Evidence for Big Leaps?

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michael...@worldnet.att.net

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Jul 6, 2006, 5:36:44 PM7/6/06
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July 07, 2006
An Evolution Saga: Beach Mice Mutate and Survive

It's a pitiless lesson-adapt or die-but the sand-colored mice that
scurry around the beaches of Florida's Gulf Coast seem to have learned
the lesson well. Now researchers have identified a genetic mutation
that underlies natural selection for the sand-matching coat color of
the beach mice, an adaptive trait that camouflages them from aerial
predators.

In the July 7, 2006, issue of the journal Science, evolutionary
geneticist Hopi Hoekstra and colleagues at the University of
California, San Diego, report that a single mutation causes the
lifesaving color variation in beach mice (Peromyscus polionotus) and
provides evidence that evolution can occur in big leaps.

"This is a striking example of how protein-coding changes can play a
role in adaptation and divergence in populations, and ultimately
species."
Hopi Hoekstra

The Gulf Coast barrier islands of Florida and Alabama where the beach
mice are found are less than 6,000 years old-quite young from an
evolutionary standpoint. Hoekstra said that the identification of a
single mutation that contributes to the color change that has arisen in
these animals argues for a model of evolution in which populations
diverge in big steps.

This model, in which change is driven by large effects produced by
individual mutations, contrasts with a popular model that sees
populations diverging via small changes accumulated over long periods
of time.

More at:
http://www.hhmi.org/news/hoekstra20060707.html

Inez

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Jul 6, 2006, 5:50:57 PM7/6/06
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michael...@worldnet.att.net wrote:
> July 07, 2006
> An Evolution Saga: Beach Mice Mutate and Survive
>
> It's a pitiless lesson-adapt or die-but the sand-colored mice that
> scurry around the beaches of Florida's Gulf Coast seem to have learned
> the lesson well. Now researchers have identified a genetic mutation
> that underlies natural selection for the sand-matching coat color of
> the beach mice, an adaptive trait that camouflages them from aerial
> predators.
>
> In the July 7, 2006, issue of the journal Science, evolutionary
> geneticist Hopi Hoekstra and colleagues at the University of
> California, San Diego, report that a single mutation causes the
> lifesaving color variation in beach mice (Peromyscus polionotus) and
> provides evidence that evolution can occur in big leaps.
>
That doesn't seem like such a drastic change to me. For example, my
hair has gone from blonde to red and back to blonde again.

R Brown

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Jul 6, 2006, 6:01:22 PM7/6/06
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<michael...@worldnet.att.net> wrote in message
news:1152221804.5...@j8g2000cwa.googlegroups.com...
I can hear it now: "Yes, but they're still mice. Call us when one of them
gives birth to a cat."

bullpup

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Jul 6, 2006, 7:15:26 PM7/6/06
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<michael...@worldnet.att.net> wrote in message
news:1152221804.5...@j8g2000cwa.googlegroups.com...
>

<Obligatory creationist dismissal>

1 But it's still a mouse!

2 Moths, mice, same difference, big deal!

3 All mutations are bad! (But the mutation increases the probability of
sucessful reproduction.) All mutatons are bad!

4 (Stuffs head up arse) <muffled mumbling> I can't hear you!</muffled
mumbling>

5 The genetic information for sand covered fur was always there!

6 So, where's the new and novel structure requred for proof of evolution?
Mice already had hair to begin with!

7 <Nashty-poop> So, how does that same anyone's life? </Nashty-poop>

8 <nando> Who owns the decision point of the chance if the mutation where
things could go one way or the other, why didn't spiritual love appear in
the research? It's nothing but secular propaganda because it doesn't make
me feel *special*!</nando>

9 It was designed that way!

10 <ave> What does a different color of hare have to do with beach mice?
</ave>

11 <ed> I have a rock shaped like a mouse penis for sale on eBay, and it's
five feet long!</ed>

12 <McNameless> Ron Wyatt found the Ark shaped rock, and since they said the
islands were only about 6000 years old, that proves it Wyatt Ark is *the*
Ark!</McNameless>

</Obligatory creationist dismissal>

Boikat

michael...@worldnet.att.net

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Jul 6, 2006, 7:41:23 PM7/6/06
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bullpup wrote:
>
>[snip]
<Obligatory creationist dismissal>
>
> Boikat

There is a picture with the original article, so we can add:

It's obviously a stuffed mouse that has been spray-painted with Glidden
interior enamel.

-- Mike Palmer

Desertphile

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Jul 6, 2006, 10:14:53 PM7/6/06
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michael...@worldnet.att.net wrote:

> July 07, 2006
> An Evolution Saga: Beach Mice Mutate and Survive
>
> It's a pitiless lesson-adapt or die-but the sand-colored mice that
> scurry around the beaches of Florida's Gulf Coast seem to have learned
> the lesson well. Now researchers have identified a genetic mutation
> that underlies natural selection for the sand-matching coat color of
> the beach mice, an adaptive trait that camouflages them from aerial
> predators.

Yes, but they are STILL moths!

Oh, wait. That's a different argument.

> In the July 7, 2006, issue of the journal Science, evolutionary
> geneticist Hopi Hoekstra and colleagues at the University of

"Hopi Hoekstra?!" What a great name!

> California, San Diego, report that a single mutation causes the
> lifesaving color variation in beach mice (Peromyscus polionotus) and
> provides evidence that evolution can occur in big leaps.

Note that it is also a single gene in humans that controls skin color.

Desertphile

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Jul 6, 2006, 10:22:29 PM7/6/06
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bullpup wrote:

Awww hell: you beat me to it.

> 3 All mutations are bad! (But the mutation increases the probability of
> sucessful reproduction.) All mutatons are bad!

3b "It was a loss of information that made the mice sand-colored."

> 4 (Stuffs head up arse) <muffled mumbling> I can't hear you!</muffled
> mumbling>

That's 90% of Creationists right there.

> 5 The genetic information for sand covered fur was always there!

5b "It survived the flood in Noah's sister-in-law, along with
gonorrhea, tuberculosis, and Mycobacterium leprae!"

> 6 So, where's the new and novel structure requred for proof of evolution?
> Mice already had hair to begin with!

Hee! That's a good 'un.

> 7 <Nashty-poop> So, how does that [save] anyone's life? </Nashty-poop>

7b "And duz the mice wan' fries wid' 'dat?"

> 8 <nando> Who owns the decision point of the chance if the mutation where
> things could go one way or the other, why didn't spiritual love appear in
> the research? It's nothing but secular propaganda because it doesn't make
> me feel *special*!</nando>

Wow. You got him down pat!

> 9 It was designed that way!
>
> 10 <ave> What does a different color of hare have to do with beach mice?
> </ave>
>
> 11 <ed> I have a rock shaped like a mouse penis for sale on eBay, and it's
> five feet long!</ed>

11b "That wasn't a mouse: it was Bill Clinton."

> 12 <McNameless> Ron Wyatt found the Ark shaped rock, and since they said the
> islands were only about 6000 years old, that proves it Wyatt Ark is *the*
> Ark!</McNameless>

13 <Ray Martinez>I'm writing a research paper on these mice right now
proving they did not evolve and are not brown and actually have six
legs and I'll publish this research paper in April.</Ray Martinez>

> </Obligatory creationist dismissal>
>
> Boikat

Nic

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Jul 6, 2006, 10:40:32 PM7/6/06
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Not bad for a single mutation though. Does anyone know how many loci
are different for the Manchester moths?

David Wilson

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Jul 7, 2006, 1:24:07 PM7/7/06
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In article <1152229283.0...@s26g2000cwa.googlegroups.com> on

July 6th in talk.origins michael...@worldnet.att.net wrote:

> bullpup wrote:
> >
> >[snip]
> <Obligatory creationist dismissal>
> >
> > Boikat
>

> There is a picture with the original article, ...

It was faked by gluing dead mice to the tree trunks.

---------------------------------------------------------------------
David Wilson

SPAMMERS_fingers@WILL_BE_fwi_PROSECUTED_.net.au
(Remove underlines and upper case letters to obtain my email address.)

Kermit

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Jul 7, 2006, 1:27:12 PM7/7/06
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bullpup wrote:
> <michael...@worldnet.att.net> wrote in message
<snip>

>
> <Obligatory creationist dismissal>
>
> 1 But it's still a mouse!
>
> 2 Moths, mice, same difference, big deal!
>
> 3 All mutations are bad! (But the mutation increases the probability of
> sucessful reproduction.) All mutatons are bad!
>
> 4 (Stuffs head up arse) <muffled mumbling> I can't hear you!</muffled
> mumbling>
>
> 5 The genetic information for sand covered fur was always there!
>
> 6 So, where's the new and novel structure requred for proof of evolution?
> Mice already had hair to begin with!
>
> 7 <Nashty-poop> So, how does that same anyone's life? </Nashty-poop>
>
> 8 <nando> Who owns the decision point of the chance if the mutation where
> things could go one way or the other, why didn't spiritual love appear in
> the research? It's nothing but secular propaganda because it doesn't make
> me feel *special*!</nando>
>
> 9 It was designed that way!
>
> 10 <ave> What does a different color of hare have to do with beach mice?
> </ave>
>
> 11 <ed> I have a rock shaped like a mouse penis for sale on eBay, and it's
> five feet long!</ed>
>
> 12 <McNameless> Ron Wyatt found the Ark shaped rock, and since they said the
> islands were only about 6000 years old, that proves it Wyatt Ark is *the*
> Ark!</McNameless>
>
> </Obligatory creationist dismissal>
>

14 <robin> I have posted here many times, trying to be fair and
explaining that I embrace many possibilites, but the Creationists are
upset. While it's true that Darwin didn't disown the racist
implications in his books, he really didn't do worse than many of his
contemporaries, and the English gentlemen were hard pressed to explain
themselves in any event. I think there are many possibilities in
evolutionism, just as there are in the glory of True Christian love. I
wish you people could consider the possibility that God used evolution
to accomplish his goal, that science is not necesarily unrighteous, and
Darwin, while unwitting and flawed, was his spokesman on this issue.
Compare Darwin's racism to Thomas Merton's "Seven Storey Mountain", and
see how science could be. </robin>


> Boikat
Kermit

Dwib

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Jul 7, 2006, 1:52:45 PM7/7/06
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michael...@worldnet.att.net wrote:
> July 07, 2006
> An Evolution Saga: Beach Mice Mutate and Survive
> It's a pitiless lesson-adapt or die-but the sand-colored mice that
> scurry around the beaches of Florida's Gulf Coast seem to have learned
> the lesson well. Now researchers have identified a genetic mutation
> that underlies natural selection for the sand-matching coat color of
> the beach mice, an adaptive trait that camouflages them from aerial
> predators.

This sounds more like an example of "survival of the fittest".

I mean, it's not like "the mice adapted a new hair color". The hair
color was selected because those mice survived predation.

Perhaps I'm splitting hairs.

Dwib

hersheyhv

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Jul 7, 2006, 9:19:29 PM7/7/06
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Life's a beach and if you are the wrong color, you die.
>
> More at:
> http://www.hhmi.org/news/hoekstra20060707.html

TCE

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Jul 7, 2006, 9:39:25 PM7/7/06
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15 <topmind> This is exactly what SETI can't prove and I've been
telling you that all along. Those mice were genetically altered by
alien spores easily found by generic pattern searching based on an
algorithm I don't understand. It also proves you're all part of a
conspiracy to suppress the true nature of the universe. Talk about
calling the camel a pot. </topmind>

---
Strange

nightlight

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Jul 7, 2006, 10:51:49 PM7/7/06
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michael...@worldnet.att.net wrote:

> Now researchers have identified a genetic mutation
> that underlies natural selection for the sand-matching
> coat color of the beach mice, an adaptive trait that

> camouflages them from aerial predators....

It doesn't appear they have shown that the mutation
was _random_. They only found a variant of a gene
which is responsible for the lighter color.

a) If the given population size for a given time can
produce altogether N mutations for all individuals,

b) and if there are total of T theoretically possible
mutations at a comparable distance from the baseline
mice genome as the Mc1r mutation they found,

then the probability that this mutation will happen by
chance at least once in these N available tries is:

P(N,T) = 1 - (1-1/T)^N ~ 1 - exp(-N/T) ... (1)

For small values of N/T this is approximately:

P(N,T) ~ N/T ... (2)

(If there are F favorable color mutations among T, then
N/T in (2) would be multiplied by F. That refinement is
irrelevant for the point being made below.)

I don't see in the article any hint of estimates for P(N,T)
in order to establish what are the odds that a _random_ mutation
can "find" the right solution (any of the F favorable color mutations)
in the given number of tries N.

They need to estimate P(N,T), then show that P(N,T) is fairly
high e.g. 50% or above in order to claim that neo-Darwinian model
(ND = RM + NS = Random Mutation + Natural Selection) has better
than 50% chance of producing this adaptation. Otherwise,
what is left is guided (intelligent) mutation.

Hence, this particular discovery as it stands, seems at
least as favorable to ID = IM + NS as to ND = RM + NS,
since all they have shown is the existence of M + NS,
a fact consistent with ID and ND models of evolution.


Windy

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Jul 7, 2006, 11:41:22 PM7/7/06
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nightlight wrote:
> michael...@worldnet.att.net wrote:
> > Now researchers have identified a genetic mutation
> > that underlies natural selection for the sand-matching
> > coat color of the beach mice, an adaptive trait that
> > camouflages them from aerial predators....
>
> It doesn't appear they have shown that the mutation
> was _random_. They only found a variant of a gene
> which is responsible for the lighter color.
>
> a) If the given population size for a given time can
> produce altogether N mutations for all individuals,
>
> b) and if there are total of T theoretically possible
> mutations at a comparable distance from the baseline
> mice genome as the Mc1r mutation they found,

Ooo, fancy words. What is this "baseline mice genome"? Are the baseline
mice kept in a vault somewhere for comparisons?

> then the probability that this mutation will happen by
> chance at least once in these N available tries is:
>
> P(N,T) = 1 - (1-1/T)^N ~ 1 - exp(-N/T) ... (1)
>
> For small values of N/T this is approximately:
>
> P(N,T) ~ N/T ... (2)

No, the possibility of independent events (T) does not bring down the
probability of a given nucleotide from mutating, moron.

> They need to estimate P(N,T), then show that P(N,T) is fairly
> high e.g. 50% or above in order to claim that neo-Darwinian model
> (ND = RM + NS = Random Mutation + Natural Selection) has better
> than 50% chance of producing this adaptation. Otherwise,
> what is left is guided (intelligent) mutation.

The goalposts are moving in a completely new direction, I'll give you
that.

> Hence, this particular discovery as it stands, seems at
> least as favorable to ID = IM + NS as to ND = RM + NS,
> since all they have shown is the existence of M + NS,
> a fact consistent with ID and ND models of evolution.

So the designer actively intervened in the evolution of these mice
during the last 6000 years? Interesting.... how, exactly?

-- w.

nightlight

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Jul 8, 2006, 2:59:45 AM7/8/06
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Windy wrote:
>
>>a) If the given population size for a given time can
>> produce altogether N mutations for all individuals,
>>
>>b) and if there are total of T theoretically possible
>> mutations at a comparable distance from the baseline
>> mice genome as the Mc1r mutation they found,
>
>
> Ooo, fancy words. What is this "baseline mice genome"? Are the baseline
> mice kept in a vault somewhere for comparisons?

I called "baseline genome" the initial state of the genome of
the entire population. That is a set of DNA configurations, call
it S0 (initial set), which is a subset of the combinatorial space
S1, consisting of all DNA configurations which are at a distance
of 1 mutation away from elements of S0.

The number of elements in the set S1 was denoted in (b) as T. Now,
the adaptation process for the given population size and the
given duration will be able to explore some set of points (DNA
configurations) from the set S1, call it SN, starting from
various points in S0. The size of the set SN was denoted as
N in (a).

For the argument being made, it doesn't matter whether we can
compute numbers T and N in practice with present-day technology.
We are discussing different mathematical models of the observed
process and we only need to know that such finite sets S0, S1
and SN exist (and thus have sizes, such as integers T and N),
as mathematical elements of the models. The neo-Darwinian model
is one conceivable way to construct set SN from S0 -- it says
that the N points of SN are chosen randomly from the set S1
(of all configurations which are 1 mutuation away from S0).

That model then implies certain probability for the adaptation to
occur, as indicated in eq. (1). Again, it doesn't matter whether
we can presently compute P(N,T). It only matters that neo-Darwinian
model mathematically implies some P(N,T), a number that exists
whether we can calculate it at present or not.

In contrast, the ID model says that those N points are not
chosen randomly from S1, but are guided by some 'intelligent
agency' which allows it to find favorable configurations
from S1 faster than the random search does i.e. the ID model
says that if we observe a series of such adaptation processes,
then the rate of observed favorable adaptations will be
greater than the rate predicted by the neo-Darwinian model
(implied by particular P(N,T) in each process instance).

The point of my argument is that there is nothing in the article
for neo-Darwinians to crow about. All that was shown is that
the adaptation process consisted of a certain mutation plus the
natural selection i.e. they observed M + NS. The neo-Darwinian
model requires _RM_ + NS.

To show that their observation favors neo-Darwinian model, they
would have to obtain prediction of that model, at least some
rough estimate for P(N,T), and compare it to the observed facts
(the appearance of the favorable mutation for the given population
size and duration). If the ND model estimate for P(N,T) turns
out much smaller than 1, then the ND model is not a probable
mechanism behind the observed adpatation. Of course, the ND
model is not excluded by the P(N,T) << 1, since random mutation
can in principle produce the observed result. It can only be
shown to be a highly improbable mechanism for the observed
adaptation and one would have to consider the remaining
more probable possibility, the guided mutations.

>
>>then the probability that this mutation will happen by
>>chance at least once in these N available tries is:
>>
>> P(N,T) = 1 - (1-1/T)^N ~ 1 - exp(-N/T) ... (1)
>>
>>For small values of N/T this is approximately:
>>
>> P(N,T) ~ N/T ... (2)
>
>
> No, the possibility of independent events (T) does not bring down the
> probability of a given nucleotide from mutating, moron.
>

Where did I "bring down" any probability. If you roll a dice with T=6
possible outcomes, N=2 times, the probability that you will _not_ get,
say, number 5 in those 2 throws, is P(no_5) = (1-1/6)^2. Hence the
probability that you will get 5 at least once is 1 - P(no_5) =
1 - (1-1/6)^2, which is what eq. (1) is for some general numbers T
and N (which are the sizes of sets S1 and SN). Now Mr. Genius, show
us your formulae for this type of probabilities.

>>They need to estimate P(N,T), then show that P(N,T) is fairly
>>high e.g. 50% or above in order to claim that neo-Darwinian model
>>(ND = RM + NS = Random Mutation + Natural Selection) has better
>>than 50% chance of producing this adaptation. Otherwise,
>>what is left is guided (intelligent) mutation.
>
>
> The goalposts are moving in a completely new direction, I'll give you
> that.
>

What goalpost has moved? I am saying that there is nothing in the
reported result that suggests _random_ mutation is responsible for
the observed adaptation. At best it shows that the particular
mutation they found was responsible. But they show nothing that
would indicate whether the mutation was random or guided/intelligent.

As already explained, the neo-Darwinian random mutation model
implies certain probabilty P(N,T) of occurrence of particular
adaptation. To claim that their oobservation supports the
neo-Darwinian model, they would need to estimate this P(N,T)
and compare its implied rates favorable mutations to those
observed. They do nothing of the sort. Their empirical result
is completely non-discriminating between the ID and ND models
of the observed adaptation.


>
>>Hence, this particular discovery as it stands, seems at
>>least as favorable to ID = IM + NS as to ND = RM + NS,
>>since all they have shown is the existence of M + NS,
>>a fact consistent with ID and ND models of evolution.
>
>
> So the designer actively intervened in the evolution of these mice
> during the last 6000 years? Interesting.... how, exactly?

There could be an intelligent agency guiding mutation faster than
random search toward the favorable DNA configuration. We do know
that numerous 'intelligent agencies' do exist in nature, such
as human or animal brains, immune systems and variety of other
intelligent networks (complex systems) at all scales. There is
no a priori reason why the biochemical reaction network of a
cell, which in turn is a sub-net in a hierarchy of larger
adaptable networks (organism, population, ecosystem), cannot
be at least a part of the 'intelligent agency' guiding mutations
faster than a purely random process. After all, we know that
some other perfectly natural processes do exist which guide
mutations purposefully (e.g. those occurring in brains of
molecular biologists while designing some new GM plant).
There is no fundamental reason why those known intelligent
processes guiding mutations are the only ones that can
exist.

There is also no a priori reason why the biochemical
reaction network of a cell has to be the innermost/smallest
or the most important such network implementing the
'intelligent agency' which guides the mutations. For
example, our physical space-time is meaningful (within
present-day physics) down to Planck scale which is 1e-33m.
The elementary particles, which are elemental building
blocks for atoms, molecules, cells, organs, organisms,
human brains, human societies, sciences and technologies,
are above the scale of 1e-16m. Hence, there are as many
orders of magnitude between the Planckian scale objects
and our 'elementary' particles as there are between the
'elementary' particles and the intelligent agencies
built from them (e.g. human brain which is at the
scale ~ 1e-1m). Thus, there is as much space for
Planckian scale objects to build complex intelligent
networks below the levels of our elementary particles
as there is between these particles and us.

The frequencies at which these Planckian objects
interact are 1e16 times faster than those occurring
between our elementary particles i.e. any complex
networks (distributed computers) built up on Planckian
scale objects would run 1e16 times faster than the
networks built from our 'elementary particles' (our
brains and technologies). Now, try extrapolating where
the evolution at our scale, including our science and
technology, might be at some future time which is
1e16 times longer than the few billions years we had
to evolve, biologically and culturally, so far. It is
beyond what we could imagine.

Hence, it is perfectly conceivable that our physical,
chemical, biological... laws are an extremely crude
picture of an activity by an unimaginably powerful
underlying intelligence (vast distributed computer
running 1e16 times faster and having (1e16)^3 ~ 1e50
times more components than the intelligent processes
we are familiar with at our level). In addition to
providing support for ID model of evolution, this
kind of model could also be a rational alternative
to the 'anthropic principle' in explaining the fine
tuning of physical constants.


In any case, these are just couple ways one might
conceive the nature of the 'intelligent agency'
guiding mutations and evoution.


Windy

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Jul 8, 2006, 8:54:47 AM7/8/06
to

OK.. if favorable adaptations occur at a high rate, this is evidence
for ID? What about if favorable adaptations did not occur or occur at a
lower rate? Is that evidence against ID?

> The point of my argument is that there is nothing in the article
> for neo-Darwinians to crow about.

Sez you.

> All that was shown is that
> the adaptation process consisted of a certain mutation plus the
> natural selection i.e. they observed M + NS. The neo-Darwinian
> model requires _RM_ + NS.

> To show that their observation favors neo-Darwinian model, they
> would have to obtain prediction of that model, at least some
> rough estimate for P(N,T), and compare it to the observed facts
> (the appearance of the favorable mutation for the given population
> size and duration).

No, *you* are adding an unnecessary intelligent agent into the equation
and making the explanation more complex. It is your job to prove that
the process is non-random.

> >>then the probability that this mutation will happen by
> >>chance at least once in these N available tries is:
> >> P(N,T) = 1 - (1-1/T)^N ~ 1 - exp(-N/T) ... (1)
> >>
> >>For small values of N/T this is approximately:
> >>
> >> P(N,T) ~ N/T ... (2)
> >
> > No, the possibility of independent events (T) does not bring down the
> > probability of a given nucleotide from mutating, moron.
>
> Where did I "bring down" any probability. If you roll a dice with T=6
> possible outcomes, N=2 times, the probability that you will _not_ get,
> say, number 5 in those 2 throws, is P(no_5) = (1-1/6)^2. Hence the
> probability that you will get 5 at least once is 1 - P(no_5) =
> 1 - (1-1/6)^2, which is what eq. (1) is for some general numbers T
> and N (which are the sizes of sets S1 and SN). Now Mr. Genius, show
> us your formulae for this type of probabilities.

The genome is not a die. Mutations can occur independently of other
mutations (but in rare occasions don't, but that is irrelevant here).
At the very least you would have to represent all nucleotides with
their own dice. Then *each* nucleotide has some probability of mutating
represented by the mutation rate. Adding more nucleotides to your
observation is like adding more dice, not adding more sides to the die.
(Which is what you are doing now with your assumption that T=possible
outcomes).

> >>They need to estimate P(N,T), then show that P(N,T) is fairly
> >>high e.g. 50% or above in order to claim that neo-Darwinian model
> >>(ND = RM + NS = Random Mutation + Natural Selection) has better
> >>than 50% chance of producing this adaptation. Otherwise,
> >>what is left is guided (intelligent) mutation.
> >
> > The goalposts are moving in a completely new direction, I'll give you
> > that.
>
> What goalpost has moved? I am saying that there is nothing in the
> reported result that suggests _random_ mutation is responsible for
> the observed adaptation. At best it shows that the particular
> mutation they found was responsible. But they show nothing that
> would indicate whether the mutation was random or guided/intelligent.

We can consider guided mutation if someone presents a hypothesis that
explains the observed adaptation better. Random mutation is the null
hypothesis and you have to present evidence against it yourself.

> >>Hence, this particular discovery as it stands, seems at
> >>least as favorable to ID = IM + NS as to ND = RM + NS,
> >>since all they have shown is the existence of M + NS,
> >>a fact consistent with ID and ND models of evolution.
> >
> > So the designer actively intervened in the evolution of these mice
> > during the last 6000 years? Interesting.... how, exactly?
>
> There could be an intelligent agency guiding mutation faster than
> random search toward the favorable DNA configuration.

And *how* is it doing that? Devise an experiment to test it.

What are you smoking?

> Hence, it is perfectly conceivable that our physical,
> chemical, biological... laws are an extremely crude
> picture of an activity by an unimaginably powerful
> underlying intelligence (vast distributed computer
> running 1e16 times faster and having (1e16)^3 ~ 1e50
> times more components than the intelligent processes
> we are familiar with at our level). In addition to
> providing support for ID model of evolution, this
> kind of model could also be a rational alternative
> to the 'anthropic principle' in explaining the fine
> tuning of physical constants.

So we're in the Matrix?

-- w.

Kermit

unread,
Jul 8, 2006, 9:42:42 AM7/8/06
to

Windy wrote:
> nightlight wrote:
> > Windy wrote:

<snip OC pseudo-equations>

Apparently it's time to acknowledge a new class of anti-evolutionists -
the Matrixers (Matrices?). They may or not be religious, but if so
they're more mystics ("Is that a real poncho, or is that a Sears
poncho?") than biblical literalists.

This is not the first time I have heard of a "universe as computer"
scenario, but they seem to be on the rise since those movies came out.

I have often presented a Matrix as one alternative to mainstream
evolutionary science, but I always present it as a non-testable model -
it fits the facts, but there is no way to get supporting *or refuting
evidence, so it doesn't matter how you try to present the null
hypothesis.

I suggest God is a nerd living in his Mom's basement, who can't get a
date, who is playing The Sims version 47 or somesuch. The ones who take
it seriously always see the computer itself as wise and conscious, and
something with which we will someday meld or something which dispenses
power or knowledge, etc. It may be true, but until Norbert the
Omnipotent Nerdness manifests himself to us subroutines, there would be
no way to confirm the universe as virtual reality, even using math :P

Besides, like aliens seeding life on Earth, it just pushes the ultimate
questions back further out of reach. I do not see this as a desirable
possibility.

>
> -- w.

Kermit,
who needs both hands to bend the spoon, just like Uri Gellar

hersheyhv

unread,
Jul 8, 2006, 11:54:44 AM7/8/06
to

nightlight wrote:
> michael...@worldnet.att.net wrote:
>
> > Now researchers have identified a genetic mutation
> > that underlies natural selection for the sand-matching
> > coat color of the beach mice, an adaptive trait that
> > camouflages them from aerial predators....
>
> It doesn't appear they have shown that the mutation
> was _random_. They only found a variant of a gene
> which is responsible for the lighter color.

All variants of genes start out as mutations. Although there are some
"domesticated" mutational processes that occur at a higher (sometimes
strikingly higher) rate in particular cells (e.g. our immune system or
the switch of mating type in haploid yeast), even these are largely
random (wrt need) events. There is no reason to believe that the
single mutational event that produced the color variant described here
is any more or less random (wrt need) than the mutation of bacteria to
strep resistance or the mutation(s) --there are several -- that
produces melanic moths or melanic mice in the desert southwest. The
mutation that produces this color variant happens from time to time.
Since you are the one claiming that this mutation is somehow different
from the vast, nay, overwhelming (in the sense that 99.99999% or more
is overwhelming), majority of mutations -- which occur from time to
time without respect to the need for the mutation, it is *your*
responsibility to demonstrate why this mutation is different from
almost all other mutations.

That said, if the mutation is a point mutation, the likely probability
of it occurring in any one individual offspring is between 10^-6 and
10^-11 (with a modal peak around 10^-8 to 10^-9). That is, admittedly,
a wide range of probabilities (because the rate of mutation *is*
dependent upon local features of sequence and the type of point
mutation involved -- e.g. transversions are rarer than transitions, not
because the rate varies according to need).

It would also help to know if the phenotypic effect is dominant or
recessive. [If recessive, there is a probability that the frequency of
the allele in the *population* of mice that invaded these islands
already had the allele.] If dominant, OTOH, when it occurred in the
population on the island, its phenotypic effect would be observed (or
not observed by predators in this case) immediately.

This probability of the mutation (actually this would only be if the
trait was dominant) needs to be multiplied by the mean number of mice
on the islands and the number of generations until the mutation
occurred. Then there would have to be a factor to take account of the
probability that that particular time the beneficial mutation would be
lost by chance. That would give you a very rough idea of the
probability of this event. Without even knowing the other numbers, I
can say that the probability of such a mutational event occurring
sometime within 6000 years is certainly within the realms of
probability.

For recessive traits, the more probable starting point is the frequency
of the allele in the founding population on the islands, which can be
significantly higher than the mutation frequency. Then the amount of
inbreeding would play a significant role in producing the mice with the
now beneficial variant trait, resulting in their exposure to the
selective environment.

> a) If the given population size for a given time can
> produce altogether N mutations for all individuals,
>
> b) and if there are total of T theoretically possible
> mutations at a comparable distance from the baseline
> mice genome as the Mc1r mutation they found,
>
> then the probability that this mutation will happen by
> chance at least once in these N available tries is:
>
> P(N,T) = 1 - (1-1/T)^N ~ 1 - exp(-N/T) ... (1)
>
> For small values of N/T this is approximately:
>
> P(N,T) ~ N/T ... (2)
>
> (If there are F favorable color mutations among T, then
> N/T in (2) would be multiplied by F. That refinement is
> irrelevant for the point being made below.)
>
> I don't see in the article any hint of estimates for P(N,T)
> in order to establish what are the odds that a _random_ mutation
> can "find" the right solution (any of the F favorable color mutations)
> in the given number of tries N.
>
> They need to estimate P(N,T), then show that P(N,T) is fairly
> high e.g. 50% or above in order to claim that neo-Darwinian model
> (ND = RM + NS = Random Mutation + Natural Selection) has better
> than 50% chance of producing this adaptation. Otherwise,
> what is left is guided (intelligent) mutation.

No mutation has ever been observed to be guided by any intelligence.
You are proposing a mechanism (guided mutation or mutation that occurs
as a result of need) that has been diligently searched for and has
never been observed. Lamarckism is dead. Killed by a lack of
evidence. If you can resurect that particular rancid corpse by
presenting evidence that *some* specific point mutations (which is what
we are talking about) occur as a result of need please to so. Until
then, you are proposing a mechanism that has uniformly and consistently
has been shown not to occur in nature. If your claim is that an
intelligent agent capable of altering the genome of the island mice was
responsible, one way to support your claim would be to present
empirical evidence of such an intelligent agent capable of performing
such genomic magic having existed at the right time and place.

> Hence, this particular discovery as it stands, seems at
> least as favorable to ID = IM + NS as to ND = RM + NS,
> since all they have shown is the existence of M + NS,
> a fact consistent with ID and ND models of evolution.

Not really. ID = IM + NS requires the existence of the hypothetical
"I" agent, for which there is zero evidence. RM, OTOH, is consistent
with all known mechanisms of natural mutation. And the probability of
RM producing a point mutation for any normal point mutation variant
within, say, 500 years, with a mean population size of, say, 10,000
mice with 2-3 generations per year, is actually pretty good. And if
the mutant allele is recessive, the starting point might not involve a
"new" mutation but a variant that is already present (but it would be a
deleterious variant in the other environment). That the same variant
can be deleterious in one environment and beneficial in another would
simply mean something that creationists have a hard time grasping, that
the terms "deleterious" and "beneficial" are conditional adjectives,
not inherent properties, of the variant being described.

Because the ID = IM + NS hypothesis requires something that is neither
supported by independent evidence (unlike the 'random wrt need' nature
of point mutations) nor is such an entity necessary to explain what has
been observed, the famous blade of Ockham must slice it off.

nightlight

unread,
Jul 8, 2006, 12:06:37 PM7/8/06
to
Windy wrote:

>>In contrast, the ID model says that those N points are not
>>chosen randomly from S1, but are guided by some 'intelligent
>>agency' which allows it to find favorable configurations
>>from S1 faster than the random search does i.e. the ID model
>>says that if we observe a series of such adaptation processes,
>>then the rate of observed favorable adaptations will be
>>greater than the rate predicted by the neo-Darwinian model
>>(implied by particular P(N,T) in each process instance).
>
>
> OK.. if favorable adaptations occur at a high rate, this is evidence
> for ID?

It would be an evidence that neo-Darwinian model (RM+NS) is
an unlikely explanation of the observed adaptation and that
a more efficient (than random) search algorithm is responsible
for the adaptation. By convention, we can call this more
efficient algorithm an 'intelligent' or guided mutation,
or generally an ID algorithm.

> What about if favorable adaptations did not occur or occur at a
> lower rate? Is that evidence against ID?
>

I think you meant "higher rate" not "lower rate" above (otherwise
what you wrote is a gibberish). Assuming this correction,
it would be an evidence that the 'intelligent agency' (IA) model
is not necessary to explain that particular adaptation. That
doesn't exclude a need for the IA model in order to explain
some other adaptations. It doesn't even exclude the IA
participation in that example. It only means that what
was observed does not discriminate for or against IA and
that one might need additional data to make such discrimination.

(The latter observation is important since a coherent IA theory
should not cherry pick in which processes the IA participates
and in which it choses not to be involved with.)

Consider an 'intelligent agency' which we know to exist in nature
(human brain) applying its efforts to stock market trading. One
could trade using all his knowledge and foresight and not do
any better than chance on any particular day or a week or
throughout the whole trading career. Could you declare that
he was picking randomly if his gains don't exceed random
ones for some given span of time? You can't. You would
need more data and possibly different kind of data (such as
direct observation of his trading or an interview) to support
such conclusion.

In any case, what is your point? How is your question related
to my observation that there is nothing in the article, no
calculation or estimation of predictions of any mutation model
(random or any other), let alone any comparison of such
prediction with the empirical facts observed. There is simply
nothing there for neo-Darwinians to crow about. If you saw
something to crow about, you haven't shown as yet what that
might be.

Instead, so far you have been quite desperate in trying
to divert the discussion to your little collection of pet
strawmen while showing off your repertoire of explitives.
Either say something of substance or stay quiet and let
somene who may have a better understanding of the subject
being discussed have a turn defending the neo-Darwinian
model. Your response was and continues to be so inpet that
you may well be a supporter of Pat Robertson's theory of
evolution acting here under the false flag, trying to
make neo-Darwinians look stupid and primitive.

>
>>The point of my argument is that there is nothing in the article
>>for neo-Darwinians to crow about.
>
>
> Sez you.

Well, can you cite some calculation from the paper demonstrating
that the observed mutation was 'most probably' (e.g. 50% or
better) random.

>>Where did I "bring down" any probability. If you roll a dice with T=6
>>possible outcomes, N=2 times, the probability that you will _not_ get,
>>say, number 5 in those 2 throws, is P(no_5) = (1-1/6)^2. Hence the
>>probability that you will get 5 at least once is 1 - P(no_5) =
>>1 - (1-1/6)^2, which is what eq. (1) is for some general numbers T
>>and N (which are the sizes of sets S1 and SN). Now Mr. Genius, show
>>us your formulae for this type of probabilities.
>
>
> The genome is not a die. Mutations can occur independently of other
> mutations (but in rare occasions don't, but that is irrelevant here).
> At the very least you would have to represent all nucleotides with
> their own dice. Then *each* nucleotide has some probability of mutating
> represented by the mutation rate. Adding more nucleotides to your
> observation is like adding more dice, not adding more sides to the die.
> (Which is what you are doing now with your assumption that T=possible
> outcomes).

In this case they were talking about a particular _single_
nucleotide mutation (not some chain of mutations compunding
in the presence of natural selection which would require conditional
probabilities in the reasoning). The number of sides for
the neo-Darwinian dice in the case of single nucleotide mutation
is then simply the number of all DNA configurations which differ
from the starting configuration by a single nucleotide. Hence,
to roughly estimate the size of this set of configuration, the
number T, one would need to multiply number of nucleotides with
some average number of variants per nucleotide.

Note also that since radnom mutations model does not have a 'look
ahead' capability, and since natural selection occurs _after_
the mutation, you cannot reduce the size of T by discarding
'non-viable' mutations in your count of configurations that
RM has to explore. You have one configuration available,
viable or otherwise, per random mutation and only the natural
selection can decide what is viable and what unviable (hence
each try costs you one potentially available offspring).

Let's also note here that you're again not answering the original
objection: where does the paper compute any 'random mutation'
model predictions, much less compare such predictions with
the observed data? The argument you are pursuing, such as what
is the best way to obtain such estimates, is entirely irrelevant
since they haven't shown any way, optimal or subpotimal, to be
debated.


>>What goalpost has moved? I am saying that there is nothing in the
>>reported result that suggests _random_ mutation is responsible for
>>the observed adaptation. At best it shows that the particular
>>mutation they found was responsible. But they show nothing that
>>would indicate whether the mutation was random or guided/intelligent.
>
>
> We can consider guided mutation if someone presents a hypothesis that
> explains the observed adaptation better. Random mutation is the null
> hypothesis and you have to present evidence against it yourself.

The article does not make any estimates as to how any hypothesis,
radnom or any other, performs against the observed data. Hence
it provides no evidence in support or against any particular
mutation model. If you wish to crow that their empirical data
support 'RM' model, you need to calculate prediction of the RM
model and compare them to the data. Otherwise, in the absence of
any model calculations and comparisons to the data, the data is
neutral with respect to the mutation model. Absent any model
predictions, your "RM is the null hypothesis" is a vacuous
euphemism, providing precisely zero bits of information about
the nature of the observed mutation.


>>>So the designer actively intervened in the evolution of these mice
>>>during the last 6000 years? Interesting.... how, exactly?
>>
>>There could be an intelligent agency guiding mutation faster than
>>random search toward the favorable DNA configuration.
>
>
> And *how* is it doing that? Devise an experiment to test it.


There are plenty of ways that an 'intelligent agency' could exist
and perform directed mutations. I merely pointed out couple
possibilities which are not a priori excluded by the presently
known laws of physics.

We also already know that natural processes which intelligently
guide mutations exist in nature (e.g. brains of molecular
biologists). The empirically established existence of such
processes is a direct counter-example to a conjecture
that such natural processes are excluded by laws of nature.
They are obviously not excluded by the laws of nature since
they do exist in nature.

Hence your "point" about '6000 years', which is what I was
responding to above, is a vacuous strawman. Pat Robertson's
model of evolution is certainly not the sole alternative
to the neo-Darwinian model.


>>Hence, it is perfectly conceivable that our physical,
>>chemical, biological... laws are an extremely crude
>>picture of an activity by an unimaginably powerful
>>underlying intelligence (vast distributed computer
>>running 1e16 times faster and having (1e16)^3 ~ 1e50
>>times more components than the intelligent processes
>>we are familiar with at our level). In addition to
>>providing support for ID model of evolution, this
>>kind of model could also be a rational alternative
>>to the 'anthropic principle' in explaining the fine
>>tuning of physical constants.
>
>
> So we're in the Matrix?

I suppose, if one had to put it in terms understandible to
a simpleton whose science education consists of going to
the movies, one might put it that way.

nightlight

unread,
Jul 8, 2006, 1:34:29 PM7/8/06
to
hersheyhv wrote:

>>It doesn't appear they have shown that the mutation
>>was _random_. They only found a variant of a gene
>>which is responsible for the lighter color.
>
>

> random (wrt need) events. There is no reason to believe that the
> single mutational event that produced the color variant described here
> is any more or less random (wrt need) than the mutation of bacteria to
> strep resistance or the mutation(s) --there are several -- that
> produces melanic moths or melanic mice in the desert southwest.

You are confusing the absence of evidence due to 'no reason to
believe' (as far as you know) with the evidence of absence of
such phenomenon (directed mutation).

> That said, if the mutation is a point mutation, the likely probability
> of it occurring in any one individual offspring is between 10^-6 and
> 10^-11 (with a modal peak around 10^-8 to 10^-9).

You are confusing empirically observed rates of mutations
with the predictions of such rates by some mathematical model,
such as random mutation model. As explained in the first post,
the RM model is an assumption about the algorithm used to explore
the space of DNA configurations. Specifically, the RM assumes
that the 'next' configuration to be explored is randomly selected
among all accessible configurations (consistent with physical laws).
Like any such search algorithm, the RM assumption implies a certain
probability of success for a given space of physically accessible
configurations (size of which was denoted as number T in (b))
and given number of tries (denoted as number N in (a)). To test
whether the RM search algorithm is likely explanation of the
observed adaptation (under the given population size and time
constraints) one needs to estimate these spaces and compute
the RM implied probability. Only if the computed probability is
high enough, you can crow that the observation confirms the
RM model (as the likely mechanism). Neither you nor the article
provide any such RM model prediction.

The figures of empirical rates of mutations have no relation
with their origin. After all, there is also some empirical
rate of mutations which are known to be intelligently guided,
such as those within the bio-technology (in agriculture,
academic research etc). By your logic, merely measuring
the empirical rate of these mutations and citing the obtained
figure, "proves" that these mutations are random. Of course not.

The empirical rate of mutation is relevant only if you wish
to show that a mutation (of whatever nature) is responsible
for the observed adaptation. That is not being debated here.
We take for granted that the paper has demonstrated not just
the genetic nature of this adaptation but also found the
specific mutation responsible. Hence, your citations of
the empirical rates of mutations are a strawman argument in
the context of this debate.


> No mutation has ever been observed to be guided by any intelligence.

How about those in bio-technology? That merely shows that a
natural processes which guide mutations intelligently do
not contradict the natural laws. Such natural processes can
exist and do exist.

> You are proposing a mechanism (guided mutation or mutation that occurs
> as a result of need) that has been diligently searched for and has
> never been observed.

Again, you're confusing absence of evidence, or even the failure
to examine and recognize the evidence, with the evidence of
absence.

If you want to demonstrate that the mice adaptation discussed
shows that the search algorithm in the space of DNA configuration
was random (this was just a single nucleotide mutation, the
simplest case you can have), go ahead. Compute the prediction
of success for such random search algorithm for the given space
of possibilities (all configuration with one nucleotide change
away from the initial state) and the given number of tries
(which requires population sizes, conception rates, duration)
and show that this algorithm has a 'good' probability of success
under the constraints given.

Recall that ID and ND differ for these simple adaptations only
in the their search algorithm, in how each picks the 'next'
configuration to explore (which in turn implies probabilities
of success of each algorithm under any given constraints).


> If your claim is that an intelligent agent capable of
> altering the genome of the island mice was responsible,
> one way to support your claim would be to present
> empirical evidence of such an intelligent agent capable
> of performing such genomic magic having existed at the
> right time and place.

My claim is that the article shows nothing in favor or against
the ND = RM + NS vs ID = IM + NS models of adaptaion observed.
It shows only M + NS, which is common to both models. Hence
there is nothing here for neo-Darwinians to crow about.

As to what might be the nature of 'intelligent agency' guiding
the mutations, that is a separate issue from the point I was
making. We all agree that natural processes exist on Earth
which guide mutations intelligently (the natural processes
we call bio-technology or genetic engineering). Your argument
above seems to be based on conjecture that no such natural
process is consistent with natural laws. The direct
counter-example (pointing you to the existence of such
natural processes) invalidates your conjecture. Try
something better.


>>Hence, this particular discovery as it stands, seems at
>>least as favorable to ID = IM + NS as to ND = RM + NS,
>>since all they have shown is the existence of M + NS,
>>a fact consistent with ID and ND models of evolution.
>
>
> Not really. ID = IM + NS requires the existence of the hypothetical
> "I" agent, for which there is zero evidence.

This paper, which is what is I was referring to above, has no
discussion, let alone tests, of the I-agentcy hypothesis. Now, you
and I may have this or that view on the existence or plausibility
of the I-agency, but that is unrelated to what the paper and its
empirical facts show, or fail to show. In particular they do not
show that the observed adaptation and its genetic mechanism
favor any particular search algorithm, the RM or IM based method,
in the space of DNA configurations accessible to mutations.


> Because the ID = IM + NS hypothesis requires something that is neither
> supported by independent evidence (unlike the 'random wrt need' nature
> of point mutations) nor is such an entity necessary to explain
> what has been observed, the famous blade of Ockham must slice it
> off.


Ockham razor doesn't apply unless you can show that the
alternative models are equally consistent with the empirical
evidence. Merely failing to evaluate the consistency of the
alternative models A and B against the empirical evidence
does not allow you to declare that A is simpler, hence it
is a better model by Ockham's razor.

Otherwise, someone could have a "theory" A of free fall, which
says that all objects fall at a constant speed, then refuse
to make a specific prediction of his "theory" since by
_your_ interpretation of Ockham's razor, that prediction is
not necessary because his "theory" is preferable to the
alternative theory B, which says that the free fall motion
is accelerated, since theory A is simpler than theory B.


nightlight

unread,
Jul 8, 2006, 1:47:10 PM7/8/06
to
nightlight wrote:

> Windy wrote:
>
>> What about if favorable adaptations did not occur or occur at a
>> lower rate? Is that evidence against ID?
>>
>
> I think you meant "higher rate" not "lower rate" above (otherwise

> what you wrote is a gibberish). Assuming this correction, ...

Oops, your wording was merely grammatically incorrect (mixed up
tenses), but not ambiguous semantically as I suggested. Hence,
scratch my correction since my reply that followed the correction
responded to what you actually meant to say above.

Lee Bowman

unread,
Jul 8, 2006, 2:51:34 PM7/8/06
to
On Sat, 08 Jul 2006 13:34:29 -0400, nightlight
<nightli...@skip.omegapoint.com> wrote:

>hersheyhv wrote:

>This paper, which is what is I was referring to above, has no
>discussion, let alone tests, of the I-agentcy hypothesis. Now, you
>and I may have this or that view on the existence or plausibility
>of the I-agency, but that is unrelated to what the paper and its
>empirical facts show, or fail to show. In particular they do not
>show that the observed adaptation and its genetic mechanism
>favor any particular search algorithm, the RM or IM based method,
>in the space of DNA configurations accessible to mutations.

To go a step further with the interventionary model (ID = IM + NS),
would you consider as a possibility ID = IM + IS?
(or + ISS, 'Intelligently Specified Selection)?

> > Because the ID = IM + NS hypothesis requires something that is neither
> > supported by independent evidence (unlike the 'random wrt need' nature
> > of point mutations) nor is such an entity necessary to explain
> > what has been observed, the famous blade of Ockham must slice it
> > off.
>
>
>Ockham razor doesn't apply unless you can show that the
>alternative models are equally consistent with the empirical
>evidence. Merely failing to evaluate the consistency of the
>alternative models A and B against the empirical evidence
>does not allow you to declare that A is simpler, hence it
>is a better model by Ockham's razor.
>
>Otherwise, someone could have a "theory" A of free fall, which
>says that all objects fall at a constant speed, then refuse
>to make a specific prediction of his "theory" since by
>_your_ interpretation of Ockham's razor, that prediction is
>not necessary because his "theory" is preferable to the
>alternative theory B, which says that the free fall motion
>is accelerated, since theory A is simpler than theory B.

I agree. Given the observed complexity of biologic systems, I feel
that Ockham's Razor is an outdated philosophy, and quite risky to
invoke. Richard Dawkins once referred to it to rule out a supernatural
causation of life, stating that a naturalistic cause was simpler, and
thus more viable.

i.e. "God as an unnecessary rider in an otherwise perfectly acceptable
scientific theory of life's origins"

Didn't mean to take this thread in a new direction by the above
philosophical rant. Primarily wanted to get your (and others) take
on:

ID = IM + IS or
ID = IM + ISS

*assuming* an intelligent agency other than human existed

Windy

unread,
Jul 8, 2006, 4:52:25 PM7/8/06
to

nightlight wrote:
> Windy wrote:
(snip)

> > What about if favorable adaptations did not occur or occur at a
> > lower rate? Is that evidence against ID?
> >
> I think you meant "higher rate" not "lower rate" above (otherwise
> what you wrote is a gibberish). Assuming this correction,
> it would be an evidence that the 'intelligent agency' (IA) model
> is not necessary to explain that particular adaptation. That
> doesn't exclude a need for the IA model in order to explain
> some other adaptations. It doesn't even exclude the IA
> participation in that example. It only means that what
> was observed does not discriminate for or against IA and
> that one might need additional data to make such discrimination.
> (The latter observation is important since a coherent IA theory
> should not cherry pick in which processes the IA participates
> and in which it choses not to be involved with.)

Good. But you are aware, I trust, that a low rate of favourable
adaptations emerging in nature is often cited as evidence against
evolution? I was therefore wondering why now a high rate of favourable
adaptations is evidence against evolution, too. It couldn't be because
evolution skeptics are twisting their theories to accommodate all
possible results, now could it?

> There is simply
> nothing there for neo-Darwinians to crow about. If you saw
> something to crow about, you haven't shown as yet what that
> might be.

You haven't shown as yet why the null hypothesis of random mutation
should be discarded. Like it or not, that is the null hypothesis at
present. If you don't like it, do your own research.

> Instead, so far you have been quite desperate in trying
> to divert the discussion to your little collection of pet
> strawmen while showing off your repertoire of explitives.

Now I'm hurt. I would have used much better expletives if I'd known you
were counting, douchebag.

> Either say something of substance or stay quiet

Says a veritable veteran with a total of five posts.

> and let
> somene who may have a better understanding of the subject
> being discussed have a turn defending the neo-Darwinian
> model.

I imagine most people are rather turned off by your wordy,
self-important bullshit.

> Your response was and continues to be so inpet that

Perhaps you mean "inept"?

> you may well be a supporter of Pat Robertson's theory of
> evolution acting here under the false flag, trying to
> make neo-Darwinians look stupid and primitive.

Fuck you and the mouse you rode in on.

> >>Where did I "bring down" any probability. If you roll a dice with T=6
> >>possible outcomes, N=2 times, the probability that you will _not_ get,
> >>say, number 5 in those 2 throws, is P(no_5) = (1-1/6)^2. Hence the
> >>probability that you will get 5 at least once is 1 - P(no_5) =
> >>1 - (1-1/6)^2, which is what eq. (1) is for some general numbers T
> >>and N (which are the sizes of sets S1 and SN). Now Mr. Genius, show
> >>us your formulae for this type of probabilities.
> >
> > The genome is not a die. Mutations can occur independently of other
> > mutations (but in rare occasions don't, but that is irrelevant here).
> > At the very least you would have to represent all nucleotides with
> > their own dice. Then *each* nucleotide has some probability of mutating
> > represented by the mutation rate. Adding more nucleotides to your
> > observation is like adding more dice, not adding more sides to the die.
> > (Which is what you are doing now with your assumption that T=possible
> > outcomes).
>
> In this case they were talking about a particular _single_
> nucleotide mutation (not some chain of mutations compunding
> in the presence of natural selection which would require conditional
> probabilities in the reasoning). The number of sides for
> the neo-Darwinian dice in the case of single nucleotide mutation
> is then simply the number of all DNA configurations which differ
> from the starting configuration by a single nucleotide.

No, it's not the "number of sides", and I just explained why. Fine,
stay stupid.

> Let's also note here that you're again not answering the original
> objection: where does the paper compute any 'random mutation'
> model predictions, much less compare such predictions with
> the observed data?

Such computations are not customary since the body of evidence points
to mutations being random. Again, if you don't like it, do your own
research.

> >>What goalpost has moved? I am saying that there is nothing in the
> >>reported result that suggests _random_ mutation is responsible for
> >>the observed adaptation. At best it shows that the particular
> >>mutation they found was responsible. But they show nothing that
> >>would indicate whether the mutation was random or guided/intelligent.
> >
> > We can consider guided mutation if someone presents a hypothesis that
> > explains the observed adaptation better. Random mutation is the null
> > hypothesis and you have to present evidence against it yourself.
>
> The article does not make any estimates as to how any hypothesis,
> radnom or any other, performs against the observed data. Hence
> it provides no evidence in support or against any particular
> mutation model. If you wish to crow that their empirical data
> support 'RM' model, you need to calculate prediction of the RM
> model and compare them to the data. Otherwise, in the absence of
> any model calculations and comparisons to the data, the data is
> neutral with respect to the mutation model. Absent any model
> predictions, your "RM is the null hypothesis" is a vacuous
> euphemism, providing precisely zero bits of information about
> the nature of the observed mutation.

Sour grapes.

> >>>So the designer actively intervened in the evolution of these mice
> >>>during the last 6000 years? Interesting.... how, exactly?
> >>
> >>There could be an intelligent agency guiding mutation faster than
> >>random search toward the favorable DNA configuration.
> >
> > And *how* is it doing that? Devise an experiment to test it.
>
> There are plenty of ways that an 'intelligent agency' could exist
> and perform directed mutations. I merely pointed out couple
> possibilities which are not a priori excluded by the presently
> known laws of physics.
>
> We also already know that natural processes which intelligently
> guide mutations exist in nature (e.g. brains of molecular
> biologists).

They can't "guide mutations", they either accelerate the rate of random
mutations using mutagens or develop transgenic organisms through a
laborious process. The second approach tends to leave plenty of
physical evidence.

> Hence your "point" about '6000 years', which is what I was
> responding to above, is a vacuous strawman. Pat Robertson's
> model of evolution is certainly not the sole alternative
> to the neo-Darwinian model.

The mice have existed on the dunes for at most 6000 years (real years,
not biblical), hence the time limit for the adaptation. Way to read for
comprehension, dunce.

> >>Hence, it is perfectly conceivable that our physical,
> >>chemical, biological... laws are an extremely crude
> >>picture of an activity by an unimaginably powerful
> >>underlying intelligence (vast distributed computer
> >>running 1e16 times faster and having (1e16)^3 ~ 1e50
> >>times more components than the intelligent processes
> >>we are familiar with at our level). In addition to
> >>providing support for ID model of evolution, this
> >>kind of model could also be a rational alternative
> >>to the 'anthropic principle' in explaining the fine
> >>tuning of physical constants.
> >
> > So we're in the Matrix?
>
> I suppose, if one had to put it in terms understandible to
> a simpleton whose science education consists of going to
> the movies, one might put it that way.

Not really, but better that than a moron pushing idiotic word salad
without understanding a single thing about the probability of
mutations.

-- w.

nightlight

unread,
Jul 8, 2006, 6:29:22 PM7/8/06
to
Lee Bowman wrote:

> On Sat, 08 Jul 2006 13:34:29 -0400, nightlight
> <nightli...@skip.omegapoint.com> wrote:
>
>
>>hersheyhv wrote:
>
>
>>This paper, which is what is I was referring to above, has no
>>discussion, let alone tests, of the I-agentcy hypothesis. Now, you
>>and I may have this or that view on the existence or plausibility
>>of the I-agency, but that is unrelated to what the paper and its
>>empirical facts show, or fail to show. In particular they do not
>>show that the observed adaptation and its genetic mechanism
>>favor any particular search algorithm, the RM or IM based method,
>>in the space of DNA configurations accessible to mutations.
>
>
> To go a step further with the interventionary model (ID = IM + NS),
> would you consider as a possibility ID = IM + IS?
> (or + ISS, 'Intelligently Specified Selection)?
>
>
>>>Because the ID = IM + NS hypothesis requires something that is neither
>>>supported by independent evidence (unlike the 'random wrt need' nature
>>>of point mutations) nor is such an entity necessary to explain
>>>what has been observed, the famous blade of Ockham must slice it
>>>off.
>>
>>

>

> I agree. Given the observed complexity of biologic systems, I feel
> that Ockham's Razor is an outdated philosophy, and quite risky to
> invoke. Richard Dawkins once referred to it to rule out a supernatural
> causation of life, stating that a naturalistic cause was simpler, and
> thus more viable.
> i.e. "God as an unnecessary rider in an otherwise perfectly acceptable
> scientific theory of life's origins"

He was misapplying the Ockham's razor. The proper caveat was best
stated by A. Einstein: "Make everything as simple as possible,
but not simpler."

> Didn't mean to take this thread in a new direction by the above
> philosophical rant. Primarily wanted to get your (and others) take
> on:
>
> ID = IM + IS or
> ID = IM + ISS
>
> *assuming* an intelligent agency other than human existed

The selection of reproductive mates is an 'intelligent selection'
(IS & ISS). In my view the 'intelligence' (foresight, strategizing)
and the 'mind stuff' (the stuff that answers for 'you' a question:
what is it like to be such and such arrangement of atoms and
fields that make up 'you') is manifest not just in humans or
higher animals, and not just in 'live' or 'material' nature,
but in everything from the most elemental 'elementary' particles
and fields, through the larger complex systems (intelligent
networks) in the material and the abstract realms, such as
biochemcial reacton webs within cells, immune systems, animal
and human brains, technologies, sciences, languages, cultures,
religions, human societies, gene pools, ecosystems,...

I visualize the overall structure of this vast hierarchy of
mutually permeating, overlapping and nesting intelligent
networks and sub-networks, sharing the same elements
and motions, each network in 'pursuit of its own happiness',
as a gigantic, multi-dimensional crossword puzzle, with words
at one level serving as letters at the next level, and where
each 'letter' belongs to multitudes of 'words', 'super-words'...
all in unceasing, busy little motions at all levels and along
all dimensions, endlessly harmonizing itself in pursuit of an
ever more perfect 'solution', at ever higher levels. As the
near perfect harmonization is achieved at the lower/inner
levels, the motions of their elements become increasingly
more regular and repetitive (such as the simple periodic
oscillations at the level of physical particles and fields),
their creative spark extinguished and the disquietudes of
fragile individuality given away in return for a safe,
predicatable harmony and eternal fulfillment in serving
obediently the increasingly more delicate flame as it
advances its ever narrowing edge to the levels above.

In this kind of larger picture, the 'natural selection' and
'mutations' can be seen as slightly different forms of these
little harmonizing motions, where each organism is continually
adapting to (or harmonizing with) its environment and the
environment adapting/harmonizing with the organism. Each
seeks to become more predicatable to the other by harmonizing
its own motions to the internal model the other has of these
motions, while the respective models in turn are seeking to
anticipate the motions of the other as closely as possible.

Nic

unread,
Jul 8, 2006, 6:51:06 PM7/8/06
to

Not sure I see.

Intelligent selection is often used when an intelligent agent cannot
influence what is originally on offer. I mean if you're a would-be
meddler, then you can meddlingly select from a set you can't meddlingly
control, or you can simply meddlingly control. You wouldn't need to do
both.

Or am I missing the point?

Lee Bowman

unread,
Jul 8, 2006, 7:33:03 PM7/8/06
to
On 8 Jul 2006 15:51:06 -0700, "Nic" <harris...@hotmail.com> wrote:

>
>Lee Bowman wrote:

>>
>> ID = IM + IS or
>> ID = IM + ISS
>>
>> *assuming* an intelligent agency other than human existed
>
>Not sure I see.
>
>Intelligent selection is often used when an intelligent agent cannot
>influence what is originally on offer. I mean if you're a would-be
>meddler, then you can meddlingly select from a set you can't meddlingly
>control, or you can simply meddlingly control. You wouldn't need to do
>both.

Gene tweaking could entail an allele alteration (mutation) followed by
manual selection (IS or ISS).

Hmm ... how about ID = IAA + ISS

>
>Or am I missing the point?
>

What point? My ramblings are often pointless.

I know, how about IM instead of ID
(Intelligent Meddling)

Lee Bowman

unread,
Jul 8, 2006, 7:49:11 PM7/8/06
to
On Sat, 08 Jul 2006 18:29:22 -0400, nightlight
<nightli...@skip.omegapoint.com> wrote:

>Lee Bowman wrote:

>> i.e. "God as an unnecessary rider in an otherwise perfectly acceptable
>> scientific theory of life's origins"
>
>He was misapplying the Ockham's razor. The proper caveat was best
>stated by A. Einstein: "Make everything as simple as possible,
>but not simpler."

Right. Or its corollary, KISS (keep it simple stupid). It probably
refers more to organizing your investments, office, projects, etc.
than to cosmology.

How about KICK (keep it cogent, kiddo).

>> Didn't mean to take this thread in a new direction by the above
>> philosophical rant. Primarily wanted to get your (and others) take
>> on:
>>
>> ID = IM + IS or
>> ID = IM + ISS
>>
>> *assuming* an intelligent agency other than human existed

>The selection of reproductive mates is an 'intelligent selection'
>(IS & ISS). In my view the 'intelligence' (foresight, strategizing)
>and the 'mind stuff' (the stuff that answers for 'you' a question:
>what is it like to be such and such arrangement of atoms and

>fields ...

<snip>

>... each seeking to

>become more predicatable to the other by harmonizing
>its own motions to the internal model the other has of these
>motions, while the respective models in turn are seeking to
>anticipate the motions of the other as closely as possible.

Hey, didn't I read that in "Hitchhiker's Guide to the Astral Plane??

Nic

unread,
Jul 8, 2006, 7:54:14 PM7/8/06
to

Lee Bowman wrote:
> On 8 Jul 2006 15:51:06 -0700, "Nic" <harris...@hotmail.com> wrote:
>
> >
> >Lee Bowman wrote:
>
> >>
> >> ID = IM + IS or
> >> ID = IM + ISS
> >>
> >> *assuming* an intelligent agency other than human existed
> >
> >Not sure I see.
> >
> >Intelligent selection is often used when an intelligent agent cannot
> >influence what is originally on offer. I mean if you're a would-be
> >meddler, then you can meddlingly select from a set you can't meddlingly
> >control, or you can simply meddlingly control. You wouldn't need to do
> >both.
>
> Gene tweaking could entail an allele alteration (mutation) followed by
> manual selection (IS or ISS).

In management speak, that would be micro-meddling! If that goes on,
then there's no possible excuse for there being any evil in the world.

nightlight

unread,
Jul 8, 2006, 8:56:54 PM7/8/06
to
Lee Bowman wrote:
> Hey, didn't I read that in "Hitchhiker's Guide to the
> Astral Plane??

Never heard of that book, although I have probably
absorbed those images from somewhere. As to Astral
Projection, I haven't read about that subject
since a brief interest in high school.

John Wilkins

unread,
Jul 8, 2006, 10:15:37 PM7/8/06
to
nightlight <nightli...@skip.omegapoint.com> wrote:

Don't go there...
--
John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
University of Queensland - Blog: scienceblogs.com/evolvingthoughts
"He used... sarcasm. He knew all the tricks, dramatic irony, metaphor,
bathos, puns, parody, litotes and... satire. He was vicious."

hersheyhv

unread,
Jul 9, 2006, 1:50:42 AM7/9/06
to

nightlight wrote:
> hersheyhv wrote:
>
> >>It doesn't appear they have shown that the mutation
> >>was _random_. They only found a variant of a gene
> >>which is responsible for the lighter color.
> >
> >
> > random (wrt need) events. There is no reason to believe that the
> > single mutational event that produced the color variant described here
> > is any more or less random (wrt need) than the mutation of bacteria to
> > strep resistance or the mutation(s) --there are several -- that
> > produces melanic moths or melanic mice in the desert southwest.
>
> You are confusing the absence of evidence due to 'no reason to
> believe' (as far as you know) with the evidence of absence of
> such phenomenon (directed mutation).

I am NOT confusing the absence of evidence with my statement. I am
doing a standard scientific inference. I am specifically *including*
as evidence relevant to this particular case the clear and
quantitatively massive evidence that no, zero, nada point mutational
event in nature that has actually been studied has ever been observed
to be guided. Saying that mutation is random wrt need is like saying
that the sun rises in the east. The sun has repeatedly been observed
to rise in the east.

Your claim that this particular point mutation could have been due to a
magical mutation fairy makes as much sense in science as saying that
the sun rose in the west on July 4th in 1777. You can certainly make
such a claim, and make up all sorts of excuses as to why nobody alive
at the time noticed, but no one would take such a claim seriously. In
science, if you are proposing an extraordinary explanation, *you* are
responsible for demonstrating that such an explanation is both possible
and at least as likely as one that is consistent with the way that
things are known to work. You are *specifically* claiming that this
mutation, unlike other similar point mutations in DNA from organisms
across the phylogenetic spectrum, is just as likely to have been poofed
into existence by a mutation fairy as to have occurred by known
mechanisms that produce point mutations. *You* need something to back
up such an extraordinary and unnecessary claim, such as independence
evidence that there actually is a mutation fairy that could have done
what you claim was done. Without that, your explanation is most
definately NOT as good as an explanation that uses known mechanisms
without needing to posit the apparently hypothetical mutation fairy.

> > That said, if the mutation is a point mutation, the likely probability
> > of it occurring in any one individual offspring is between 10^-6 and
> > 10^-11 (with a modal peak around 10^-8 to 10^-9).
>
> You are confusing empirically observed rates of mutations
> with the predictions of such rates by some mathematical model,
> such as random mutation model.

No. I am saying that this is the *empirically observed* rate of point
mutation seen in a wide range of organisms and a wide range of genes
and a wide range of possible point mutations. Unless you have a better
estimate of the probability of point mutations, this is the range to
use. BTW, if the mutation needed to produce the phenotype is *any*
mutation that knocks out the gene's function, the rate of mutation to
the phenotype would be more frequent by a factor of 10-1000 since any
of the mutations that knock out the gene would produce the selective
phenotype.

> As explained in the first post,
> the RM model is an assumption about the algorithm used to explore
> the space of DNA configurations.

And the probability I gave is the rate of point mutation at a
particular nucleotide per generation. That is the rate of exploration
of the DNA configuration of the ancestral organism by point mutations.
And this example is an example of a single point mutation.

> Specifically, the RM assumes
> that the 'next' configuration to be explored is randomly selected
> among all accessible configurations (consistent with physical laws).
> Like any such search algorithm, the RM assumption implies a certain
> probability of success for a given space of physically accessible
> configurations (size of which was denoted as number T in (b))
> and given number of tries (denoted as number N in (a)). To test
> whether the RM search algorithm is likely explanation of the
> observed adaptation (under the given population size and time
> constraints) one needs to estimate these spaces and compute
> the RM implied probability. Only if the computed probability is
> high enough, you can crow that the observation confirms the
> RM model (as the likely mechanism). Neither you nor the article
> provide any such RM model prediction.

You are engaged in babbling incoherently. RM is the rate of change in
the genome. In this case, all that is needed is the probability of
point mutations per nucleotide.

> The figures of empirical rates of mutations have no relation
> with their origin. After all, there is also some empirical
> rate of mutations which are known to be intelligently guided,
> such as those within the bio-technology (in agriculture,
> academic research etc).

The vast majority of mutations in bio-tech have been random mutations
and the intelligent guidance came about by arranging conditions that
selected for the desired mutations by virtue of their phenotype.
Directed mutation has been rather recent phenomenon. But there is no
mechanism of this type directed mutation accounting for mutations in
the absence of very recent modern humans. The agent (the mutation
fairy) necessary to perform directed mutation on the gene in question
is unevidenced (as well as being unnecessary).

> By your logic, merely measuring
> the empirical rate of these mutations and citing the obtained
> figure, "proves" that these mutations are random. Of course not.

No. All I claim is that there is no need to posit a mutation fairy to
explain the result. The known rate of random mutation (followed by
selection) is quite capable of producing the observed results. That
is, the observed phenomena does not need a mutation fairy. It can be
explained without positing one, by using *known* mutational mechanisms
and *known* empirically observed mutation rates. If an event can be
explained by *known* mechanisms, positing other mechanisms is
unnecessary *unless* you have some independent evidence that the other
mechanism actually did produce the result. Positing an unnecessary and
unevidenced mutation fairy explanation is not good science.

> The empirical rate of mutation is relevant only if you wish
> to show that a mutation (of whatever nature) is responsible
> for the observed adaptation. That is not being debated here.

All it shows is that known mechanisms of RM and NS are sufficient to
explain this result. There is no need to posit a mutation fairy
*unless* you have some independent evidence that it was involved.

> We take for granted that the paper has demonstrated not just
> the genetic nature of this adaptation but also found the
> specific mutation responsible.

Of course they found the specific mutation responsible for the color
change. They undoubtedly did the genetic experiments that show that
this allele is responsible and showed where the two alleles differ in
sequence. Are you claiming that they are lying about the color
difference being due to a point mutation in a particular gene to
produce a variant allele?

> Hence, your citations of
> the empirical rates of mutations are a strawman argument in
> the context of this debate.

No they aren't. They are quite relevant to showing that there is no
*need* to posit a mutation fairy. That RM and NS can explain these
observations just fine without the need to posit an unnecessary and
unevidenced guided mutation fairy.

> > No mutation has ever been observed to be guided by any intelligence.
>
> How about those in bio-technology?

For most of human history and that of bio-tech, mutation was always
randomly generated wrt need (although the rate of *all* mutations was
sometimes increased by adding mutagens, and different mutagens do cause
different types of mutation -- in the sense of transition or
frameshift, not mutations specific according to need). Directed
mutation requires a lab and an intelligent agent with modern human
capabilities existing at the right time and place to perform the
directed mutation. At present there is no independent evidence that
such an agent (the mutation fairy) existed. And no evidence has been
presented that such an agent is necessary. Such an agent is
superfluous and unnecessary. One can always posit a mutation fairy to
do whatever one wants done.

> That merely shows that a
> natural processes which guide mutations intelligently do
> not contradict the natural laws. Such natural processes can
> exist and do exist.

How, then, if intelligently guided mutations occur by natural processes
and at rates that are indistinguishable from unintelligently (as far as
we can tell) unguided mutations, can we distinguish between them? The
only way I can see is to have direct independent evidence that some
mutations are directed and others aren't. We don't have any such
evidence (except for recent human endeavors, and humans are clearly not
the agent you are interested in). That makes intelligently guided and
unintelligently unguided mutations indistinguishable and makes the
results of intelligent guidance indistinguishable from the results of
random chance mutation. How does making intelligent guidance
indistinguishable from chance help you?

> > You are proposing a mechanism (guided mutation or mutation that occurs
> > as a result of need) that has been diligently searched for and has
> > never been observed.
>
> Again, you're confusing absence of evidence, or even the failure
> to examine and recognize the evidence, with the evidence of
> absence.

The sun still rises in the east. And, I predict, will do so tomorrow
and tomorrow and tomorrow as it creeps in this petty pace. I certainly
agree that just because all the flamingos I have seen (at least the
ones fed the right diet) are pink doesn't mean that non-pink flamingos
cannot exist. But *you* are the one that has to demonstrate that they
do. Until then it remains an empirical inference *from massive amounts
of evidence* that the sun rises in the east, flamingos fed shrimp are
pink, and mutations occur at random wrt need. If someone asks me which
direction the sun will rise, what color the next flamingo will be, or
whether any particular mutation occurred at random wrt need, I (unlike
you) will not reply that the sun is equally likely to arise from the
east or west or north or south, that the next flamingo will be just as
likely to be blue or green or purple as pink, or that any mutation I
did not directly observe was just as likely to have been produced by
the mutation fairy as by chance chemical or radiological events.

> If you want to demonstrate that the mice adaptation discussed
> shows that the search algorithm in the space of DNA configuration
> was random (this was just a single nucleotide mutation, the
> simplest case you can have), go ahead. Compute the prediction
> of success for such random search algorithm for the given space
> of possibilities (all configuration with one nucleotide change
> away from the initial state) and the given number of tries
> (which requires population sizes, conception rates, duration)
> and show that this algorithm has a 'good' probability of success
> under the constraints given.

That is just what I did. I gave an empirically determined rate for
mutation per nucleotide per generation. You didn't like that, even
though it is clearly the best estimate one can give in this case.
Since we are talking about a single nucleotide change, that is the
right rate for "searching" the DNA configuration of the ancestor. I
might be able to narrow it down some, by knowing, say, if the mutation
is a transition (more frequent) or transversion (less frequent). I
also pointed out that if the mutation is recessive, the frequency of
the recessive mutation in the founder population might be more
important. And I certainly estimated the population size, the number
of generations per year, and the probability of fixation of a new
mutation. All of those, and the intensity of selection for phenotype,
affect the probability of a new mutation becoming fixed.

I don't know what algorithm one can use for a magical mutation fairy
poofing a new mutation into existence, because no such mechanism has
ever been observed. One could use human directed mutation, but since
humans clearly are not our magical mutation fairy, there is no evidence
that this mutation was produced by directed mutation, and there is not
a shred of evidence that a magical mutation fairy is needed or exists,
it would be rather pointless.

> Recall that ID and ND differ for these simple adaptations only
> in the their search algorithm, in how each picks the 'next'
> configuration to explore (which in turn implies probabilities
> of success of each algorithm under any given constraints).
>
>
> > If your claim is that an intelligent agent capable of
> > altering the genome of the island mice was responsible,
> > one way to support your claim would be to present
> > empirical evidence of such an intelligent agent capable
> > of performing such genomic magic having existed at the
> > right time and place.
>
> My claim is that the article shows nothing in favor or against
> the ND = RM + NS vs ID = IM + NS models of adaptaion observed.
> It shows only M + NS, which is common to both models. Hence
> there is nothing here for neo-Darwinians to crow about.

The article does not propose IM because there was no such mechanism in
existence at the time and proposing it is unnecessary, using, as it
does, a hypothetical unevidenced mutation fairy to do whatever the
poser wants done. One can always posit a magical mutation fairy to
explain anything. Such an explanation is not science until one has
evidence that mutation fairies existed at the right time and place.
Otherwise, the mutation fairy is a superfluous and unnecessary
explanation (in addition to being unevidenced).

> As to what might be the nature of 'intelligent agency' guiding
> the mutations, that is a separate issue from the point I was
> making.

That is why I call it the magical mutation fairy. The agent, if there
is one, *is* the issue.

> We all agree that natural processes exist on Earth
> which guide mutations intelligently (the natural processes
> we call bio-technology or genetic engineering).

And we can all agree that those agents have only existed on the Earth,
as far as we know, in the last 10-15 years. And that they are modern
humans in science labs. As far as we know, no such agent existed even
25 years ago. Before that time humans *did* intelligently direct
selection, but did not intelligently direct mutation.

> Your argument
> above seems to be based on conjecture that no such natural
> process is consistent with natural laws. The direct
> counter-example (pointing you to the existence of such
> natural processes) invalidates your conjecture. Try
> something better.

No. My argument is based on the fact that no known agent capable of
doing what you claim existed at the time and place and that such an
agency is unnecessary and superfluous and unevidenced (a trifecta).
Moreover, *known* natural mechanisms working at *known* empirically
observed rates can produce the observed results.

> >>Hence, this particular discovery as it stands, seems at
> >>least as favorable to ID = IM + NS as to ND = RM + NS,
> >>since all they have shown is the existence of M + NS,
> >>a fact consistent with ID and ND models of evolution.
> >
> >
> > Not really. ID = IM + NS requires the existence of the hypothetical
> > "I" agent, for which there is zero evidence.
>
> This paper, which is what is I was referring to above, has no
> discussion, let alone tests, of the I-agentcy hypothesis.

How can a legitimate scientific article say "Oh, and by the way, a
magical mutation fairy could have poofed this mutation into existence."
when such an explanation is unnecessary, superfluous, and unevidenced?

> Now, you
> and I may have this or that view on the existence or plausibility
> of the I-agency, but that is unrelated to what the paper and its
> empirical facts show, or fail to show. In particular they do not
> show that the observed adaptation and its genetic mechanism
> favor any particular search algorithm, the RM or IM based method,
> in the space of DNA configurations accessible to mutations.

How does one go about producing evidence for your magical mutation
fairy when you say that one cannot distinguish between the results of
such a fairy and RM wrt the rates at which they occur?

> > Because the ID = IM + NS hypothesis requires something that is neither
> > supported by independent evidence (unlike the 'random wrt need' nature
> > of point mutations) nor is such an entity necessary to explain
> > what has been observed, the famous blade of Ockham must slice it
> > off.
>
>
> Ockham razor doesn't apply unless you can show that the
> alternative models are equally consistent with the empirical
> evidence.

I said, specifically, that the observed results are quite consistent
with known point mutation rates. One does not need to posit a magical
mutation fairy. The magical mutation fairy is unnecessary,
superfluous, and unevidenced. Unlike the random (wrt need) nature of
natural mutation, which has evidence up its whazoo.

> Merely failing to evaluate the consistency of the
> alternative models A and B against the empirical evidence
> does not allow you to declare that A is simpler, hence it
> is a better model by Ockham's razor.

How does one model a magical mutation fairy poofing mutations that you
choose at will? You refuse the only type of test that would actually
work -- namely independent tests that an agent capable of doing what
you claim existed at the right time and place.

nightlight

unread,
Jul 9, 2006, 4:29:01 PM7/9/06
to
hersheyhv wrote:

> I am NOT confusing the absence of evidence with my statement. I am
> doing a standard scientific inference. I am specifically *including*
> as evidence relevant to this particular case the clear and
> quantitatively massive evidence that no, zero, nada point mutational
> event in nature that has actually been studied has ever been observed
> to be guided.

To decide whether mutation is "guided", you would need to
know what is it being guided toward, or the utility function
being optimized. Having more offspring one of few generations
forward may not be the same function as having more offspring
farther into the future, just as in chess, where grabbing an
opponent's pawn now may cost you a game thirty moves later.

Further, multitudes of adaptable networks (in the ecosystem,
societies) overlap and permeate each other, with variety of
objectives being pursued by different networks. Some networks
are in the 'material' realm (such as biochemical reaction
networks within cells, immune systems, brains, various social
networks), while others are networks in the 'abstract'
realms, such as cultures, languages, religions, sciences,...

Any element of the system (such as individual cell or an
individual organism) is a member of multitudes of such
networks, overlapping at all levels (e.g. you may be be
a node or a link or their building block, in the 'Christian'
or 'Muslim' network, American economy network, biologist network,
English language network, your ethnic group network, gene pool
network,...), with all networks optimizing their own punishments
and rewards through the movements/actions of their elements,
using strategies and means, internal models and languages
mostly unknown to us. The count of 'selfish genes' few or many
generations ahead is merely one element of one utility function
optimized by one (the intra-cellular genetic network) of
many networks sharing the particular organism and each
guiding its actions for its own benefit, in subtle ways
largely imperceptible to us. The science is just beginning
to recognize these intelligent networks (complex systems)
and to uncover some of their laws, structural and functional
patterns, but it is still quite immature discipline. Claiming
detailed knowledge of all the utility functions that DNA,
cells or organisms are optimizing is preposterous, hence
claiming that there is no correlation between mutations
and any utility function is vacuous boasting.

Consider, for example, giving a 19th century scientist a modern
computer with instruction to check whether electric & magnetic
fields they observe make any sense or have any relation to the
pictures shown on the screen. He will hook up his best voltmeters
at various points, get hundreds of thousands of readings and he
will find _no statistically significant_ correlation between what
is shown on the computer screen and his voltage readings.

The voltages will appear completely random. He may observe
that disconnecting some connectors will make pictures or sounds
go away, some may shut everything down. He may also notice
the particular frequencies some of the lines carry. But he will
be clueless as to how the content he can see on the screen, or
the algorithms executed by the computer, are related to the
thousands of recorded voltages. A single voltage oscillation
lasting less than one thousandth of one billionth of a second,
out of trillions such oscillations from various points, going
constantly up or down, may mean a single bit being 1 or 0,
which in turn may mean entirely different program and
algorithms running thousands of billions oscillations later.
Hence, there would be no _statistically_ significant
correlation here between present voltages and the later
behaviors of the computer. But there would certainly be
a relation (understood by a team of engineers and programmers
who designed the machine and wrote the programs), that is
invisible through the statistical significance pinhole.

The molecular biology is in no better position with respect the
the extremely complex multi-layered web of chemical reactions,
tightly interwoven with a complex chains of electro-mechanical
interactions, classical and quantum, at microscopic level,
along with the innumerable interactions with even more complex
networks (of which the intra-cellular network is a tiny sub-net)
at the level of tissues, organs, organism, populations...

As someone looking from the perspective of a much 'harder'
science (theoretical physics) than comparatively 'softer'
disciplines of biology and biochemistry, I know that even
far simpler systems, with just few electrons and protons
and for behaviors spanning only few tiny fractions of a
second, are essentially unsolvable puzzles, especially if
one wishes to know the dynamical/time dependent non-periodic
behaviors (in contrast to periodic and static properties,
such as energy spectra, which are simpler to compute),
with the longer time spans being much more difficult
to model.

The biological processes are time dependent problems with
tens of orders of magnitude greater number of interacting
components and tens of orders of magnitude longer time
intervals of relevant non-periodic dynamics, than what
is already very difficult to impossible to model. The
statistical physics or solid state physics models, which
physicists use for systems with large number of particles,
are completely useless for biological systems since the
core simplifying assumptions made for those physical
models (such as ergodicity, quasi-stationarity, closed
systems, small fluctuations around the thermodynamical
equilibrium without amplification, negative feedback)
are violated by the biological systems. The best one
can do with biological systems with present computational
and mathematical tools is extremely coarse grained, crude
modeling covering the tip of a tip ... of a tip of the
iceberg making these phenomena.

Of course, if one talks to molecular biologists, one may
get an impression they're in a fairly complete control
of all the key phenomena, and are just filling in few
smaller details here and there. Of course, if one were
to talk to the ancient Egyptian priesthoods, one would
have gotten equally self-assured response, claiming
full knowledge of all things, from calendar seasons
and floods, through knowledge of secrets of health
and illness, life and death, Earth and stars. If
there was anything they couldn't answer safely, then
those things were declared intrinsically 'random',
un-answerable, un-knowable, the will of gods.

In retrospect, they were a handful of clever guys who
managed to pick out few genuine patterns about the
calendar seasons and floods. The rest was self-promotion,
mostly self-delusional i.e. they actually believed they
knew what they were talking about (especially those
still learning the secrets). The disciples had to go
through long process of testing and elimination of
unsuitables (those not bright enough and those lacking
a gift for self-deception needed to uphold convincingly
enough the pretense of omniscience), learning the arcane
symbolism and secret language of the discipline,...
before his initiation into the inner circle. That's the
human nature, back then and as it is today. The
scientists in various disciplines are essentially our
modern day priesthoods with similar patterns of behavior,
pretense, self-promotion, self-deception as those of
ancient Egyptian priesthoods.

Hence, I take all excessively self-assured declarations
that there are no patterns in the mutations (or in general
transformation of DNA from generation to generation)
correlating them with future states of the environment
the same way I would take Egyptian priests assuring me
that any phenomenon for which they don't see any
patterns _has no_ pattern, it is irreducibly random.
Doubly suspicious are any such declarations which are
also backed up by censorship, lawsuits, intimidations...


> Your claim that this particular point mutation could have been due to a
> magical mutation fairy makes as much sense in science as saying that
> the sun rose in the west on July 4th in 1777.

I was only claiming that the 'random' nature of the mutation
behind the color adaptation being reported in the article
was not established in any way. All that was established was
that an adaptation was due to particular very small mutation
(a single nucleotide).

There is nothing in the paper, or in any subsequent discussion,
that shows how did they establish that the astronomically
tiny fraction among the all possible DNA configurations (which
are one nucleotide change away from the initial configuration,
the set S0 in my original post in this thread) that were explored
by the given comparatively small number of tries available,
constitutes a 'random' set of configurations, _unbiased in
any way_ to find the suitable solution to the survival
problem.

Just saying that there were so many mutations in given a
time, as you keep doing, says nothing about their relation
to the problem being solved by the genetic search algorithm
or the nature of the algorithm. Both, the guided (intelligent)
and the 'random' mutations will have some number of mutations
per given time. The _only_ difference you could extract
statistically is that the intelligent mutations will find
the solution faster on average than the random ones. Now, to
check whether the search was faster than random, you cannot
get around the task of estimating what the random _model_
predicts for the expected number of tries needed to solve
the problem. Only then you can say whether the _empirically
observed_ search and solution time is comparable to that
predicted by the random search model, or whether it is slower
(malicious intelligence) or faster (benevolent intelligence).

Just pointing out at the empirically observed rates of
mutations, without any comparison to the search space
being explored, tells you nothing about the efficiency
of the search compared to the random search.

For example, if you know that I can guess a number that
another player writes down, in ten tries on average, that
doesn't tell you whether I am guessing randomly or using
some more intelligent strategy. You wouldn't even know,
whether a strategy used, if any, was aiming speed up or
to slow down the guessing. To know any of that, you also
need to know the size of space being explored by the
search, in this case the maximum range of numbers
being guessed.

If the maximum allowed number is 20, then a random search
will find it on average in 10 tries. But if the maximum
number allowed is 1000, then a random search will not
find it in ten tries on average (but in 500 tries),
hence one would conclude that the algorithm used was
not random guessing but some more intelligent strategy
(such a binary search). But if the maximum allowed number
is 1 million, then even the binary search will not work
with the observed success rate, and one would need to
look for a different hypothesis as how the observed
success rate might have been achieved (human psychology,
cheating, sub-conscious clues etc). Further, if the
maximum number was 12, then you could conclude that I
was (in some way) purposefully avoiding the correct
guess and if the maximum number was 10 or lower, you
would also know how I was avoiding it (by repeating
the same incorrect guess multiple times).

The kind of answer that you have been repeating here (for
the genetic search) is that since you can empirically
observe ten tries on average before the solution is found,
the search must be random (since there were many more
failures than successes), and that you don't need to
know the size of the space being searched and the size
of the 'solution' sub-set, let alone compute how
well would random search would perform here on average.

My point is that you can't say whether the guessing was
random or intelligent unless you estimate the sizes of
the search and solution spaces and compute the performance
characteristics (such as the average number of guesses
until the solution) of different search algorithms, then
compare this theoretically obtained number with the
empirically observed average number of guesses. Just
citing the empirically observed number of guesses tells
you nothing about the type of algorithm used to guess the
number.

All the other points you make rest on this fundamental
flaw in your methodology. Until you understand why
in the number guessing game you need to know the
sizes of search & solution spaces, and not just the
numbers of tries (which are an equivalent of the
empirical mutation rates you keep repeating as the
"answer"), in order to declare that the observed
success rate of ten tries on average can be
explained by the random guessing model, you won't
get what is the objection to the neo-Darwinian RM+NS
model being made here.

All I am saying (in this thread and the earlier ones)
is that you do need the estimates for the sizes
of the search and solution spaces, and not just the
empirically observed number of tries (or mutation rates
and population sizes), before you can make declarations
about the kind of the search algorithm being used in
the evolution at _all_ levels, from the simplest minor
adaptations, through new species and new body plans,
up to the origin of life.

Even if we were to observe, from start to end, the
emergence of an entirely new phylum in some habitat,
that would still leave a question of what search algorithm
was used by the genetic networks (and numerous other
networks involved) to find a solutions to great many
problems that such gigantic transformation would create.
Just because the observers didn't see an old guy with a
white beard, in a mideastern robe and a voice of Charlton
Heston, materialize from the thundering clouds and snap
his fingers at the original creatures, that doesn't
imply that the algorithm was a random search or that
the religiously and ideologically loaded neo-Darwinian
dogma (of RM+NS being the sole algorithm behind evolution)
was confirmed by the observation. As suggested at the
end of an earlier post in this thread:

http://groups.google.com/group/talk.origins/msg/651222ff530cbe4e

there are plenty of perfectly natural ways (even restricting
ourselves to what we know as natural laws at present, the
knowledge which will be laughable in few centuries) that
a) an 'intelligent agency' with intelligence many orders of
magnitude greater than our own can exist b) which can guide
the genetic transformations of organisms c) without
appearing to observers as some human look-alike (in size,
shape, methods and objectives) intelligence.

Depending on how subtle that kind of process may be, or how
small or large its 'gears' are, it may not be directly
recognizable as such, or even perceptible directly at
all, and one would have to infer its existence, properties
and role in the evolution via mathematical modeling, as we
already do for most of the objects and phenomena being
researched in high energy physics.

Hence, repeatedly trotting out the Pat Robertson's "theory
of evolution" as the sole alternative to the neo-Darwinism,
as it is reflexively done here by you and other defenders
of the neo-Darwinian dogma, is a childish strawman which,
being a clear indicator of ultimate desperation and
retreat from a rational argument, only further emphasizes
the fundamental weakness of the theory you are defending.

The nature of the search algorithm behind evolution (how
close or how far from the random search is it?) is a
perfectly legitimate scientific question that presently
has no answer. It is also a fact which the neo-Darwinian
priesthood is fighting tooth and nail to keep away
from being recognized outside of the priesthood, even
that there is a question, by all means available --
through censorship, lawsuits, bureaucratic and social
intimidation, threats to academic career, funding,...

hersheyhv

unread,
Jul 10, 2006, 12:42:22 AM7/10/06
to

nightlight wrote:
> hersheyhv wrote:
>
> > I am NOT confusing the absence of evidence with my statement. I am
> > doing a standard scientific inference. I am specifically *including*
> > as evidence relevant to this particular case the clear and
> > quantitatively massive evidence that no, zero, nada point mutational
> > event in nature that has actually been studied has ever been observed
> > to be guided.
>
> To decide whether mutation is "guided", you would need to
> know what is it being guided toward, or the utility function
> being optimized. Having more offspring one of few generations
> forward may not be the same function as having more offspring
> farther into the future, just as in chess, where grabbing an
> opponent's pawn now may cost you a game thirty moves later.

IOW, you have to posit (because you have no evidence) the existence of
a teleological goal. _Ex post facto_ determination of what the goal or
utility function was is a snap: whatever actually exists now was the
goal of the process. Anybody can always claim that whatever currently
exists was the purpose that the magic mutation fairy had in mind. It
is easy to draw a bull's eye around the holes you shot in the barn's
side and call yourself a sharpsman extraordinaire. Painting the bull's
eyes first and subsequently hitting the center is what is difficult.

> Further, multitudes of adaptable networks (in the ecosystem,
> societies) overlap and permeate each other, with variety of
> objectives being pursued by different networks. Some networks
> are in the 'material' realm (such as biochemical reaction
> networks within cells, immune systems, brains, various social
> networks), while others are networks in the 'abstract'
> realms, such as cultures, languages, religions, sciences,...

And this is supposed to be relevant how...?

> Any element of the system (such as individual cell or an
> individual organism) is a member of multitudes of such
> networks, overlapping at all levels (e.g. you may be be
> a node or a link or their building block, in the 'Christian'
> or 'Muslim' network, American economy network, biologist network,
> English language network, your ethnic group network, gene pool
> network,...), with all networks optimizing their own punishments
> and rewards through the movements/actions of their elements,
> using strategies and means, internal models and languages
> mostly unknown to us. The count of 'selfish genes' few or many
> generations ahead is merely one element of one utility function
> optimized by one (the intra-cellular genetic network) of
> many networks sharing the particular organism and each
> guiding its actions for its own benefit, in subtle ways
> largely imperceptible to us.

It always seems that that which is imperceptible to us (aka ignorance)
is the evidence that IDeologues use.

> The science is just beginning
> to recognize these intelligent networks (complex systems)
> and to uncover some of their laws, structural and functional
> patterns, but it is still quite immature discipline. Claiming
> detailed knowledge of all the utility functions that DNA,
> cells or organisms are optimizing is preposterous, hence
> claiming that there is no correlation between mutations
> and any utility function is vacuous boasting.

Science has several mechanisms for disecting out whether a particular
feature out of many possible environmental features has a significant
impact on a result. You might try learning some of them. This is the
very basis of controlled experiment and/or factor analysis. But all
you are doing is claiming that all the repeated experiments in the
world that show that mutation is random wrt need is irrelevant if you
can somehow *believe* that there is something more going on.

Where do you make up this utter bullshit? Do you have a bull in the
corner? Until you have some actual *evidence* that mutation is
non-random wrt need, that Lamarck was somehow right, you have to go
with the actual *evidence* that we do have. Namely, that to all
extents and purposes mutation (and point mutation specifically) is
random wrt need. Waving your hands and wildly claiming that because
*you* don't understand (It's too complex!) or don't want to believe the
results of controlled experiment that you get to assert that it is just
as likely that the sun will set in the north or west or south tomorrow
doesn't make that an *equally likely* result. Just because you want to
believe that there is a mutation fairy that makes some mutations (but
just the beneficial ones) that are indistinguishable from all those
naturally made (and hence bad) mutations doesn't make the mutation
fairy explanation just as likely as the explanation that mutations


occur at random wrt need.

> As someone looking from the perspective of a much 'harder'


> science (theoretical physics) than comparatively 'softer'
> disciplines of biology and biochemistry, I know that even
> far simpler systems, with just few electrons and protons
> and for behaviors spanning only few tiny fractions of a
> second, are essentially unsolvable puzzles, especially if
> one wishes to know the dynamical/time dependent non-periodic
> behaviors (in contrast to periodic and static properties,
> such as energy spectra, which are simpler to compute),
> with the longer time spans being much more difficult
> to model.

Everything is a mystery to the mind of an IDeologue who does not want
to accept the empirical evidence, which clearly says: Mutation is
random wrt need. Let me repeat. Mutation is random wrt need. There
is NO difference in this between mutations that are selectively
beneficial and mutations that selectively detrimental. In fact, the
very same mutation can be selectively beneficial in one environment and
detrimental in a different one and neutral in yet a third environment.

> The biological processes are time dependent problems with
> tens of orders of magnitude greater number of interacting
> components and tens of orders of magnitude longer time
> intervals of relevant non-periodic dynamics, than what
> is already very difficult to impossible to model. The
> statistical physics or solid state physics models, which
> physicists use for systems with large number of particles,
> are completely useless for biological systems since the
> core simplifying assumptions made for those physical
> models (such as ergodicity, quasi-stationarity, closed
> systems, small fluctuations around the thermodynamical
> equilibrium without amplification, negative feedback)
> are violated by the biological systems. The best one
> can do with biological systems with present computational
> and mathematical tools is extremely coarse grained, crude
> modeling covering the tip of a tip ... of a tip of the
> iceberg making these phenomena.

You mean that you cannot accept the results of controlled experiment.
So you blabber and obfusticate that it is, oh so complex that
*anything* is possible. What utter bs. The fact remains that the
finding that mutation is random wrt need has been about as convincingly
demonstrated as the idea that the sun rises in the east. Maybe not
quite as convincingly, but any deviant mutations are rare exceptions
and not the rule. You also seem to be deluded in thinking that the
'beneficial' or 'detrimental' adjectives applied to particular
mutations are inherent in the mutation rather than conditional to a
particular environment and its interaction with the phenotypes these
alleles produce.

> Of course, if one talks to molecular biologists, one may
> get an impression they're in a fairly complete control
> of all the key phenomena, and are just filling in few
> smaller details here and there. Of course, if one were
> to talk to the ancient Egyptian priesthoods, one would
> have gotten equally self-assured response, claiming
> full knowledge of all things, from calendar seasons
> and floods, through knowledge of secrets of health
> and illness, life and death, Earth and stars. If
> there was anything they couldn't answer safely, then
> those things were declared intrinsically 'random',
> un-answerable, un-knowable, the will of gods.

*When* you have something other than your personal incredulity and
misunderstanding of the difference between *scientists* and
*post-modernist priesthoods* (one will change its understanding when
presented with evidence, which you are NOT presenting; the other is
wedded to the idea that everything is a mystery and any explanation is
as good as any other). I am perfectly willing to examine any actual
*evidence* you have that mutations are not random wrt need. But you
haven't presented any. All you have done is wave some fancy,
schmantsy, mumbo jumbo and asserted, like a good post-modernist, that
there is no empirical reality one has to really deal with. Any
explanation is as good as any other you keep repeating. I say that
that is something that can get you killed if you believe that the idea
that Comet Tuttle is hiding a spaceship that will wisk you out of here.

> In retrospect, they were a handful of clever guys who
> managed to pick out few genuine patterns about the
> calendar seasons and floods. The rest was self-promotion,
> mostly self-delusional i.e. they actually believed they
> knew what they were talking about (especially those
> still learning the secrets). The disciples had to go
> through long process of testing and elimination of
> unsuitables (those not bright enough and those lacking
> a gift for self-deception needed to uphold convincingly
> enough the pretense of omniscience), learning the arcane
> symbolism and secret language of the discipline,...
> before his initiation into the inner circle. That's the
> human nature, back then and as it is today. The
> scientists in various disciplines are essentially our
> modern day priesthoods with similar patterns of behavior,
> pretense, self-promotion, self-deception as those of
> ancient Egyptian priesthoods.

So you cannot tell the difference between scientists and voodoo
priests, eh. I agree. You probably can't.

> Hence, I take all excessively self-assured declarations
> that there are no patterns in the mutations (or in general
> transformation of DNA from generation to generation)
> correlating them with future states of the environment
> the same way I would take Egyptian priests assuring me
> that any phenomenon for which they don't see any
> patterns _has no_ pattern, it is irreducibly random.
> Doubly suspicious are any such declarations which are
> also backed up by censorship, lawsuits, intimidations...

Oh, mutation in fact does have a very specific pattern. It is a
pattern which is indistinguishable from the specific pattern one would
expect if mutation were random wrt need. It does not have a pattern
which, to all the degrees of sensitivity one wishes to apply or has
applied, that shows the slightest indication of any significant
deviation from the specific expectations of randomness in this regard.
There are specific tests that have been applied. The easiest to
understand is replica plating of bacterial colonies to selective or
non-selective plates. The rate of mutation to resistance is
independent of whether or not the colony is replica plated to selective
or non-selective plates.

> > Your claim that this particular point mutation could have been due to a
> > magical mutation fairy makes as much sense in science as saying that
> > the sun rose in the west on July 4th in 1777.
>
> I was only claiming that the 'random' nature of the mutation
> behind the color adaptation being reported in the article
> was not established in any way. All that was established was
> that an adaptation was due to particular very small mutation
> (a single nucleotide).

You are saying, in fact, that this particular mutation could have
arisen in a way that is equivalent to the sun rising in the west (by
the never seen and unevidenced mechanism of a mutation fairy), that
that explanation is just as likely as the idea that the sun rose in the
east (by natural random wrt need mutation). You are wrong. The
probability that this mutation arose by standard random mutation is
very high. The probability that this mutation arose by a mechanism of
intelligently guided mutation (a mechanism with no evidence, no agency,
and one that is unnecessarily complex because it requires such a
mechanism when known natural processes would suffice) is extremely low.
Now, if you had some actual evidence that this particular mutation, of
all the mutations in the world, *required* or actually was produced by
a mutation fairy, you would have something. But you don't. All you
have is the hand-waving post-modernist assertion, rejected by all
scientists, that *any* explanation is as good as any other. It's all a
mystery to you.

> There is nothing in the paper, or in any subsequent discussion,
> that shows how did they establish that the astronomically
> tiny fraction among the all possible DNA configurations (which
> are one nucleotide change away from the initial configuration,
> the set S0 in my original post in this thread) that were explored
> by the given comparatively small number of tries available,
> constitutes a 'random' set of configurations, _unbiased in
> any way_ to find the suitable solution to the survival
> problem.

The point I am making is that your whole thesis is based on a false
disection of the problem. There is no genetic search algorithm
searching through all possible DNA configurations. There is no
teleologic goal in the process. There is a single point mutation
altering one *pre-existing* gene by a single nucleotide change
resulting in a change in the phenotype of the allele in certain
genotypic combinations. This altered phenotype then underwent
selection in the local environment. The rate of point mutation that
produces this type of change (since mutations in other sites could well
produce the same phenotype) in the *pre-existing* gene is the relevant
rate. Your calculation of a genetic search through *all possible DNA
configurations* is utterly irrelevant.

> Just saying that there were so many mutations in given a
> time, as you keep doing, says nothing about their relation
> to the problem being solved by the genetic search algorithm
> or the nature of the algorithm.

Mutation is not for the purpose of solving a genetic search algorithm.
It is simply something that happens due to the nature of the chemistry
of DNA and its replication.

> Both, the guided (intelligent)
> and the 'random' mutations will have some number of mutations
> per given time. The _only_ difference you could extract
> statistically is that the intelligent mutations will find
> the solution faster on average than the random ones.

IOW, there is no detectable difference. Exactly how would you
determine that any given mutation is "intelligently designed"? We are
talking about a single nucleotide change here, not some long drawn out
search of all DNA sequence space. Are you saying that mutations that
occur at a higher frequency are more likely to be beneficial than
mutations that occur at low frequency in a population? You would, of
course, be wrong as the 80% of achondroplastic dwarfs due to new
mutation (one which occurs at very high frequency) could tell you.

> Now, to
> check whether the search was faster than random, you cannot
> get around the task of estimating what the random _model_
> predicts for the expected number of tries needed to solve
> the problem.

The random model does not predict the rate of mutation for any given
mutational event (there are local sequence features that affect rates).
That is something that is empirically determined not established as a
feature of theory.

> Only then you can say whether the _empirically
> observed_ search and solution time is comparable to that
> predicted by the random search model, or whether it is slower
> (malicious intelligence) or faster (benevolent intelligence).

Again. There is no correlation between the rate of mutation that
produces a given phenotype and the need for that mutation. Nor is
there any correlation between the rates of mutation and whether or not
the effects are generally deleterious. Nor is there any correlation
between the rate of mutation and the *degree* of
deleteriousness/benefit. Nor is there any evidence of intelligent
agency involved at all. One *can* speed up the rate (and determine the
general type of mutational event) by adding mutagens or reduce the
rates by amplifying repair enzymes (although at a cost). But neither
of these can speed up the rates of mutation of beneficial over
detrimental mutations. And, as I keep pointing out, there is no
evidence of any intelligent agent capable of doing this at the right
time and place.

> Just pointing out at the empirically observed rates of


> mutations, without any comparison to the search space
> being explored, tells you nothing about the efficiency
> of the search compared to the random search.

The search space in this case is a single nucleotide in a pre-existing
gene (although it is possible that other mutations could have produced
the same phenotype). The rate of mutation at that site is quite
clearly the correct rate for the search of this particular search
space. Were you claiming that one must re-invent the entire gene from
scratch like creation claims to do rather than produce a modified gene
by descent as *evolution* would?

> For example, if you know that I can guess a number that
> another player writes down, in ten tries on average, that
> doesn't tell you whether I am guessing randomly or using
> some more intelligent strategy.

I could certainly tell whether or not you were rotating through the
numbers in a way significantly different from what would occur by
chance. In the simplest case, if all you did was chose 3 each time, it
would be obvious that you were using a strategy or that you could not
think of another number and thus were extraordinarily stupid rather
than intelligent. Even if you tried to produce a pattern that mimicked
a random pattern, it is likely that your false human intuition of what
was a random pattern would betray you eventually. I would have more
trouble if you chose a true randomly repeating number, like pi, unless
I happened to guess what number you were using.

But all that is irrelevant.

> You wouldn't even know,
> whether a strategy used, if any, was aiming speed up or
> to slow down the guessing. To know any of that, you also
> need to know the size of space being explored by the
> search, in this case the maximum range of numbers
> being guessed.
>
> If the maximum allowed number is 20, then a random search
> will find it on average in 10 tries. But if the maximum
> number allowed is 1000, then a random search will not
> find it in ten tries on average (but in 500 tries),
> hence one would conclude that the algorithm used was
> not random guessing but some more intelligent strategy
> (such a binary search). But if the maximum allowed number
> is 1 million, then even the binary search will not work
> with the observed success rate, and one would need to
> look for a different hypothesis as how the observed
> success rate might have been achieved (human psychology,
> cheating, sub-conscious clues etc). Further, if the
> maximum number was 12, then you could conclude that I
> was (in some way) purposefully avoiding the correct
> guess and if the maximum number was 10 or lower, you
> would also know how I was avoiding it (by repeating
> the same incorrect guess multiple times).

Again, I could, quite often, determine if you were rotating through
your numbers in a random fashion. I would only have significant
difficulty if you actually were "intelligently" using a pattern which
exactly mimicked some random pattern and was thus indistinguishable
from a random pattern. But if you are using a randomly generated
pattern, it is still a randomly generated pattern, intelligent or not.
If your "intelligently" generated mutations occur in a pattern
completely indistinguishable from that expected by random mutation wrt
need, which would also occur in "unintelligently" "undirected"
mutation, how can you tell it was "intelligently" generated?

> The kind of answer that you have been repeating here (for
> the genetic search) is that since you can empirically
> observe ten tries on average before the solution is found,
> the search must be random (since there were many more
> failures than successes), and that you don't need to
> know the size of the space being searched and the size
> of the 'solution' sub-set, let alone compute how
> well would random search would perform here on average.
>
> My point is that you can't say whether the guessing was
> random or intelligent unless you estimate the sizes of
> the search and solution spaces and compute the performance
> characteristics (such as the average number of guesses
> until the solution) of different search algorithms, then
> compare this theoretically obtained number with the
> empirically observed average number of guesses. Just
> citing the empirically observed number of guesses tells
> you nothing about the type of algorithm used to guess the
> number.

I can certainly learn wether the pattern of numbers is randomly
generated among the numbers being rotated among. Obviously, the larger
the set, the longer it would take to detect a pattern.

> All the other points you make rest on this fundamental
> flaw in your methodology. Until you understand why
> in the number guessing game you need to know the
> sizes of search & solution spaces, and not just the
> numbers of tries (which are an equivalent of the
> empirical mutation rates you keep repeating as the
> "answer"), in order to declare that the observed
> success rate of ten tries on average can be
> explained by the random guessing model, you won't
> get what is the objection to the neo-Darwinian RM+NS
> model being made here.

In our particular example, the size of the search and solution space is
the single nucleotide that needs to be changed. The rate of change at
that site is all you need.

> All I am saying (in this thread and the earlier ones)
> is that you do need the estimates for the sizes
> of the search and solution spaces, and not just the
> empirically observed number of tries (or mutation rates
> and population sizes), before you can make declarations
> about the kind of the search algorithm being used in
> the evolution at _all_ levels, from the simplest minor
> adaptations, through new species and new body plans,
> up to the origin of life.

There is no search algorithm because there is no teleologic goal.

> Even if we were to observe, from start to end, the
> emergence of an entirely new phylum in some habitat,
> that would still leave a question of what search algorithm
> was used by the genetic networks (and numerous other
> networks involved) to find a solutions to great many
> problems that such gigantic transformation would create.
> Just because the observers didn't see an old guy with a
> white beard, in a mideastern robe and a voice of Charlton
> Heston, materialize from the thundering clouds and snap
> his fingers at the original creatures, that doesn't
> imply that the algorithm was a random search or that
> the religiously and ideologically loaded neo-Darwinian
> dogma (of RM+NS being the sole algorithm behind evolution)
> was confirmed by the observation. As suggested at the
> end of an earlier post in this thread:
>
> http://groups.google.com/group/talk.origins/msg/651222ff530cbe4e
>
> there are plenty of perfectly natural ways (even restricting
> ourselves to what we know as natural laws at present, the
> knowledge which will be laughable in few centuries) that
> a) an 'intelligent agency' with intelligence many orders of
> magnitude greater than our own can exist b) which can guide
> the genetic transformations of organisms c) without
> appearing to observers as some human look-alike (in size,
> shape, methods and objectives) intelligence.

Yes. He/it/she/they can be the mutation fairies. Any evidence?


> Depending on how subtle that kind of process may be, or how
> small or large its 'gears' are, it may not be directly
> recognizable as such, or even perceptible directly at
> all, and one would have to infer its existence, properties
> and role in the evolution via mathematical modeling, as we
> already do for most of the objects and phenomena being
> researched in high energy physics.
>
> Hence, repeatedly trotting out the Pat Robertson's "theory
> of evolution"

Pat Robertson doesn't have a "theory of evolution". He believes in the
mutation fairy and even believes in the magical creation fairy.

> as the sole alternative to the neo-Darwinism,

I am perfectly willing to look at any *evidenced* alternative you can
present. So far all I see is hand-waving and post-modernist "any idea
is as good as any other" claptrap.

> as it is reflexively done here by you and other defenders
> of the neo-Darwinian dogma, is a childish strawman which,
> being a clear indicator of ultimate desperation and
> retreat from a rational argument, only further emphasizes
> the fundamental weakness of the theory you are defending.
>
> The nature of the search algorithm behind evolution (how
> close or how far from the random search is it?)

Since evolution is constrained to search only within the genomes of
ancestral organisms (for vertical evolution anyway), the non-search
(since there is no teleologic goal) that happens to produce new alleles
or new genes is decidedly non-random. If a new feature cannot be
produced by some modification of a pre-exisiting feature (descent with
modification), it generally won't happen. In creationism, of course,
there are no limits. The magical mutation fairy can produce whatever
it wants and, lo and behold, miracle of miracles, the magical mutation
fairy you posit just happens to produce what actually exists. Just by
positing it. See, wasn't that easy?

michael...@worldnet.att.net

unread,
Jul 10, 2006, 1:08:59 AM7/10/06
to

nightlight wrote:
>
> P(N,T) = 1 - (1-1/T)^N ~ 1 - exp(-N/T) ... (1)
>
> For small values of N/T this is approximately:
>
> P(N,T) ~ N/T ... (2)
> [considerable snipping]

> (If there are F favorable color mutations among T, then
> N/T in (2) would be multiplied by F. That refinement is
> irrelevant for the point being made below.)
>

Let the nightlight special shine his heaven of a light on me.

-- Mike Palmer

Windy

unread,
Jul 10, 2006, 3:49:38 AM7/10/06
to

hersheyhv wrote:

> nightlight wrote:
> > Just pointing out at the empirically observed rates of
> > mutations, without any comparison to the search space
> > being explored, tells you nothing about the efficiency
> > of the search compared to the random search.
>
> The search space in this case is a single nucleotide in a pre-existing
> gene (although it is possible that other mutations could have produced
> the same phenotype).

And very likely.

> The rate of mutation at that site is quite
> clearly the correct rate for the search of this particular search
> space. Were you claiming that one must re-invent the entire gene from
> scratch like creation claims to do rather than produce a modified gene
> by descent as *evolution* would?

No, he is talking about a single nucleotide change, he just wrongly
thinks that the probability of the single change is 1/(number of all
theoretically possible point mutations).

-- w.

Andrew McClure

unread,
Jul 10, 2006, 5:07:11 AM7/10/06
to
michael...@worldnet.att.net wrote:
> July 07, 2006
> An Evolution Saga: Beach Mice Mutate and Survive
>
> It's a pitiless lesson-adapt or die-but the sand-colored mice that
> scurry around the beaches of Florida's Gulf Coast seem to have learned
> the lesson well. Now researchers have identified a genetic mutation

> that underlies natural selection for the sand-matching coat color of
> the beach mice, an adaptive trait that camouflages them from aerial
> predators.
>
> In the July 7, 2006, issue of the journal Science, evolutionary
> geneticist Hopi Hoekstra and colleagues at the University of
> California, San Diego, report that a single mutation causes the
> lifesaving color variation in beach mice (Peromyscus polionotus) and
> provides evidence that evolution can occur in big leaps.
>
> "This is a striking example of how protein-coding changes can play a
> role in adaptation and divergence in populations, and ultimately
> species."
> Hopi Hoekstra
>
> The Gulf Coast barrier islands of Florida and Alabama where the beach
> mice are found are less than 6,000 years old-quite young from an
> evolutionary standpoint. Hoekstra said that the identification of a
> single mutation that contributes to the color change that has arisen in
> these animals argues for a model of evolution in which populations
> diverge in big steps.
>
> This model, in which change is driven by large effects produced by
> individual mutations, contrasts with a popular model that sees
> populations diverging via small changes accumulated over long periods
> of time.
>
> More at:
> http://www.hhmi.org/news/hoekstra20060707.html

That's one small step for mouse, one giant leap for mousekind


Ba dum ching

Richard Forrest

unread,
Jul 8, 2006, 1:32:03 PM7/8/06
to

nightlight wrote:
> Windy wrote:
>
> >>In contrast, the ID model says that those N points are not
> >>chosen randomly from S1, but are guided by some 'intelligent
> >>agency' which allows it to find favorable configurations
> >>from S1 faster than the random search does i.e. the ID model
> >>says that if we observe a series of such adaptation processes,
> >>then the rate of observed favorable adaptations will be
> >>greater than the rate predicted by the neo-Darwinian model
> >>(implied by particular P(N,T) in each process instance).
> >
> >
> > OK.. if favorable adaptations occur at a high rate, this is evidence
> > for ID?
>
> It would be an evidence that neo-Darwinian model (RM+NS) is
> an unlikely explanation of the observed adaptation and that
> a more efficient (than random) search algorithm is responsible
> for the adaptation. By convention, we can call this more
> efficient algorithm an 'intelligent' or guided mutation,
> or generally an ID algorithm.
>

No we don't.
Not in science, anyway.
If, in science, we don't know what is responsible, we say
"We don't know what's responsible. How can we find out?"

In ID, which isn't science, they say
"We don't know what's responsible, so GodImeananintelligentdesigner
must be responsible. Well, now that's settled, let's go and spend those
fat cheques the DI has sent us."

> > What about if favorable adaptations did not occur or occur at a
> > lower rate? Is that evidence against ID?
> >
>
> I think you meant "higher rate" not "lower rate" above (otherwise
> what you wrote is a gibberish). Assuming this correction,
> it would be an evidence that the 'intelligent agency' (IA) model
> is not necessary to explain that particular adaptation.

Oh, I see.
So the position is that there *must* be an intelligent designer, but if
any particular test doesn't uncover his actions, it's the wrong test.

Hard to falsify.

> That
> doesn't exclude a need for the IA model in order to explain
> some other adaptations. It doesn't even exclude the IA
> participation in that example. It only means that what
> was observed does not discriminate for or against IA and
> that one might need additional data to make such discrimination.
>
> (The latter observation is important since a coherent IA theory
> should not cherry pick in which processes the IA participates
> and in which it choses not to be involved with.)

To form a theory, you have to start by testing hypotheses. So far, no
IDer has tested a single hypothesis about the action of any intelligent
designer.

This is called trying to run before you can even crawl. Or more
acurately, trying to run before you are even conceived.


>
> Consider an 'intelligent agency' which we know to exist in nature
> (human brain) applying its efforts to stock market trading. One
> could trade using all his knowledge and foresight and not do
> any better than chance on any particular day or a week or
> throughout the whole trading career. Could you declare that
> he was picking randomly if his gains don't exceed random
> ones for some given span of time? You can't. You would
> need more data and possibly different kind of data (such as
> direct observation of his trading or an interview) to support
> such conclusion.

Quite what the relevance of this is to evolution is a mystery to me.
I supose that if you have not one scrap or tittle of evidence, then all
you can do is to argue from analogy.

By the way, science does not construct arguments from analogy. It
constructs them from evidence.

>
> In any case, what is your point? How is your question related
> to my observation that there is nothing in the article, no
> calculation or estimation of predictions of any mutation model
> (random or any other), let alone any comparison of such
> prediction with the empirical facts observed. There is simply
> nothing there for neo-Darwinians to crow about. If you saw
> something to crow about, you haven't shown as yet what that
> might be.
>
> Instead, so far you have been quite desperate in trying
> to divert the discussion to your little collection of pet
> strawmen while showing off your repertoire of explitives.
> Either say something of substance or stay quiet and let
> somene who may have a better understanding of the subject
> being discussed have a turn defending the neo-Darwinian
> model. Your response was and continues to be so inpet that
> you may well be a supporter of Pat Robertson's theory of
> evolution acting here under the false flag, trying to
> make neo-Darwinians look stupid and primitive.
>

So what was the hypothesis which ID is testing?

> >
> >>The point of my argument is that there is nothing in the article
> >>for neo-Darwinians to crow about.
> >
> >
> > Sez you.
>
> Well, can you cite some calculation from the paper demonstrating
> that the observed mutation was 'most probably' (e.g. 50% or
> better) random.

And this demonstrates what, exactly?

On the other hand, there is plenty of other evidence to support
evolution by natural selection, and no evidence whatsoever to support
the idea that an "intelligent designer" occasionally interferes with
normal biological processes.

Science forms paradigms because they form a consistent and coherent
model of how systems behave, and builds those paradigms because that is
where the evidence leads. Whether you like it or not, evolution by
natural selection is the ruling paradigm in the biological sciences
because it is supported by a vast amount of evidence.

>
> >>>So the designer actively intervened in the evolution of these mice
> >>>during the last 6000 years? Interesting.... how, exactly?
> >>
> >>There could be an intelligent agency guiding mutation faster than
> >>random search toward the favorable DNA configuration.
> >
> >
> > And *how* is it doing that? Devise an experiment to test it.
>
>
> There are plenty of ways that an 'intelligent agency' could exist
> and perform directed mutations. I merely pointed out couple
> possibilities which are not a priori excluded by the presently
> known laws of physics.

So propose a test which could *falsify* the intervention of an
intelligent agency.

>
> We also already know that natural processes which intelligently
> guide mutations exist in nature (e.g. brains of molecular
> biologists). The empirically established existence of such
> processes is a direct counter-example to a conjecture
> that such natural processes are excluded by laws of nature.
> They are obviously not excluded by the laws of nature since
> they do exist in nature.

So propose a test which could *falsify* the intervention of an
intelligent agency.


>
> Hence your "point" about '6000 years', which is what I was
> responding to above, is a vacuous strawman. Pat Robertson's
> model of evolution is certainly not the sole alternative
> to the neo-Darwinian model.

What was that scientific alternative to evolution by natural selection
again?
It isn't ID - Michael Behe, one of it's leaders conceeded under oath
that it isn't science, so you must be talking about something else.

>
>
> >>Hence, it is perfectly conceivable that our physical,
> >>chemical, biological... laws are an extremely crude
> >>picture of an activity by an unimaginably powerful
> >>underlying intelligence (vast distributed computer
> >>running 1e16 times faster and having (1e16)^3 ~ 1e50
> >>times more components than the intelligent processes
> >>we are familiar with at our level). In addition to
> >>providing support for ID model of evolution, this
> >>kind of model could also be a rational alternative
> >>to the 'anthropic principle' in explaining the fine
> >>tuning of physical constants.
> >
> >
> > So we're in the Matrix?
>
> I suppose, if one had to put it in terms understandible to
> a simpleton whose science education consists of going to
> the movies, one might put it that way.

Cutting, cutting.
What is *your* education in science, by the way?

RF

Windy

unread,
Jul 10, 2006, 2:13:51 PM7/10/06
to
Richard Forrest wrote:

> nightlight wrote:
> > >>Hence, it is perfectly conceivable that our physical,
> > >>chemical, biological... laws are an extremely crude
> > >>picture of an activity by an unimaginably powerful
> > >>underlying intelligence (vast distributed computer
> > >>running 1e16 times faster...

> > >
> > > So we're in the Matrix?
> >
> > I suppose, if one had to put it in terms understandible to
> > a simpleton whose science education consists of going to
> > the movies, one might put it that way.
>
> Cutting, cutting.
> What is *your* education in science, by the way?

He wrote something about that in a later post:

"As someone looking from the perspective of a much 'harder'
science (theoretical physics) than comparatively 'softer'
disciplines of biology and biochemistry, I know that even
far simpler systems, with just few electrons and protons
and for behaviors spanning only few tiny fractions of a

second, are essentially unsolvable puzzles..."

Too bad, since many physicists' insights into biology have been
valuable. I guess there are always a few filled with nothing but hot
air, like John Barrow and the dimly glowing nightlight.

And shouldn't persons educated in theoretical physics know how to apply
statistics?

-- w.

nightlight

unread,
Jul 10, 2006, 6:13:34 PM7/10/06
to
> The point I am making is that your whole thesis is based
> on a false disection of the problem. There is no genetic
> search algorithm searching through all possible DNA
> configurations. There is no teleologic goal in the
> process.

Term "algorithm" here is merely a shorthand for a specific
sequence of steps which transforms a system from state A to
state B. Similarly the "search algorithm" in this context is
a sequence of steps which transforms the genetic network
(possibly spanning multiple generations) from state A which
does not have the particular favorable mutation to state B
which does have it.

For adaptable networks (such as brain, genetic network, neural
network) and the sequences of steps they go through one often
uses term "algorithm" (e.g. the pattern recognition algorithms
or search algorithms realized via neural networks) since such
sequences of state transformations can be mapped into conventional
computer algorithms solving the same problems. No teleological
premise is introduced by use of such shorthand. It is simply a
terminological convenience since the theory of computer
algorithms brings in cleanly defined, high resolution terms
and concepts particularly suitable for analyzing such
sequences of steps, states they traverse, their effects,
performance characteristics, alternatives.... etc.


>>Both, the guided (intelligent)
>>and the 'random' mutations will have some number of mutations
>>per given time. The _only_ difference you could extract
>>statistically is that the intelligent mutations will find
>>the solution faster on average than the random ones.
>
>
> IOW, there is no detectable difference. Exactly how would you
> determine that any given mutation is "intelligently designed"?

Statistical difference is detectable. The difference here would
be between the theoretically predicted success rate (or probability
of success for a given number of tries) of a 'random search' in
the space of DNA configuration (accessible via 1 nucleotide change)
vs the empirically observed success rate of the actual algorithm.

> We are
> talking about a single nucleotide change here, not some long drawn out
> search of all DNA sequence space.

It may have slipped your mind, but we are discussing this single
nucleotide change in the context of its alleged support for
the neo-Darwinian conjecture, which prescribes a particular
way/algorithm as to how such single nucleotide change is picked
out (e.g. by the biochemical reaction web of the cell) among
all possible single nucleotide changes that could be picked
out from a given initial state.

The ND algorithm/prescription requires that the change is
picked "randomly" i.e. that the picking process cannot
systematically (= with statistical significance) show
preference/bias at the time of the pick for any particular
nucleotide (or any of their possible final states) whose
change will turn out (with statistical significance) to
be more useful _later_ over the nucleotides & their final
states whose change will turn out to be less useful _later_
(or even outright fatal shortly the the change).

Otherwise, we would characterize the picking process which
systematically gives preference _now_ to particular nucleotide
changes which will be more useful _later_ as anticipatory or
intelligent picking process.

The ND theology absolutely prohibits that kind of picking
processes. If there are only two physically/chemically
possible changes A and B, and A will turn out statistically
useful _later_, while B will turn out almost always fatal
_later_, the ND dogma still prohibits picking processes
which give preference to A at the time of the pick i.e.
it requires that A and B have to be picked with equal
probability and only the natural selection that follows
later is allowed to terminate B type offspring and continue
the A type offspring.

Now, if you suddenly declare that your view of ND
allows for the 'change picking processes' that give
statistically significant preference to A over B
at the time of the picking, hence before the later
state of the environment would perform the natural
selection, then you already agree that the change
picking process can be _anticipatory_ -- the changes
statistically preferred _now_ among the alternatives
will turn out statistically more useful later than
the alternatives.

You are then, for theological reasons, merely refusing
to attach attribute "anticipatory" to the 'change
picking processes' which anticipate usefulness of the
change.

You will defend (as you did before on this same point
in Cairn's bacteria discussion) that you are not refusing
it for theological reasons but simply because the changes
on A are more probable due to the particular physical/chemical
DNA properties around the sites A and B at the time of the
change i.e. the greater probability of the A change is due
to the physical and chemical laws and not due to the
anticipation.

But as noted before, with that kind of criteria, you cannot
then call any processes anticipatory, including those
occurring in human brain since the human "anticipation"
is also _implemented_ by neurons through some physical
and chemical processes. Similarly, you would refuse to
say that a metereological program predicting weather is
an anticipatory process since its computation and output
are also produced by the physical processes in its
hardware. Or, you will reject to say that a chess program
anticipating your next move is "anticipating" your next move
since its computations is also implemented as a physical
process in the computer hardware.

In other words, your underlying premise appears to be that
the attribute "anticipation" can be applied only to the
super-natural processes, the processes which do not comply
with the laws of physics & chemistry i.e. you have merely
defined the attribute "anticipation" away from its common
meaning, while in substance agreeing that such processes
do in fact exist, be it in the genetic networks or in
the networks of neurons such as human brain, or in the
conventional computers.

{ Note: I use above the phrase "change picking processes"
since the commonly used term "mutation" seems to throw
you (and some others here) into your usual 'vapid dictums
parroting loop', which then leads to waste of time and
efforts required to snap you out of the loop. }


> Are you saying that mutations that
> occur at a higher frequency are more likely to be beneficial than
> mutations that occur at low frequency in a population?

One cannot make an absolute evaluation like that without any
regard to the context. If a high mutation rate at some site
is the result of the past memory (by the cellular genetic
network) of the environmental challenges for which that
mutation has turned out useful, then if the similar
environmental challenges recur (which is often a useful
probabilistic assumption), the change will likely turn
out useful again.

As to how that usefulness might compare to some arbitrary
changes on arbitrary sites in arbitrary environments, is a
matter of specific evaluation of consequences. For example
one can put an organism into a different environment
in which any particular mutation, which was generally useful
in the previous environments, will turn out harmful.

>
> The search space in this case is a single nucleotide in a pre-existing
> gene (although it is possible that other mutations could have produced
> the same phenotype).

That is the core element of your confusion. Reminding you again,
as explained above we are discussing the implication of the
observed adaptation, which indeed was due to a single nucleotide
change, for the vaiablity (as a mathematical model of the observed
process) of the neo-Darwinian 'change picking' algorithm among
all possible changes. Hence, the space of all possible states
(the set denoted as S0 earlier) available for any 'change picking'
algorithm is essential for deciding which algorithm might have
been used to pick the change observed. This is no different
than using the knowledge of the space of allowed numbers in
the number guessing game in order to decide which algorithm
might have been used to pick the guesses.

Whether we can compute such number or not, any particular
nucleotide X can be changed (mutated) in some finite number
of ways, call it NX, under the physical and chemical conditions
given as initial state. Therefore, for all NN nucleotides, there
is another number T, which is the total number of DNA
configurations which differ from the initial state by a
single nucleotide change. If NX were constant for all
nucleotides X, then one could compute T = NN * NX. If the
NX varies with X, as it normally would, T would be the sum
of NX for all X. In any case, there is such integer T,
regardless of how well we may be able to estimate in practice
its value with present computational tools.

Let's say, for the sake of argument, that you obtain that
T = 10^20 configurations which differ by one nucleotide change
(including all possible ways that any changed nucleotide
can be changed under the initial state physical-chemical
conditions) from the initial configuration. Note that we
can't do anticipatory pre-filtering (from among all possible
nucleotides changes) based on the future viability of the
organism, since within ND algorithm, that filtering can be
done only _after_ the pick, when the natural selection takes
place and when the cost of one potential offspring is already
paid. Hence our NX for nucleotide X includes changes which may
result in what would be a 'defective' DNA (including all the
possible fatal defects).

Suppose now that the total number of offspring by the mice
population during this adaptive "big leap" is 100 million,
i.e. N = 10^8. Hence, the mice population was able to explore
only N/T = 10^-12 fraction of the possible DNA configurations
which differ by one nucleotide from the initial one. The odds,
_within the random pick algorithm_, that one of the changes
would hit the right nucleotide the right way, from some set
of F favorable mutations of this type, would be P(N,) = F*N/T.

Let's say that F=1000 configurations qualify as favorable
under the circumstances. Hence the _random pick algorithm_
yields the odds of any favorable 1 nucleotide mutation as
10^-9 or one in billion. That kind of low odds would
automatically exclude the _random pick algorithm_ as
a probable algorithm capable of mathematically modeling the
empirically observed mutation, since it would model it
correctly once in a billion experiments, failing the rest.
One would then have to look for some other algorithm to
mathematically model the observed adaptation.

This is mathematically the same problem setup as in the
number guessing game, only with different values for
N, T and F. If the 'random guess' algorithm is shown to
need many more tries (or offspring in the mice example)
to guess the right number than what was observed as the
average number of tries to guess, then one can conclude
that the random guessing algorithm is a poor model for
the observed success rate. For example, if a random guessing
is computed to have a chance 1 in billion to yield a correct
guess in 10 tries on average, the implication is that I
have used some other strategy, more efficient than
random guessing.

> I could certainly tell whether or not you were rotating through the
> numbers in a way significantly different from what would occur by
> chance.

Yes you might be able to do that, but you don't have that kind
of knowledge by your own rules. Namely, you are claiming (via
your empirical rates argument) that _all_ you need to declare
that my guessing strategy was 'random guessing' is how many
tries on average I need to guess (which is equivalent here to
knowing the average rate of my tries, such as 5 tries per minute,
and the duration of the guessing).

I am saying that this number alone (which is equivalent to the
knowledge of the empirical rates of various mutations) is not
enough for such conclusion. Short of being able in some cases
to eyeball the pattern of my guesses (which is an irrelevant
artifact of the intentional simplicity of the example), any
deduction of the algorithm used, based solely on the statistical
properties of its performance, requires the knowledge of
the range of the available numbers i.e. the size of the
space of all possibilities (denoted earlier as the integer T).

In other words, we are discussing whether you can legitimately
deduce from the observed _statistical properties_ of mutations
alone, as reported in this or similar experiments, that the
'change picking algorithm' was a random pick (unbiased to
prefer changes _now_ which will turn out useful _later_, as
explained earlier).

That you may be able to sometimes eyeball some kind of pattern
in my sequence of number guesses in a simplified example where
you can count everything on your fingers is, to put it politely,
not relevant for the present argument. You are trotting out the
emirical rates of mutations, claiming that such rate numbers
_alone_ allow you to conclude that the algorithm which models
best the observed success rates is the neo-Darwinian RM
algorithm -- that is the algorithm which randomly picks among
all possible 1 nucleotide changes without any statistical bias
toward the changes which will turn out more useful later. I am
saying that the rate numbers are not enough for such conclusion.

Or, expressed in terms of the number guessing game, you can't
deduce that I am guessing randomly from knowning the empirical
average number of trie before a guess. You need to know the
range of the numbers allowed (the size of the space of all
possible configurations being explored) to conclude that the
random guessing algorithm models well enough the observed
performance of the guessing.


> In our particular example, the size of the search and solution space is
> the single nucleotide that needs to be changed. The rate of change at
> that site is all you need.
>

The rate of change (accounting also for the rate of repairs)
is dependent on the immediate physical and chemical
environment in which it occurs. That immediate environment
is in turn dependent on its own physico-chemical environment,...
and so on, until you reach the state of the organism's
environment and any survival challenges that it may contain
(such as presence of certain predators, which may result
in particular type of physiological stress response, possibly
specific to the predator type, which eventually affects the
individual cells and their biochemical reaction webs,
including the immediate environment of the favorable mutation
site). Hence, the rate of that nucleotide change is, at least
in principle, dependent on the environmental challenge for
the organism.

Obviously, if you were to measure mutation rate of that
site in vitro, maintaining its immediate environment fixed,
you will probably get fixed mutation rate at that site.
We do know of examples, though, where mutation rates do
change drastically under the environmental stress. I
didn't see anything mentioned about the mutation rates
for this nucleotide under different circumstances.

In any case, your argument wouldn't be helped even if
one were to measure the rate and found that in the
variety of circumstances, with or without predators
or stress, the net rate of retained change (allowing
for repair) is sufficient to account for the observed
adaptation for the available number of tries. While I
didn't see any such fact cited, and I suspect it isn't
quite true, for the sake of argument I will grant it
fora moment. So, let's assume that this rate was high
enough to likely produce the observed adaptation
in those circumstances.

Going back to the number guessing game, that would be
analogous to, say, using strategy of trying number 7 more
often as the initial guess, since, for example, I may
have noticed that the other players tend to pick 7 most
often.

Similarly, the genetic network of the mice may have in
the past generations accumulated knowledge of usefulness
of changing that nucleotide that way, more often than
some others and has already built in the structural &
chemical properties (perhaps stored in the "junk DNA")
which make that particular nucleotide more prone to
that particular change. That kind of memory and recall
of previously useful patterns of change/action is common
to adaptable networks (e.g. animal brains, immune systems).

Does this help your argument? Quite the contrary. It would
be like declaring that my calling number 7 more often
or sooner than others proves that my guessing strategy
was random guess. It actually shows exactly the opposite.
Random guessing strategy would pick any number within the
allowed range equiprobably. The fact that my guessing
distribution is skewed toward something that may work
better when guessing numbers produced by humans (knowing
the common human biases toward 'lucky number 7'), shows
a guessing strategy which is trying to anticipate the
values of the numbers which will be uncovered at some
later time. It is a look-ahead algorithm, an algorithm
which maintains an internal model of the number generating
process, plays 'internally' this model forward in time
to find out what numbers it will generate, and uses
these results from the model space to select its action
(the guess) in the real world.

With genetic networks of animals, the changing of colors
via mutations may similarly be a generally useful strategy,
hence the relatively higher rates of such mutations are
a form of anticipatory or intelligent mutations -- the
mutation is done more often in anticipation of need for
it, since the past experience of the genetic network of
mice, spanning perhaps many generations, has shown it to
be useful to mutate that nucleotide that way. I would
guess that "junk DNA" stores great many such patterns
or strategies, allowing it to perform combined changes
of multiple sites simultaneously, with a single "recall"
control switch (which may turn on/off via a mutation or
some other type of the biochemical activation).

Alternatively, you may argue that this mutation is not
done by the genetic network "more often" than "others".
Well, that brings back into the argument the "other"
possible mutations i.e. it raises the question:
is this particular change of this nucleotide more or
less likely than any other change of any other nucleotide?
But that puts you right back were we started with
the number guessing game -- you need to know how big is
the space of possible changes in order to know whether
this particular change is occurring more or less often
than a randomly picked change from the entire space
of possible changes.

You may try twisting the above defense, in order to
avoid recognizing that you need to know the size of the
search space, by claiming that this mutation is not
occurring "more often" than the other _observed_
mutation rates for other sites. But that still leaves
the point of the question unchanged -- how do you know
that all these other _observed_ mutations, including
the nucleotide discussed, are an unbiased random pick
from all possible 1 nucleotide changes, without knowing
how many possible 1 nucleotide changes are there.

Hence, neither of the last two variants allows you
to claim that this is a "random 1 nucleotide change
pick" without having to compute/estimate how many
possible 1 nucleotide changes are there.

You can try hanging some more onto the earlier
position i.e. you can say you allow that the observed
rate of mutation is greater than what a random pick from
all possible 1 nucleotide changes would yield, but now
you will claim that there is nothing intelligent about
it since, say, you can show exactly, via hypothetical
detailed biochemical analysis that the rate observed
is perfectly predictable from the biochemical properties
of that site and its surrounding. Hence you maintain
that the mutation strategy was still the plain old
random mutation, but now under the particular
physico-chemical constraints, it is the constraints
which are responsible for the biased picks, and not
the picking algorithm, which thus, by these shifting
definitions, remains dumb and simultaneously stripped
of any connection with physical and chemical laws,
thus leaving only the 'supernatural anticipation' as
the sole alternative to the RM conjecture.

(That is the old argument you have used earlier for
the Cairn's experiments and their followups, as you
were struggling to make the RM conjecture coexist,
somehow, with these results, at least at a superficial
verbal level via the childish semantic games.)

Well, try the same "fix" for the number guessing game
and my strategy of calling number 7 more often. Say,
you measure my EEG, or use some other probes on
specific neurons, and from the electric patterns there
somehow show that I will call 7, 500 ms before I
consciously "decide" to call it. Does that discovery
somehow make my use of anticipatory (look-ahead) guessing
strategy suddenly into a random guessing strategy?
_Your_ knowledge of the precise neurological mechanism
by which my neurons implement my guessing strategy
does not change my guessing strategy into some other
non-anticipatory strategy or to an absence of any
strategy at all.

Claiming that the knowledge of the detailed mechanism
will somehow change the anticipatory process into
a non-anticipatory/dumb/random process, would be
like recording the orchestra playing Beethoven's ninth
and defending a thesis that they are not playing the
Beethoven's ninth. How? By displaying the sound waves
as electric voltage curves on the oscilloscope, and
then declaring that since you can see the sounds as
voltage curves, the orchestra is merely playing the
voltage curves and not the Beethoven's ninth.

That is essentially what your ND defense via pointing
at the biochemical mechanisms (and their resulting mutation
rates) implementing anticipation, as a "proof" that there
is no anticipation, amounts to.

Windy

unread,
Jul 10, 2006, 7:11:05 PM7/10/06
to
nightlight wrote:
> > We are
> > talking about a single nucleotide change here, not some long drawn out
> > search of all DNA sequence space.
>
> It may have slipped your mind, but we are discussing this single
> nucleotide change in the context of its alleged support for
> the neo-Darwinian conjecture, which prescribes a particular
> way/algorithm as to how such single nucleotide change is picked
> out (e.g. by the biochemical reaction web of the cell) among
> all possible single nucleotide changes that could be picked
> out from a given initial state.

There is no "picking", random or otherwise. You are talking as if a
process (random or not) first determines that a mutation must happen
somewhere in the genome, and then the mutation must find a place where
to happen. It is not so, the mutations are independent of each other.

> Whether we can compute such number or not, any particular
> nucleotide X can be changed (mutated) in some finite number
> of ways, call it NX, under the physical and chemical conditions
> given as initial state. Therefore, for all NN nucleotides, there
> is another number T, which is the total number of DNA
> configurations which differ from the initial state by a
> single nucleotide change. If NX were constant for all
> nucleotides X, then one could compute T = NN * NX. If the
> NX varies with X, as it normally would, T would be the sum
> of NX for all X. In any case, there is such integer T,
> regardless of how well we may be able to estimate in practice
> its value with present computational tools.

Your strategy is flawed. Consider two theoretical organisms where one
has more DNA than the other, but which share the gene we want to
observe and have similar mutation rates. In your scenario, the
likelihood of the desired mutation is always lower in the organism with
more DNA, since it has more possible mutational states. Do you think
that's realistic?

By the way, what is your prediction of the rate of neutral to
non-neutral mutations, if the mutations are picked intelligently?

-- w.

nightlight

unread,
Jul 10, 2006, 9:11:01 PM7/10/06
to
Richard Forrest wrote:

>>It would be an evidence that neo-Darwinian model (RM+NS) is
>>an unlikely explanation of the observed adaptation and that
>>a more efficient (than random) search algorithm is responsible
>>for the adaptation. By convention, we can call this more
>>efficient algorithm an 'intelligent' or guided mutation,
>>or generally an ID algorithm.
>>
>
>
> No we don't.
> Not in science, anyway.
> If, in science, we don't know what is responsible, we say
> "We don't know what's responsible. How can we find out?"

If some algorithm is more efficient than a dumb/random search
it is perfectly reasonable to call it _by convention_
'intelligent' search. There is nothing to "research" and
"find out" about a perfectly natural naming convention,
which merely indicates the basic property (greater efficiency)
of such alternative algorithm.

>
> In ID, which isn't science, they say
> "We don't know what's responsible, so GodImeananintelligentdesigner
> must be responsible. Well, now that's settled, let's go and spend those
> fat cheques the DI has sent us."

You seem to have mistakenly cut and pasted something from your
debate with Pat Robertson. Or maybe you just prefer to wrestle
with your little strawman.


>>it would be an evidence that the 'intelligent agency' (IA) model
>>is not necessary to explain that particular adaptation.
>
>
> Oh, I see.
> So the position is that there *must* be an intelligent designer, but if
> any particular test doesn't uncover his actions, it's the wrong test.
>
> Hard to falsify.

Not at all. I am simply pointing out that one can imagine a
hypothetical experiment or observation which provide no data
which can discriminate between the various models. That is
not equivalent to saying that no observation can discriminate
between the ID and ND models. After all, this whole series of
posts is arguing precisely the opposite -- that there exist
ways to falsify either of the two models of the evolutionary
algorithm.

> To form a theory, you have to start by testing hypotheses. So far, no
> IDer has tested a single hypothesis about the action of any intelligent
> designer.
>

The hypothesis is that there is an 'intelligent agency' (IA) guiding
the mutations (or generally all transformations of genetic networks
across generations). This results in a more efficient search of the
space of all "possible" (=consistent with the laws of physics &
chemistry) DNA configurations for the 'favorable' configuration than
the neo-Darwinian search algorithm (random mutation, unbiased toward
possible mutations which may turn out favorable later) can achieve.
Hence the testable hypothesis, as explained at length in previous
posts, is that the observed rates of the new 'favorable'
configurations should be greater than those that a random search
algorithm would find.

The single nucleotide mutation described in the paper being discussed
is a particularly convenient case for discussing what is meant above
since the search space is relatively simple to define - it is a space
of all DNA configurations which differ from the initial state by a
single nucleotide change (of any kind of change i.e. the change need
not result in a valid nucleotide, it needs only to be consistent with
the laws of physics/QM and chemistry applied to the initial state).

Mathematically, this problem is equivalent to the problem of finding
whether the algorithm I am using in the number guessing game
performs better than the random guessing. If you only know that I
guess the hidden number in 10 tries on average, my claim is that
this fact alone is not enough to decide whether my guessing
performance is better than a random guessing algorithm. You
also need to know what is the range of allowed numbers, before
arriving to such conclusion. The basic neo-Darwinist claim here
(the crowing about how the mice paper confirms the neo-Darwinist
RM conjecture) is equivalent to claiming that from just knowing
that I use 10 tries per correct guess one can conclude that my
guessing performs no better than the "random guessing" algorithm.

In the mice adaptation example, knowing the empirical rate of mutations
at the site where they found the 1 nucleotide mutation, is not enough
to conclude that the neo-Darwinian RM algorithm (the random search
in the space of configurations 1 nucleotide away from the initial
state) is the model which explains the observed adaptation. Namely,
all that the empirical mutation rates (taken together with the
number of organisms and the time for adaptation to arise) give
you is the number of tries that the search algorithm had to find
the favorable adaptation. The number of tries alone is insufficient
data to decide whether the search algorithm performed better
or worse or equally as the random search. You need to know what
the search space was, before declaring that the empirically
observed performance is no better than random search. Hence,
there is nothing there for neo-Darwinists to crow about.


>>Consider an 'intelligent agency' which we know to exist in nature
>>(human brain) applying its efforts to stock market trading. One
>>could trade using all his knowledge and foresight and not do
>>any better than chance on any particular day or a week or
>>throughout the whole trading career. Could you declare that
>>he was picking randomly if his gains don't exceed random
>>ones for some given span of time? You can't. You would
>>need more data and possibly different kind of data (such as
>>direct observation of his trading or an interview) to support
>>such conclusion.
>
>
> Quite what the relevance of this is to evolution is a mystery to me.
> I supose that if you have not one scrap or tittle of evidence, then all
> you can do is to argue from analogy.
>

The intent was to illustrate just how far the neo-Darwinists
are willing to go in twisting the common language and concepts
in order to uphold their religiously/ideologically motivated
dogma (of 'random search' being the sole search algorithm used
to explore the space of DNA configurations). By placing their
absurd criteria into an analogous context but in which they don't
have so strong emotional investment as they do in the context
of evolution, makes the absurdity of the rigged criteria more
obvious.


> So what was the hypothesis which ID is testing?

The hypothesis is that the random search algorithm for
favorable configurations in the space of all physically
possible DNA configurations would under-perform the empirically
observed evolutionary algorithm i.e. the random search would
take much longer to find the successful evolutionary novelties
than the observed rates of such novelties. As explained
earlier, the single nucleotide adaptation with the mice,
greatly simplifies the formulation of the hypothesis and
its test criteria.

> On the other hand, there is plenty of other evidence to support
> evolution by natural selection, and no evidence whatsoever to support
> the idea that an "intelligent designer" occasionally interferes with
> normal biological processes.


You are again pasting here from your debate with Pat Robertson or
some such. Nothing I said here or in other threads implies the
strawman "theory" you are mocking above. First, "intelligent designer"
is quite loaded term, implying among others a deistic perspective
(which I think is wrong). I prefer term "intelligent agency" (IA),
which is more consistent with a pantheistic perspective which I
find more coherent. Namely the IA is continuously active, not just
in evolution, but also in forming and upholding the uniform physical
laws across the universe, from incredibly finely tuned physical
constants (e.g. google on "anthropic principle") down to the
elemental properties of our space-time. A bit more about the
possible model for IA is given at the end of an earlier post here:

http://groups.google.com/group/talk.origins/msg/651222ff530cbe4e

I bring up the general view underlying my arguments only to
avoid various caricatures being tossed in by the neo-Darwinists
here as their presumed best guess as to what perspective one
must have to make those arguments.

>>There are plenty of ways that an 'intelligent agency' could exist
>>and perform directed mutations. I merely pointed out couple
>>possibilities which are not a priori excluded by the presently
>>known laws of physics.
>
>
> So propose a test which could *falsify* the intervention of an
> intelligent agency.

Well, showing that the neo-Darwinian random search algorithm can
perform at the level of the empirically observed evolutionary
algorithm, would make the IA model subject to Ockham's razor.

On the other hand, if the random search algorithm were to
perform better than the observed one, that would imply a
'malevolent' (to life) IA, while the performance of random
search worse than the observed would imply a 'benevolent' IA
(this is the variant assumed by default as IA).

One can also easily flip upside-down these value loaded
attributes (malevolent & benevolent) by viewing the emergence
and evolution of life as a shortcut or a short-circuit speeding
up the approach of the whole system to the maximum entropy state,
the heat death of the universe (since the processes of life
accelerate the total entropy generation for the whole system).

> What was that scientific alternative to evolution by natural
> selection again?

The alternative that I have in mind is a hypothesis that
the neo-Darwinian 'random mutation' search algorithm would
under-perform the actual/empirical evolutionary algorithm.
Since that core aspect of the neo-Darwinism was never put
to test (it may be computationally too complex at present to
test decisively), all three types of algorithms, the neo-Darwinian,
the benevolent IA and the malevolent IA, are equally open
and falsifiable hypotheses, none so far shown or known to be
better than the others.

> It isn't ID - Michael Behe, one of it's leaders conceeded under oath
> that it isn't science, so you must be talking about something else.

He is welcome to believe and say as he wishes. I don't share that
particular view.

> What is *your* education in science, by the way?

Theoretical physics. Since the grad school (Brown Univ.),
though, I have been working in industry, R&D, mostly in
research and design of practical combinatorial and optimization
algorithms (used for forecasting, compression, search,...).

nightlight

unread,
Jul 11, 2006, 3:17:40 AM7/11/06
to
Windy wrote:
> There is no "picking", random or otherwise. You are talking as if a
> process (random or not) first determines that a mutation must happen
> somewhere in the genome, and then the mutation must find a place where
> to happen.

The term "pick" doesn't imply a human-like conscious decision. If one
looks at the processes of DNA transformation as a sequence of steps
connecting one DNA state to the next, from the initial state A
t