An experimental Darwinist hits the edge...

[Steady Eddie]

From Thornton's Lab, More Strong Experimental Support for a Limit to Darwinian Evolution


*****
Thornton himself -- apparently a conventional Darwinist, and certainly no sympathizer with intelligent design -- does not attribute the protein receptor's new function to Darwinian processes. Rather, he ascribes it mostly to "historical contingency." That's another way of saying "dumb luck."

*****

-by Michael Behe

[Athel Cornish-Bowden]

You seem to have forgotten to quote what Joe Thornton thought of Behe's
conclusions, so here it is:

"Thanks for asking for my reaction to Behe’s post on our recent paper
in Nature. His interpretation of our work is incorrect. He confuses
“contingent” or “unlikely” with “impossible.” He ignores the key role
of genetic drift in evolution. And he erroneously concludes that
because the probability is low that some specific biological form will
evolve, it must be impossible for ANY form to evolve.

"Behe contends that our findings support his argument that adaptations
requiring more than one mutation cannot evolve by Darwinian processes.
The many errors in Behe’s Edge of Evolution — the book in which he
makes this argument — have been discussed in numerous publications.

"In his posts about our paper, Behe’s first error is to ignore the fact
that adaptive combinations of mutations can and do evolve by pathways
involving neutral intermediates. Behe says that if it takes more than
one mutation to produce even a crude version of the new protein
function, then selection cannot drive acquisition of the adaptive
combination."


--
athel

[jillery]

Behe equates historical contingency with dumb luck, but it really mean
only what has happened in the past. Unless one subscribes to
omphalism, one necessarily acknowledges that living organisms have a
past. The events of the past shaped their current genomes, just as
current events shape their future genomes.

[Steady Eddie]

On Friday, 1 August 2014 10:47:38 UTC-6, Athel Cornish-Bowden wrote:
> On 2014-08-01 16:30:06 +0000, Steady Eddie said:
>
>
>
> > From Thornton's Lab, More Strong Experimental Support for a Limit to
>
> > Darwinian Evolution
>
> >
>
> >
>
> > *****
>
> > Thornton himself -- apparently a conventional Darwinist, and certainly
>
> > no sympathizer with intelligent design -- does not attribute the
>
> > protein receptor's new function to Darwinian processes. Rather, he
>
> > ascribes it mostly to "historical contingency." That's another way of
>
> > saying "dumb luck."
>
> >
>
> > *****
>
> >
>
> > -by Michael Behe
>
>
>
> You seem to have forgotten to quote what Joe Thornton thought of Behe's
>
> conclusions, so here it is:
>
>
>
> "Thanks for asking for my reaction to Behe's post on our recent paper
>
> in Nature. His interpretation of our work is incorrect. He confuses
>
> "contingent" or "unlikely" with "impossible."

Behe accurately defined contingency as "dumb luck".

As for "unlikely" vs "impossible":
That's a vaporous argument without the NUMBERS to determine HOW unlikely.
And that's what Behe's The Edge of Evolution is all about - the numbers.

> He ignores the key role
>
> of genetic drift in evolution.

"Genetic drift" is another term for "dumb luck", the invisible guiding hand behind Darwin's ghost.

> And he erroneously concludes that
>
> because the probability is low that some specific biological form will
>
> evolve, it must be impossible for ANY form to evolve.

Without putting words into Behe's mouth, I submit that he is saying:
'because the probability is low that some specific biological form will
evolve, it must be impossible for the MANY forms of functional protein to evolve.'

Finally Evolutionists are running into the brick wall that they have so ardently claimed as
their own - SCIENCE - true, factual science.
Science has finally got to the point where Thornton can carry out his experiments - as Behe
pointed out, this is the first experiment of its kind. There are MANY more protein mutation
experiments coming down the pipeline, which will throw more shit on Darwin.

>
>
>
> "Behe contends that our findings support his argument that adaptations
>
> requiring more than one mutation cannot evolve by Darwinian processes.

I think that is more than TWO mutations, if I remember correctly...
>
> The many errors in Behe's Edge of Evolution -- the book in which he
>
> makes this argument -- have been discussed in numerous publications.

And which 'error' is he referring to in this case?

>
>
>
> "In his posts about our paper, Behe's first error is to ignore the fact
>
> that adaptive combinations of mutations can and do evolve by pathways
>
> involving neutral intermediates.

But there's only a SLIM chance of that.
Again, that's what Behe's book 'The Edge of Evolution' is all about; looking at the
quantitative chance of a particular mutation showing up in a population.

> Behe says that if it takes more than
>
> one mutation to produce even a crude version of the new protein
>
> function, then selection cannot drive acquisition of the adaptive
>
> combination."

This guy either doesn't know how to read, or is intentionally misrepresenting Behe's
claim.
He never claimed that 'more than ONE mutation is impossible'. He claimed that
more than TWO simultaneous mutations is improbable enough to be considered
mathematically impossible.

If i remember correctly...
>
>
>
>
>
> --
>
> athel

[Steady Eddie]

On Friday, 1 August 2014 11:03:42 UTC-6, jillery wrote:
> On Fri, 1 Aug 2014 09:30:06 -0700 (PDT), Steady Eddie
>
>
>
>

You make a very good point.
What specific events are you referring to?
When did the specific protein under investigation evolve?
How? What was the mechanism?

Without these details, 'contingency' still equals 'dumb luck', the guiding hand of Darwin's ghost.

[Bob Casanova]

On Fri, 1 Aug 2014 18:47:38 +0200, the following appeared in
talk.origins, posted by Athel Cornish-Bowden
<acor...@imm.cnrs.fr>:

Thanks for the context.

Gee, Eddie, nice petard you have there...
--

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

[jillery]

Perhaps you should read his book.

[Greg Guarino]

I just computed the odds of dealing a particular pair of ten-card hands
for gin rummy (in order). It is roughly one in 3 x 10^32. This is of
course more hands of gin rummy than have ever been dealt, or ever will
be dealt, by a tremendous multiple. But every time you deal the cards,
you have produced an arrangement with those spectacularly low odds.

I have no doubt that the odds for the evolution of the Yellow-Banded
Poison Arrow Frog from a distant ancestor species are similarly
unlikely; unlikely enough that we could consider it impossible for that
set of evolutionary steps to be repeated. Perhaps the same could be said
of the evolution of a particular protein.

But if we deal two hands of Gin, SOME combination of cards will result;
the probability of that outcome is in fact 1. And unless a lineage goes
extinct, SOME *working* organism will be produced. The chance that it
will be the Yellow-Banded Poison Arrow Frog is infinitesimal, but it
will be an organism of some kind.

Behe tries to dodge this by saying that Thornton's lab tried "thousands"
of permutations, none of which could perform the same function; the
"target" function is then "particular", like a particular hand of cards.
But life has no requirement to produce the Yellow-Banded Poison Arrow
Frog, or a particular enzyme, or even a particular function; it need
only produce creatures that survive and reproduce.

The inventory of life on Earth is not a predetermined set of species and
features; it is those working combinations that HAVE been able to be
"reached" by evolutionary processes.

---
This email is free from viruses and malware because avast! Antivirus protection is active.
http://www.avast.com

[jillery]

Wrong again. Historical contingency has nothing to do with dumb luck.
Nor do I need to refer to any specific events or proteins.

You seem to recognize that living organisms have some genome sequence
from the past. It's that sequence, modified in past generations
according to the environment of those generations, that is modified
according to the environment of the present generation.

[jillery]

On Fri, 01 Aug 2014 10:21:03 -0700, Bob Casanova <nos...@buzz.off>
wrote:

Maybe he's just happy to see you.

[Steady Eddie]

On Friday, 1 August 2014 11:26:04 UTC-6, jillery wrote:
> On Fri, 1 Aug 2014 10:09:58 -0700 (PDT), Steady Eddie
>
>
>
>

Why, am I wrong?

[RSNorman]

On Fri, 01 Aug 2014 13:35:58 -0400, Greg Guarino <gdgu...@gmail.com>
wrote:

Finally an explanation of the probability fallacy that is on the mark.
Thank you for that. Too many people argue "gee, this particular deal
of cards is exceptionally unlikely but I just got it. Events of
extremely low probability really do happen!" You hit it exactly: the
point is not the probability of "this particular" hand but the
probability of geting "some" hand which is actually 1.0 (not counting
the dealer being hit by lightening before finishing the deal),.

You also describe exactly the misapplication of probability to
evolution. "What is the probability of hemoglobin?" must be replaced
by "what is the probability of some amino acid sequence binding to
some cofactors that can bind oxygen reversibly, no matter how weakly?"

[broger...@gmail.com]

On Friday, August 1, 2014 2:00:36 PM UTC-4, Steady Eddie wrote:

> Why, am I wrong?

[Eddie, I'm just using your response as a springboard. I'm not writing for you, so, no need to reply, I'll be happy to stipulate that my post made you LOL and confirmed your belief that I'm an idiot.]

Contingency versus determinism in evolution is about the question of to what extent if you re-ran the history of life from the beginning, you would end up with the same suite of organisms that we have now. Virtually every biologist who thinks about this says "No" if you ask the question in the broadest possible terms. However, the question remains whether some sorts of organisms or particular proteins are such "good tricks" that they, or something very like them would be likely to recur. So, there seems little question that the particular arrangement of the mammalian eye is "contingent" in that the particular form it takes depends on chance events that happened early in the lineage that ultimately led to mammals. On the other hand, evolution of some form of focusing eye sensitive to light in the range of wavelengths most strongly delivered to earth from the sun may be pretty much a deterministic outcome. That's what Thornton means when he talks about contingency versus determinism.

In his particular case of the GC receptor, he was curious if there were alternate routes to the modern GC receptor from the reconstructed primordial GC receptor. He couldn't find any. That means that the modern GC receptor is contingent in the sense I described above; the form of the modern GC receptor depends on the particular primordial GC receptor that it started to evolve from. That does not mean that SOME possible modern GC receptor is highly unlikely to evolve, or that divine intervention is required to produce it. It only means that not all roads lead to Rome; if we had started with a different primordial GC receptor, or had not happened to accumulate the required neutral mutations, we'd have ended up with a different modern GC receptor.

[John Bode]

"Dumb luck" doesn't exactly help Behe's case, though.

The way I understand it, you have a neutral (or nearly neutral) mutation in
an individual; this neutral mutation is passed on to that individual's offspring
without affecting their overall fitness (it's not subject to selection in the
Darwinian sense).

One of that individual's descendants then has a second mutation that, together
with the ancestral mutation, leads to a new function. This new function didn't
arise as a result of Darwinian selection; however, it will be selected for
(or against, depending on environment) going forward.

IINM, something similar happened with Lenski's citrate-digesting E. coli.

[RSNorman]

On Fri, 1 Aug 2014 10:09:58 -0700 (PDT), Steady Eddie

<1914o...@gmail.com> wrote:

<snip to get to one important point>

>"Genetic drift" is another term for "dumb luck", the invisible guiding hand behind Darwin's ghost.

That hand is by no means invisible except to those ignorant of biology
and evolution.

Some people may object to the pejorative phrase "dumb luck" but it
really just means "outcome of a random process". The word "Darwinism"
or "Darwinistic evolution" is often applied strictly to the selection
part of evolution. However selection requires variability and random
processes, mutations, are the foundation for variation. And mutations
are, indeed, "blind" or "dumb luck". The chance of having your first
child a girl rather than a boy is also "dumb luck" (if you use the
usual method of internal fertilization and conception). That doesn't
mean it doesn't extremely frequently. It is a historical contingency
(what you call "dumb luck") that Queen Elizabeth II has a younger
sister and no brothers and so inherited the royal title. In other
words, she is queen by dumb luck.

By railing against "dumb luck" you are simply echoing a standard
creationist objection to science in general, the mindless working out
of the universe according to the laws of science rather than the
infinite intelligence and guidig hand of the creator.

[Steady Eddie]

Which primordial GC receptor do you have in mind as the evolutionary precursor to the modern one?

[Steady Eddie]

On Friday, 1 August 2014 12:31:22 UTC-6, John Bode wrote:
> On Friday, August 1, 2014 11:30:06 AM UTC-5, Steady Eddie wrote:
>
> > From Thornton's Lab, More Strong Experimental Support for a Limit to
>
> > Darwinian Evolution
>
> >
>
> > *****
>
> >
>
> > Thornton himself -- apparently a conventional Darwinist, and certainly no
>
> > sympathizer with intelligent design -- does not attribute the protein
>
> > receptor's new function to Darwinian processes. Rather, he ascribes it mostly
>
> > to "historical contingency." That's another way of saying "dumb luck."
>
> >
>
> > *****
>
> >
>
> > -by Michael Behe
>
>
>
> "Dumb luck" doesn't exactly help Behe's case, though.
>
>
>
> The way I understand it, you have a neutral (or nearly neutral) mutation in
>
> an individual; this neutral mutation is passed on to that individual's offspring

Why would NEUTRAL mutations be passed on to that individual's offspring?
Neutral mutations are automatically overwhelmed and cancelled out in the gene pool
by the sheer numbers of the original allele.
Remember: NEUTRAL means UNSELECTED.

[Steady Eddie]

On Friday, 1 August 2014 12:40:39 UTC-6, RSNorman wrote:
> On Fri, 1 Aug 2014 10:09:58 -0700 (PDT), Steady Eddie
>
>
>
>

> <snip to get to one important point>
>
>
>
> >"Genetic drift" is another term for "dumb luck", the invisible guiding hand behind Darwin's ghost.
>
>
>
> That hand is by no means invisible except to those ignorant of biology
>
> and evolution.
>
>
>
> Some people may object to the pejorative phrase "dumb luck" but it
>
> really just means "outcome of a random process". The word "Darwinism"
>
> or "Darwinistic evolution" is often applied strictly to the selection
>
> part of evolution. However selection requires variability and random
>
> processes, mutations, are the foundation for variation. And mutations
>
> are, indeed, "blind" or "dumb luck". The chance of having your first
>
> child a girl rather than a boy is also "dumb luck" (if you use the
>
> usual method of internal fertilization and conception). That doesn't
>
> mean it doesn't extremely frequently.

That's the rub, isn't it? Speculation about the frequency of an occurrence is easy;
facing the FACTS about the frequency of an occurrence is not so easy.
And it's called SCIENCE. You should read up on it some time.

[broger...@gmail.com]

You would know if you'd actually read Thornton's paper, or, since this one is firewalled, any of the several earlier ones in which he described reconstruction of a primordial GC receptor. Now you would think that his work in reconstructing this primordial GC receptor was shot through with Darwinian assumptions, but if his work is therefore invalid, so are Behe's arguments which are based on Thornton's work. So, choose your poison.

[Greg Guarino]

On 8/1/2014 2:46 PM, Steady Eddie wrote:

> Why would NEUTRAL mutations be passed on to that individual's offspring?

I likely have at least several dozen mutations in my DNA; "letters" that
do not match either my mother's or father's genome at those sites. None
of them were fatal, and none of them have prevented me from reproducing.

Even though we could describe those mutations as "copying errors", they
are nonetheless part of my genome now; copied (mostly) faithfully
trillions of times into the cells in my body, notably including my sperm
cells.

What would prevent (some of) those mutations from being passed on to my
offspring? "Selection" is no answer, as I have successfully reproduced.
Statistically speaking, roughly half a parent's mutations should be
inherited by each child.

[alias Ernest Major]

On 01/08/2014 19:46, Steady Eddie wrote:
> On Friday, 1 August 2014 12:31:22 UTC-6, John Bode wrote:
>> On Friday, August 1, 2014 11:30:06 AM UTC-5, Steady Eddie wrote:
>>
>>> From Thornton's Lab, More Strong Experimental Support for a Limit to
>>
>>> Darwinian Evolution
>>
>>>
>>
>>> *****
>>
>>>
>>
>>> Thornton himself -- apparently a conventional Darwinist, and certainly no
>>
>>> sympathizer with intelligent design -- does not attribute the protein
>>
>>> receptor's new function to Darwinian processes. Rather, he ascribes it mostly
>>
>>> to "historical contingency." That's another way of saying "dumb luck."
>>
>>>
>>
>>> *****
>>
>>>
>>
>>> -by Michael Behe
>>
>>
>>
>> "Dumb luck" doesn't exactly help Behe's case, though.
>>
>>
>>
>> The way I understand it, you have a neutral (or nearly neutral) mutation in
>>
>> an individual; this neutral mutation is passed on to that individual's offspring
>
> Why would NEUTRAL mutations be passed on to that individual's offspring?
> Neutral mutations are automatically overwhelmed and cancelled out in the gene pool
> by the sheer numbers of the original allele.
> Remember: NEUTRAL means UNSELECTED.

Remember: *neutral* means *not subject to selection*. They are not
automatically eliminated from the gene pool. Consider the case of a
mutation rate of 10^-8, and a population size of of 10^20 diploid
organisms. Then in every generation you have roughly 10^12 de novo
mutant individuals, plus half the offspring of the de novo mutant
individuals from the previous generation, and so for generation after
generation. In a sufficiently large population genetic drift is less
effective and mutation pressure become the dominant force is determining
allele frequencies. The frequency depends on the relative probabilities
of the mutation and the reverse mutation (or rather of the sets of
mutations with the same effect of the amino acid sequence, if we're
talking of protein-coding genes).

Consequently the mean proportion of mutants in the population is greater
than the mutation rate, and the odds of sequential or simultaneous
mutations is greater than the odds of simultaneous mutations, by some
factor that depends on the population. My intuition is that over short
periods of time for Plasmodium falciparum the factor is about 2. (Over
sufficiently long periods of time, under conditions in which drift
dominates, the factor is 5*10^7, but I suspect that the sufficiently
long periods of time are longer than is relevant to real populations.)

>>
>> without affecting their overall fitness (it's not subject to selection in the
>>
>> Darwinian sense).
>>
>>
>>
>> One of that individual's descendants then has a second mutation that, together
>>
>> with the ancestral mutation, leads to a new function. This new function didn't
>>
>> arise as a result of Darwinian selection; however, it will be selected for
>>
>> (or against, depending on environment) going forward.
>>
>>
>>
>> IINM, something similar happened with Lenski's citrate-digesting E. coli.
>

--
alias Ernest Major

[Steady Eddie]

That's one of the most idiotic arguments I've heard today.
Come on guys, stick to the science, okay?

[Steady Eddie]

On Friday, 1 August 2014 13:13:44 UTC-6, Greg Guarino wrote:
> On 8/1/2014 2:46 PM, Steady Eddie wrote:
>
>
>
> > Why would NEUTRAL mutations be passed on to that individual's offspring?
>
>
>
> I likely have at least several dozen mutations in my DNA; "letters" that
>
> do not match either my mother's or father's genome at those sites. None
>
> of them were fatal, and none of them have prevented me from reproducing.
>
>
>
> Even though we could describe those mutations as "copying errors", they
>
> are nonetheless part of my genome now; copied (mostly) faithfully
>
> trillions of times into the cells in my body, notably including my sperm
>
> cells.
>
>
>
> What would prevent (some of) those mutations from being passed on to my
>
> offspring? "Selection" is no answer, as I have successfully reproduced.
>
> Statistically speaking, roughly half a parent's mutations should be
>
> inherited by each child.

Yes, then half of that in the next generation, until your particular mutations exponentially approach zero.
Meaning, as your progeny continues to reproduce, your particular mutations get CANCELLED OUT
quite quickly by the original genome in the population (unless, in the case of the wild, a mutation
confers an evolutionary advantage).

[alias Ernest Major]

On 01/08/2014 20:30, Steady Eddie wrote:
>>> Why would NEUTRAL mutations be passed on to that individual's offspring?
>> >
>> >
>> >
>> >I likely have at least several dozen mutations in my DNA; "letters" that
>> >
>> >do not match either my mother's or father's genome at those sites. None
>> >
>> >of them were fatal, and none of them have prevented me from reproducing.
>> >
>> >
>> >
>> >Even though we could describe those mutations as "copying errors", they
>> >
>> >are nonetheless part of my genome now; copied (mostly) faithfully
>> >
>> >trillions of times into the cells in my body, notably including my sperm
>> >
>> >cells.
>> >
>> >
>> >
>> >What would prevent (some of) those mutations from being passed on to my
>> >
>> >offspring? "Selection" is no answer, as I have successfully reproduced.
>> >
>> >Statistically speaking, roughly half a parent's mutations should be
>> >
>> >inherited by each child.

In the "creationists live in a different world" category.

> Yes, then half of that in the next generation, until your particular mutations exponentially approach zero.
> Meaning, as your progeny continues to reproduce, your particular mutations get CANCELLED OUT
> quite quickly by the original genome in the population (unless, in the case of the wild, a mutation
> confers an evolutionary advantage).


--

alias Ernest Major

[jillery]

Yes, on so many levels.

[Greg Guarino]

Hey! That is a reasonable facsimile of a substantive reply. Wrong, but
welcome nonetheless.

You confuse what happens "on average" with what happens to each and
every mutation. Some will spread through the population without selection.

That sounds counterintuitive, doesn't it? I thought so too.

Suppose you have a population of 100 individuals in an asexual species.
Each one reproduces, making two copies of itself. In each generation,
half the population dies, keeping the population at 100 members. Which
ones die is random.

Suppose one of the 100 organisms has a mutation, we'll call it "blue".
The rest are "red". My original intuition told me that the "blue"
mutation would never be able to spread to the whole population.

I was wrong. Want to see it happen? Check this out:

http://meechme.com/beads.html

The program implements the rules I described above. Someone on T.O.
wrote it a ways back.

Set Blue to 1 and Red to 99. Set the others to zero. Click Start.

Watch the numbers of the individual colors. You should see the Blue go
to zero in just a few generations most of the time, as expected. But
sometimes the "blue" number will fluctuate for a longer time, getting up
to higher numbers. Occasionally it will become "fixed", meaning it hits
100. How often is "occasionally"? About 1% of the time. If you let the
experiment go long enough you should get a number of about 1% for "Blue"
fixations.

What if there was only one "Blue" mutation in a population of 1000? Try
it. You'll find the mutation gets fixed approximately .1% of the time.
Are you starting to deduce the rule? (for asexual species). It is much
the same for sexual reproduction, except the mutation gets fixed half as
often (1/2N, where N is the effective population).

[alias Ernest Major]

He has also failed to take into account the fact that the average number
of children is greater than 1. When you take that into account his
description doesn't apply to what happens "on average" either.

--
alias Ernest Major

[deadrat]

On 8/1/14 11:30 AM, Steady Eddie wrote:
> From Thornton's Lab, More Strong Experimental Support for a Limit to Darwinian Evolution
>
>
> *****
> Thornton himself -- apparently a conventional Darwinist, and certainly no sympathizer with intelligent design -- does not attribute the protein receptor's new function to Darwinian processes. Rather, he ascribes it mostly to "historical contingency." That's another way of saying "dumb luck."
>
> *****
>
> -by Michael Behe
>

There a lot of "dumb luck" in survival.

[deadrat]

On 8/1/14 12:09 PM, Steady Eddie wrote:
> On Friday, 1 August 2014 10:47:38 UTC-6, Athel Cornish-Bowden wrote:
>> On 2014-08-01 16:30:06 +0000, Steady Eddie said:
>>
>>
>>
>>> From Thornton's Lab, More Strong Experimental Support for a Limit to
>>
>>> Darwinian Evolution
>>
>>>
>>
>>>
>>
>>> *****
>>
>>> Thornton himself -- apparently a conventional Darwinist, and certainly
>>
>>> no sympathizer with intelligent design -- does not attribute the
>>
>>> protein receptor's new function to Darwinian processes. Rather, he
>>
>>> ascribes it mostly to "historical contingency." That's another way of
>>
>>> saying "dumb luck."
>>
>>>
>>
>>> *****
>>
>>>
>>
>>> -by Michael Behe
>>
>>
>>
>> You seem to have forgotten to quote what Joe Thornton thought of Behe's
>>
>> conclusions, so here it is:
>>
>>
>>
>> "Thanks for asking for my reaction to Behe's post on our recent paper
>>
>> in Nature. His interpretation of our work is incorrect. He confuses
>>
>> "contingent" or "unlikely" with "impossible."
>
> Behe accurately defined contingency as "dumb luck".

You don't think luck isn't involved? What would've happened to you if
your mother hadn't dropped you on your head when you were an infant?

> As for "unlikely" vs "impossible":
> That's a vaporous argument without the NUMBERS to determine HOW unlikely.
> And that's what Behe's The Edge of Evolution is all about - the numbers.

The wrong numbers, but numbers nevertheless.

>> He ignores the key role
>>
>> of genetic drift in evolution.
>
> "Genetic drift" is another term for "dumb luck", the invisible guiding hand behind Darwin's ghost.

It's called probability. Another thing you apparently know nothing about.

>> And he erroneously concludes that
>>
>> because the probability is low that some specific biological form will
>>
>> evolve, it must be impossible for ANY form to evolve.
> Without putting words into Behe's mouth, I submit that he is saying:
> 'because the probability is low that some specific biological form will
> evolve, it must be impossible for the MANY forms of functional protein to evolve.'

Cite?

> Finally Evolutionists are running into the brick wall that they have so ardently claimed as
> their own - SCIENCE - true, factual science.
> Science has finally got to the point where Thornton can carry out his experiments - as Behe
> pointed out, this is the first experiment of its kind. There are MANY more protein mutation
> experiments coming down the pipeline, which will throw more shit on Darwin.

Cite?

>> "Behe contends that our findings support his argument that adaptations
>>
>> requiring more than one mutation cannot evolve by Darwinian processes.
>
> I think that is more than TWO mutations, if I remember correctly...

So what?

>> The many errors in Behe's Edge of Evolution -- the book in which he
>>
>> makes this argument -- have been discussed in numerous publications.
>
> And which 'error' is he referring to in this case?
>>
>>
>>
>> "In his posts about our paper, Behe's first error is to ignore the fact
>>
>> that adaptive combinations of mutations can and do evolve by pathways
>>
>> involving neutral intermediates.
>
> But there's only a SLIM chance of that.
> Again, that's what Behe's book 'The Edge of Evolution' is all about; looking at the
> quantitative chance of a particular mutation showing up in a population.

Wrong, but quantitative nevertheless.

>> Behe says that if it takes more than
>>
>> one mutation to produce even a crude version of the new protein
>>
>> function, then selection cannot drive acquisition of the adaptive
>>
>> combination."
>
> This guy either doesn't know how to read, or is intentionally misrepresenting Behe's
> claim.
> He never claimed that 'more than ONE mutation is impossible'. He claimed that
> more than TWO simultaneous mutations is improbable enough to be considered
> mathematically impossible.
>
> If i remember correctly...

You don't do much "correctly." Neither does Behe. The mutations
needn't be simultaneous.

[deadrat]

On 8/1/14 12:21 PM, Bob Casanova wrote:
> On Fri, 1 Aug 2014 18:47:38 +0200, the following appeared in
> talk.origins, posted by Athel Cornish-Bowden
> <acor...@imm.cnrs.fr>:
>
>> On 2014-08-01 16:30:06 +0000, Steady Eddie said:
>
>>> From Thornton's Lab, More Strong Experimental Support for a Limit to
>>> Darwinian Evolution
>>> *****
>>> Thornton himself -- apparently a conventional Darwinist, and certainly
>>> no sympathizer with intelligent design -- does not attribute the
>>> protein receptor's new function to Darwinian processes. Rather, he
>>> ascribes it mostly to "historical contingency." That's another way of
>>> saying "dumb luck."
>>>
>>> *****
>>>
>>> -by Michael Behe
>
>> You seem to have forgotten to quote what Joe Thornton thought of Behe's
>> conclusions, so here it is:
>>

>> "Thanks for asking for my reaction to Behe�s post on our recent paper

>> in Nature. His interpretation of our work is incorrect. He confuses

>> �contingent� or �unlikely� with �impossible.� He ignores the key role

>> of genetic drift in evolution. And he erroneously concludes that
>> because the probability is low that some specific biological form will
>> evolve, it must be impossible for ANY form to evolve.
>>
>> "Behe contends that our findings support his argument that adaptations
>> requiring more than one mutation cannot evolve by Darwinian processes.

>> The many errors in Behe�s Edge of Evolution � the book in which he
>> makes this argument � have been discussed in numerous publications.
>>
>> "In his posts about our paper, Behe�s first error is to ignore the fact

>> that adaptive combinations of mutations can and do evolve by pathways
>> involving neutral intermediates. Behe says that if it takes more than
>> one mutation to produce even a crude version of the new protein
>> function, then selection cannot drive acquisition of the adaptive
>> combination."
>
> Thanks for the context.
>
> Gee, Eddie, nice petard you have there...
>

Yeah, it would be a shame for someone to get hoisted by it.

Oh, too late.

[RSNorman]

On Fri, 01 Aug 2014 21:21:42 +0100, alias Ernest Major
<{$to$}@meden.demon.co.ukl> wrote:


<snip to isolate one point -- and to eliminate steady's nonsense>

>He has also failed to take into account the fact that the average number
>of children is greater than 1. When you take that into account his
>description doesn't apply to what happens "on average" either.

Average number of children can be tricky. If a population is constant
over time then the average number of offspring per member of the
current population is 1. However for population dynamics in sexually
reproducing populations you often only count females and then the
average number of children per female is 2 and the average number of
female offspring per female is 1. Many females do not reproduce at
all so the average number of total offspring for those females that do
is greater than 2. Still if the population is in replacement mode --
constant number -- then necessarily the average number of offspring
per individual (or the average number of female offspring per female)
is 1.

The fact that not all females reproduce in some species makes the
effective population size smaller than the total number of individuals
and that makes genetic drift more significant. However except in
weird situations like honeybees, it is usually the males who are
divided into a small number of studs vs. a large number of horny
bystanders who lost the battles of sexual selection but are ready and
eager to step in at any opportunity.

[jillery]

Wrong again:

<http://en.wikipedia.org/wiki/Founder_effect>

[Steady Eddie]

On Friday, 1 August 2014 10:30:06 UTC-6, Steady Eddie wrote:
> From Thornton's Lab, More Strong Experimental Support for a Limit to Darwinian Evolution
>
>
>
>
>
> *****
>
> Thornton himself -- apparently a conventional Darwinist, and certainly no sympathizer with intelligent design -- does not attribute the protein receptor's new function to Darwinian processes. Rather, he ascribes it mostly to "historical contingency." That's another way of saying "dumb luck."
>
>
>
> *****
>
>
>
> -by Michael Behe

Sorry, I forgot the link to the article I am discussing:
http://www.evolutionnews.org/2014/06/more_strong_exp087061.html

[Steady Eddie]

On Friday, 1 August 2014 15:00:16 UTC-6, jillery wrote:
> On Fri, 1 Aug 2014 12:30:59 -0700 (PDT), Steady Eddie
>
>
>
>

Off-topic Darwinian bluster and quote-mongering again.

[John Bode]

On Friday, August 1, 2014 1:46:11 PM UTC-5, Steady Eddie wrote:
> On Friday, 1 August 2014 12:31:22 UTC-6, John Bode wrote:
> > On Friday, August 1, 2014 11:30:06 AM UTC-5, Steady Eddie wrote:
> >
> > > From Thornton's Lab, More Strong Experimental Support for a Limit to
> > > Darwinian Evolution
> > >
> > > *****
> > >
> > > Thornton himself -- apparently a conventional Darwinist, and certainly no
> > > sympathizer with intelligent design -- does not attribute the protein
> > > receptor's new function to Darwinian processes. Rather, he ascribes it mostly
> > > to "historical contingency." That's another way of saying "dumb luck."
> > >
> > > *****
> > >
> > > -by Michael Behe
> >
> > "Dumb luck" doesn't exactly help Behe's case, though.
> >
> > The way I understand it, you have a neutral (or nearly neutral) mutation in
> > an individual; this neutral mutation is passed on to that individual's offspring
>
> Why would NEUTRAL mutations be passed on to that individual's offspring?
> Neutral mutations are automatically overwhelmed and cancelled out in the gene pool
> by the sheer numbers of the original allele.
>

You're confusing population genetics with individual genetics. Offspring
will inherit the genome of their parent(s), mutations (neutral or otherwise)
and all. Whether the mutation becomes fixed *in the population over multiple
generations* will depend on how that mutation affects reproductive success.
If the mutation is neutral, it can persist in a subset of the population
for generations.

> Remember: NEUTRAL means UNSELECTED.

No. NEUTRAL means NEITHER BENEFICIAL NOR DELETERIOUS. It doesn't affect
selection.

[jillery]

You're correct:

<http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment>

<http://www.pnas.org/content/105/23/7899.long>


Short version: Lenski's E.coli evolved the ability to metabolize
citrate in oxic conditions (Cit+) shortly after 33,000 generations.
Further analysis identified at least two neutral potentiating
mutations some time after 20,000 generations, followed by several
actualizing and refining mutations following each other relatively
rapidly.

Lenski also cultured samples taken before 20,000 generations and the
potentiating mutations, and before 33,000 generations and the
actualizing mutations. The cultures taken before 20,000 generations
didn't evolve Cit+ again, but the cultures taken before 33,000
generations did. This illustrates that the evolution of Cit+ is
partially historically contingent.

[RSNorman]

You are misstating the population genetics. If the mutation is
neutral, it can grow in the population and become fixed so that every
member carries it. The probability of that happening and the expected
time to fixation are all part of standard population genetics theory.
So to say that a neutral mutation can "persist in a subset of the
population for generations" is very much understating the case.

Genetic drift is extremely important for small populations and plays a
truly major role during population bottlenecks or with founder systems
where a small number of individuals leaves one region to start a new
population elsewhere. Its role is even amplified following mass
extinction events.

The role of genetic drift fixing neutral alleles was originally (a
half century ago) such a departure from classical evolution that it
was called "nonDarwinian evolution" , Darwinian meaning evolution
through selection. However it quickly became part of the standard
notion so that modern evolutionary change is mediated through both
drift and selection. In fact, when you look at the genomic level,
most changes that you see are drift, not selection.

Steady (and probably Behe) completely fails to understand that neutral
mutations can become established and accumulate so that several
neutral mutations can be combined to produce a result that does
increase fitness. In fact with sexual reproduction, the two different
mutations can occur in very different groups and then get assembled
through sexual recombination.

[jillery]

On Fri, 01 Aug 2014 21:21:42 +0100, alias Ernest Major
<{$to$}@meden.demon.co.ukl> wrote:

Steadly also failed to take into account that children don't inherit
probabilities. Each child gets an entire gene, with 100% certainty.

[jillery]

On Fri, 01 Aug 2014 16:38:54 -0400, RSNorman <r_s_n...@comcast.net>
wrote:

The above isn't accurate. Some percentage of the offspring almost
certainly die before they reproduce. If the average number of
offspring were is just one (or two females), the population will
decline.

So it isn't the average number of offspring, but the average number of
offspring surviving to reproduce. Same requirement applies for female
offspring.

[jillery]

On Fri, 1 Aug 2014 14:07:57 -0700 (PDT), Steady Eddie
<1914o...@gmail.com> wrote:

>On Friday, 1 August 2014 15:00:16 UTC-6, jillery wrote:
>> On Fri, 1 Aug 2014 12:30:59 -0700 (PDT), Steady Eddie
>>
>>
>>
>>
>> >On Friday, 1 August 2014 13:13:44 UTC-6, Greg Guarino wrote:

[...]

>> >> What would prevent (some of) those mutations from being passed on to my
>> >> offspring? "Selection" is no answer, as I have successfully reproduced.
>> >> Statistically speaking, roughly half a parent's mutations should be
>> >> inherited by each child.
>>
>> >Yes, then half of that in the next generation, until your particular mutations exponentially approach zero.
>> >Meaning, as your progeny continues to reproduce, your particular mutations get CANCELLED OUT
>> > quite quickly by the original genome in the population (unless, in the case of the wild, a mutation
>> >confers an evolutionary advantage).
>>
>> Wrong again:
>>
>> <http://en.wikipedia.org/wiki/Founder_effect>
>
>Off-topic Darwinian bluster and quote-mongering again.

What the heck is quote-mongering?

Most likely you didn't even read the cite, but if you did, most likely
you didn't understand it.

[RSNorman]

On Fri, 01 Aug 2014 17:59:58 -0400, jillery <69jp...@gmail.com>

That is true and is another reason why counting "average number of
children" is tricky.

In population genetics, offspring that don't themselves contribute to
the gene pool are effectively eliminated from the population. Counting
children who die in infancy as "offspring" is then the equivalent of
counting embryos that die unnoticed or, to go to the extreme case,
counting unfertilized eggs and sperm as "offspring that fail to
survive to reproductive age". Are eggs that are laid but eaten before
hatching really "offspring"? What about external fertilization where
eggs are laid but not fertilized? It really is tricky just how you
count things. We humans define "offspring" as "births" (except those
fundamentalists who try to insist that a fertilized egg must count as
an individual). In that case you are entirely correct.

[Steady Eddie]

On Friday, 1 August 2014 16:03:17 UTC-6, jillery wrote:
> On Fri, 1 Aug 2014 14:07:57 -0700 (PDT), Steady Eddie
>
>
>
>

> >On Friday, 1 August 2014 15:00:16 UTC-6, jillery wrote:
>
> >> On Fri, 1 Aug 2014 12:30:59 -0700 (PDT), Steady Eddie
>
> >>
>
> >>
>
> >>
>
> >>
>
> >> >On Friday, 1 August 2014 13:13:44 UTC-6, Greg Guarino wrote:
>
>
>
> [...]
>
>
>
> >> >> What would prevent (some of) those mutations from being passed on to my
>
> >> >> offspring? "Selection" is no answer, as I have successfully reproduced.
>
> >> >> Statistically speaking, roughly half a parent's mutations should be
>
> >> >> inherited by each child.
>
> >>
>
> >> >Yes, then half of that in the next generation, until your particular mutations exponentially approach zero.
>
> >> >Meaning, as your progeny continues to reproduce, your particular mutations get CANCELLED OUT
>
> >> > quite quickly by the original genome in the population (unless, in the case of the wild, a mutation
>
> >> >confers an evolutionary advantage).
>
> >>
>
> >> Wrong again:
>
> >>
>
> >> <http://en.wikipedia.org/wiki/Founder_effect>
>
> >
>
> >Off-topic Darwinian bluster and quote-mongering again.
>
>
>
>
>
> What the heck is quote-mongering?

Sorry, i was referring to quote-bluffing.

>
>
>
> Most likely you didn't even read the cite, but if you did, most likely
>
> you didn't understand it.

This is pointless. We're just accusing each other of poor reading skills.
Nevertheless, there is my OP, on the record as an example of an experimental
Darwinist who hit the wall...or, at least, grazed it.

[deadrat]

On 8/1/14 12:35 PM, Greg Guarino wrote:

> On 8/1/2014 12:30 PM, Steady Eddie wrote:
>> From Thornton's Lab, More Strong Experimental Support for a Limit to
>> Darwinian Evolution
>>
>>
>> ***** Thornton himself -- apparently a conventional Darwinist, and
>> certainly no sympathizer with intelligent design -- does not
>> attribute the protein receptor's new function to Darwinian processes.
>> Rather, he ascribes it mostly to "historical contingency." That's
>> another way of saying "dumb luck."
>>
>> *****
>>
>> -by Michael Behe
>>

> I just computed the odds of dealing a particular pair of ten-card hands
> for gin rummy (in order). It is roughly one in 3 x 10^32. This is of
> course more hands of gin rummy than have ever been dealt, or ever will
> be dealt, by a tremendous multiple. But every time you deal the cards,
> you have produced an arrangement with those spectacularly low odds.
>
> I have no doubt that the odds for the evolution of the Yellow-Banded
> Poison Arrow Frog from a distant ancestor species are similarly
> unlikely; unlikely enough that we could consider it impossible for that
> set of evolutionary steps to be repeated. Perhaps the same could be said
> of the evolution of a particular protein.
>
> But if we deal two hands of Gin, SOME combination of cards will result;
> the probability of that outcome is in fact 1. And unless a lineage goes
> extinct, SOME *working* organism will be produced. The chance that it
> will be the Yellow-Banded Poison Arrow Frog is infinitesimal, but it
> will be an organism of some kind.
>
> Behe tries to dodge this by saying that Thornton's lab tried "thousands"
> of permutations, none of which could perform the same function; the
> "target" function is then "particular", like a particular hand of cards.
> But life has no requirement to produce the Yellow-Banded Poison Arrow
> Frog, or a particular enzyme, or even a particular function; it need
> only produce creatures that survive and reproduce.
>
> The inventory of life on Earth is not a predetermined set of species and
> features; it is those working combinations that HAVE been able to be
> "reached" by evolutionary processes.

I've said before that a "scientific" cretinist or an IDiot is like
someone playing poker who stands up, triumphantly throws his cards
face-up on the table, yells "Bingo!" and is surprised when the other
players don't give him the pot.

"You can't prove that. Bingo!"
"The Bible tells me so. Bingo!"
"If you don't know the answer, it must be supernatural. Bingo!"
"It looks designed, so there must be a designer. Bingo!"

But here we have another card analogy. Steadfastly is playing gin with
a bunch of "Darwinists." He picks up his hand, looks at it for a
moment, and says, "Wait a minute. The odds against my getting this hand
are impossibly small, about one in 3x10^32. You're cheating!"

[deadrat]

On 8/1/14 1:00 PM, Steady Eddie wrote:
> On Friday, 1 August 2014 11:26:04 UTC-6, jillery wrote:
>> On Fri, 1 Aug 2014 10:09:58 -0700 (PDT), Steady Eddie

>>
>>
>>
>>
>>> On Friday, 1 August 2014 10:47:38 UTC-6, Athel Cornish-Bowden wrote:
>>

>>>> On 2014-08-01 16:30:06 +0000, Steady Eddie said:
>>
>>>>
>>
>>>>
>>
>>>>
>>

>>>>> From Thornton's Lab, More Strong Experimental Support for a Limit to
>>
>>>>
>>
>>>>> Darwinian Evolution
>>
>>>>
>>
>>>>>
>>
>>>>
>>
>>>>>
>>
>>>>
>>
>>>>> *****
>>
>>>>
>>
>>>>> Thornton himself -- apparently a conventional Darwinist, and certainly
>>
>>>>
>>
>>>>> no sympathizer with intelligent design -- does not attribute the
>>
>>>>
>>
>>>>> protein receptor's new function to Darwinian processes. Rather, he
>>
>>>>
>>
>>>>> ascribes it mostly to "historical contingency." That's another way of
>>
>>>>
>>
>>>>> saying "dumb luck."
>>
>>>>
>>
>>>>>
>>
>>>>
>>
>>>>> *****
>>
>>>>
>>
>>>>>
>>
>>>>
>>
>>>>> -by Michael Behe
>>
>>>>
>>
>>>>
>>
>>>>
>>

>>>> You seem to have forgotten to quote what Joe Thornton thought of Behe's
>>
>>>>
>>
>>>> conclusions, so here it is:
>>
>>>>
>>
>>>>
>>
>>>>
>>

>>>> "Thanks for asking for my reaction to Behe's post on our recent paper

>>
>>>>
>>
>>>> in Nature. His interpretation of our work is incorrect. He confuses
>>
>>>>
>>

>>>> "contingent" or "unlikely" with "impossible."
>>
>>>
>>
>>> Behe accurately defined contingency as "dumb luck".
>>
>>>
>>

>>> As for "unlikely" vs "impossible":
>>
>>> That's a vaporous argument without the NUMBERS to determine HOW unlikely.
>>
>>> And that's what Behe's The Edge of Evolution is all about - the numbers.
>>
>>>
>>

>>>> He ignores the key role
>>
>>>>
>>
>>>> of genetic drift in evolution.
>>
>>>
>>

>>> "Genetic drift" is another term for "dumb luck", the invisible guiding hand behind Darwin's ghost.
>>

>>>> And he erroneously concludes that
>>
>>>>
>>
>>>> because the probability is low that some specific biological form will
>>
>>>>
>>
>>>> evolve, it must be impossible for ANY form to evolve.
>>

>>> Without putting words into Behe's mouth, I submit that he is saying:
>>
>>> 'because the probability is low that some specific biological form will
>>
>>> evolve, it must be impossible for the MANY forms of functional protein to evolve.'
>>
>>>
>>

>>> Finally Evolutionists are running into the brick wall that they have so ardently claimed as
>>
>>> their own - SCIENCE - true, factual science.
>>
>>> Science has finally got to the point where Thornton can carry out his experiments - as Behe
>>
>>> pointed out, this is the first experiment of its kind. There are MANY more protein mutation
>>
>>> experiments coming down the pipeline, which will throw more shit on Darwin.
>>
>>>
>>
>>>>
>>
>>>>
>>
>>>>
>>

>>>> "Behe contends that our findings support his argument that adaptations
>>
>>>>
>>
>>>> requiring more than one mutation cannot evolve by Darwinian processes.
>>
>>>
>>

>>> I think that is more than TWO mutations, if I remember correctly...
>>
>>>>
>>

>>>> The many errors in Behe's Edge of Evolution -- the book in which he
>>
>>>>
>>
>>>> makes this argument -- have been discussed in numerous publications.
>>
>>>
>>
>>> And which 'error' is he referring to in this case?
>>
>>>>
>>
>>>>
>>
>>>>
>>

>>>> "In his posts about our paper, Behe's first error is to ignore the fact

>>
>>>>
>>
>>>> that adaptive combinations of mutations can and do evolve by pathways
>>
>>>>
>>
>>>> involving neutral intermediates.
>>
>>>
>>

>>> But there's only a SLIM chance of that.
>>
>>> Again, that's what Behe's book 'The Edge of Evolution' is all about; looking at the
>>
>>> quantitative chance of a particular mutation showing up in a population.
>>
>>>
>>

>>>> Behe says that if it takes more than
>>
>>>>
>>
>>>> one mutation to produce even a crude version of the new protein
>>
>>>>
>>
>>>> function, then selection cannot drive acquisition of the adaptive
>>
>>>>
>>
>>>> combination."
>>
>>>
>>

>>> This guy either doesn't know how to read, or is intentionally misrepresenting Behe's
>>
>>> claim.
>>
>>> He never claimed that 'more than ONE mutation is impossible'. He claimed that
>>
>>> more than TWO simultaneous mutations is improbable enough to be considered
>>
>>> mathematically impossible.
>>
>>>
>>
>>> If i remember correctly...
>>
>>
>>
>>
>>

>> Perhaps you should read his book.
>
> Why, am I wrong?

No doubt. But you should really ask yourself the question with the
comma removed.

[RSNorman]

On Fri, 1 Aug 2014 11:52:54 -0700 (PDT), Steady Eddie
<1914o...@gmail.com> wrote:

>On Friday, 1 August 2014 12:40:39 UTC-6, RSNorman wrote:
>> On Fri, 1 Aug 2014 10:09:58 -0700 (PDT), Steady Eddie
>>
>>
>>
>>

>> <snip to get to one important point>

>>
>>
>>
>> >"Genetic drift" is another term for "dumb luck", the invisible guiding hand behind Darwin's ghost.
>>
>>
>>

>> That hand is by no means invisible except to those ignorant of biology
>>
>> and evolution.
>>
>>
>>
>> Some people may object to the pejorative phrase "dumb luck" but it
>>
>> really just means "outcome of a random process". The word "Darwinism"
>>
>> or "Darwinistic evolution" is often applied strictly to the selection
>>
>> part of evolution. However selection requires variability and random
>>
>> processes, mutations, are the foundation for variation. And mutations
>>
>> are, indeed, "blind" or "dumb luck". The chance of having your first
>>
>> child a girl rather than a boy is also "dumb luck" (if you use the
>>
>> usual method of internal fertilization and conception). That doesn't
>>
>> mean it doesn't extremely frequently.
>
>That's the rub, isn't it? Speculation about the frequency of an occurrence is easy;
>facing the FACTS about the frequency of an occurrence is not so easy.
>And it's called SCIENCE. You should read up on it some time.
>

What are the FACTS about the frequency of an occurence. Pick one of
your choice and you tell me a number along with all the FACTS about
how you derived that number.

Scientists do this kind of calculation frequently. You might also
read, for example, Greg Guarino's post about how creationists and
IDers abuse probability theory. You should also consider the correct
method of calculating the probability of two mutations occuring in any
one individual even if those two are neutral in isolation.

[deadrat]

On 8/1/14 1:40 PM, Steady Eddie wrote:
> On Friday, 1 August 2014 12:25:26 UTC-6, broger...@gmail.com wrote:
>> On Friday, August 1, 2014 2:00:36 PM UTC-4, Steady Eddie wrote:
>>
>>
>>
>>> Why, am I wrong?
>>
>>
>>
>> [Eddie, I'm just using your response as a springboard. I'm not writing for you, so, no need to reply, I'll be happy to stipulate that my post made you LOL and confirmed your belief that I'm an idiot.]
>>
>>
>>
>> Contingency versus determinism in evolution is about the question of to what extent if you re-ran the history of life from the beginning, you would end up with the same suite of organisms that we have now. Virtually every biologist who thinks about this says "No" if you ask the question in the broadest possible terms. However, the question remains whether some sorts of organisms or particular proteins are such "good tricks" that they, or something very like them would be likely to recur. So, there seems little question that the particular arrangement of the mammalian eye is "contingent" in that the particular form it takes depends on chance events that happened early in the lineage that ultimately led to mammals. On the other hand, evolution of some form of focusing eye sensitive to light in the range of wavelengths most strongly delivered to earth from the sun may be pretty much a deterministic outcome. That's what Thornton means when he talks about contingency versus det
erminism.

>>
>>
>>
>> In his particular case of the GC receptor, he was curious if there were alternate routes to the modern GC receptor from the reconstructed primordial GC receptor. He couldn't find any. That means that the modern GC receptor is contingent in the sense I described above; the form of the modern GC receptor depends on the particular primordial GC receptor that it started to evolve from. That does not mean that SOME possible modern GC receptor is highly unlikely to evolve, or that divine intervention is required to produce it. It only means that not all roads lead to Rome; if we had started with a different primordial GC receptor, or had not happened to accumulate the required neutral mutations, we'd have ended up with a different modern GC receptor.
>
> Which primordial GC receptor do you have in mind as the evolutionary precursor to the modern one?
>

Which Feynman diagrams explain how you read your screen?

[jillery]

On Fri, 1 Aug 2014 16:22:47 -0700 (PDT), Steady Eddie
<1914o...@gmail.com> wrote:

>On Friday, 1 August 2014 16:03:17 UTC-6, jillery wrote:
>> On Fri, 1 Aug 2014 14:07:57 -0700 (PDT), Steady Eddie
>>
>>
>>
>>
>> >On Friday, 1 August 2014 15:00:16 UTC-6, jillery wrote:
>>
>> >> On Fri, 1 Aug 2014 12:30:59 -0700 (PDT), Steady Eddie
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >>
>>
>> >> >On Friday, 1 August 2014 13:13:44 UTC-6, Greg Guarino wrote:
>>
>>
>>
>> [...]
>>
>>
>>
>> >> >> What would prevent (some of) those mutations from being passed on to my
>>
>> >> >> offspring? "Selection" is no answer, as I have successfully reproduced.
>>
>> >> >> Statistically speaking, roughly half a parent's mutations should be
>>
>> >> >> inherited by each child.
>>
>> >>
>>
>> >> >Yes, then half of that in the next generation, until your particular mutations exponentially approach zero.
>>
>> >> >Meaning, as your progeny continues to reproduce, your particular mutations get CANCELLED OUT
>>
>> >> > quite quickly by the original genome in the population (unless, in the case of the wild, a mutation
>>
>> >> >confers an evolutionary advantage).
>>
>> >>
>>
>> >> Wrong again:
>>
>> >>
>>
>> >> <http://en.wikipedia.org/wiki/Founder_effect>
>>
>> >
>>
>> >Off-topic Darwinian bluster and quote-mongering again.
>>
>>
>>
>>
>>
>> What the heck is quote-mongering?
>
>Sorry, i was referring to quote-bluffing.

What the heck is quote-bluffing?

>> Most likely you didn't even read the cite, but if you did, most likely
>>
>> you didn't understand it.
>
>This is pointless. We're just accusing each other of poor reading skills.

There is a difference. I posted relevant comments and accurate
summaries.

>Nevertheless, there is my OP, on the record as an example of an experimental
>Darwinist who hit the wall...or, at least, grazed it.

A vague reference and a quote is nothing to brag about, but you get a
brownie point for not LOLing anywhere in the topic.

[deadrat]

On 8/1/14 1:46 PM, Steady Eddie wrote:
> On Friday, 1 August 2014 12:31:22 UTC-6, John Bode wrote:
>> On Friday, August 1, 2014 11:30:06 AM UTC-5, Steady Eddie wrote:
>>

>>> From Thornton's Lab, More Strong Experimental Support for a Limit to
>>
>>> Darwinian Evolution
>>
>>>
>>
>>> *****
>>
>>>
>>
>>> Thornton himself -- apparently a conventional Darwinist, and certainly no
>>
>>> sympathizer with intelligent design -- does not attribute the protein
>>
>>> receptor's new function to Darwinian processes. Rather, he ascribes it mostly
>>
>>> to "historical contingency." That's another way of saying "dumb luck."
>>
>>>
>>
>>> *****
>>
>>>
>>
>>> -by Michael Behe
>>
>>
>>

>> "Dumb luck" doesn't exactly help Behe's case, though.
>>
>>
>>
>> The way I understand it, you have a neutral (or nearly neutral) mutation in
>>

>> an individual; this neutral mutation is passed on to that individual's offspring

>
> Why would NEUTRAL mutations be passed on to that individual's offspring?

Why wouldn't they?

> Neutral mutations are automatically overwhelmed and cancelled out in the gene pool
> by the sheer numbers of the original allele.

Could we see your computations? Show your work. Be sure to take
account of population size.

> Remember: NEUTRAL means UNSELECTED.

Neutral means on the whole having no advantage or disadvantage in the
environment, and implies not selected for or against.

<snip/>

[deadrat]

On 8/1/14 1:52 PM, Steady Eddie wrote:
> On Friday, 1 August 2014 12:40:39 UTC-6, RSNorman wrote:
>> On Fri, 1 Aug 2014 10:09:58 -0700 (PDT), Steady Eddie
>>
>>
>>
>>
>> <snip to get to one important point>
>>
>>
>>
>>> "Genetic drift" is another term for "dumb luck", the invisible guiding hand behind Darwin's ghost.
>>
>>
>>
>> That hand is by no means invisible except to those ignorant of biology
>>
>> and evolution.
>>
>>
>>
>> Some people may object to the pejorative phrase "dumb luck" but it
>>
>> really just means "outcome of a random process". The word "Darwinism"
>>
>> or "Darwinistic evolution" is often applied strictly to the selection
>>
>> part of evolution. However selection requires variability and random
>>
>> processes, mutations, are the foundation for variation. And mutations
>>
>> are, indeed, "blind" or "dumb luck". The chance of having your first
>>
>> child a girl rather than a boy is also "dumb luck" (if you use the
>>
>> usual method of internal fertilization and conception). That doesn't
>>
>> mean it doesn't extremely frequently.
>
> That's the rub, isn't it? Speculation about the frequency of an occurrence is easy;
> facing the FACTS about the frequency of an occurrence is not so easy.
> And it's called SCIENCE. You should read up on it some time.

Says Steadfastly, who won't read anything presented to him.

[Glenn]

"Steady Eddie" <1914o...@gmail.com> wrote in message news:d1ef609b-6a7e-4099...@googlegroups.com...

> On Friday, 1 August 2014 10:47:38 UTC-6, Athel Cornish-Bowden wrote:
>> On 2014-08-01 16:30:06 +0000, Steady Eddie said:
>>
>>
>>

>> > From Thornton's Lab, More Strong Experimental Support for a Limit to
>>
>> > Darwinian Evolution
>>
>> >
>>
>> >
>>
>> > *****
>>
>> > Thornton himself -- apparently a conventional Darwinist, and certainly
>>
>> > no sympathizer with intelligent design -- does not attribute the
>>
>> > protein receptor's new function to Darwinian processes. Rather, he
>>
>> > ascribes it mostly to "historical contingency." That's another way of
>>
>> > saying "dumb luck."
>>
>> >
>>
>> > *****
>>
>> >
>>
>> > -by Michael Behe
>>
>>
>>

>> You seem to have forgotten to quote what Joe Thornton thought of Behe's
>>
>> conclusions, so here it is:
>>
>>
>>
>> "Thanks for asking for my reaction to Behe's post on our recent paper
>>
>> in Nature. His interpretation of our work is incorrect. He confuses
>>
>> "contingent" or "unlikely" with "impossible."
>
> Behe accurately defined contingency as "dumb luck".
>
> As for "unlikely" vs "impossible":
> That's a vaporous argument without the NUMBERS to determine HOW unlikely.
> And that's what Behe's The Edge of Evolution is all about - the numbers.
>
>> He ignores the key role
>>
>> of genetic drift in evolution.
>

> "Genetic drift" is another term for "dumb luck", the invisible guiding hand behind Darwin's ghost.

Of course he is. If he didn't, he'd have to agree, and that would blackball him.

> He never claimed that 'more than ONE mutation is impossible'. He claimed that
> more than TWO simultaneous mutations is improbable enough to be considered
> mathematically impossible.
>
> If i remember correctly...
>>
>>
>>
>>
>>

>> --
>>
>> athel
>

[deadrat]

Translation: I either didn't read or read and failed to understand the
refutation of my claim.

fail #(n++)

[deadrat]

On 8/1/14 6:22 PM, Steady Eddie wrote:
> On Friday, 1 August 2014 16:03:17 UTC-6, jillery wrote:
>> On Fri, 1 Aug 2014 14:07:57 -0700 (PDT), Steady Eddie
>>
>>
>>
>>
>>> On Friday, 1 August 2014 15:00:16 UTC-6, jillery wrote:
>>
>>>> On Fri, 1 Aug 2014 12:30:59 -0700 (PDT), Steady Eddie
>>
>>>>
>>
>>>>
>>
>>>>
>>
>>>>
>>
>>>>> On Friday, 1 August 2014 13:13:44 UTC-6, Greg Guarino wrote:
>>
>>
>>
>> [...]
>>
>>
>>
>>>>>> What would prevent (some of) those mutations from being passed on to my
>>
>>>>>> offspring? "Selection" is no answer, as I have successfully reproduced.
>>
>>>>>> Statistically speaking, roughly half a parent's mutations should be
>>
>>>>>> inherited by each child.
>>
>>>>
>>
>>>>> Yes, then half of that in the next generation, until your particular mutations exponentially approach zero.
>>
>>>>> Meaning, as your progeny continues to reproduce, your particular mutations get CANCELLED OUT
>>
>>>>> quite quickly by the original genome in the population (unless, in the case of the wild, a mutation
>>
>>>>> confers an evolutionary advantage).
>>
>>>>
>>
>>>> Wrong again:
>>
>>>>
>>
>>>> <http://en.wikipedia.org/wiki/Founder_effect>
>>
>>>
>>
>>> Off-topic Darwinian bluster and quote-mongering again.
>>
>>
>>
>>
>>
>> What the heck is quote-mongering?
>
> Sorry, i was referring to quote-bluffing.

To call a quote-bluff, you actually have to read and understand the
quote. Clearly the latter obtained; most likely both.

>
>> Most likely you didn't even read the cite, but if you did, most likely
>>
>> you didn't understand it.
>
> This is pointless. We're just accusing each other of poor reading skills.

For values of poor equal to not reading.

> Nevertheless, there is my OP, on the record as an example of an experimental
> Darwinist who hit the wall...or, at least, grazed it.

You didn't even read your own cite in your OP, did you?

You certainly didn't read the explanations of why it doesn't say what
you claimed.

[broger...@gmail.com]

On Friday, August 1, 2014 3:25:48 PM UTC-4, Steady Eddie wrote:

> > > Which primordial GC receptor do you have in mind as the evolutionary precursor to the modern one?

> > You would know if you'd actually read Thornton's paper, or, since this one is firewalled, any of the several earlier ones in which he described reconstruction of a primordial GC receptor. Now you would think that his work in reconstructing this primordial GC receptor was shot through with Darwinian assumptions, but if his work is therefore invalid, so are Behe's arguments which are based on Thornton's work. So, choose your poison.
>
>
>
> That's one of the most idiotic arguments I've heard today.
>
> Come on guys, stick to the science, okay?

Well, it's odd that you post about Thornton's work and yet don't know about the reconstruction of the ancient GC receptor that is critical to that work. In fact, I doubt you could describe, in your own words, the approach he took to making and then validating the reconstruction. Prove me wrong, if you like.

But even odder is the fact that you seem skeptical of the reconstruction. Your man Behe is perfectly fine with Thornton's reconstruction. And, indeed, Behe's argument depends critically on the assumption that Thornton's reconstruction was correct. I keep getting the impression that not only don't you understand the theory of evolution, you don't even understand the arguments advanced by the ID crowd whose sites you keep linking to.

[Glenn]

<broger...@gmail.com> wrote in message news:cba4c0d2-7c24-40a0...@googlegroups.com...

> On Friday, August 1, 2014 3:25:48 PM UTC-4, Steady Eddie wrote:
>
>> > > Which primordial GC receptor do you have in mind as the evolutionary precursor to the modern one?
>
>> > You would know if you'd actually read Thornton's paper, or, since this one is firewalled, any of the several earlier ones in which he described reconstruction of a primordial GC receptor. Now you would think that his work in reconstructing this primordial GC receptor was shot through with Darwinian assumptions, but if his work is therefore invalid, so are Behe's arguments which are based on Thornton's work. So, choose your poison.

Note the question was not answered.
>>
"The immediate, obvious implication (which he clearly wants to keep far away from) is that the 2009 results render problematic even pretty small changes in structure/function for all proteins - not just the ones he worked on. (Thornton himself is betting on this: "We predict that future investigations, like ours, will support a molecular version of Dollo's law: as evolution proceeds, shifts in protein structure-function relations become increasingly difficult to reverse whenever those shifts have complex architectures..") (1) So how, other than begging the question, are we now to know that even the small differences we see in related protein systems came about by random mutation/selection (and, yes, drift)? Quite simply, we can't. Yet if even small changes are problematic, then larger changes will be prohibitive, and very big changes essentially unattainable. Thanks to Thornton's impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed."

http://behe.uncommondescent.com/page/2/

>>
>> That's one of the most idiotic arguments I've heard today.
>>
>> Come on guys, stick to the science, okay?

Good luck with getting evolutionists to stick to anything.

>
> Well, it's odd that you post about Thornton's work and yet don't know about the reconstruction of the ancient GC receptor that is critical to that work. In fact, I doubt you could describe, in your own words, the approach he took to making and then validating the reconstruction. Prove me wrong, if you like.
>
> But even odder is the fact that you seem skeptical of the reconstruction. Your man Behe is perfectly fine with Thornton's reconstruction. And, indeed, Behe's argument depends critically on the assumption that Thornton's reconstruction was correct. I keep getting the impression that not only don't you understand the theory of evolution, you don't even understand the arguments advanced by the ID crowd whose sites you keep linking to.
>

Childish rhetoric.

[Glenn]

"RSNorman" <r_s_n...@comcast.net> wrote in message news:3caot9pr7qofe17sm...@4ax.com...

> On Fri, 1 Aug 2014 11:52:54 -0700 (PDT), Steady Eddie

snip

>>
>>That's the rub, isn't it? Speculation about the frequency of an occurrence is easy;
>>facing the FACTS about the frequency of an occurrence is not so easy.
>>And it's called SCIENCE. You should read up on it some time.
>>
>
> What are the FACTS about the frequency of an occurence. Pick one of
> your choice and you tell me a number along with all the FACTS about
> how you derived that number.
>
> Scientists do this kind of calculation frequently. You might also
> read, for example, Greg Guarino's post about how creationists and
> IDers abuse probability theory. You should also consider the correct
> method of calculating the probability of two mutations occuring in any
> one individual even if those two are neutral in isolation.
>

I do not have access to Nature. Two news sources use this language:

"Thornton and Harms tested many thousands of variants but found none that restored the function of GR other than the historical mutations that occurred in actuality. "Among the huge numbers of alternate possible histories, there were no other permissive mutations that could have opened an evolutionary path to the modern-day GR," Thornton said."

"other than the historical mutations"...
"there were no other permissive mutations"...

I would like to know if these test subjects did gain the historical mutations and had the function of GR restored.
If that did not happen, the statement is misleading, and I would wonder why.

[Chris Thompson]

On 8/1/2014 3:30 PM, Steady Eddie wrote:
> On Friday, 1 August 2014 13:13:44 UTC-6, Greg Guarino wrote:

>> On 8/1/2014 2:46 PM, Steady Eddie wrote:
>>
>>
>>
>>> Why would NEUTRAL mutations be passed on to that individual's offspring?
>>
>>
>>
>> I likely have at least several dozen mutations in my DNA; "letters" that
>>
>> do not match either my mother's or father's genome at those sites. None
>>
>> of them were fatal, and none of them have prevented me from reproducing.
>>
>>
>>
>> Even though we could describe those mutations as "copying errors", they
>>
>> are nonetheless part of my genome now; copied (mostly) faithfully
>>
>> trillions of times into the cells in my body, notably including my sperm
>>
>> cells.
>>
>>
>>

>> What would prevent (some of) those mutations from being passed on to my
>>
>> offspring? "Selection" is no answer, as I have successfully reproduced.
>>
>> Statistically speaking, roughly half a parent's mutations should be
>>
>> inherited by each child.
>
> Yes, then half of that in the next generation, until your particular mutations exponentially approach zero.
> Meaning, as your progeny continues to reproduce, your particular mutations get CANCELLED OUT
> quite quickly by the original genome in the population (unless, in the case of the wild, a mutation
> confers an evolutionary advantage).

I was going to post a one-liner about just how profoundly you're
misunderstanding things but that's pointless.

Please think on what you wrote here. You are NOT describing something
that's "unselected" (as you wrote in a different post). You are
describing (without realizing it) a mutation under significant selection
pressure- probably more powerful selection pressure than you'd ever see
in the wild, other than for a lethal dominant allele.

Remember when you asked where Ernest Major got that number 10E-08? This
is where it where it comes into play. 10E-08 seems to be a pretty good
estimate of the mutation rate in eukaryotes. So every individual born,
hatched, whatever, has a number of mutations. Some number of these are
deleterious (but NOT lethal, please remember that for later), most are
neutral, and a very few might be beneficial.

Let's stick to the mutations that are neutral. Do you know how a
mutation can be neutral? A moment's calculation will tell you there are
64 possible combinations of the four nucleotides (adenine, guanine,
cytosine, thymine) that make the DNA triplets- each triplet codes for a
particular amino acid. One triplet codes for AUG, the "start" codon, and
three code for "stop" codons, so there's actually 60 triplets for 20
amino acids (AUG also codes for methionine, so line up quick for pedant
points...)

This allows for some redundancy. Many amino acids will be produced by
more than one triplet. Proline is an example. Proline is coded for by
several DNA triplets, including GGG and GGT. So we could have a mutation
in a DNA triplet, changing G to T or vice versa, and it's completely
neutral.

Another way to get a neutral mutation becomes obvious when you look at
the structure of enzymes. Most enzymes are pretty large proteins. The
most critical region is the binding site, where the substrate attaches.
A change in an amino acid there is likely to alter or even wreck the
function of the enzyme- the substrate just won't be able to bind there
anymore. Second, the enzyme has to have a particular shape to it. Ever
hear the phrase "form follows function"? It's true with a vengeance in
enzymes. The shape is determined by other "levels" of protein structure,
in particular things like van der Waal's forces and disulfide bonds
between amino acids that are distant from the binding site. A change
here is slightly less likely to result in change or loss of function,
but mutations can be serious. Sickle-cell disease is an example: the
mutation is not a change at the oxygen binding site, but the molecular
structure is altered such that the hemoglobin is liable to collapse if
it is depleted of oxygen too rapidly, causing the erythrocyte to change
shape or "sickle".

Now, neutral mutations are not "cancelled out" by the population's
genome. There's a real chance that a mutation will be lost due to drift
("dumb luck" as you correctly put it). Remember- an organism might die
without progeny, and even if it does reproduce, there's only a 50%
chance that the mutation will be inherited by any given one of its
offspring. But neutral mutations are accumulated over time. Heck,
compare how long it takes to eliminate a _lethal_ recessive allele from
a population and it becomes obvious that _neutral_ recessive mutations
are just going to stick around forever.

How do they accumulate, you ask? Well, they just keep happening, over
and over and over again. 10E-08, remember? How many nucleotides do you
have in your genome? On average, we've all got about a dozen mutations
that we're stuck with, and that doesn't even include the ones that
happened in our parents, grandparents, great-grandparents etc. If you
have any kids, each one will get about 6 of your mutations, and have a
dozen of their own. Most are neutral, some might be deleterious, and
some might be beneficial. Some might be back-mutations that actually
revert an earlier mutation to its previous state.

Now, why did I say to remember the difference between deleterious and
lethal? Lethal alleles are obviously a subset of deleterious alleles,
but by no means are they the whole of the set. Too many people equate
the two, and as we see in sickle-cell disease (and for that matter
Huntington's disease, a lethal _dominant_ disorder, although there's a
complicating factor there) even a disease that can kill you will not
necessarily prevent you from reproducing. "Deleterious" in the sense of
population genetics really just means "reduced fertility" or "lower
reproductive success". Might kill you, might not, but on average, you'll
have _fewer_ surviving progeny than someone not carrying that particular
allele or pair of alleles, but probably not _zero_ progeny.

This obviously applies to Behe's work, and I have not seen anyone bring
it up yet. A mutation may very well be deleterious (the mutations in
_Plasmodium_ were apparently neutral, or nearly so) but so what? Unless
it's a lethal dominant allele, it is NOT going to be removed from the
population by selection in a single generation.It might persist for a
very long time indeed.

And if it is a deleterious recessive allele, its very rarity will help
it persist, wrt selection, at least. If it's recessive, it will not
exert deleterious effects unless it is paired with another copy of the
mutation- and that means it's highly unlikely to be exerting any
ill-effects on the organism's reproductive success.

This is why inbreeding/incest can have consequences. It's not so much
that one person might be a mutant- we're all mutants. But the more
closely related you are to your mate, the more likely it is that you're
carrying the SAME deleterious recessive alleles, rather than a
completely different set.

Chris

[ognj...@gmail.com]

On Saturday, August 2, 2014 7:46:19 AM UTC+2, Glenn wrote:
> <brogers...@gmail.com> wrote in message news:cba4c0d2-7c24-40a0-870f-...@googlegroups.com...

Yet you have no complaints when Eddie's responds to any arguments is a variation of "Idiotic!" with no actual counterarguments?

[ognj...@gmail.com]

On Friday, August 1, 2014 8:46:11 PM UTC+2, Steady Eddie wrote:
> On Friday, 1 August 2014 12:31:22 UTC-6, John Bode wrote:
>
> > On Friday, August 1, 2014 11:30:06 AM UTC-5, Steady Eddie wrote:
>
> >
>

> > > From Thornton's Lab, More Strong Experimental Support for a Limit to
>
> >
>
> > > Darwinian Evolution
>
> >
>
> > >
>
> >
>
> > > *****
>
> >
>
> > >
>
> >
>
> > > Thornton himself -- apparently a conventional Darwinist, and certainly no
>
> >
>
> > > sympathizer with intelligent design -- does not attribute the protein
>
> >
>
> > > receptor's new function to Darwinian processes. Rather, he ascribes it mostly
>
> >
>
> > > to "historical contingency." That's another way of saying "dumb luck."
>
> >
>
> > >
>
> >
>
> > > *****
>
> >
>
> > >
>
> >
>
> > > -by Michael Behe
>
> >
>
> >
>
> >
>

> > "Dumb luck" doesn't exactly help Behe's case, though.
>
> >
>
> >
>
> >
>
> > The way I understand it, you have a neutral (or nearly neutral) mutation in
>
> >
>

> > an individual; this neutral mutation is passed on to that individual's offspring

>
>
>
> Why would NEUTRAL mutations be passed on to that individual's offspring?
>

> Neutral mutations are automatically overwhelmed and cancelled out in the gene pool
>
> by the sheer numbers of the original allele.
>

> Remember: NEUTRAL means UNSELECTED.
>
<snip>

Are you actually confusing populations with individuals? You are trying to disprove the theory of evolution without knowledge of such basic subjects?

You are stating that the alleles in the gene pool of the population are somehow canceling the mutations in an individual's genome while they are producing an offspring. Do you even know how reproduction works?

To put it in your language: idiotic.

[RSNorman]

You are skilled at pointing to irrelevant issues and adding comments
to obscure the original point.

Whether you would like to know something is quite irrelevant. Also
irrelevant is whether the test subjects did gain the historical
mutations and, especially whether the function of GR was restored.
Even more irrelevant is whether you would wonder one such thing or
another.

You did not attend to the points I raised: the correect method of

calculating the probability of two mutations occuring in any one

individual even if those two are neutral in isolation. You did not
attend the the really significant point Greg Guarino raised and that I
referred to about incorrect use of probabilities.

[Steady Eddie]

No, I don't understand how macroevolution works. Neither do you. You're making it up as you
go along.

[Greg Guarino]

On 8/2/2014 1:46 AM, Glenn wrote:
> "The immediate, obvious implication (which he clearly wants to keep
> far away from) is that the 2009 results render problematic even
> pretty small changes in structure/function for all proteins - not
> just the ones he worked on. (Thornton himself is betting on this: "We
> predict that future investigations, like ours, will support a
> molecular version of Dollo's law: as evolution proceeds, shifts in
> protein structure-function relations become increasingly difficult to
> reverse whenever those shifts have complex architectures..") (1) So
> how, other than begging the question, are we now to know that even
> the small differences we see in related protein systems came about by
> random mutation/selection (and, yes, drift)? Quite simply, we can't.
> Yet if even small changes are problematic, then larger changes will
> be prohibitive, and very big changes essentially unattainable. Thanks
> to Thornton's impressive work, we can now see that the limits to
> Darwinian evolution are more severe than even I had supposed."
>
> http://behe.uncommondescent.com/page/2/

The more I read of Behe, the less I think of him. The low probability of
*reversing* the (exact) course of evolutionary changes makes the forward
process unlikely?

Suppose I have a deck of cards that is initially in the following order:
Ace through King of Spades, Ace through King of Hearts, etc.I shuffle
them three times, yielding some other order. Nothing special has
happened, right? Now let's try it in reverse. It's unlikely as to be
essentially impossible, right? Ergo, the first set of shuffles did not
happen?

When drift is involved - a random process - how could we ever expect the
course to be reversible? And why would non-reversibility have any
bearing on the likelihood of the "forward" course?

I'm sure someone will say that my example represents order becoming
disordered. But in the case of life on Earth, any "disorderings" that
prove fatal or greatly deleterious are weeded out; thus the "shuffled"
genomes are merely "differently ordered".

[jillery]

Nominated for POTM. It's so good, it's a shame that it's designed for
someone who will almost certainly dismiss it out of hand.

[Malygris]

<snipped to save bits>

Probably wasted on Eddie but I found it interesting, thanks!

--
Malygris

[deadrat]

Ya had me right there, Sparky. The rest is talking past the close.
<snip/>

[Bob Casanova]

On Fri, 01 Aug 2014 13:45:44 -0400, the following appeared
in talk.origins, posted by jillery <69jp...@gmail.com>:

>On Fri, 01 Aug 2014 10:21:03 -0700, Bob Casanova <nos...@buzz.off>
>wrote:
>
>>On Fri, 1 Aug 2014 18:47:38 +0200, the following appeared in
>>talk.origins, posted by Athel Cornish-Bowden
>><acor...@imm.cnrs.fr>:

>>
>>>On 2014-08-01 16:30:06 +0000, Steady Eddie said:
>>

>>>> From Thornton's Lab, More Strong Experimental Support for a Limit to
>>>> Darwinian Evolution
>>>> *****
>>>> Thornton himself -- apparently a conventional Darwinist, and certainly
>>>> no sympathizer with intelligent design -- does not attribute the
>>>> protein receptor's new function to Darwinian processes. Rather, he
>>>> ascribes it mostly to "historical contingency." That's another way of
>>>> saying "dumb luck."
>>>>
>>>> *****
>>>>
>>>> -by Michael Behe
>>

>>>You seem to have forgotten to quote what Joe Thornton thought of Behe's
>>>conclusions, so here it is:
>>>
>>>"Thanks for asking for my reaction to Behe�s post on our recent paper
>>>in Nature. His interpretation of our work is incorrect. He confuses

>>>�contingent� or �unlikely� with �impossible.� He ignores the key role
>>>of genetic drift in evolution. And he erroneously concludes that

>>>because the probability is low that some specific biological form will
>>>evolve, it must be impossible for ANY form to evolve.
>>>

>>>"Behe contends that our findings support his argument that adaptations

>>>requiring more than one mutation cannot evolve by Darwinian processes.
>>>The many errors in Behe�s Edge of Evolution � the book in which he
>>>makes this argument � have been discussed in numerous publications.

>>>
>>>"In his posts about our paper, Behe�s first error is to ignore the fact
>>>that adaptive combinations of mutations can and do evolve by pathways

>>>involving neutral intermediates. Behe says that if it takes more than

>>>one mutation to produce even a crude version of the new protein
>>>function, then selection cannot drive acquisition of the adaptive
>>>combination."
>>

>>Thanks for the context.
>>
>>Gee, Eddie, nice petard you have there...
>
>
>Maybe he's just happy to see you.

Thanks for the mental image. :-(
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[Bob Casanova]

On Fri, 1 Aug 2014 12:25:48 -0700 (PDT), the following
appeared in talk.origins, posted by Steady Eddie
<1914o...@gmail.com>:

<snip>

>Come on guys, stick to the science, okay?

My upgraded Irony Meter barely handled that one.

[jillery]

I forgot to change the subject. Silly me.

On Sat, 02 Aug 2014 09:26:18 -0400, jillery <69jp...@gmail.com>
wrote:

[Vincent Maycock]

On Sat, 2 Aug 2014 05:08:42 -0700 (PDT), Steady Eddie
<1914o...@gmail.com> wrote:
snip

>> Are you actually confusing populations with individuals? You are trying to disprove the theory of evolution without knowledge of such basic subjects?
>>
>>
>>
>> You are stating that the alleles in the gene pool of the population are somehow canceling the mutations in an individual's genome while they are producing an offspring. Do you even know how reproduction works?
>>
>>
>>
>> To put it in your language: idiotic.
>
>No, I don't understand how macroevolution works.

How come you try to criticize then?

>Neither do you. You're making it up as you
>go along.

Neutral mutations can spread throughout a population by genetic drift.
Natural selection does not have to be involved for this to happen.

[Chris Thompson]

One of the more incompetent attempts at topic-switching, even for you.

How did you go from individual reproduction and its effect on population
genetics (a quite well-studied topic) to macroevolution (another
well-studied, but entirely different, topic)?

Lame.

Chris

[Burkhard]

seconded

[Chris Thompson]

On 8/1/2014 6:15 PM, RSNorman wrote:
> On Fri, 01 Aug 2014 17:59:58 -0400, jillery <69jp...@gmail.com>
> wrote:
>
>> On Fri, 01 Aug 2014 16:38:54 -0400, RSNorman <r_s_n...@comcast.net>
>> wrote:
>>
>>> On Fri, 01 Aug 2014 21:21:42 +0100, alias Ernest Major
>>> <{$to$}@meden.demon.co.ukl> wrote:
>>>
>>>
>>> <snip to isolate one point -- and to eliminate steady's nonsense>
>>>
>>>> He has also failed to take into account the fact that the average number
>>>> of children is greater than 1. When you take that into account his
>>>> description doesn't apply to what happens "on average" either.
>>>
>>> Average number of children can be tricky. If a population is constant
>>> over time then the average number of offspring per member of the
>>> current population is 1. However for population dynamics in sexually
>>> reproducing populations you often only count females and then the
>>> average number of children per female is 2 and the average number of
>>> female offspring per female is 1. Many females do not reproduce at
>>> all so the average number of total offspring for those females that do
>>> is greater than 2. Still if the population is in replacement mode --
>>> constant number -- then necessarily the average number of offspring
>>> per individual (or the average number of female offspring per female)
>>> is 1.
>>>
>>> The fact that not all females reproduce in some species makes the
>>> effective population size smaller than the total number of individuals
>>> and that makes genetic drift more significant. However except in
>>> weird situations like honeybees, it is usually the males who are
>>> divided into a small number of studs vs. a large number of horny
>>> bystanders who lost the battles of sexual selection but are ready and
>>> eager to step in at any opportunity.
>>
>>
>> The above isn't accurate. Some percentage of the offspring almost
>> certainly die before they reproduce. If the average number of
>> offspring were is just one (or two females), the population will
>> decline.
>>
>> So it isn't the average number of offspring, but the average number of
>> offspring surviving to reproduce. Same requirement applies for female
>> offspring.
>
> That is true and is another reason why counting "average number of
> children" is tricky.
>
> In population genetics, offspring that don't themselves contribute to
> the gene pool are effectively eliminated from the population. Counting
> children who die in infancy as "offspring" is then the equivalent of
> counting embryos that die unnoticed or, to go to the extreme case,
> counting unfertilized eggs and sperm as "offspring that fail to
> survive to reproductive age". Are eggs that are laid but eaten before
> hatching really "offspring"? What about external fertilization where
> eggs are laid but not fertilized? It really is tricky just how you
> count things. We humans define "offspring" as "births" (except those
> fundamentalists who try to insist that a fertilized egg must count as
> an individual). In that case you are entirely correct.

And that, of course, is why wildlife managers and population biologists
are in such demand, and why they get paid the big bucks.

Oh, wait...

Chris

[Burkhard]

Chris Thompson wrote:
<snip>

Friends of mine just hired a wildlife manager for their twins...

[Roger Shrubber]

Two pedant points. Mutations in coding regions that do not
change the amino acid are generally termed silent mutations
as opposed to neutral mutations. Silent mutations are defined
as mutations that do not change the protein sequence. For
added technical reasons, not all silent mutations are neutral
but most are. The reasons they might not be neutral involve
codon usage and RNA structure.

The second pedant point is that your emphasis on enzymes is
overly specific. It would be better to simply refer to
proteins and the effect of a single substitution on structure
and function. Most single amino acid changes to proteins
have minor effects, often difficult to measure. And, even
those point mutations that do change amino acids often change
to a similar amino acid as a function of the the way the
genetic code is structured. (more often than randomly picking
a different amino acid out of a hat).

Beyond that, nice post.

[Nick Roberts]

In message <qqaot9l496reii1ar...@4ax.com>
jillery <69jp...@gmail.com> wrote:

> On Fri, 1 Aug 2014 16:22:47 -0700 (PDT), Steady Eddie
> <1914o...@gmail.com> wrote:
>
> >On Friday, 1 August 2014 16:03:17 UTC-6, jillery wrote:
> >> On Fri, 1 Aug 2014 14:07:57 -0700 (PDT), Steady Eddie
> >>
> >>
> >>
> >>
> >> >On Friday, 1 August 2014 15:00:16 UTC-6, jillery wrote:
> >>
> >> >> On Fri, 1 Aug 2014 12:30:59 -0700 (PDT), Steady Eddie
> >>
> >> >>
> >>
> >> >>
> >>
> >> >>
> >>
> >> >>
> >>

> >> >> >On Friday, 1 August 2014 13:13:44 UTC-6, Greg Guarino wrote:
> >>
> >> >> >> What would prevent (some of) those mutations from being
> >> >> >> passed on to my offspring? "Selection" is no answer, as I
> >> >> >> have successfully reproduced. Statistically speaking,
> >> >> >> roughly half a parent's mutations should be inherited by
> >> >> >> each child.
> >>
> >> >>
> >>
> > > > > > Yes, then half of that in the next generation, until your
> > > > > > particular mutations exponentially approach zero. Meaning,
> > > > > > as your progeny continues to reproduce, your particular
> > > > > > mutations get CANCELLED OUT quite quickly by the original
> > > > > > genome in the population (unless, in the case of the wild,
> > > > > > a mutation confers an evolutionary advantage).
> > >
> > > > >

> > > > > Wrong again:
> > > > >
> > > > > <http://en.wikipedia.org/wiki/Founder_effect>
> >> >
> > > > Off-topic Darwinian bluster and quote-mongering again.
> >>
> >> What the heck is quote-mongering?
> >
> >Sorry, i was referring to quote-bluffing.
>
>

> What the heck is quote-bluffing?

It's SEs code phrase for "I have no response", when even he realises
that he can't ask for a cite becausehe's so obviously been given one.
Basically, he's playing for time.

> >> Most likely you didn't even read the cite, but if you did, most
> >> likely you didn't understand it.
> >
> > This is pointless. We're just accusing each other of poor reading
> > skills.

> There is a difference. I posted relevant comments and accurate
> summaries.

> > Nevertheless, there is my OP, on the record as an example of an
> > experimental Darwinist who hit the wall...or, at least, grazed it.
>
>

> A vague reference and a quote is nothing to brag about, but you get a
> brownie point for not LOLing anywhere in the topic.

Is it really fair to keep challenging Stately to a battle of wits? He
comes to the battleground so obviously unarmed, it just seems a bit
cruel.

--
Nick Roberts tigger @ orpheusinternet.co.uk

Hanlon's Razor: Never attribute to malice that which
can be adequately explained by stupidity.

[jillery]

Almost all of Steadly's replies can be reasonably understood that way.

>> >> Most likely you didn't even read the cite, but if you did, most
>> >> likely you didn't understand it.
>> >
>> > This is pointless. We're just accusing each other of poor reading
>> > skills.
>> There is a difference. I posted relevant comments and accurate
>> summaries.
>> > Nevertheless, there is my OP, on the record as an example of an
>> > experimental Darwinist who hit the wall...or, at least, grazed it.
>>
>>
>> A vague reference and a quote is nothing to brag about, but you get a
>> brownie point for not LOLing anywhere in the topic.
>
>Is it really fair to keep challenging Stately to a battle of wits? He
>comes to the battleground so obviously unarmed, it just seems a bit
>cruel.

It may be cruel to pull wings off flies, but swatting them away from
one's face is a matter of good hygiene.

[Steady Eddie]

"Tracing these alternative evolutionary paths, the researchers discovered that the protein -- the cellular receptor for the stress hormone cortisol -- could not have evolved its modern-day function unless two extremely unlikely mutations happened to evolve first. These "permissive" mutations had no effect on the protein's function, but without them the protein could not tolerate the later mutations that caused it to evolve its sensitivity to cortisol. In screening thousands of alternative histories, the researchers found no alternative permissive mutations that could have allowed the protein's modern-day form to evolve. [Emphasis added.]

The above is taken from a news item from the University of Chicago Medical Center titled: "Evolution depends on rare chance events, 'molecular time travel' experiments show."

It continues:

"This very important protein exists only because of a twist of fate," said study senior author Joe Thornton, PhD, professor of ecology & evolution and human genetics at the University of Chicago. "If our results are general -- and we think they probably are -- then many of our body's systems work as they do because of very unlikely chance events that happened in our deep evolutionary past," he added."
http://www.evolutionnews.org/2014/06/playing_roulett087011.html

[Greg Guarino]

Here is the crux of what is wrong with the "Evolution News" argument:

====================================
From the article:
"What Thornton's saying, I think, is that many mutations had to happen,
with no help from natural selection, in order to make other mutations
possible."
====================================

This is imprecise, but I won't dwell on it. The earlier mutations did
not make the later ones "possible", only useful in a way that they would
not have been otherwise.

====================================
From the article:
"And all these mutations somehow came together to make the proteins
necessary to build functioning organisms. In other words, we were
incredibly lucky."
====================================

The mutations, neutral and selected, came together to produce a
*particular set* of *modified* organisms; which developed from prior
organisms that were *already* functioning. But for certain neutral
mutations, the particular set of descendant organisms that we find would
not have come to exist and that lineage would have taken different
paths. "Incredibly lucky" only comes into play if we define a certain
permutation as a "target". But life has no requirement to produce any
particular "target" organism or trait, only ones that survive and
reproduce.

[broger...@gmail.com]

On Wednesday, August 13, 2014 11:00:33 AM UTC-4, Steady Eddie wrote:
> "Tracing these alternative evolutionary paths, the researchers discovered that the protein -- the cellular receptor for the stress hormone cortisol -- could not have evolved its modern-day function unless two extremely unlikely mutations happened to evolve first. These "permissive" mutations had no effect on the protein's function, but without them the protein could not tolerate the later mutations that caused it to evolve its sensitivity to cortisol. In screening thousands of alternative histories, the researchers found no alternative permissive mutations that could have allowed the protein's modern-day form to evolve. [Emphasis added.]

There's no need to go to all the trouble of thinking about cortisol receptors to show how impossible evolution is. Just consider yourself, Steady Eddie. What are the chances that you would have descended by natural processes from your great-great grandparents, never mind from some proto-chimp/human millions of years ago? Here's the calculation you need:

An average woman makes 1 x 10^6 eggs in a lifetime. An average man makes more than 1 x 10^11 sperm in a lifetime. Therefore the chance that your parents mating would produce you is at least 1 in 10^-17. But even to get there, we needed two parents, four grandparents, eight great grandparents, and sixteen great-great-grandparents, so that's a total of 30 precursors each of which has a probability of 1 in 10^-17. So to actually get to you by random processes we would have a probability of 1 in (10^-17) raised to the 31st power or 1 in 10^-527. That's such a staggeringly small number that there's not the slightest chance that you descended from your great great grandparents by natural processes, never mind evolving from proto-apes or pond-scum. Clearly evolution is impossible, since it cannot account for you. That's a rock solid argument. Take it to the bank. Count on it. Seriously. Really. Damn sure.

[Glenn]

<broger...@gmail.com> wrote in message news:0f31cb8a-1d28-4e29...@googlegroups.com...

> On Wednesday, August 13, 2014 11:00:33 AM UTC-4, Steady Eddie wrote:
>> "Tracing these alternative evolutionary paths, the researchers discovered that the protein -- the cellular receptor for the stress hormone cortisol -- could not have evolved its modern-day function unless two extremely unlikely mutations happened to evolve first. These "permissive" mutations had no effect on the protein's function, but without them the protein could not tolerate the later mutations that caused it to evolve its sensitivity to cortisol. In screening thousands of alternative histories, the researchers found no alternative permissive mutations that could have allowed the protein's modern-day form to evolve. [Emphasis added.]
>
> There's no need to go to all the trouble of thinking about cortisol receptors to show how impossible evolution is. Just consider yourself, Steady Eddie.


>What are the chances that you would have descended by natural processes from your great-great grandparents

Fairly good, considering sex and all.

>, never mind from some proto-chimp/human millions of years ago? Here's the calculation you need:
>
> An average woman makes 1 x 10^6 eggs in a lifetime. An average man makes more than 1 x 10^11 sperm in a lifetime. Therefore the chance that your parents mating would produce you is at least 1 in 10^-17. But even to get there, we needed two parents, four grandparents, eight great grandparents, and sixteen great-great-grandparents, so that's a total of 30 precursors each of which has a probability of 1 in 10^-17. So to actually get to you by random processes we would have a probability of 1 in (10^-17) raised to the 31st power or 1 in 10^-527. That's such a staggeringly small number that there's not the slightest chance that you descended from your great great grandparents by natural processes, never mind evolving from proto-apes or pond-scum. Clearly evolution is impossible, since it cannot account for you. That's a rock solid argument. Take it to the bank. Count on it. Seriously. Really. Damn sure.
>

"You" are an idiot, notwithstanding the specific sperm that caused you to be so.

[Athel Cornish-Bowden]

R. A. Fisher described rather a nice example along these lines:

"Consideration of the conditions prevailing in bisexual organisms shows
that ... the chance of an organism leaving at least one offspring of
his own sex has a calculable value of about 5/8. Let the reader imagine
this simple condition were true of his own species, and attempt to
calculate the prior probability that a hundred generations of his
ancestry in the direct male line should each have left at least one
son. The odds against such a contingency as it would have appeared to
his hundredth ancestor (about the time of King Solomon) would require
for their expression forty-four figures of the decimal notation."

R. A. Fisher (1954) in "Evolution as a Process", edited by J. Huxley,
A. C. Hardy and E. B. Ford, George Allen & Unwin, London.


--
athel

[deadrat]

On 8/13/14 11:24 AM, broger...@gmail.com wrote:
> On Wednesday, August 13, 2014 11:00:33 AM UTC-4, Steady Eddie wrote:
>> "Tracing these alternative evolutionary paths, the researchers discovered that the protein -- the cellular receptor for the stress hormone cortisol --
>> could not have evolved its modern-day function unless two extremely unlikely mutations happened to evolve first. These "permissive" mutations had no
>> effect on the protein's function, but without them the protein could not tolerate the later mutations that caused it to evolve its sensitivity to
>> cortisol. In screening thousands of alternative histories, the researchers found no alternative permissive mutations that could have allowed the
>> protein's modern-day form to evolve. [Emphasis added.]
>
> There's no need to go to all the trouble of thinking about cortisol receptors to show how impossible evolution is. Just consider yourself, Steady Eddie.
> What are the chances that you would have descended by natural processes from your great-great grandparents, never mind from some proto-chimp/human
> millions of years ago? Here's the calculation you need:

> An average woman makes 1 x 10^6 eggs in a lifetime. An average man makes more than 1 x 10^11 sperm in a lifetime. Therefore the chance that your parents
> mating would produce you is at least 1 in 10^-17. But even to get there, we needed two parents, four grandparents, eight great grandparents, and sixteen
> great-great-grandparents, so that's a total of 30 precursors each of which has a probability of 1 in 10^-17. So to actually get to you by random processes
> we would have a probability of 1 in (10^-17) raised to the 31st power or 1 in 10^-527. That's such a staggeringly small number

Wow! What staggeringly bad luck for the rest of us.

[deadrat]

On 8/13/14 11:53 AM, Glenn wrote:
>
> <broger...@gmail.com> wrote in message news:0f31cb8a-1d28-4e29...@googlegroups.com...
>> On Wednesday, August 13, 2014 11:00:33 AM UTC-4, Steady Eddie wrote:
>>> "Tracing these alternative evolutionary paths, the researchers discovered that the protein -- the cellular receptor for the stress hormone cortisol -- could not have evolved its modern-day function unless two extremely unlikely mutations happened to evolve first. These "permissive" mutations had no effect on the protein's function, but without them the protein could not tolerate the later mutations that caused it to evolve its sensitivity to cortisol. In screening thousands of alternative histories, the researchers found no alternative permissive mutations that could have allowed the protein's modern-day form to evolve. [Emphasis added.]
>>
>> There's no need to go to all the trouble of thinking about cortisol receptors to show how impossible evolution is. Just consider yourself, Steady Eddie.
>
>
>> What are the chances that you would have descended by natural processes from your great-great grandparents
>
> Fairly good, considering sex and all.

The chances are fairly good that someone would have descended. The
chances that it would have been Steadfastly are vanishingly small.

>
>
>> , never mind from some proto-chimp/human millions of years ago? Here's the calculation you need:
>>
>> An average woman makes 1 x 10^6 eggs in a lifetime. An average man makes more than 1 x 10^11 sperm in a lifetime. Therefore the chance that your parents mating would produce you is at least 1 in 10^-17. But even to get there, we needed two parents, four grandparents, eight great grandparents, and sixteen great-great-grandparents, so that's a total of 30 precursors each of which has a probability of 1 in 10^-17. So to actually get to you by random processes we would have a probability of 1 in (10^-17) raised to the 31st power or 1 in 10^-527. That's such a staggeringly small number that there's not the slightest chance that you descended from your great great grandparents by natural processes, never mind evolving from proto-apes or pond-scum. Clearly evolution is impossible, since it cannot account for you. That's a rock solid argument. Take it to the bank. Count on it. Seriously. Really. Damn sure.
>>
> "You" are an idiot, notwithstanding the specific sperm that caused you to be so.

What's your excuse?

[Bob Casanova]

On Wed, 13 Aug 2014 09:53:18 -0700, the following appeared
in talk.origins, posted by "Glenn" <g...@invalid.invalid>:

><broger...@gmail.com> wrote in message news:0f31cb8a-1d28-4e29...@googlegroups.com...

>>What are the chances that you would have descended by natural processes from your great-great grandparents

>Fairly good, considering sex and all.

Nope, that only indicates that *someone* would probably be
descended from them; that the someone was you was a very
small chance indeed considering the number of possible
combinations.

[Glenn]

"Bob Casanova" <nos...@buzz.off> wrote in message news:k9anu95iv6devu195...@4ax.com...

> On Wed, 13 Aug 2014 09:53:18 -0700, the following appeared
> in talk.origins, posted by "Glenn" <g...@invalid.invalid>:
>
>><broger...@gmail.com> wrote in message news:0f31cb8a-1d28-4e29...@googlegroups.com...
>
>>>What are the chances that you would have descended by natural processes from your great-great grandparents
>
>>Fairly good, considering sex and all.
>
> Nope, that only indicates that *someone* would probably be
> descended from them; that the someone was you was a very
> small chance indeed considering the number of possible
> combinations.
> --

You may think that you are not someone, and I might agree.

[Bob Casanova]

On Wed, 13 Aug 2014 11:35:55 -0700, the following appeared

in talk.origins, posted by "Glenn" <g...@invalid.invalid>:

>
>"Bob Casanova" <nos...@buzz.off> wrote in message news:k9anu95iv6devu195...@4ax.com...
>> On Wed, 13 Aug 2014 09:53:18 -0700, the following appeared
>> in talk.origins, posted by "Glenn" <g...@invalid.invalid>:
>>
>>><broger...@gmail.com> wrote in message news:0f31cb8a-1d28-4e29...@googlegroups.com...
>>
>>>>What are the chances that you would have descended by natural processes from your great-great grandparents
>>
>>>Fairly good, considering sex and all.
>>
>> Nope, that only indicates that *someone* would probably be
>> descended from them; that the someone was you was a very
>> small chance indeed considering the number of possible
>> combinations.

>You may think that you are not someone, and I might agree.

And yet another non sequitur in an attempt to spin a
refutation...

Given the worth of your usual opinions I'll take that as a
compliment.

[Steady Eddie]

On Friday, 1 August 2014 10:47:38 UTC-6, Athel Cornish-Bowden wrote:
> On 2014-08-01 16:30:06 +0000, Steady Eddie said:
>
>
>
> > From Thornton's Lab, More Strong Experimental Support for a Limit to
>
> > Darwinian Evolution
>
> >
>
> >
>
> > *****
>
> > Thornton himself -- apparently a conventional Darwinist, and certainly
>
> > no sympathizer with intelligent design -- does not attribute the
>
> > protein receptor's new function to Darwinian processes. Rather, he
>
> > ascribes it mostly to "historical contingency." That's another way of
>
> > saying "dumb luck."
>
> >
>
> > *****
>
> >
>
> > -by Michael Behe
>
>
>
> You seem to have forgotten to quote what Joe Thornton thought of Behe's
>
> conclusions, so here it is:
>
>
>
> "Thanks for asking for my reaction to Behe's post on our recent paper
>
> in Nature. His interpretation of our work is incorrect. He confuses
>
> "contingent" or "unlikely" with "impossible." He ignores the key role
>
> of genetic drift in evolution. And he erroneously concludes that
>
> because the probability is low that some specific biological form will
>
> evolve, it must be impossible for ANY form to evolve.
>
>
>
> "Behe contends that our findings support his argument that adaptations
>
> requiring more than one mutation cannot evolve by Darwinian processes.

Again, a Darwinist who does NOT KNOW what Behe wrote, falsely attributing
to him a straw man argument and proceeding to beat the stuffing out of it.
HE's as bad as MORON.

>
> The many errors in Behe's Edge of Evolution -- the book in which he
>
> makes this argument -- have been discussed in numerous publications.

>
>
>
> "In his posts about our paper, Behe's first error is to ignore the fact
>
> that adaptive combinations of mutations can and do evolve by pathways
>
> involving neutral intermediates. Behe says that if it takes more than
>
> one mutation to produce even a crude version of the new protein
>
> function, then selection cannot drive acquisition of the adaptive
>
> combination."

Again, I think he'd better read The Edge of Evolution before he tries to critique it.
>
>
>
>
>
> --
>
> athel

[Steady Eddie]

On Friday, 1 August 2014 11:45:28 UTC-6, jillery wrote:
> On Fri, 1 Aug 2014 10:15:14 -0700 (PDT), Steady Eddie
>
>
>
>
> >On Friday, 1 August 2014 11:03:42 UTC-6, jillery wrote:
>
> >> On Fri, 1 Aug 2014 09:30:06 -0700 (PDT), Steady Eddie

>
> >>
>
> >>
>
> >>
>
> >>
>
> >> >From Thornton's Lab, More Strong Experimental Support for a Limit to Darwinian Evolution
>
> >>
>
> >> >
>
> >>
>
> >> >
>
> >>
>
> >> >*****
>
> >>
>
> >> >Thornton himself -- apparently a conventional Darwinist, and certainly no sympathizer with intelligent design -- does not attribute the protein receptor's new function to Darwinian processes. Rather, he ascribes it mostly to "historical contingency." That's another way of saying "dumb luck."
>
> >>
>
> >> >
>
> >>
>
> >> >*****
>
> >>
>
> >> >
>
> >>
>
> >> >-by Michael Behe
>
> >>
>
> >>
>
> >>
>
> >>
>
> >>
>

> >> Behe equates historical contingency with dumb luck, but it really mean
>
> >>
>
> >> only what has happened in the past. Unless one subscribes to
>
> >>
>
> >> omphalism, one necessarily acknowledges that living organisms have a
>
> >>
>
> >> past. The events of the past shaped their current genomes, just as
>
> >>
>
> >> current events shape their future genomes.
>
> >
>
> >You make a very good point.
>
> >What specific events are you referring to?
>
> >When did the specific protein under investigation evolve?
>
> >How? What was the mechanism?
>
> >
>
> >Without these details, 'contingency' still equals 'dumb luck', the guiding hand of Darwin's ghost.
>
>
>
>
>
> Wrong again. Historical contingency has nothing to do with dumb luck.
>
> Nor do I need to refer to any specific events or proteins.
>
>
>
> You seem to recognize that living organisms have some genome sequence
>
> from the past. It's that sequence, modified in past generations
>
> according to the environment of those generations, that is modified
>
> according to the environment of the present generation.

LOL!!!!!
Another way of saying "We don't know how the hell it happened, but we know God didn't do it!"

[broger...@gmail.com]

On Thursday, August 14, 2014 2:49:45 PM UTC-4, Steady Eddie wrote:

> Again, I think he'd better read The Edge of Evolution before he tries to critique it.
>

Wait, you mean you think you should understand an argument before you try to critique it? No, that can't be what you mean. In that case, you'd be able to accurately describe what the theory of evolution claims and provide some of the lines of evidence that support it. And do so well enough that an evolutionist would agree that you'd stated their case just as they would have. But you can't do that. So why would you demand that standard of others?

[Steady Eddie]

On Friday, 1 August 2014 12:31:22 UTC-6, John Bode wrote:
> On Friday, August 1, 2014 11:30:06 AM UTC-5, Steady Eddie wrote:
>

> > From Thornton's Lab, More Strong Experimental Support for a Limit to
>
> > Darwinian Evolution
>
> >
>
> > *****
>
> >
>
> > Thornton himself -- apparently a conventional Darwinist, and certainly no
>
> > sympathizer with intelligent design -- does not attribute the protein
>
> > receptor's new function to Darwinian processes. Rather, he ascribes it mostly
>
> > to "historical contingency." That's another way of saying "dumb luck."
>
> >
>
> > *****
>
> >
>
> > -by Michael Behe
>
>
>

> "Dumb luck" doesn't exactly help Behe's case, though.
>
>
>
> The way I understand it, you have a neutral (or nearly neutral) mutation in
>

> an individual; this neutral mutation is passed on to that individual's offspring
>
> without affecting their overall fitness (it's not subject to selection in the
>
> Darwinian sense).
>
>
>
> One of that individual's descendants then has a second mutation that, together
>
> with the ancestral mutation, leads to a new function. This new function didn't
>
> arise as a result of Darwinian selection; however, it will be selected for
>
> (or against, depending on environment) going forward.
>
>
>
> IINM, something similar happened with Lenski's citrate-digesting E. coli.

Yes, something similar to 'dumb luck'.

[Steady Eddie]

On Friday, 1 August 2014 12:40:39 UTC-6, RSNorman wrote:
> On Fri, 1 Aug 2014 10:09:58 -0700 (PDT), Steady Eddie
>
>
>
>
> <snip to get to one important point>
>
>
>
> >"Genetic drift" is another term for "dumb luck", the invisible guiding hand behind Darwin's ghost.
>
>
>
> That hand is by no means invisible except to those ignorant of biology
>
> and evolution.
>
>
>
> Some people may object to the pejorative phrase "dumb luck" but it
>
> really just means "outcome of a random process". The word "Darwinism"
>
> or "Darwinistic evolution" is often applied strictly to the selection
>
> part of evolution. However selection requires variability and random
>
> processes, mutations, are the foundation for variation. And mutations
>
> are, indeed, "blind" or "dumb luck". The chance of having your first
>
> child a girl rather than a boy is also "dumb luck" (if you use the
>
> usual method of internal fertilization and conception). That doesn't
>
> mean it doesn't extremely frequently. It is a historical contingency
>
> (what you call "dumb luck") that Queen Elizabeth II has a younger
>
> sister and no brothers and so inherited the royal title. In other
>
> words, she is queen by dumb luck.
>
>
>
> By railing against "dumb luck" you are simply echoing a standard
>
> creationist objection to science in general, the mindless working out
>
> of the universe according to the laws of science rather than the
>
> infinite intelligence and guidig hand of the creator.

...Which is shown to be virtually impossible considering the necessary changes, and each one of them
depending on "dumb Luck".
What a joke.

[Steady Eddie]

He's a professional scientist, idiot. I believe they are expected to understand an argument before
describing it incorrectly.

The problem with understanding neo Darwinian evolution is that you have to ACCEPT IT HOOK, LINE, AND
SINKER

[broger...@gmail.com]

On Thursday, August 14, 2014 3:19:57 PM UTC-4, Steady Eddie wrote:

> He's a professional scientist, idiot. I believe they are expected to understand an argument before describing it incorrectly.

So, no problem if YOU describe the theory of evolution incorrectly.
>
>
>
> The problem with understanding neo Darwinian evolution is that you have to ACCEPT IT HOOK, LINE, AND SINKER.

Well, certainly, if you do understand Darwinian evolution and the massive evidence in support of it, you'll be very likely to accept it hook, line, and sinker. But not necessarily. I can describe ID well enough to masquerade as a real ID theorist, but I don't accept it in the least.

You don't mean to be saying this, of course, but it looks to me like when you understand ID well you can reject it, but when you understand the theory of evolution well you can't help but accept it. But all you need to do to prove me wrong is read some standard explanation of the evidence for evolution (e.g. Jerry Coyne's Why Evolution is True) and repeat the main arguments in your own words. There's no reason that should make you change your mind. None at all....

[Steady Eddie]

(continuation...) ...before you can start to understand some of the terms they use.
Their definitions of terms beg the question of whether neo-Darwinian evolution, that is
biological and chemical 'evolution' starting from the origin of life, really happened.

[John Harshman]

Thank you for being the only person in my recent memory to use the term
"beg the question" correctly.

[deadrat]

Another way of saying "We don't know how the hell it happened, and we
hope more study can tell us, so we won't give up and say "Goddidit."

[jillery]

On Thu, 14 Aug 2014 11:56:30 -0700 (PDT), Steady Eddie
<1914o...@gmail.com> wrote:

>On Friday, 1 August 2014 11:45:28 UTC-6, jillery wrote:
>> On Fri, 1 Aug 2014 10:15:14 -0700 (PDT), Steady Eddie
>>
>>
>>
>>
>> >On Friday, 1 August 2014 11:03:42 UTC-6, jillery wrote:
>>
>> >> On Fri, 1 Aug 2014 09:30:06 -0700 (PDT), Steady Eddie
>>
>> >> >From Thornton's Lab, More Strong Experimental Support for a Limit to Darwinian Evolution
>>

>> >> >Thornton himself -- apparently a conventional Darwinist, and certainly no sympathizer with intelligent design -- does not attribute the protein receptor's new function to Darwinian processes. Rather, he ascribes it mostly to "historical contingency." That's another way of saying "dumb luck."
>>
>>

>> >> Behe equates historical contingency with dumb luck, but it really mean
>> >> only what has happened in the past. Unless one subscribes to
>> >> omphalism, one necessarily acknowledges that living organisms have a
>> >> past. The events of the past shaped their current genomes, just as
>> >> current events shape their future genomes.
>>
>> >You make a very good point.
>>
>> >What specific events are you referring to?
>> >When did the specific protein under investigation evolve?
>> >How? What was the mechanism?
>> >Without these details, 'contingency' still equals 'dumb luck', the guiding hand of Darwin's ghost.
>>
>> Wrong again. Historical contingency has nothing to do with dumb luck.
>> Nor do I need to refer to any specific events or proteins.
>> You seem to recognize that living organisms have some genome sequence
>> from the past. It's that sequence, modified in past generations
>> according to the environment of those generations, that is modified
>> according to the environment of the present generation.
>
>LOL!!!!!
>Another way of saying "We don't know how the hell it happened, but we know God didn't do it!"

You took two weeks and still that's the best you can do?

[jillery]

Yes, mutations are more-or-less random. So what?

[broger...@gmail.com]

On Thursday, August 14, 2014 3:39:30 PM UTC-4, Steady Eddie wrote:

> (continuation...) ...before you can start to understand some of the terms they use.
>
> Their definitions of terms beg the question of whether neo-Darwinian evolution, that is
>
> biological and chemical 'evolution' starting from the origin of life, really happened.

And why would that stop you from understanding their argument well enough to recapitulate it in your own words? If you need to explain their definitions, go ahead. Understanding an argument does not commit you to agreeing with it.

[jillery]

Neither you, Behe, nor anyone else has shown the necessary changes to
be virtually impossible. To the contrary, Behe's example of
chloroquine resistance shows that "dumb luck" happens quite regularly.
Didn't you read his book?

[jillery]

But in the process, he evades the question of how biological evolution
works, and makes a false dichotomy that how life originated determines
how life evolves.