Re: [asa] Amazing Proteins

Mike Gene: One then wonders if there exists a more versatile design
material in the entire Universe. But it gets even better. At the heart
of all this mind-numbing functionality and versatility that has served
Life so well for billions of years is the very same manufacturing
process. Now that's a design material: one manufacturing process
coupled to thousands upon thousands of functions.

Indeed, and since design is an ambiguous term to denote our ignorance,
may I point out that the existence of a single manufacturing process
coupled to thousands of functions is well explained by evolutionary
theory. And although the ID perspective lacks any guiding principles
to constrain their hypotheses, there is ample evidence that there were
multiple designers involved... In fact, a single design material seems
unnecessarily constraining for an Intelligent Designer who can pick
and chose most any method and approach. But Mike Gene's thesis is one
of front loading where the 'design' event is conveniently hidden from
our view and natural processes are allowed to do their 'magic'. While
front loading is indeed the best philosophical response to
evolutionary science, it fails as a scientific contributor.

Mike Gene: This all raises some interesting questions. For example,
without proteins, and their manufacturing process, what becomes of the
blind watchmaker? Without proteins, and the latent functions contained
within, might not the blind watchmaker exist as the impotent,
crippled, blind watchmaker with no one to notice its existence? If so,
how much credit does the blind watchmaker really deserve?

Without the blind watchmaker, there would not have been observers to
miss its existence, that seems simple. But Mike is right, the blind
watchmaker does not owe its success to just chance but also
regularities such as the laws of physics. Now one may wonder, who or
what caused the laws of physics but that seems to be a question mostly
outside the direct view of science.

What is ironic is how the blind watchmaker argument has been abused
when it relates to proteins to suggest that pure chance could never
explain why or how proteins fold. And yet more recent research has
shown why such an argument is flawed.

In "How much of protein sequence space has been explored by life on
Earth? ", Dryden and collaborators show

---
We suggest that the vastness of protein sequence space is actually
completely explorable during the populating of the Earth by life by
considering upper and lower limits for the number of organisms, genome
size, mutation rate and the number of functionally distinct classes of
amino acids. We conclude that rather than life having explored only an
infinitesimally small part of sequence space in the last 4 Gyr, it is
instead quite plausible for all of functional protein sequence space
to have been explored and that furthermore, at the molecular level,
there is no role for contingency.
---
Somewhat surprisingly to me the research goes back to at least early 90's
In Polymer principles and protein folding, Dill writes
---
This paper surveys the emerging role of statistical mechanics and
polymer theory in protein folding. In the polymer perspective, the
folding code is more a solvation code than a code of local phipsi
propensities. The polymer perspective resolves two classic puzzles:
(1) the Blind Watchmaker's Paradox that biological proteins could not
have originated from random sequences, and (2) Levinthal's Paradox
that the folded state of a protein cannot be found by random search.
Both paradoxes are traditionally framed in terms of random unguided
searches through vast spaces, and vastness is equated with
impossibility. But both processes are partly guided. The searches are
more akin to balls rolling down funnels than balls rolling aimlessly
on flat surfaces. In both cases, the vastness of the search is largely
irrelevant to the search time and success. These ideas are captured by
energy and fitness landscapes. Energy landscapes give a language for
bridging between microscopics and macroscopics, for relating folding
kinetics to equilibrium fluctuations, and for developing new and
faster computational search strategies.
----
The solution to the 'classic puzzles' of the Blind Watchmaker Paradox
for proteins and the Levinthal paradox seem to both be related to a
flawed application of probability calculations. We see such
calculations extended in time to reach the same flawed conclusions in
the works by ID proponents such as Dembski and Behe.
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