Reflectorites
On Sun, 30 Jan 2000 14:36:35 EST, MikeBGene@aol.com wrote:
[...]
>CC>Further, there is the fact that we know that the watch is designed partly
>>precisely because it does *not* have the *non-*designed look of biological
>>organisms and such. It's parts are put together differently. It has screws
>>and such holding it together. Living organisms do *not* have such "design"
>>features.
MG>But cells do and that's the point. Of course, cells don't have tiny metal
>screws; instead, things are secured to each other through packing interactions
>as a consequence of complementary conformations and specific placement
>of amino acid side chains. It used to be thought that diffusion dominated
>in the cytoplasm of the cell. But it has become increasingly clear that basic
>cellular processes work more like the gears of a watch, where specific
>placement and shapes make possible inter-protein handoffs that channel products from
>one protein to the next directly so that intermediates never see the aqueous
>phase. Protein complexes work exactly like assembly lines.
This reminded me of something Denton wrote about the a (alpha) helix of
proteins fitting almost perfectly into the major groove of the DNA helix:
"From first principles, proteins, because of their limitless variety, functional
diversity and inherent flexibility, and their ability to undergo allosteric
transitions, etc., are obvious candidates for the crucial function of
recognizing and binding to a particular section of a DNA molecule. But on
top of their general properties, which tailor them so superbly for almost any
conceivable biochemical task, there is a fascinating and highly specific
aspect of protein structure that appears to fit them precisely for DNA
recognition: the fact that the a helix of a protein, one of the most common
conformations found in proteins, fits almost perfectly into the major groove
of the DNA helix." (Denton M.J., "Nature's Destiny", 1998, p189).
Denton continues:
"The fact that one of the most fundamental protein conformations fits very
neatly into the large groove of the DNA obviously greatly facilitates
protein DNA recognition because it allows the protein to have intimate
access to the DNA sequence. ... if a protein is "to read" a particular base
sequence in a particular region of the DNA, the protein must be able to
distinguish between the different base pairs along the helix. Of course, the
protein cannot actually "see" but must feel the sequence of the DNA like a
blind person reading braille until it finds (feels) the sequence it is looking
for. It turns out, and this is surely another coincidence of great significance,
that of the two grooves in the DNA, the major and the minor, it is the
major groove-the one into which the a helix happens to fit so perfectly-that
provides hydrogen bond patterns which are distinctive for each of the four
base pairs and can therefore be felt by the or helix.... So the actual base
sequence of the DNA can be "felt" most readily by a protein feeling the
sequence in the major groove. In effect, the major groove is fit for protein
recognition not only because its dimensions match that of the a helix but
also because in the large groove each base pair presents a unique
electrostatic pattern which greatly facilitates sequence recognition-quite
literally the "feeling" by the a helix of the base sequence of the DNA. The
large groove therefore exhibits two independent adaptations for its role in
protein-DNA recognition-its electrostatic variability and its dimensions,
which match closely that of the a helix. The mutual fitness of the large
groove and the a helix for DNA-protein recognition must be considered a
coincidence of very great significance, as recent work in this area has
revealed that a great many DNA-recognizing proteins insert a protruding a
helix into the major groove of the DNA helix when binding to the DNA."
(Denton M.J., 1998, p190).
At the end of his next chapter, after considering the cell, Denton concludes
by pointing out that: a) in molecular biology we have found a `watch'
"more complicated and more harmonious than any conceived by William
Paley"; and b) it is a watch which the `blind watchmaker', natural selection,
could not have produced, because natural selection *needs* this watch to
be already working before it can work:
"The emerging picture is obviously consistent with the teleological view of
nature. That each constituent utilized by the cell for a particular biological
role, each cog in the watch, turns out to be the only and at the same time
the ideal candidate for its role is particularly suggestive of design. That the
whole, the end to which all this teleological wizardry leads-the living cell-
should be also ideally suited for the task of constructing the world of
multicellular life reinforces the conclusion of purposeful design. The
prefabrication of parts to a unique end is the very hallmark of design.
Moreover, there is simply no way that such prefabrication could be the
result of natural selection. Design in the very components which make an
organism possible cannot be, as Carl Pantin pointed out some time ago,
*the result of natural selection*. The many vital mutual adaptations in the
constituents of life were given by physics long before any living thing
existed and long before natural selection could have begun to operate. In
the current molecular biological picture of life, we have found a "watch"
more complicated and more harmonious than any conceived by William
Paley, exhibiting in its design precisely what Richard Bentley was looking
for, a "*usefulness conspicuous not in one or a few only, but in a long train
and series of things*." (My [Denton's] emphasis.)" (Denton M.J., 1998,
p233)
[...]
Steve
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"It was-and still is-very hard to arrive at this concept from inside biology.
The trouble lay in an unremitting cultural struggle which had developed
from 1860 onward between biologists on the one hand and the supporters
of old beliefs on the other. The old believers said that rabbits had been
created by God using methods too wonderful for us to comprehend. The
new believers said that rabbits had been created from sludge, by methods
too complex for us to calculate and by methods likely enough involving
improbable happenings. Improbable happenings replaced miracles and
sludge replaced God, with believers both old and new seeking to cover up
their ignorance in clouds of words, but different words. It was over the
words that passions raged, passions which continue to rumble on in the
modern world, passions that one can read about with hilarious satisfaction
in the columns of the weekly science magazine Nature and listen to in
basso profundo pronouncements from learned scientific societies." (Hoyle
F., "Mathematics of Evolution", [1987], Acorn Enterprises: Memphis TN,
1999, p3).
Stephen E. Jones | sejones@iinet.net.au | http://www.iinet.net.au/~sejones
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