Re: ID and the Difference Between Spheres and Cubes

On 10 May 2006 12:31:40 -0700, "nightlight"
<nightlight@xxxxxxxxxxxxxx> wrote:

The random mutation (RM) + natural selection (NS) do
not explain even the microevolution, much less the
macroevolution. The key missing piece is a proof
that RM can yield the observed rates of adaptation.


That is easy, if, of course, you accept standard timeframes.

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

Humans and chimpanzees diverged from a common ancestor some 5
million years ago. Random mutation and *neutral drift* to
fixation, unlike the much faster random mutation plus positive
selection, occurs at a relatively constant (it does not need
to be absolutely constant to make the point) rate for
selectively neutral sites.

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). An intelligent
agency could model the possible DNA changes internally, performing
look-ahead and elimination/selection before committing to the physical
changes. While running as an internal model could be many orders of
magnitude faster than the corresponding physical process, its net
effect may well be precisely the _observed_ rate of evolutionary
novelty, be it for steady or for highly variable (e.g. Cambrian
explosion) forms of evolution.

What we see is easily accounted for based on the chemistry of DNA and
the ability of cells to repair DNA. There is no need for an outside
agency to account for the drift observed.

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).
All the biological evolution patterns, such as those in your examples,
commonly trotted out by neo-Darwinists in support of the sufficiency of
"random" mutations, occur in the evolution of natural and artificial
(such as mathematical formalisms) languages, religions, arts,
scientific theories, technologies,... (just recall Dawkins memes).
Curiously, in all other observed instances of such evolutionary
patterns, there is always an intelligent agency behind. The sole
exception is, according to neo-Darwinist Gospel, the biological
evolution.

You are confusing models with reality.


The constant (or variable) _observed_ rate of DNA change is only an
easy half of the criteria needed to discern between intelligent
(guided, anticipatory) and random generation of novelty. The present
molecular biology is still much too primitive to evaluate the other
half, since it cannot _compute_ either how many total DNA
configurations could be produced in a given setting, much less how
would every DNA change at the atomic level affect the phenotype (in
order to enumerate the 'favorable' or at least neutral outcomes).


WTH are DNA configurations? That certainlly is not a term used by us
mol bio folks. And is "change at the atomic level" just an akward way
of saying mutation? DNA is pretty much DNA at an atomic level. You
gots your A's, C's, G's. and T's. There some finessing in various
organisms with methyl groups and/or other modifications acting as
party hats, but DNA is not that exciting at an atomic level.

Evolution is certainlly not guided, it is contingent. Look at the
Luria Delbruck experiment for a simple example.

The problem is therefore too complex to tackle with the present
technological and scientific tools, hence the question of ID vs ND is
an open and a perfectly legitimate scientific problem. The "irreducible
complexity" examples offered by the ID proponents are a qualitative
plausibility argument. Its effect in terms of the more precise criteria
described in the previous posts is to enlarge (exponentially in the
number of required changes) the space of possible configurations, thus
reduce the probability of favorable combined DNA change for any given
number of tries. Since the full combinatorial spaces relevant for the
precise criteria are enormous (e.g. of 10^C kind, where C is of the
order of number of atoms in the DNA), the handfuls of components used
in "irreducible complexity" arguments merely add relatively tiny
numbers to the exponent C for the total number of combinations. Arguing
those examples is like arguing fiscal policies based only on the last
digit of the figure for US national debt expressed in millicent units.

Ahhh, no. You seem to be caught in the logical loop of "if DNA has X
# of atoms, then something like 10^X degrees of freedom are possible,
therefore evolution would take Y^10^X sample size". While you
certainly can shuffle numbers all you like you are confused about some
basic chemistry and biology. Using that sort of logic we preclude any
cell from existing for more than an fraction of a second. Using that
sort of logic, there is no way that any enzyme could exist or
function. It seems to me that a reasonable person would notice that
life did not logically depoof at the original assertion, and look for
the error.

Organisms are not free to explore the entire phase space available
based on their genome size and randomlly rearranging the DNA. There
is actually a relativelly small area of the phase space to explore,
and it's almost always nearby (lateral gene transfer is an exeption).
Kinda explains why species tend to go extinct.


But it does mean that there is more than enough random
mutation to account for the difference between humans
and chimps *even if* all the difference between these
species were merely random neutral fixation.

As explained, the empirical mutation rate is a fact orthogonal to the
question of whether the mutations which differentiated humans from apes
were random or guided (selected with look-ahead).

What we see in comparison of the genomes shows that the changes are
biased towards genes implicated in neural development, diet, and
disease. Sort of what you would expect based on the biology. And
linkage disequilibrium of genes near these genes showing strong
selection indicate either a) evolution or b)
incompetant/malevolent/trickster designer.

Which is simpler, and which has actual evidence?


In my book of science, actual observation of organisms
trumps your hypothetical mathematics.

I am not arguing against the value of empirical data. After all, the
observed counts of viable novelties O (in my first post) is the number
to be compared with the expected number of viable novelties from random
mutations (within given time & population sizes). The problem is that
there are no empirical facts that addresses the point of contention
between ID and ND.

Bad model, and even worse conclusion.


Consider a simple analogy -- I tell you I am "randomly" tossing 10
coins behind a curtain and then you are allowed to check the outcome
and deduce whether I am tossing them "randomly" or putting them down by
hand. You are not allowed to look behind the curtain until I say the
coins have settled down. If we were to perform a "large" number of such
experiments, you could apply various random number tests on the
observed outcomes and deduce the probability of "random" tossing vs
putting the coins down by hand for the given number of tests. Since you
can't see or hear what is going on behind the curtain, the observation
is not enough -- you need a mathematical model for the "random coin
tossing" (binomial distribution), then you need to compute numbers
(various frequencies) within that model and compare them with the
observed numbers.



In nature, our current most fundamental theory (Quantum Theory; QT) is
irreducibly non-deterministic i.e. you're seeing the outcomes of
quantum transitions, you know the probabilities of various outcomes,
but neither the theory nor any observation can "see" behind the quantum
curtain. Hence if you wish to show _scientifically_ (instead of relying
on Lysenkoists methods used by the present neo-Darwinian priesthood)
that the mutations (which eventually come down to quantum dice)
involved in evolution (at any scale, micro and macro) are "random" you
need to work out the mathematical model for truly random DNA changes
and compare its predictions with the observed outcomes as sketched in
my first post.

Actually, most mutations fall into the macroscopic realm, at least for
QT. We are talking about relatively large chuncks of stuff being
moved- deamination of cytosine, oxidative adducts, strand breakage and
repair etc. You are blathering nonsense here if you think there are
any Schrodinger cats involved. On the off chance you and think that
most mutations involve radioactive decay, you are very much mistaken.

And before you call someone a Lysonkoist, please learn what a
Lysenkoist is. He certainlly did not beleive in random changes as a
driving force for changes in organisms. If you are refering to his
suppresion of what you would call "Neo-Darwinists" in the former USSR,
then you should use the term "Stalinist". Calling a biologist a
"Lysenkoist" is confusing.

As far as your math goes, GIGO. If you don't understand either the
biology or the chemistry, you really cannot make a sensible model.
Your model would make life impossible, so I suggest a change in model
parameters. Just a suggestion.

And as a final point, the real problem of ID is the invisible pink
unicorn (or it's hipper cousin the FSM). Any agent that can be
postulated to do anything, in any way, and hide itself from
inspection, is by definition unscientific. No predictive basis, no
testibility, no way to falsify.

As far as IC goes, it just means you are A) not current with biology a
la Behe or B) or willing to assume we now know all that is ever
possible to know about a system a la Dembski. I am not willing to say
I am god-like in my knowledge, but am always amazed at the relegious
folk who seem to think that ID is reasonable given that conclusion.
And that is the basis of most "scientific" ID- I can't explain it
fully, therefore God/IPU/FSM. To me, I can't explain it means that
that's something worth looking into. That's part of the joy, and most
of the frustration of being a scientist.


B Miller


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Relevant Pages

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