Re: ID and the Difference Between Spheres and Cubes

My argument is not about or based on short times available
for evolution.

Meaning that you do accept standard timeframes?

Of course. Anything that has empirical support is fine within its
uncertainty margins (provided you state them). That wasn't my argument.
The argument was about the sufficiency, at the mathematical and the
empirical level, of the "random" mutations in replicating the observed
rates and quality (complexity) of evolutionary novelties. You are
welcome to point out what data and what calculations show that "random"
mutations can replicate the observed rates of novelty. Note that you
can't avoid the mathematical modeling part due, at the very least, to
the quantum dice curtain which doesn't allow you to see the precise
mechanism behind the individual choices (QT only lets you have
probabilities of various choices and no theory or present observation
will let you peak behind the QT curtain). In practice and at the
present technological level the domain of ignorance of the precise
detail of individual choices is much larger than what the final quantum
curtain prescribes.

The (approximately) "constant rate" of DNA change is an
empirical fact. It tells you absolutely nothing about
the presence or absence of any guidance (or anticipation,
foresight...) in the generation of those DNA changes
(which are then subject to natural selection).

You mean does science exclude the possiblity of
theistic evolution?

That's not what I meant and it has no relation to what I said. If you
are looking at a sequence of say, presumed coin tosses, just counting,
say totals for heads and tails doesn't tell you whether the sequence
was from genuine "random" coin tosses or from hand put outcomes. You
can eliminate (in the probabilistic sense) the latter by comparing the
prediction of "random" model (binomial distribution for genuine coin
tosses) with the observed frequencies of various subsequences (e.g.
counts of 01 vs 00 etc). Your RM argument seems to be that since you
don't see any pattern by just eyeballing the sequence of 0's and 1's,
then it must be due to random coin tosses. My argument is that, since
you're not allowed to watch the tossing but only to see the results (in
biology, due to quantum and technological indeterminisms), you need a
mathematical model for the generator, such as binomial distribution for
coin tosses. Then you need to compare whether its predictions match
(and how well) the empirical counts you can obtain from the actual
sequence. That was not done for RM conjecture in ND theory. Just
declaring it so and applying Lysenkoist methods to academically destroy
anyone doubting the RM conjecture merely emphasizes its fundamental
hollowness and sterility.

No. Nothing can exclude the possibility of an unspecified
and unobservable appearing to act via naturalistic methods.

Well, if logic, facts and imagination fail you, there is always that
strawman of 'supernatural' to fall on.

One can propose a magical entity as the cause for
*anything*. But what you have to do is demonstrate
that such a magical entity is *necessary*.

Again the same strawman. You're the only one bringing in the magic. I
am asking you to show results that confirm "random" nature of
mutations, specifically the predictions of adaptation/innovation rates
based on "random" model and their comparison to empirical frequencies.
The difference between the two would imply the degree of likelihood of
the "random" mutation model of observed evolution rates (micro and
macro). If you don't have any, then the question is open whether the
mutations are random or not (which is my position here).

In the case they're not "random" (poor predictions), there are plenty
of alternative models (some of which I pointed out before e.g.
subquantum complexity between the current "elementary" particles,
10^-16 cm, down to Planckian scale objects, 10^-33 cm). In fact you
don't even need subquantum complexity, since you already know that
there _are_ natural processes guiding non-random, even purposeful and
anticipatory, generation of genetic novelty (e.g. brain of a molecular
biologist, or for that matter even the brain and senses of any animal
looking for a mate).

There is no magic or supernatural elements (assuming you exclude the
existence of "mind stuff" which, even though it exists, is presently
not modeled by the natural science of matter-energy transformations) in
any of them. I see no reason, much less a proof, that those must be the
sole examples of such purposeful natural processes. I don't even see
how would one express such exception in a precise scientific
mathematical language so one can model it.

Yet the neo-Darwinist RM dogma claims it is so, that those exceptions
(which it can't even describe in a precise mathematical language) are
the only exceptions to RM conjecture. Why is it so? My guess is that
such intelligent, purposeful processes exist at all levels, at least
from the ecoweb scale down to the biochemical reaction webs within
cells (including the "junk" DNA which I think is a key part of a highly
intelligent neural network which models and evaluates internally the
possible transformations of DNA and their phenotopic consequences
before committing its best pick to the much more costly physical
implementation/offspring).

After all, the linguists use similar methods as
evolutionary molecular biologists to study the
evolution and relations among natural languages
(which are created and transformed by intelligent/
purposeful agents).

Yes. There is a lot of similarity in the two processes.
A difference, of course, is that the intelligent/purposeful
agent involved in the evolution of languages are not
undetectable or magical.

That little strawman is quite busy in the debate here. Just because
your imagination fails to come up with anything else besides magic for
a given phenomenon, it doesn't mean that everyone else must also be
assuming magic as the "answer".

There is nothing magical or grossly undetectable in the examples above
of natural processes, that we all know to exist and which intelligently
and purposefully guide DNA transformations from generation to
generation. There is also nothing mathematically or computationally
special about the intelligent networks which act as intelligent agents
behind those DNA transformations. Such networks exist at all scales,
above and below human brain. They all interact in some way with
genomes, hence they build (as we do at our own level) their own
internal models of genomes and their envirnments. The most natural
position is to assume that they all exert in some way their
anticipatory influences on the genome, each one affecting the aspects
of DNA relevant for its own intearactions with it and the related
punishments/rewards. The ND conjecture -- that only one particular
network (the brain of 'molecular biologist') can guide mutations, and
all others are somehow excluded (despite interactions) so that except
for that one unique case, the mutations must be "random" -- is
strained, unnatural and ambiguous (e.g. how do you give precise
mathematical characterization or model this single odd exception).

Note also that molecular physics, which is an applied quantum
mechanics, is subject to quantum dice behind the curtain. No
theoretical result or existent experiment gives any clue what (if
anything) is behind the quantum indeterminism i.e. how do quantum
outcomes get picked. There are also plenty of technological and
mathematical modeling unknowns in molecular biology e.g. what does the
"junk" DNA do and how does it do it? How do biochemical reaction webs
which include the "junk" DNA work, what do they model, what do they
"think"? Just because you can sequence it, it doesn't mean you know or
understand how it works, how it affect phenotype and by which chain of
reactions.

The present level of knowledge in the molecular biology is not much
better than that of a caveman looking at a computer -- he can figure
out that by pressing this or that key he can get some light dots on the
screen or that pulling the cord darkens the screen and other such
superficial correlations. But he has no clue (or even a language to
conceptualize what the question is) about the underlying processes that
make such correlations happen or the (perfectly natural) intelligent
agency (modern technology & science) that designed it and built it. For
him it's a magic, yet we know that no magic is needed. Assigning magic
to phenomena you may not understand, as you repeatedly do, is a
primitive form of thinking which short-circuits any further query by
attaching to the puzzling the empty label "magic" as an sedative.
Scientific thinking is to look at it as a puzzle or an open question, a
challenge to ones imagination.

Languages, unlike organisms, do not self-reproduce.

Neither do ecosystems (or species). But the elements/building blocks of
languages do reproduce, just as the building blocks of ecosystems or
species (organisms) reproduce. For example, you add suffix "ed" to
verbs to form past participle. The pattern "ed" is thus reproducing
itself (in its particular realm). Numerous forms of pattern
reproduction exist at every level (e.g. semantic, grammatical,
phonetic) of natural and artificial (mathematical, scientific)
languages, propagating via analogies. There is an even more elemental
reproduction (analogous to cellular reproduction) of patterns -- every
time someone learns or uses such patterns the pattern has managed to
reproduce. How many times have patterns DNA or "is" or "the" reproduced
in this post? Of course, this reproduction uses humans, books and
computers, instead of atoms and fields, as its substratum, but that is
a matter of network implementation. The basic mathematical properties
of such networks with adaptible (to punishments & rewards) links are
deduced independently of the implementation for the links, nodes and
punishments/rewards.

They are manufactured by a known intelligent agent.

Known? Really. That's like the cavemen with computer saying he "knows"
how it works and to demonstrate that he "knows", he shows how when he
hits a key the light pattern pops up, just as he predicted it would. As
far as he knows he "knows" it. Similarly, with humans generating
languages -- for example, there is no scientific model at present which
tells you anything about the mind-stuff (what is it like to be some
arrangement of atoms and fields? what is redness like? what is it like
to get an idea?). We don't know whether the mind-stuff is an
epiphenomenon or a causal agent (which can affect the matter-energy
transformations). I am not talking about telekinesis but about quantum
dice. We don't know how it picks its quantum outcomes when "brain"
thinks (perhaps the mind-stuff does the job as von Neumann and Wigner
conjectured). Hence, you don't know the "intelligent agent" behind
language much better than the cavemen knows the one behind the
computer. Just as he can predict pattern from a button pressed we can
roughly predict neurological and behavioral effects of stimulation of
certain brain regions. In both cases there is also some "little" stuff
going on that is sort of mysterious, but that probably doesn't matter
much. We got these handful of correlations, so we both "know" the
agent. We can also name it as a "proof" that we know it. Yeah, sure.
(The same goes for "knowing" how evolution works.)


I have explicitly pointed out that no DNA configuration is
so deviant from configurations held in common by both
chimps and humans that any search of some hypothetical
total sequence space of possible sequences ever is likely
to have occurred. *All* that is needed is *modification*
of the subset of total sequence space that existed in
the common ancestor.

You should read more carefully before responding. I was not talking
about space of all possible arrangements of a given numbers of atoms
but about all arrangements reachable by a single (or by some number n)
mutagenic event from a given initial state. That space (labeled as M in
the first post) is huge, too. To test "random" mutation conjecture
behind evolution, for single or for some n>1 mutations, you still need
to have combinatorial or probabilistic model of that "n-mutation
neighborhood" space and compare its predictions with the empirically
observed frequencies of favorable novelties at the distance of
n-mutations from the same initial state.

The ID conjecture is that the empirical frequencies of favorable
novelties (being offered to natural selection to weed out) are much
greater than what a "random" mutation model would predict. The
neo-Darwinian conjecture is that the observed empirical frequencies are
exactly what the "random" mutation model would predict. Neither side
can at present work out the math and computations of the model to prove
their case (due to our present limited computational and modeling
capabilities). The ND priesthood had not won this argument but has
merely bullied the alternatives out of academia through Lysenkoist
style censorship, economic and professional intimidation. The side
which has to reach for these kinds of "scientific" methods in order to
cling on just a bit longer, is as a rule the weaker one on the
substance (recall USSR and its communism).

The underlying assumption of these arguments is a
specific non-evolutionary mechanism that involves
inventing a sequence from total sequence space rather
than modifying a sequence from an ancestor.

Your sloppy reading again. The space M of possible DNA configurations
is the space at distance n mutagenic events from the original sequence,
where n=1,2... It is not a space of all possible configurations of
given numbers of atoms (which would be much bigger).

Given that such calculations are utter nonsense wrt
to modelling how evolution *actually* claims to work (and,
from direct, observable *evidence*, actually did so in
the case of chimps and humans), what is the use of
presenting these ignorant "747 forming in a tornado"
calculations? Evolution works by descent with modification.

You're getting quite a mileage out of that strawman. Read again in the
1st post what the 'total space of configurations' and M mean.


Anyone can always claim that mutations occcurred by a
God producing them, just as you can claim that Lady
Luck is responsible for the cards you received.

There are quantitative criteria to distinguish whether the deck and
shuffling are stacked or fair. This is no different than testing a
quality of random number generator by applying random number tests. The
idea is to use presumed model of the random generator (such as binomial
or multinomial distribution) and produce its predictions for the
empirical counts obtained from the sequence. That lets you decide
whether the "random" model is valid and how valid.

But you seem to be claiming that the rate of such mutations
is too slow to be happening in the absence of a God (or
that you could not have gotten those cards in the absence
of Lady Luck).

No, I am only claiming that no one has computed whether "random"
mutations are too slow to generate the observed rates and quality of
evolutionary novelties. I am saying that this is an unsolved problem
which has, at least given sufficient computational and modeling
resources, a precise answer.

All I am doing is pointing out that there is no *need* for
such an outside agent.

You can "point out" whatever you want. That doesn't show that the
"random" mutations are just right. To show that there is no need for
any other but "random" mutations, you need to make prediction from the
random mutation statistical/combinatorial model of DNA mutations and
compare them with the observed frequencies.

As to "outside agent" that's your strawman again. "Outside" of what?
Outside of backward & forward light cones of a DNA molecule (which is
the space-time region which can propagate interactions at maximum light
speed)? Well that would cover the entire visible universe.

Until ID presents a testable idea that would require the
*necessity* of the action by some outside agent, my thesis
that such an agent is *unnecessary* because *all* of
the observed differences between humans and chimps are
consistent with known rates and types of mutation from
ancestral sequences, it remains ignored by and irrelevant
to science because it fails the razor test.

I described a test. It is the same kind of test you would use to test
"random" generator for any other sequence, such as that of coin tosses.
Make prediction from that RM model of DNA and lets see whether it
matches the empirical frequencies of the evolutionary novelties being
submitted to the natural selection. There is plenty of unknown, from
quantum dice to present limitations of technology and mathematics, for
entire universe of intelligent agents to fit in and causally interface
to the DNA mutations.


And that is relevant to the modification of pre-existing
useful sequences how? That is an interesting model of
the "747 in a tornado" explanation.

Shadow boxing again...

There have been many, many, many empirical tests of the
idea that mutation occurs *independently* of need for
the mutation. In every case, from the Luria/Delbruck
experiments on, the finding is that mutation occurs
*independently* of the need for that mutation.

I responded to LD and similar experiments in the previous post:

http://groups.google.com/group/talk.origins/msg/748587b6e86a28c8?hl=en&;

These experiments have nothing to do with question of "random" mutation
vs guided (anticipatory, intelligent,...) mutation. Namely, the same
kind of statistical behaviour can be observed for technological
innovations which clearly do have intelligent agents behind (see my
previous post for details on LD). Generally, any kind of statistical
phenomena and patterns you can observe in the technological evolution
(or of science, languages, cultures, etc) where the intelligent agents
are clearly behind, cannot be claimed as a proof that the similar or
analogous statistical phenomena and patterns imply "random" mutations
in the biological evolution.

.