.

[Bob Casanova]

On Sat, 16 Feb 2019 14:14:53 -0500, the following appeared
in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:

<snip>

>I think we are missing a golden opportunity by ignoring the recently
>discovered homeobox genes.

....for values of "recently" equal to "35 years ago"...
--

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

[Ron Dean]

On 2/20/2019 1:41 PM, Bob Casanova wrote:
> On Sat, 16 Feb 2019 14:14:53 -0500, the following appeared
> in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:
>
> <snip>
>
>> I think we are missing a golden opportunity by ignoring the recently
>> discovered homeobox genes.
>
> ....for values of "recently" equal to "35 years ago"...
>

Yes, relative to almost 160 years since Darwin's book on Evolution, was
published 1859.

[Bob Casanova]

On Wed, 20 Feb 2019 14:16:13 -0500, the following appeared

in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:

>On 2/20/2019 1:41 PM, Bob Casanova wrote:
>> On Sat, 16 Feb 2019 14:14:53 -0500, the following appeared
>> in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:
>>
>> <snip>
>>
>>> I think we are missing a golden opportunity by ignoring the recently
>>> discovered homeobox genes.
>>
>> ....for values of "recently" equal to "35 years ago"...
>>
>Yes, relative to almost 160 years since Darwin's book on Evolution, was
>published 1859.

So now it's *relatively* recent? Both are "relatively
recent" compared to Plato's "eternal forms" As is phlogiston
theory. Your point?

[Ron Dean]

On 2/21/2019 12:28 PM, Bob Casanova wrote:
> On Wed, 20 Feb 2019 14:16:13 -0500, the following appeared
> in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:
>
>> On 2/20/2019 1:41 PM, Bob Casanova wrote:
>>> On Sat, 16 Feb 2019 14:14:53 -0500, the following appeared
>>> in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:
>>>
>>> <snip>
>>>
>>>> I think we are missing a golden opportunity by ignoring the recently
>>>> discovered homeobox genes.
>>>
>>> ....for values of "recently" equal to "35 years ago"...
>>>
>> Yes, relative to almost 160 years since Darwin's book on Evolution, was
>> published 1859.
>
> So now it's *relatively* recent? Both are "relatively
> recent" compared to Plato's "eternal forms" As is phlogiston
> theory. Your point?
>

OK, but it should have been clear, I had previously mentioned
homeobox genes which were discovered in 1983 by the late
Walter Gehring A Swiss developmental biologist at Basel University
Basel, Switzerland.
Considering the role these master control genes play throughout the
animal kingdom, their highly conserved nature and the ancient origin of
these genes, before the Cambrian. The question arises as to how and
when did evolution occur? Take for example the eye. It was once
believed that eyes had evolved independently at least 40 times
throughout the history of life, however, with the discovery of the
Pax6 gene which controls the development of fruit-fly eyes, mouse,
Zebra fish, trilobite eyes etc and human eyes when and how did the
40 eyes evolve independently?

[Ernest Major]

I explained a little about the evolution of homeobox genes to you a few
months back. Do you remember anything of that?

--
alias Ernest Major

[Ron Dean]

I've read a considerable amount retarding Homeobox genes and by several
writers, posters and papers. These genes were present during the
appearance of The denizens of the Cambrian.
So, they must have arisen prior to the Cambrian radiation, so there are
hypothesis and theories as to how they arose. But like most or the
animals there is little empirical evidence as to their origin. But there
are reasonable theories and hypotheses regarding the origin of these
highly stable genes. I probably read what you wrote, but I don't always
respond due to limited time on my part.

[jillery]

Apparently not, else he would know that Pax6 doesn't control the
development of eyes directly, but instead is a regulatory gene which
controls the expression of many genes, only some of which control the
development of eyes.

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

Evelyn Beatrice Hall
Attributed to Voltaire

[Ron Dean]

The Pax6 gene, as I understand it, is upstream from the genes that
actually sculpt eyes of the various animals of the animal kingdom. It
also plays a part in the formation of the brain and other body parts.

From Wikipedia:
"PAX6 is a member of the Pax gene family which is responsible for
carrying the genetic information that will encode the Pax-6 protein. It
acts as a "master control" gene for the development of eyes and other
sensory organs, certain neural and epidermal tissues as well as other
homologous structures, usually derived from ectodermal tissues."

[jillery]

On Fri, 22 Feb 2019 00:23:29 -0500, Ron Dean <"Ron Dean"@gmail.net>
wrote:

So do you now retract your claim above, about the existence of Pax6
challenging the independent evolution of eyes? If not, why not?

[Bob Casanova]

On Thu, 21 Feb 2019 17:18:48 -0500, the following appeared

in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:

>On 2/21/2019 12:28 PM, Bob Casanova wrote:
>> On Wed, 20 Feb 2019 14:16:13 -0500, the following appeared
>> in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:
>>
>>> On 2/20/2019 1:41 PM, Bob Casanova wrote:
>>>> On Sat, 16 Feb 2019 14:14:53 -0500, the following appeared
>>>> in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:
>>>>
>>>> <snip>
>>>>
>>>>> I think we are missing a golden opportunity by ignoring the recently
>>>>> discovered homeobox genes.
>>>>
>>>> ....for values of "recently" equal to "35 years ago"...
>>>>
>>> Yes, relative to almost 160 years since Darwin's book on Evolution, was
>>> published 1859.
>>
>> So now it's *relatively* recent? Both are "relatively
>> recent" compared to Plato's "eternal forms" As is phlogiston
>> theory. Your point?
>>
>OK, but it should have been clear, I had previously mentioned
>homeobox genes which were discovered in 1983 by the late
>Walter Gehring A Swiss developmental biologist at Basel University
>Basel, Switzerland.

Exactly, as I noted.

>Considering the role these master control genes play throughout the
>animal kingdom, their highly conserved nature and the ancient origin of
>these genes, before the Cambrian. The question arises as to how and
>when did evolution occur? Take for example the eye. It was once
>believed that eyes had evolved independently at least 40 times
>throughout the history of life, however, with the discovery of the
>Pax6 gene which controls the development of fruit-fly eyes, mouse,
>Zebra fish, trilobite eyes etc and human eyes when and how did the
>40 eyes evolve independently?

Assuming you are correct in your assertion, they evolved
through natural selection in the various lineages. If they
hadn't evolved independently they would have the same
structure, which they emphatically do not. The regulatory
genes only needed to arise once.

You seem to think that the existence of a particular gene
across multiple lines of descent means that those lines of
descent didn't evolve independently once the genes existed;
I confess I don't see where that idea came from.

[Ron Dean]

Pax6 gene had to exist before the split from the common ancestor of mice
and fruit flies, since the Pax6 gene is shared by both forms currently.
Also certain animals during the Cambrian had complex eyes, meaning the
Pax6 gene had to have been present and functioning during the Cambrian
radiation. So, since this is the case, how could eyes have evolved
independently through 40 different pathways? And this applies to the
more then 300 described master control genes.

[Ron Dean]

On 2/22/2019 1:28 PM, Bob Casanova wrote:
> On Thu, 21 Feb 2019 17:18:48 -0500, the following appeared
> in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:
>
>> On 2/21/2019 12:28 PM, Bob Casanova wrote:
>>> On Wed, 20 Feb 2019 14:16:13 -0500, the following appeared
>>> in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:
>>>
>>>> On 2/20/2019 1:41 PM, Bob Casanova wrote:
>>>>> On Sat, 16 Feb 2019 14:14:53 -0500, the following appeared
>>>>> in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:
>>>>>
>>>>> <snip>
>>>>>
>>>>>> I think we are missing a golden opportunity by ignoring the recently
>>>>>> discovered homeobox genes.
>>>>>
>>>>> ....for values of "recently" equal to "35 years ago"...
>>>>>
>>>> Yes, relative to almost 160 years since Darwin's book on Evolution, was
>>>> published 1859.
>>>
>>> So now it's *relatively* recent? Both are "relatively
>>> recent" compared to Plato's "eternal forms" As is phlogiston
>>> theory. Your point?
>>>
>> OK, but it should have been clear, I had previously mentioned
>> homeobox genes which were discovered in 1983 by the late
>> Walter Gehring A Swiss developmental biologist at Basel University
>> Basel, Switzerland.
>
> Exactly, as I noted.
>

OK, I erroneously assumed it was common knowledge.

>
>> Considering the role these master control genes play throughout the
>> animal kingdom, their highly conserved nature and the ancient origin of
>> these genes, before the Cambrian. The question arises as to how and
>> when did evolution occur? Take for example the eye. It was once
>> believed that eyes had evolved independently at least 40 times
>> throughout the history of life, however, with the discovery of the
>> Pax6 gene which controls the development of fruit-fly eyes, mouse,
>> Zebra fish, trilobite eyes etc and human eyes when and how did the
>> 40 eyes evolve independently?
>
> Assuming you are correct in your assertion, they evolved
> through natural selection in the various lineages. If they
> hadn't evolved independently they would have the same
> structure, which they emphatically do not. The regulatory
> genes only needed to arise once.
>

From what I've read is that the Pax6 gene contains the genetic
information, so it's how the Pax6 gene is played as to how the
structures are fashioned. In an experiment to prove a point Dr Gehring
placed a mouse eye gene in a fruit fly: it produced a fly eye - the
mouse Pax6 gene produced a complex fruit fly eye - not a mouse eye.
As I understand it, homeobox genes are "center stage" there are
upstream genes which select switches in the master control genes
which in turn activate downstream gene which actually accomplish the
formation and the sculpting of body shapes, sizes, organs, limbs etc.
This is the overall meaning I've received from two books, I've
read. 1) - The New Science of EVO DEVo Endless Forms Most beautiful
by Sean Carroll (2005) and 2) Master control Genes in Development and
Evolution
by Walter J. Gehring. (1998). I read Carroll's booK twice, but
Gehring's book is difficult and hard to understand.

>
> You seem to think that the existence of a particular gene
> across multiple lines of descent means that those lines of
> descent didn't evolve independently once the genes existed;
> I confess I don't see where that idea came from.
>

I suspect that the genetic information (within these master
control genes) existed from the beginning of life as observed
during the Cambrian. But during the passage of vast spans of
time tensions built up resulting from environmental changes
causing extinction or rapid change, as seen in the fossil
record and explained by Stephen Gould and Niles Eldredge.

[jillery]

On Fri, 22 Feb 2019 15:07:40 -0500, Ron Dean <"Ron Dean"@gmail.net>

IIUC your argument above is that eyes appeared during the Cambrian,
and Pax6 is involved in the development of eyes, and since Pax6 is
common to all organisms with eyes, therefore eyes didn't evolve
independently.

However, Pax6 regulates other genes besides eyes, so it's no surprise
that Pax6 appeared before eyes appeared. And once again, Pax6 does
*not* have anything to do with the complexity of eyes, so your
conclusion above is a non-sequitur. That Pax6 *regulates* the
expression of eye genes does not mean those separate eye genes were
inherited along with Pax6. How do you not understand this?

[Ernest Major]

There are (at least) a couple of models that he could consider.

Firstly, on the basis that one of the functions of homeobox proteins is
to specify parts of the body, one could postulate that Pax6, among other
functions, and in conjunction with other regulatory proteins, specified
the front of the head, and as that the front of the head is the best
place to put eyes Pax6 was pressed into service in eye development as
eyes evolved in other lineages. This hypothesis can be probed by
considering eye development in groups that have eyes in other locations,
e.g. starfish. If I read Google right starfish eyes also involve Pax6,
which puts doubt on this first hypothesis, but it's conceivable that the
homeobox protein network was restruction during the transition from
bilateral to radial symmetry - we'd need a more detailed study for a
firm conclusions.

Secondly, one could hypothesise that in the ancestral metazoan Pax6 was
involved in the construction of eyespots, and that its role has been
conserved as eyespots evolved into a diversity of eyes in various lineages.

--
alias Ernest Major

[Bob Casanova]

On Fri, 22 Feb 2019 16:12:12 -0500, the following appeared

That is also the way I understand it, and why the genes only
needed to arise once. Once in existence they regulated the
expression of all sorts of genes in all sorts of lineages.

>This is the overall meaning I've received from two books, I've
>read. 1) - The New Science of EVO DEVo Endless Forms Most beautiful
>by Sean Carroll (2005) and 2) Master control Genes in Development and
>Evolution
>by Walter J. Gehring. (1998). I read Carroll's booK twice, but
>Gehring's book is difficult and hard to understand.

>> You seem to think that the existence of a particular gene
>> across multiple lines of descent means that those lines of
>> descent didn't evolve independently once the genes existed;
>> I confess I don't see where that idea came from.

>I suspect that the genetic information (within these master
>control genes) existed from the beginning of life as observed
>during the Cambrian. But during the passage of vast spans of
>time tensions built up resulting from environmental changes
>causing extinction or rapid change, as seen in the fossil
>record and explained by Stephen Gould and Niles Eldredge.

OK. Now how about stating why you seem to think that the

existence of a particular gene across multiple lines of
descent means that those lines of descent didn't evolve

independently once the genes (which are genes controlling
the expression of other genes of multiple types, not genes
directly controlling development) existed, which your
comment does not address.

[Ron Dean]

There is some overlapping of homeobox genes. But the Pax6 gene was
the first of these master control genes to be discovered. But the Pax6
is the primary gene for the development and formation of eyes.
>
https://journals.plos.org/plosgenetics/article?id=10.1371
/journal.pgen.1003357

And once again, Pax6 does
> *not* have anything to do with the complexity of eyes,
>

It does, it's the timing and combination of how switches are
played that determines the structure of eyes.

>
so your
> conclusion above is a non-sequitur. That Pax6 *regulates* the
> expression of eye genes does not mean those separate eye genes were
> inherited along with Pax6. How do you not understand this?
>

As I understand it from everything I've read, the genes are
downstream in the various seeing organisms. They are played differently.
The Homeobox gene, such as Pax, timman, Dill etc bind proteins which
selects and activates streams of genes in conjunction with timing which
is controlled by switches of these homeobox gene.
Endless forms most beautiful by Sean Carroll pg 75.

[jillery]

On Sat, 23 Feb 2019 15:07:53 -0500, Ron Dean <"Ron Dean"@gmail.net>

Incorrect. Mouse PAX6 triggers eye development in fruit flies.
However, those fruit flies grow fruit fly eyes, not mouse eyes.

>so your
>> conclusion above is a non-sequitur. That Pax6 *regulates* the
>> expression of eye genes does not mean those separate eye genes were
>> inherited along with Pax6. How do you not understand this?
>>
>As I understand it from everything I've read, the genes are
>downstream in the various seeing organisms. They are played differently.
>The Homeobox gene, such as Pax, timman, Dill etc bind proteins which
>selects and activates streams of genes in conjunction with timing which
>is controlled by switches of these homeobox gene.
>Endless forms most beautiful by Sean Carroll pg 75.

[jillery]

On Sat, 23 Feb 2019 13:55:27 +0000, Ernest Major

At it's most primitive, an "eye" is merely some light-sensitive
protein collected in some spot on an animal, which allows it to
recognize the presence or absence of light and so respond to it
appropriately. There are eels with such spots on their tails, to help
them sense when their backsides are exposed.

Put that primitive eyespot in a shallow cavity, and now it provides
directional information. Scallops have these more complex eyespots
all around their shells, to detect the approach and direction of
possible predatory starfish.

Both of these simple eyes require little in the way of genetics, so
it's no surprise that many animal lineages would have independently
evolved them.

Make the entrance to that eyespot cavity small enough, and it acts as
pinhole camera, where the light is more-or-less focused and provides
information about shapes. The hard part here is not in the creation
of a pinhole, which can be almost any shape, but in the ability to
make sense of the information it provides. So the complexity of eyes
goes hand-in-hand with the complexity of brains to process the
information eyes provide.

This is true not just for eyes, but for many other sensory organs. And
it's helpful to keep the connection between these sensory organs and
the brain as short as possible, in order to minimize the time between
sensing danger and responding to it. And it's helpful to put these
sensory organs forward in the direction of travel, to sense danger
sooner from where the organism is going rather than where it's been.

This is where the development of animals requires distinguishing head
from tail, left from right, and growing the sensory organs in specific
locations around the brain. Animals which can't tell their head from
their tail wouldn't know whether they were coming or going.

My impression is, the above is such a natural and necessary
progression, that any biosphere on any planet in the universe would
evolve organisms along the same lines. Which means I would expect to
see extraterrestrial bilaterians with brains and sensory organs
centralized at their leading end. This is not to say that would be
the only extraterrestrial body plan. After all, there are many other
body plans right here on Earth. I would also expect to see on other
planets other body plans which don't exist on Earth.

[Trolidan Troltar]

Well, I think there was an Oxyaena poster a while back that argued
that inferences about the theoretical existence of millions of years in
the past was similar to inferences made in the forensic sciences.

However forensics tends to deal with incidents that often have statutes
of limitations that mean that the events studied may have possibly
happened at times that are comparable with the life span of the
investigators.

The idea that thousands of years ago might have existed are the results
of theoretical speculation in the minds of present persons pieced
together from books and archaeology, and the idea that millions of years
ago existed are also based upon theoretical speculation in the minds
of persons in the present based upon geology and paleontology
and also books and television.

Forensic evidence deals with theoretical events that are more recent.

No one is verified to have direct memories of events that may have
happened before 1900.

If you ask a forensic scientist whether one year ago existed or
ten years ago existed they might be able to call up their direct
memories to verify that such time periods existed.

They wouldn't be able to do that if you were referring to the
theoretical existence of 1850, 500 BC, or 1.8 million BC.

So did Charles Darwin ever exist as a living person? No
one can testify today that they have direct knowledge of
this because no one alive today lived when Darwin was
theoretically alive and thus could be verified by direct
knowledge to be a living person in the past using direct
memory.

The idea that he once lived in the past is solely a theory
based upon indirect inference.

Philosophically, if you want to use absurdity in relation to
our lives to dismiss last tuesdayism then if you want to start
talking about theoretical lengths of time such as four billion
years, then it is not a great leap to say that the existence
of four billion BC is only a theory.

[Bob Casanova]

On Sat, 23 Feb 2019 11:52:41 -0700, the following appeared
in talk.origins, posted by Bob Casanova <nos...@buzz.off>:

[Crickets...]

OK.

[Ron Dean]

We know the Pax6 gene, from before the Cambrian, remains
virtually unchanged, called highly conserved by biologist
so, when you consider that Chimps share 98-99% of their
genes with humans and cats share 90% and 90% of mice genome
can be lined up with human, fruit-flies and chickens 60%
of genes are shared with us.
https://www.eupedia.com/forum/threads/25335-Percentage-of-genetic-similarity-between-humans-and-animals.


Also I found that dogs, cats and mice share so 96% of their
genome.

This is factual. By contrast, it's only hypothetical
the sub-set of genes underwent any degree of change;
the differences between eye types is embedded in the Pax6
gene. So, it's how this gene is played that determines the eye
structure in different animals.
There is no empirical evidence to the contrary.

> independently once the genes (which are genes controlling
> the expression of other genes of multiple types, not genes
> directly controlling development) existed, which your
> comment does not address.
>

There is no evidence, only theory. It's also noted that
the Pax 6 gene has been placed on various body parts on
fruit flies, such as legs, wings and antenna where eyes
have grown. So, obviously the gene is capable of producing
eyes wherever it is found.
>
There are conditions which happen because of defective Pax 6
such as small eye in mice, blindness in mice and a condition
know as Aniridia in humans. This is caused by the same defect in
in the Pax6 gene in humans and mice.

[jillery]

On Sun, 24 Feb 2019 19:13:20 -0500, Ron Dean <"Ron Dean"@gmail.net>
wrote:

<http://dev.biologists.org/content/develop/126/2/383.full.pdf>
***************************************
We have also tested whether the regulatory mechanisms
that direct Pax6 ocular expression are conserved between
mice and flies. Remarkably, when inserted upstream of
either the mouse Pax6 P1 or P0 promoter, an eye-enhancer
region of the Drosophila eyeless gene, a Pax6 homolog,
directs eye- and CNS-specific expression in transgenic mice
that accurately reproduces features of endogenous Pax6
expression. These results suggest that in addition to
conservation of Pax6 function, the upstream regulation of
Pax6 has also been conserved during evolution.
***************************************

IOW fly pax6 causes mouse embryos to grow mouse eyes, not fly eyes. So
mice have genes for growing eyes which are independent of and separate
from pax6, which is contrary to what you claim above.

[Ron Dean]

As I've pointed out before, Pax6 gene is "center stage" gene.
There are upstream and down stream genes from this master
control gene. What you've described is P1 And P0 which are
upstream genes which promote (select) pax6 switches.
This experiment demonstrated that these upstream genes
accurately reproduced the features of pax6 expression. This
experiment placed upstream fly genes in mice embryos, which
demonstrated the upstream gene in mice and fly gene in
addition to the Pax6 gene is also conserved.
This is a furtherance of the experiment by Dr. Gehring where he
placed mouse Pax6 eye genes (called small eye At the time) into
the fruit fly genome, which produced fruit fly eyes, not mouse eyes
What your article suggest is that both pax6 gene and the upstream
genes in fruit flies and mice is conserved.

Biologist refer to the mouse small eye gene and the fruit fly]
eye gene as homologous, since these genes were discovered independently.
by different researchers. Later the fly eye gene and the mouse
eye gene was termed Pax6.

[Ron Dean]

In experiments scientist placed the Pax6 gene on fruit fly legs, wings
and antennae. So obviously wherever the Pax6 is placed eye are sculpted
which somehow have sight.

www.pbs.org/wgbh/evolution/library/04/4/text_pop/l_044_01.html

> e.g. starfish. If I read Google right starfish eyes also involve Pax6,
> which puts doubt on this first hypothesis, but it's conceivable that the
> homeobox protein network was restruction during the transition from
> bilateral to radial symmetry - we'd need a more detailed study for a
> firm conclusions.
>
> Secondly, one could hypothesise that in the ancestral metazoan Pax6 was
> involved in the construction of eyespots, and that its role has been
> conserved as eyespots evolved into a diversity of eyes in various lineages.
>

The same Pax6 gene also control expression of blind spots in flatworms.
According to Sean Carroll.
Th New Science of EVO Devo pg 69.

[jillery]

On Sun, 24 Feb 2019 22:55:33 -0500, Ron Dean <"Ron Dean"@gmail.net>

You conveniently missed the point, that the mice grew mouse eyes, not
fly eyes.

[Ron Dean]

There was no reason to expect fly eyes in thus case, since the
article is _not_ referring to transplanting Pax6 gene, but
rather P1 and P0, which was placed upstream to Pax6. There
was no reason to expect this to cause the mouse Pax6 to produce
fly eyes in mouse embryos.
But it demonstrated that not only is Pax 6 conserved, but also
the genes upstream as well are conserved. So, what about
downstream genes? Is there any evidence to suggest they
evolved independently. That is withour reading evidence into
the scenario.

[Bob Casanova]

On Sun, 24 Feb 2019 19:13:20 -0500, the following appeared

Yes; so? That doesn't address the question.

>Also I found that dogs, cats and mice share so 96% of their
>genome.

Ditto.

>This is factual. By contrast, it's only hypothetical
>the sub-set of genes underwent any degree of change;
>the differences between eye types is embedded in the Pax6
>gene. So, it's how this gene is played that determines the eye
>structure in different animals.
>There is no empirical evidence to the contrary.
>
>> independently once the genes (which are genes controlling
>> the expression of other genes of multiple types, not genes
>> directly controlling development) existed, which your
>> comment does not address.
> >
>There is no evidence, only theory.

*What* is "only theory"? (Incidentally, as has been noted
many times, "theory" is a good as it gets in science, and
means "hypothesis tested multiple times and never falsified,
and which makes testable predictions". It isn't synonymous
with the common meaning of "guess".) And as even you have
noted, here and in other posts, there is plenty of evidence;
I fail to see how you can post evidence and then claim there
is none.

> It's also noted that
>the Pax 6 gene has been placed on various body parts on
>fruit flies, such as legs, wings and antenna where eyes
>have grown. So, obviously the gene is capable of producing
>eyes wherever it is found.

That's what regulatory genes apparently do - affect the
operation and expression of many different genes.

>There are conditions which happen because of defective Pax 6
>such as small eye in mice, blindness in mice and a condition
>know as Aniridia in humans. This is caused by the same defect in
>in the Pax6 gene in humans and mice.

Again, so? That also doesn't address the initial question:
"How about stating why you seem to think that the existence

of a particular gene across multiple lines of descent means

that those lines of descent didn't evolve independently?"

[Ron Dean]

We know certain genes are identical across the animal kingdom.
This is evidence of virtual chahglessness or highly conserved
as biologist say. But the evidence for independent change has
to be read into the picture.

[jillery]

On Mon, 25 Feb 2019 19:08:04 -0500, Ron Dean <"Ron Dean"@gmail.net>
wrote:

First, your repeated assertions that genes are "identical across the
animal kingdom" is an exaggeration. Even highly conserved genes have
genetic variations across species; they are not letter-for-letter
identical. Instead, what is conserved are their functions, so that
the proteins from different species function similarly, but not
necessarily identically. There can be surprisingly large variations
among genes, and the proteins which those genes make, and those
proteins still function similarly. So if your argument is that
"virtually identical" genes suggest evolution could not have created
them, then your argument would be incorrect.

Second, the evidence for independent change is manifest in the fossil
record and in extant ecosystems. There are myriad kinds of eyes, both
extinct and extant, which rely on different optical properties. There
is no "reading into the picture" required.

[jillery]

On Mon, 25 Feb 2019 10:02:40 -0500, Ron Dean <"Ron Dean"@gmail.net>

You misread, but I agree the quoted section is poorly written. P1
and P0 are specific promoters of Pax6. The article refers to them to
identify where the "eyeless" gene was inserted. "eyeless is a Pax6
homolog.

So, once again, the mice grew mouse eyes in response to regulation by
the fly "eyeless" Pax6 homolog. This would have been impossible if
the mice didn't have independent genes for controlling the details of
mouse eye development. The fly Pax6 specified where and when the
mouse eyes grew but not how they grew. This is contrary to your
claim.

>But it demonstrated that not only is Pax 6 conserved, but also
>the genes upstream as well are conserved. So, what about
>downstream genes? Is there any evidence to suggest they
>evolved independently. That is withour reading evidence into
>the scenario.

[Bob Casanova]

On Mon, 25 Feb 2019 19:08:04 -0500, the following appeared

So you have no actual reason for your assertion, just a
refusal to accept the evidence. OK.

And BTW, "identical" is a bit of a stretch, as I believe has
been noted for you recently.

[Mark Isaak]

Did you note in a passage you cited the phrase, "... the Drosophila
eyeless gene, a Pax6 homolog ..."? The word "homolog" means the genes
are recognizably similar but are NOT identical. Exactly what one would
expect from evolutionary common descent. Not at all what one would
expect from intelligent design.

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"Omnia disce. Videbis postea nihil esse superfluum."
- Hugh of St. Victor

[Ron Dean]

That was unintended. As I stated above the Pax6 and other genes
are virtually unchanged or highly conserved.

>
> And BTW, "identical" is a bit of a stretch, as I believe has
> been noted for you recently.
>

I agree it was a stretch, but I think the pax 6 gene is nearly
identically across the animal kingdom.

[jillery]

On Thu, 21 Feb 2019 17:18:48 -0500, Ron Dean <"Ron Dean"@gmail.net>
wrote:

>On 2/21/2019 12:28 PM, Bob Casanova wrote:
>> On Wed, 20 Feb 2019 14:16:13 -0500, the following appeared
>> in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:
>>
>>> On 2/20/2019 1:41 PM, Bob Casanova wrote:
>>>> On Sat, 16 Feb 2019 14:14:53 -0500, the following appeared
>>>> in talk.origins, posted by Ron Dean <"Ron Dean"@gmail.net>:
>>>>
>>>> <snip>
>>>>
>>>>> I think we are missing a golden opportunity by ignoring the recently
>>>>> discovered homeobox genes.
>>>>
>>>> ....for values of "recently" equal to "35 years ago"...
>>>>
>>> Yes, relative to almost 160 years since Darwin's book on Evolution, was
>>> published 1859.
>>
>> So now it's *relatively* recent? Both are "relatively
>> recent" compared to Plato's "eternal forms" As is phlogiston
>> theory. Your point?
>>
>OK, but it should have been clear, I had previously mentioned
>homeobox genes which were discovered in 1983 by the late
>Walter Gehring A Swiss developmental biologist at Basel University
>Basel, Switzerland.

>Considering the role these master control genes play throughout the
>animal kingdom, their highly conserved nature and the ancient origin of
>these genes, before the Cambrian. The question arises as to how and
>when did evolution occur? Take for example the eye. It was once
>believed that eyes had evolved independently at least 40 times
>throughout the history of life, however, with the discovery of the
>Pax6 gene which controls the development of fruit-fly eyes, mouse,
>Zebra fish, trilobite eyes etc and human eyes when and how did the
>40 eyes evolve independently?

In the process of looking for articles to respond to Ron Dean's claim
above, that Pax6 and other Hox genes are somehow evidence against
biological evolution, and presumably therefore for Design, I came
across a paper co-authored by the very same Walther Gehring he cites
above:

<https://www.cell.com/trends/genetics/fulltext/S0168-9525(99)01776-X?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS016895259901776X%3Fshowall%3Dtrue#%20>

<https://tinyurl.com/y3dyzus4>

***********************************
Darwin was highly self-critical in his discussion of the eye prototype
and admits that the origin of the prototype cannot be explained by
natural selection, because selection can only drive the evolution of
an eye once it is partly functional and capable of light detection.
Therefore, selection cannot explain the origin of the eye prototype,
which for Darwin represents the same problem as the origin of life.
Therefore, both the origin of life and the origin of the eye prototype
must have been very rare events, and a polyphyletic origin in over 40
different phyla is not compatible with Darwin’s theory. In this
review, we discuss more recent evidence in favor of a monophyletic
origin of the eye and propose a new hypothesis explaining how
morphogenetic pathways might have evolved.
***********************************

The article goes on to detail the "more recent evidence", which turns
to be Pax6, and presents almost exactly the same argument as Ron Dean
posts in this topic, specifically that Pax6 almost certainly was
inherited from a single common ancestor, and therefore eyes themselves
originated from a single common ancestor, contrary to the claim that
eyes evolved independently multiple times. Of course, said evidence
of monophyletic eyes is no more convincing from Walter Gehring than it
is from Ron Dean, for reasons on which I elaborate in reply to Ron
Dean.

In addition to the fact that Ron Dean and Gehring post homologous
arguments, another reason I mention this article here is the section I
quote above. It starts out by saying that Darwin was "highly
self-critical" of the concept that natural selection could have
created the modern human eye. Gehring doesn't specifically identify
Darwin's comments, but it's likely he refers to what Darwin wrote in
"On the Origin of Species":
***********************************************
To suppose that the eye, with all its inimitable contrivances for
adjusting the focus to different distances, for admitting different
amounts of light, and for the correction of spherical and chromatic
aberration, could have been formed by natural selection, seems, I
freely confess, absurd in the highest possible degree.
************************************************

Gehring goes from there to jump to several conclusions about the
limits of natural selection, and ends with his claim that eyes
themselves are too unlikely to have evolved more than once.

The irony I note here, is that in a topic whose OP argues for one
Creationist PRATT, Ron Dean alludes to an author who wrote an article
which alludes to another Creationist PRATT:

<http://www.talkorigins.org/indexcc/CA/CA113_1.html>

Specifically, it's likely Gehring indirectly quotemined Darwin,
because OoS immediately follows the above quote with this:
***********************************************
Yet reason tells me, that if numerous gradations from a perfect and
complex eye to one very imperfect and simple, each grade being useful
to its possessor, can be shown to exist; if further, the eye does vary
ever so slightly, and the variations be inherited, which is certainly
the case; and if any variation or modification in the organ be ever
useful to an animal under changing conditions of life, then the
difficulty of believing that a perfect and complex eye could be formed
by natural selection, though insuperable by our imagination, can
hardly be considered real.
************************************************

So, contrary to Gehring's claim, Darwin had no problem with natural
selection explaining the eye prototype, and so presumably would have
had no problem with natural selection explaining multiple origins of
eyes.

None of the above is relevant to Ron Dean's argument, but it's
remarkable that an authoritative scientist would invoke a Creationist
PRATT, however indirectly, in a well-cited scientific paper, to
support his hypothesis.

[jillery]

On Mon, 25 Feb 2019 23:15:29 -0500, jillery <69jp...@gmail.com>
wrote:

I recall additional evidence which suggests eyes evolved independently
at least twice. Consider cephalopod eyes:

<https://en.wikipedia.org/wiki/Cephalopod_eye>

They are functionally similar to vertebrate eyes, in that they control
both the amount of light received as well as focus. But there is a
significant difference. Vertebrate eyes have the capillaries and
nerves in front of the retina. The capillaries and nerves cast
shadows on the retina, and the nerves must go through the retina,
creating a blind spot. OTOH cephalopod eyes have the retina in front
of the nerves and capillaries, and so don't suffer from these
"undocumented features".

This difference is not a result of natural selection, but instead is a
necessary consequence of different embryological development
strategies. Cephalopods eyes develop by invaginating the ectoderm
into the mesodermal brain tissue. Vertebrate eyes develop by the
mesodermal brain tissue growing out to the surface ectoderm. These
processes begin very early in development, which means these two
different strategies are equally highly conserved. So even though
both animals use Pax6 homologs to identify where and when to grow
eyes, they necessarily must use different but equally highly conserved
suites of genes to control how to grow the eyes. This is good
evidence that at least two animal lineages evolved eyes independently.

[Bob Casanova]

On Tue, 26 Feb 2019 23:26:01 -0500, the following appeared

"Highly conserved" is not synonymous with "unchanged"
(virtually or otherwise). And Mark has explained what
"homologous" means.

>> And BTW, "identical" is a bit of a stretch, as I believe has
>> been noted for you recently.

>I agree it was a stretch, but I think the pax 6 gene is nearly
>identically across the animal kingdom.

"Nearly identical" is a rather vague term.

[Ron Dean]

OK, but the two genes are close enough that the mouse gene placed in a
fruit-fly fashioned a complex fruit fly wye.

[jillery]

On Wed, 27 Feb 2019 14:22:01 -0500, Ron Dean <"Ron Dean"@gmail.net>
wrote:

IIUC your claimed that Pax6 and other hox genes are evidence for
Design because they are identical, but you now agree that fly Pax6 and
mouse Pax6 are not identical, but have differences characteristic of
unguided natural processes. Do you now agree that Pax6 and other Hox
genes are evidence for Common Descent and not Design?

[Mark Isaak]

On 2/26/19 8:26 PM, Ron Dean wrote:
> On 2/26/2019 11:31 AM, Bob Casanova wrote:

>> [...]

>> And BTW, "identical" is a bit of a stretch, as I believe has
>> been noted for you recently.
>>
> I agree it was a stretch, but I think the pax 6 gene is nearly
> identically across the animal kingdom.

The NCBI (National Center for Biotechnology Information) lets you view
the Pax6 sequences from a variety of species. You could look.

[Mark Isaak]

On 2/27/19 11:22 AM, Ron Dean wrote:
> On 2/26/2019 12:27 PM, Mark Isaak wrote:

>> [...]

>> Did you note in a passage you cited the phrase, "... the Drosophila
>> eyeless gene, a Pax6 homolog ..."?  The word "homolog" means the genes
>> are recognizably similar but are NOT identical.  Exactly what one
>> would expect from evolutionary common descent.  Not at all what one
>> would expect from intelligent design.
>>
> OK, but the two genes are close enough that the mouse gene placed in a
> fruit-fly fashioned a complex fruit fly wye.

First: Reference please.

Second: So?

[Ernest Major]

Why do you think that reiterating that observation is a meaningful response?

>
>> e.g. starfish. If I read Google right starfish eyes also involve Pax6,
>> which puts doubt on this first hypothesis, but it's conceivable that
>> the homeobox protein network was restruction during the transition
>> from bilateral to radial symmetry - we'd need a more detailed study
>> for a firm conclusions.
>>
>> Secondly, one could hypothesise that in the ancestral metazoan Pax6
>> was involved in the construction of eyespots, and that its role has
>> been conserved as eyespots evolved into a diversity of eyes in various
>> lineages.
>>
> The same Pax6 gene also control expression of blind spots in flatworms.
> According to Sean Carroll.
> Th New Science of EVO Devo pg 69.
>

Ah, evidence for the second hypothesis. Are you abandoning your claims
that the Pax genes support an unspecified design hypothesis?

--
alias Ernest Major

[Ron Dean]

The previous comment stated that the location "front of the head",
was where eyes were pressed into service: I really wasn't disagreeing
here, pointing out that eyes on fruit flies
have appeared on wings, legs etc in fruit flies because of where Pax 6
was placed.

[Bob Casanova]

On Wed, 27 Feb 2019 15:10:10 -0800, the following appeared
in talk.origins, posted by Mark Isaak
<eciton@curiousta/xyz/xonomy.net>:

>On 2/26/19 8:26 PM, Ron Dean wrote:
>> On 2/26/2019 11:31 AM, Bob Casanova wrote:
>>> [...]
>>> And BTW, "identical" is a bit of a stretch, as I believe has
>>> been noted for you recently.
>>>
>> I agree it was a stretch, but I think the pax 6 gene is nearly
>> identically across the animal kingdom.
>
>The NCBI (National Center for Biotechnology Information) lets you view
>the Pax6 sequences from a variety of species. You could look.

What fun would that be?

[Ron Dean]

On 2/28/2019 2:53 AM, Mark Isaak wrote:
> On 2/27/19 11:22 AM, Ron Dean wrote:
>> On 2/26/2019 12:27 PM, Mark Isaak wrote:
>>> [...]
>>> Did you note in a passage you cited the phrase, "... the Drosophila
>>> eyeless gene, a Pax6 homolog ..."?  The word "homolog" means the
>>> genes are recognizably similar but are NOT identical.  Exactly what
>>> one would expect from evolutionary common descent.  Not at all what
>>> one would expect from intelligent design.
>>>
>> OK, but the two genes are close enough that the mouse gene placed in a

>> fruit-fly fashioned a complex fruit fly eye.
>
> First: Reference please.
>
This was from a Library book I no longer have access to.
>
> Second: So?
>
If true, this would mean that mice and fruit flies which separated from
a common ancestor about 500 million years ago eyes are fashioned from
the same gene.

>

[Ernest Major]

But they're not fashioned from that gene. That gene (likely in
conjunction with other genes) initiates the cascade that leads to the
development of an eye.

Write out 100 times "The genome is not a blueprint".

--
alias Ernest Major

[Alan Kleinman MD PhD]

That's brilliant. Are you one of those reptifeatharians who think they can explain the evolution of the eye but can't explain either the Kishony or Lenski experiments?
>
> --
> alias Ernest Major

[Bob Casanova]

On Fri, 1 Mar 2019 08:23:21 -0800 (PST), the following
appeared in talk.origins, posted by Alan Kleinman MD PhD
<klei...@sti.net>:

>On Friday, March 1, 2019 at 8:05:02 AM UTC-8, Ernest Major wrote:
>> On 01/03/2019 14:28, Ron Dean wrote:
>> > On 2/28/2019 2:53 AM, Mark Isaak wrote:
>> >> On 2/27/19 11:22 AM, Ron Dean wrote:
>> >>> On 2/26/2019 12:27 PM, Mark Isaak wrote:
>> >>>> [...]
>> >>>> Did you note in a passage you cited the phrase, "... the Drosophila
>> >>>> eyeless gene, a Pax6 homolog ..."?  The word "homolog" means the
>> >>>> genes are recognizably similar but are NOT identical.  Exactly what
>> >>>> one would expect from evolutionary common descent.  Not at all what
>> >>>> one would expect from intelligent design.
>> >>>>
>> >>> OK, but the two genes are close enough that the mouse gene placed in
>> >>> a fruit-fly fashioned a complex fruit fly eye.
>> >>
>> >> First: Reference please.
>> > >
>> > This was from a Library book I no longer have access to.
>> > >
>> >> Second: So?
>> >>
>> > If true, this would mean that mice and fruit flies which separated from
>> > a common ancestor about 500 million years ago eyes are fashioned from
>> > the same gene.
>> >
>> > >
>> >
>> But they're not fashioned from that gene. That gene (likely in
>> conjunction with other genes) initiates the cascade that leads to the
>> development of an eye.
>>
>> Write out 100 times "The genome is not a blueprint".

>That's brilliant.

It's also true. Look up "blueprint" and "recipe".

>Are you one of those reptifeatharians who think they can explain the evolution of the eye but can't explain either the Kishony or Lenski experiments?

So, nothing relevant to add to the discussion, as usual? OK.

[Alan Kleinman MD PhD]

Just pointing out the facts to you dimmy. Of course, facts are not relevant to the reptifeatharians. And what would you think of someone who claims they can explain the circuitry of a microprocessor yet can't explain an RLC circuit? Because that is what reptifeatharians think they can do with evolution. It make is sound like you wasted your time taking introductory electric engineering courses.

[jillery]

On Fri, 1 Mar 2019 09:28:53 -0500, Ron Dean <"Ron Dean"@gmail.net>
wrote:

Incorrect, and you know it's incorrect. Once again, Pax6 controls
when and where. Other genes control how.

[Vincent Maycock]

There's nothing difficult to understand about these experiments. The
Kishony experiment just watches bacteria evolve drug resistance and
the Lenski experiment just watches a bunch of bacteria evolving other
traits besides that.

>> --
>> alias Ernest Major
>

[Alan Kleinman MD PhD]

So watching is explaining? Why did the physics department waste all your time with those pesky math courses? All you have to do is watch the experiment and that explains it. Vincent, I really expect more than that from you.
>
> >> --
> >> alias Ernest Major
> >

[Vincent Maycock]

On Fri, 1 Mar 2019 11:13:52 -0800 (PST), Alan Kleinman MD PhD

What is there about these experiments that creationists can explain
but evolutionists can't?

>> >> --
>> >> alias Ernest Major
>> >
>

[Alan Kleinman MD PhD]

Post links where reptifeatharians have explained the Lenski and Kishony experiments. Make sure they include the mathematics which describes the experiments.
>
> >> >> --
> >> >> alias Ernest Major
> >> >
> >

[Vincent Maycock]

On Fri, 1 Mar 2019 12:20:21 -0800 (PST), Alan Kleinman MD PhD

What is it about these experiments that makes you think mainstream
biology can't explain them?

>> >> >> --
>> >> >> alias Ernest Major
>> >> >
>> >
>

[Alan Kleinman MD PhD]

These experiments show the mathematical irrationality of the ToE. Since it takes a billion replications for each evolutionary step under the best of conditions of only a single selection pressure at a time, how do you achieve the necessary replications to transform a reptile population into a bird population? You simply do not have the population sizes and recovery rates necessary for rmns to operate to make these kinds of genetic transformations. And if you have two selection pressures acting on the population simultaneously, that billion replications for each evolutionary step goes to about a trillion replications. Biologists don't want to explain these experiments, these experiments pop their bubble.
>
> >> >> >> --
> >> >> >> alias Ernest Major
> >> >> >
> >> >
> >

[Vincent Maycock]

On Fri, 1 Mar 2019 14:43:47 -0800 (PST), Alan Kleinman MD PhD

And you get this from the Kishony and Lenski experiments? For example,
does Kishony say that his experiment shows that he only has enough
replications for a single selection pressure for evolution to work?

>And if you have two selection pressures acting on the population simultaneously, that billion replications for each evolutionary step goes to about a trillion replications.

Then why are some species so spectacularly successful, if they're all
succumbing to the many natural selection pressures they encounter?

[Alan Kleinman MD PhD]

Yes, Kishony had to insure that the increase in drug concentration wasn't too large because then it would require 2 mutations to grow in that region and his experiment wouldn't work (it would require a trillion replications for that variant). And there is plenty of other empirical evidence which demonstrates this. You can start with the successful use of combination therapy for the treatment of hiv. Then there is the success of combination herbicides, pesticides, rodenticides...

>
> >And if you have two selection pressures acting on the population simultaneously, that billion replications for each evolutionary step goes to about a trillion replications.
>
> Then why are some species so spectacularly successful, if they're all
> succumbing to the many natural selection pressures they encounter?

What species do you want to talk about? Populations don't necessarily have to succumb to selection pressures, they can evolve to the pressures or drift. Drift is far, far more likely to occur.

[Vincent Maycock]

On Fri, 1 Mar 2019 15:45:59 -0800 (PST), Alan Kleinman MD PhD

But how do you get that specifically from those experiments? That is,
even if you're right, how can you derive that from those experiments?
I mean it's not as if, for example, Kishony said "Well, this looks
like I'm going to need a trillion replications for this to happen."

>And there is plenty of other empirical evidence which demonstrates this. You can start with the successful use of combination therapy for the treatment of hiv. Then there is the success of combination herbicides, pesticides, rodenticides...

Yeah, anything that involves humans deliberately trying to reduce the
population sizes under consideration.

>> >And if you have two selection pressures acting on the population simultaneously, that billion replications for each evolutionary step goes to about a trillion replications.
>>
>> Then why are some species so spectacularly successful, if they're all
>> succumbing to the many natural selection pressures they encounter?
>What species do you want to talk about?

Bison, passenger pigeons, coyotes, for example.

>Populations don't necessarily have to succumb to selection pressures, they can evolve to the pressures or drift. Drift is far, far more likely to occur.

Why would that be?

[Bob Casanova]

On Fri, 1 Mar 2019 10:20:43 -0800 (PST), the following

You wouldn't know a fact if it bit you on the ass; all you
have is your flawed "model", which is why you think(?) that
the genome is a blueprint.

> Of course, facts are not relevant to the reptifeatharians. And what would you think of someone who claims they can explain the circuitry of a microprocessor yet can't explain an RLC circuit? Because that is what reptifeatharians think they can do with evolution. It make is sound like you wasted your time taking introductory electric engineering courses.

So, still nothing relevant to add to the discussion, as
usual? OK.

[Ron Dean]

On 3/1/2019 1:41 PM, jillery wrote:
> On Fri, 1 Mar 2019 09:28:53 -0500, Ron Dean <"Ron Dean"@gmail.net>
> wrote:
>
>> On 2/28/2019 2:53 AM, Mark Isaak wrote:
>>> On 2/27/19 11:22 AM, Ron Dean wrote:
>>>> On 2/26/2019 12:27 PM, Mark Isaak wrote:
>>>>> [...]
>>>>> Did you note in a passage you cited the phrase, "... the Drosophila
>>>>> eyeless gene, a Pax6 homolog ..."?  The word "homolog" means the
>>>>> genes are recognizably similar but are NOT identical.  Exactly what
>>>>> one would expect from evolutionary common descent.  Not at all what
>>>>> one would expect from intelligent design.
>>>>>
>>>> OK, but the two genes are close enough that the mouse gene placed in a
>>>> fruit-fly fashioned a complex fruit fly eye.
>>>
>>> First: Reference please.
>>>
>> This was from a Library book I no longer have access to.
>>>
>>> Second: So?
>>>
>> If true, this would mean that mice and fruit flies which separated from
>> a common ancestor about 500 million years ago eyes are fashioned from
>> the same gene.
>
>
> Incorrect, and you know it's incorrect. Once again, Pax6 controls
> when and where. Other genes control how.
>

When and where is only part of it's purpose. The Px6 gene is a master
control gene which directs downstream genes. When the Pax6 is placed on
a fly's wing or leg or it's antennae by researchers an eye develops in
those positions.
This shows that the role of Pax6 is far more than just "where and when".
So, obviously the Pax6 can marshal cells that form the eye from where
it is physically positioned (by researchers) to the selected locations.

[Ron Dean]

On 2/28/2019 2:53 AM, Mark Isaak wrote:

> On 2/27/19 11:22 AM, Ron Dean wrote:
>> On 2/26/2019 12:27 PM, Mark Isaak wrote:
>>> [...]
>>> Did you note in a passage you cited the phrase, "... the Drosophila
>>> eyeless gene, a Pax6 homolog ..."?  The word "homolog" means the
>>> genes are recognizably similar but are NOT identical.  Exactly what
>>> one would expect from evolutionary common descent.  Not at all what
>>> one would expect from intelligent design.
>>>
>> OK, but the two genes are close enough that the mouse gene placed in a
>> fruit-fly fashioned a complex fruit fly wye.
>
> First: Reference please.
>

www.cccbiotechnology.com/WN/SUA01/master_eye_gene.php
>
www.pbs.org/wgbh/evolution/library/04/4/text_pop/l_044_01.html
>
middleschoolatsage.weebly.com/uploads/5/2/5/8/5258770/mystery
>
>
> Second: So?
>
Regardless of how this and to other "highly conserved" master control
genes came about either through natural processes 100s of millions
of years ago or by an intelligent agent, these genes are clear
examples of design.
c

[Ernest Major]

On 04/03/2019 03:28, Ron Dean wrote:
> When and where is only part of it's purpose. The Px6 gene is a master
> control gene which directs downstream genes. When the Pax6 is placed on
> a fly's wing or leg or it's antennae by researchers an eye develops in
> those positions.
> This shows that the role of Pax6 is far more than just "where and when".
> So, obviously the Pax6  can marshal cells that form the eye from where
> it is physically positioned (by researchers) to the selected locations.

How does "marshal cells that form the eye from where it is physically
positioned (by researchers) to the selected locations" differ from
"where and when"?

Are you claiming the cell fate is deterministic (it is is Caenorhabditis
elegans, but not in the majority of animals) and ectopic expression
causes the cells that are fated to form the eye to migrate to another
location? The rest of us think that ectopic expression causes cells in
that location to differentiate differently, rather than cells from other
locations to somehow follow a homeing signal.

--
alias Ernest Major

[Alan Kleinman MD PhD]

You haven't studied the design of the experiment carefully. Read their paper that gives a more detailed explanation of the video and experiment:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/
Even when using a single drug, the experiment won't work (on that size plate) if the step increase in drug concentration requires 2 mutations in order to grow in the next higher drug concentration region. That probability problem is a little more complex than the single mutation calculation and you can't use the mean value of the binomial distribution to estimate the number of replications necessary to give a reasonable probability of that event. If you want to understand how to do that calculation, read this paper:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175190/
The calculation for improvement in fitness to two drugs (a beneficial mutation for each drug) is the same as the calculation for two mutations necessary to improve fitness to a single drug. The importance to this fact in clinical medicine is don't use low drug concentrations when treating infections.

>
> >And there is plenty of other empirical evidence which demonstrates this. You can start with the successful use of combination therapy for the treatment of hiv. Then there is the success of combination herbicides, pesticides, rodenticides...
>
> Yeah, anything that involves humans deliberately trying to reduce the
> population sizes under consideration.

All selection pressures whether human applied or "natural" kill or impair the replication of some or all members of a population, that's how they select. The lesson is the same for the Lenski experiment. Of course, perhaps you don't think starvation occurs in nature? And if Lensk were to put thermal stress on his populations as well as starvation, the math is the same.

>
> >> >And if you have two selection pressures acting on the population simultaneously, that billion replications for each evolutionary step goes to about a trillion replications.
> >>
> >> Then why are some species so spectacularly successful, if they're all
> >> succumbing to the many natural selection pressures they encounter?
> >What species do you want to talk about?
>
> Bison, passenger pigeons, coyotes, for example.

Ok, describe the selection pressures, genes targeted and mutations required for any of these replicators for their evolutionary process. And then show us how to do the mathematics for their evolution.

>
> >Populations don't necessarily have to succumb to selection pressures, they can evolve to the pressures or drift. Drift is far, far more likely to occur.
>
> Why would that be?

Directional selection requires large numbers of replications for each evolutionary step of the particular lineage in order to improve fitness. If those replications aren't achieved but the population isn't driven to extinction, then drift occurs without any variants achieving improved fitness to the selection conditions.

[jillery]

On Mon, 4 Mar 2019 10:23:26 +0000, Ernest Major
<{$to$}@meden.demon.co.uk> wrote:

>On 04/03/2019 03:28, Ron Dean wrote:
>> When and where is only part of it's purpose. The Px6 gene is a master
>> control gene which directs downstream genes. When the Pax6 is placed on
>> a fly's wing or leg or it's antennae by researchers an eye develops in
>> those positions.
>> This shows that the role of Pax6 is far more than just "where and when".
>> So, obviously the Pax6  can marshal cells that form the eye from where
>> it is physically positioned (by researchers) to the selected locations.
>
>How does "marshal cells that form the eye from where it is physically
>positioned (by researchers) to the selected locations" differ from
>"where and when"?

A good question. I hope you get a good answer.

>Are you claiming the cell fate is deterministic (it is is Caenorhabditis
>elegans, but not in the majority of animals) and ectopic expression
>causes the cells that are fated to form the eye to migrate to another
>location? The rest of us think that ectopic expression causes cells in
>that location to differentiate differently, rather than cells from other
>locations to somehow follow a homeing signal.

--

[jillery]

On Sun, 3 Mar 2019 23:11:01 -0500, Ron Dean <"Ron Dean"@gmail.net>
wrote:

In your past posts, you have made it clear that you think "design"
necessarily implies designs "came about" by intelligent designer(s).
This is the very opposite of originating from unguided natural
processes, by definition. So when you say "regardless of how..."
above, that implies you no longer so think. Is that really what you
meant to write?

[Mark Isaak]

On 3/3/19 8:11 PM, Ron Dean wrote:
> On 2/28/2019 2:53 AM, Mark Isaak wrote:
>> On 2/27/19 11:22 AM, Ron Dean wrote:
>>> On 2/26/2019 12:27 PM, Mark Isaak wrote:
>>>> [...]
>>>> Did you note in a passage you cited the phrase, "... the Drosophila
>>>> eyeless gene, a Pax6 homolog ..."?  The word "homolog" means the
>>>> genes are recognizably similar but are NOT identical.  Exactly what
>>>> one would expect from evolutionary common descent.  Not at all what
>>>> one would expect from intelligent design.
>>>>
>>> OK, but the two genes are close enough that the mouse gene placed in
>>> a fruit-fly fashioned a complex fruit fly wye.
>>
>> First: Reference please.
> >
> www.cccbiotechnology.com/WN/SUA01/master_eye_gene.php
> >
> www.pbs.org/wgbh/evolution/library/04/4/text_pop/l_044_01.html
> >
> middleschoolatsage.weebly.com/uploads/5/2/5/8/5258770/mystery

Thank you.

>> Second: So?
>>
> Regardless of how this and to other "highly conserved" master control
> genes came about either through natural processes 100s of millions
> of years ago or by an intelligent agent, these genes are clear
> examples of design.

So the term "design", as you use it, does not imply intelligence or
deliberation. Perhaps it would be prudent for you to make that point up
front in your posts.

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"Omnia disce. Videbis postea nihil esse superfluum."
- Hugh of St. Victor

[Vincent Maycock]

On Mon, 4 Mar 2019 02:27:11 -0800 (PST), Alan Kleinman MD PhD

That makes sense, but I don't know that Kishony ever said it.

>That probability problem is a little more complex than the single mutation calculation and you can't use the mean value of the binomial distribution to estimate the number of replications necessary to give a reasonable probability of that event. If you want to understand how to do that calculation, read this paper:
>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175190/

How come you use Venn diagrams in the paper? Why couldn't you just
multiply the probabilities involved (for an "and" situation), without
drawing them?

>The calculation for improvement in fitness to two drugs (a beneficial mutation for each drug) is the same as the calculation for two mutations necessary to improve fitness to a single drug. The importance to this fact in clinical medicine is don't use low drug concentrations when treating infections.
>>
>> >And there is plenty of other empirical evidence which demonstrates this. You can start with the successful use of combination therapy for the treatment of hiv. Then there is the success of combination herbicides, pesticides, rodenticides...
>>
>> Yeah, anything that involves humans deliberately trying to reduce the
>> population sizes under consideration.
>All selection pressures whether human applied or "natural" kill or impair the replication of some or all members of a population,

Some forms of impairment would be milder than others, though, right?
Would variants go up in flames and be burned to death if the
temperature rose by an average of 1 degree Celsius?

> that's how they select. The lesson is the same for the Lenski experiment. Of course, perhaps you don't think starvation occurs in nature? And if Lensk were to put thermal stress on his populations as well as starvation, the math is the same.
>>
>> >> >And if you have two selection pressures acting on the population simultaneously, that billion replications for each evolutionary step goes to about a trillion replications.
>> >>
>> >> Then why are some species so spectacularly successful, if they're all
>> >> succumbing to the many natural selection pressures they encounter?
>> >What species do you want to talk about?
>>
>> Bison, passenger pigeons, coyotes, for example.
>Ok, describe the selection pressures, genes targeted and mutations required for any of these replicators for their evolutionary process. And then show us how to do the mathematics for their evolution.

All we really need to know is that enormous population sizes were
sustained for these species in North America before Europeans came
along, despite being exposed to multiple natural selection pressures.

>> >Populations don't necessarily have to succumb to selection pressures, they can evolve to the pressures or drift. Drift is far, far more likely to occur.
>>
>> Why would that be?
>Directional selection requires large numbers of replications for each evolutionary step of the particular lineage in order to improve fitness. If those replications aren't achieved but the population isn't driven to extinction,

What would prevent them from being driven to extinction? Don't you
like to say that 99% of species have gone extinct?

[Alan Kleinman MD PhD]

Read the paragraph starting with "To test the importance of the size of intermediate steps in the evolution". They don't give the number of replications but the probability calculation is quite straight-forward. They are actually relearning the fact that Edward Tatum talked about in his 1958 Nobel Laureate Lecture.

>
> >That probability problem is a little more complex than the single mutation calculation and you can't use the mean value of the binomial distribution to estimate the number of replications necessary to give a reasonable probability of that event. If you want to understand how to do that calculation, read this paper:
> >https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175190/
>
> How come you use Venn diagrams in the paper? Why couldn't you just
> multiply the probabilities involved (for an "and" situation), without
> drawing them?

You are actually computing conditional probabilities and the Venn diagrams make it easy to recognize the subset necessary to do the correct probability calculation. You are computing the probability of an AB variant occurring among a set of A, B and C (non-A, non-B variants). That probability is computed by the intersection of the A and B subsets.

>
> >The calculation for improvement in fitness to two drugs (a beneficial mutation for each drug) is the same as the calculation for two mutations necessary to improve fitness to a single drug. The importance to this fact in clinical medicine is don't use low drug concentrations when treating infections.
> >>
> >> >And there is plenty of other empirical evidence which demonstrates this. You can start with the successful use of combination therapy for the treatment of hiv. Then there is the success of combination herbicides, pesticides, rodenticides...
> >>
> >> Yeah, anything that involves humans deliberately trying to reduce the
> >> population sizes under consideration.
> >All selection pressures whether human applied or "natural" kill or impair the replication of some or all members of a population,
>
> Some forms of impairment would be milder than others, though, right?
> Would variants go up in flames and be burned to death if the
> temperature rose by an average of 1 degree Celsius?

That's correct but let's say you have two "mild" selection pressures. One selection pressure requires mutation "A" to improve fitness against one of the selection pressures and the other selection pressure requires mutation "B" to give improved fitness to that selection pressure. You still must multiply the probabilities of each of those events occurring to get the joint probabiliy of a member getting both of those mutations. It's the same math regardless of the intensity of selection. That's why if Lenski were to run his experiment at a less than optimal temperature, the experiment would slow significantly compared to the optimal temperature experiment. You are forcing the population to take a much more complex evolutionary trajectory.

>
> > that's how they select. The lesson is the same for the Lenski experiment. Of course, perhaps you don't think starvation occurs in nature? And if Lensk were to put thermal stress on his populations as well as starvation, the math is the same.
> >>
> >> >> >And if you have two selection pressures acting on the population simultaneously, that billion replications for each evolutionary step goes to about a trillion replications.
> >> >>
> >> >> Then why are some species so spectacularly successful, if they're all
> >> >> succumbing to the many natural selection pressures they encounter?
> >> >What species do you want to talk about?
> >>
> >> Bison, passenger pigeons, coyotes, for example.
> >Ok, describe the selection pressures, genes targeted and mutations required for any of these replicators for their evolutionary process. And then show us how to do the mathematics for their evolution.
>
> All we really need to know is that enormous population sizes were
> sustained for these species in North America before Europeans came
> along, despite being exposed to multiple natural selection pressures.

Compared to the population sizes achievable by microbes, the population sizes for the replicators you named are miniscule. Remember, the Kishony and Lenski experiments are demonstrating that it takes in the billions of replications for each beneficial mutation in ideal circumstances of only a single selection pressure acting on the population at a time. And it is not unusual for the "natural" environment to impose starvation, thermal stress, disease, predation... all at the same time.

>
> >> >Populations don't necessarily have to succumb to selection pressures, they can evolve to the pressures or drift. Drift is far, far more likely to occur.
> >>
> >> Why would that be?
> >Directional selection requires large numbers of replications for each evolutionary step of the particular lineage in order to improve fitness. If those replications aren't achieved but the population isn't driven to extinction,
>
> What would prevent them from being driven to extinction? Don't you
> like to say that 99% of species have gone extinct?

That 99% is not my number. All that is required it that the members of the population have sufficient fitness to reproduce against the selection conditions imposed by the environment not to go extinct. Only when some variant can replicate sufficiently is there a reasonable probability that one of its members will get a beneficial mutation.

[Mark Isaak]

On 3/4/19 11:53 AM, Alan Kleinman MD PhD wrote:
> On Monday, March 4, 2019 at 10:25:02 AM UTC-8, Vincent Maycock wrote:

>> [...]

>> Some forms of impairment would be milder than others, though, right?
>> Would variants go up in flames and be burned to death if the
>> temperature rose by an average of 1 degree Celsius?
> That's correct but let's say you have two "mild" selection pressures. One selection pressure requires mutation "A" to improve fitness against one of the selection pressures and the other selection pressure requires mutation "B" to give improved fitness to that selection pressure. You still must multiply the probabilities of each of those events occurring to get the joint probabiliy of a member getting both of those mutations.

A probability which is very nearly one. But Alan can't figure out why.

[Alan Kleinman MD PhD]

On Monday, March 4, 2019 at 2:30:03 PM UTC-8, Mark Isaak wrote:
> On 3/4/19 11:53 AM, Alan Kleinman MD PhD wrote:
> > On Monday, March 4, 2019 at 10:25:02 AM UTC-8, Vincent Maycock wrote:
> >> [...]
> >> Some forms of impairment would be milder than others, though, right?
> >> Would variants go up in flames and be burned to death if the
> >> temperature rose by an average of 1 degree Celsius?
> > That's correct but let's say you have two "mild" selection pressures. One selection pressure requires mutation "A" to improve fitness against one of the selection pressures and the other selection pressure requires mutation "B" to give improved fitness to that selection pressure. You still must multiply the probabilities of each of those events occurring to get the joint probabiliy of a member getting both of those mutations.
>
> A probability which is very nearly one. But Alan can't figure out why.

If the variant can do sufficient replications, yep, the probability approaches one and I understand exactly why BookMark. For a single selection pressure, the number of replications is about a billion, if there are two selection pressures acting, its about a trillion replications and if it is three selection pressures, you have a successful treatment for hiv. They didn't give that to you in your graduate-level course in population genetics. You know, that's the course for which you have no expertise.

[jillery]

On Mon, 4 Mar 2019 11:53:20 -0800 (PST), Alan Kleinman MD PhD
<klei...@sti.net> wrote:
>On Monday, March 4, 2019 at 10:25:02 AM UTC-8, Vincent Maycock wrote:

[...]

>> What would prevent them from being driven to extinction? Don't you
>> like to say that 99% of species have gone extinct?
>That 99% is not my number. All that is required it that the members of the population have sufficient fitness to reproduce against the selection conditions imposed by the environment not to go extinct. Only when some variant can replicate sufficiently is there a reasonable probability that one of its members will get a beneficial mutation.

Incorrect. There are always catastrophic events to which biological
organisms are incapable of adapting. Either those catastrophes exceed
the abilities of biochemical life, or because they happen so abruptly,
they provide no opportunity for life to adapt to them. When such a
catastrophe happens at just the wrong time, and over a region that
covers most of a species' range, it's going to make any species
extinct, no matter how fit. And the longer species exists, the more
likely they will experience such a catastrophe. You would know this
if you knew anything about probability theory.

[Alan Kleinman MD PhD]

So that's how reptiles grow feathers. We have all been waiting for that explanation.

[Mark Isaak]

For a population in the thousands, the probability of a member getting
both beneficial mutations is very nearly one. And Alan is clueless as
to why.

[Alan Kleinman MD PhD]

Sure I know why BookMark. Give that population of thousands a billion generations of replications and you got one of those members with the two beneficial mutations. You should write that in your last chapter of your book. You can already see the feathers growing on a lizard.

[Ron Dean]

On 2/19/2019 3:06 PM, Ernest Major wrote:
> On 19/02/2019 19:06, Burkhard wrote:
>> Ron Dean wrote:
>>> On 2/11/2019 10:55 AM, Glenn wrote:
>>>> On Monday, February 11, 2019 at 5:30:05 AM UTC-7, Burkhard wrote:
>>>>> zencycle wrote:
>>>>>> On Friday, February 8, 2019 at 2:55:09 PM UTC-5, Glenn wrote:
>>>>>>> On Friday, February 8, 2019 at 12:00:08 PM UTC-7, Burkhard wrote:
>>>>>>>> dthe...@gmail.com wrote:
>>>>>>>>
>>>>>>>> Firstly, wrong on its own terms, as these "other forms of
>>>>>>>> evidence" are
>>>>>>>> of course observations. Science frequently postulates entities and
>>>>>>>> processes that can only indirectly be observed (otherwise, you
>>>>>>>> would
>>>>>>>> really not need science, just a list of things you see)
>>>>>>>>
>>>>>>>> Second, it makes an arbitrary and ultimately meaningless
>>>>>>>> distinction
>>>>>>>> between historical sciences and other scientific disciplines.
>>>>>>>> Forensic
>>>>>>>> sciences are an obvious example where we use scientific methods to
>>>>>>>> form
>>>>>>>> reliable theories about singular past events - maybe you suggest we
>>>>>>>> should empty our prisons and only convict if there were several
>>>>>>>> eyewitnesses?
>>>>>>>>
>>>>>>> Hmmmmmm, reliable, eh.
>>>>>>>
>>>>>>> "In 2009, the National Academy of Sciences evaluated the state of
>>>>>>> forensic science and, shockingly, concluded that many of the
>>>>>>> techniques used in court actually have no scientific validity. This
>>>>>>> means that the science used to convict the accused is neither
>>>>>>> reliable, nor robust and cannot be trusted in a court of law."
>>>>>>>
>>>>>>> https://blogs.scientificamerican.com/observations/we-must-strengthen-the-science-in-forensic-science/
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Thanks for comparing evolution to forensics.
>>>>>>
>>>>>> It's always so cute when you pretend you know what you're taliking
>>>>>> about, glenn. Of course, a good analogy for your debating skills is
>>>>>> that a broken clock is right twice a day.  Burkhard may not have
>>>>>> chosen the best analogy, but as usual with half-wits like you and
>>>>>> slowstan, you don't bother to read past a headline. Guess where this
>>>>>> snippet came from:
>>>>>>
>>>>>> "Forensic techniques such as fingerprints and firearms analysis were
>>>>>> developed by law enforcement to help solve crimes. Unlike DNA
>>>>>> analysis, these practices were not borne of science, and evolved in
>>>>>> a legal system that is binary, adversarial and absolute, requiring
>>>>>> verdicts of guilty or not guilty. In contrast, mainstream science
>>>>>> functions with an acceptance that all knowledge is provisional and
>>>>>> certainty is described by probability. These two approaches create
>>>>>> tremendous tension between the ways scientists and legal
>>>>>> practitioners perceive evidence."
>>>>>>
>>>>>> thanks for playing.....
>>>>>>
>>>>>
>>>>> Glenn linked to the  NAS report on forensic science? Now that's funny
>>>>> :o). My team contributed to it, and my then co-director and
>>>>> collaborator
>>>>> Colin Aitken is cited several times. We've done more direct work
>>>>> for our
>>>>> UK review.
>>>>>
>>>>> And no, the report does not say that forensic science is unreliable -
>>>>> Glenn is of course welcome to commit a crime, leave his DNA and
>>>>> fingerprints all over the place, and then submit the report in his
>>>>> defense- should be fun. Or as the report says:
>>>>>
>>>>> "For decades, the forensic science disciplines have produced valuable
>>>>> evidence that has contributed to the successful prosecution and
>>>>> conviction of criminals as well as to the exoneration of innocent
>>>>> people. Over the last two decades, advances in some forensic science
>>>>> disciplines, especially the use of DNA technology, have demonstrated
>>>>> that some areas of forensic science have great additional potential to
>>>>> help law enforcement identify criminals. Many crimes that may have
>>>>> gone
>>>>> unsolved are now being solved because forensic science is helping to
>>>>> identify the perpetrators."
>>>>>
>>>>> If you look at the Innocence project for instance, the pretty
>>>>> consistent
>>>>> pattern is people getting exonerated through forensic (mainly DNA)
>>>>> evidence for convictions based on flawed eyewitness evidence
>>>>> (including
>>>>> false confessions, if you consider the suspect as eyewitness)
>>>>>
>>>>> Are there problems in the way forensic science is sometimes practices,
>>>>> especially in the US? Of course. Unrealistic expectations in jurors
>>>>> and
>>>>> lawyers caused by TV programs, an increasing workload with stagnating
>>>>> funding )especially for defense work), an increasing breadth of
>>>>> techniques that cause tension between the need to specialize and still
>>>>> to keep an overview of the entire investigation etc etc.
>>>>>
>>>>> The problem in most of the areas of improvement is not the science,
>>>>> but
>>>>> the forensic laboratory infrastructure. This includes lack of
>>>>> mandatory
>>>>> and robust certification standards for labs, mandatory training
>>>>> pathways
>>>>> into the profession, and also investment in things like modern
>>>>> equipment
>>>>> and comprehensive data sets. Or as the report put it right at the
>>>>> beginning:
>>>>>
>>>>> "There are scores of talented and dedicated people in the forensic
>>>>> science community, and the work that they perform is vitally
>>>>> important.
>>>>> They are often strapped in their work, however, for lack of adequate
>>>>> resources, sound policies, and national support".
>>>>>
>>>>> So what is needed is more money, and more public sector structures -
>>>>> both unfortunately anathema to the current US government, which
>>>>> promptly
>>>>> closed down the the National Commission on Forensic Science. I
>>>>> mean, why
>>>>> spend money on criminal justice if "thoughts and prayers" are so much
>>>>> cheaper
>>>>>
>>>>> There have been some forensic disciplines where the problem is more
>>>>> fundamental, bitemark evidence probably the most dramatic case. There
>>>>> the self-regulatory mechanisms of scientific practice were
>>>>> systematically sidelined. The report makes a couple of recommendations
>>>>> on how to rectify this.
>>>>>
>>>>> So yes, there is always room for improvement, but the report makes it
>>>>> clear that this is improvement of something that has already
>>>>> dramatically changed the accuracy and reliability of trial decision
>>>>> making for the better.
>>>>
>>>> As - its getting better all the time.
>>>>
>>>>> To read it as Glenn does is just your average quote mine.
>>>>
>>>> I read it the way it was printed. That's better than whitewashing it.
>>>>
>>>> Another "quotemine":
>>>>
>>>> "Historically, forensic science has had a huge impact on identifying
>>>> and confirming suspects in the courtroom, and on the judicial system
>>>> more generally. And yet, a 2009 report from the U.S. National Academy
>>>> of Sciences (NAS) identified numerous shortcomings in the field,
>>>> including an absence of a scientific basis for most forms of forensic
>>>> evidence, a lack of uniform standards and the need for independence
>>>> from law enforcement. In short, the report called for nothing less
>>>> than major reform."
>>>>
>>>> https://www.livescience.com/49929-faulty-forensic-science-failing-united-states-court-system.html
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Burkhard "DNA OK"?
>>>>
>>>> DNA tests in forensic science can't be separated from "Forensic
>>>> Science".
>>>>
>>>> "Analysts are picking up DNA transferred from one person to another by
>>>> way of an object that both of them have touched, or from one piece of
>>>> evidence to another by crime scene investigators, lab techs—or when
>>>> two items jostled against each other in an evidence bag."
>>>>
>>>> Read more at
>>>>
>>>> http://www.sciencemag.org/news/2016/03/forensics-gone-wrong-when-dna-snares-innocent
>>>>
>>>>
>>>>
>>> I think we are missing a golden opportunity by ignoring the recently
>>> discovered homeobox  genes.
>>>
>>
>> You might want to rethink this. Isn't your claim that they are highly
>> conserved? That makes them pretty useless to differentiate between
>> possible perpetrators, don't you think?
>>
>
> I thought perhaps he was changing the subject away from forensic
> science, but tens of thousands of papers (Google Scholar gives 177,000
> results for homeobox) is hardly ignoring them.
>
It's true that perhaps most biologist know about this topic and have
advanced papers regarding this discovery, but the rank and file don't
seem to know anything about them.

[Ron Dean]

No, this is not my claim but the claim of people researching the new
science of Evo Devo. This is the 1/TH. characteristic in addition other
discriptions of homeobox genes, such as: 2) ancient - existed prior to
the Cambrian explosion, 3) Universal throughout the animal kingom.

>
That makes them pretty useless to differentiate between
> possible perpetrators, don't you think?
>

I don;t understand this!

[Burkhard]

You suggested looking at homeobox for forensic DNA analysis, the issue
under discussion. If you do a DNA test, you want to exclude as many
people as possible,ideally everybody but one. That's what we call in
forensics science "discrimination". When we say that there is a "1 in a
billion etc chance that a sample comes from a person other than the
suspect, that's what we mean, that there are at best very few people who
would have the same profile. Contrast this with the older blood group
analysis e.g., where you could only say that people with say A, AB and O
could not have been the source of the blood on the broke window, which
leaves millions of suspects.

So rather obviously, in DNA fingerprinting we look not at loci that are
highly conserved (because they would be the same for all humans, or
maybe even all animalia etc, but at those microsatellites where we can
expect lots of mutations. So exactly not homeobox genes - the more
universal, the less valuable for forensic analysis. Now, if your only
suspects are a human and a vicious mushroom that has been seen
terrorizing the neighborhood, your suggestion of looking at homeobo
might just work,sometimes, to rule out one of the suspects. But I submit
tat this is not going to be the case often.

[Ernest Major]

Are the "we" who "are missing a golden opportunity" the creationists?

--
alias Ernest Major

[Ron Dean]

Anyone who has an interest in the potential of design in nature.

[Mark Isaak]

On 3/5/19 3:42 PM, Ron Dean wrote:
> On 3/5/2019 3:19 PM, Ernest Major wrote:

>>>> [...]

>>>> I thought perhaps he was changing the subject away from forensic
>>>> science, but tens of thousands of papers (Google Scholar gives
>>>> 177,000 results for homeobox) is hardly ignoring them.
>>>>
>>> It's true that perhaps most biologist know about this topic and have
>>> advanced papers regarding this discovery, but the rank and file don't
>>> seem to know anything about them.
>>
>> Are the "we" who "are missing a golden opportunity" the creationists?
>>
> Anyone who has an interest in the potential of design in nature.

Homeobox genes don't have anything to show about design that the shape
of a fern frond didn't already show people 5,000 years ago.