Re: The Pitman CSI Formula

On Jul 20, 1:12 pm, Seanpit <seanpitnos...@naturalselection.
0catch.com> wrote:
On Jul 20, 9:15 am, hersheyh <hershe...@xxxxxxxxx> wrote:



On Jul 19, 3:44 pm, Seanpit <seanpitnos...@naturalselection.

0catch.com> wrote:
On Jul 17, 2:18 am, Vend <ven...@xxxxxxxxxxx> wrote:

< snip >

Your definition of beneficial structure doesn't work:
Suppose you have three alternative homologous structures: A, B and C.
Suppose that in this enviroment their fitness is in this relation:
fitness(A) < fitness(B) < fitness(C)

A mutation changing A into B is beneficial, while a mutation changing
C into B is detrimental.
So is B beneficial, derimental or neutral?
Obviously you can't tell without knowing what it comes from.
In other words, beneficial, derimental or neutral are not properties
of a structure but they are properties of the change between
structures, that is, mutation.

The beneficial nature of a structure is always related to the organism
in question.

Beneficial is an adjective that can only be applied in a specific
*environment*. That, of course, includes the other genetic/phenotypic
properties of the organism, but is not limited to it.

Removing something that is more beneficial doesn't mean
that what remains isn't beneficial. It is. Removing something that
was more beneficial is characterized as "detrimental", but again, this
characterization is related to the new structural state that is
created. Mutations, by themselves are not "beneficial, detrimental, or
neutral".

Those adjectives are conditional upon environmental circumstances. A
mutation that allows an organism to thrive in the Arctic is rather
useless if the organism is otherwise adapted to life in Amazonia.

Only as they produce or remove structures that are or where
beneficial, detrimental, or neutral can they be classified by such
terms. It is all related to the type of structure produced or
removed.

No. It is related to the how the change in function inteacts with the
environment (including other genes of the organism). The very same
mutation can be 'beneficial', 'detrimental', or 'neutral' conditional
upon environmental conditions. And *loss* of structure can certainly
be 'beneficial'.

The environmental factor is a given . . . Obviously the external an
internal environments are what are interacting with a particular
structure to make it "beneficial", "neutral", or "detrimental". The
point here is that mutations, by themselves, don't determine the
resulting nature of the function of the organism in the given
environment. Only the resulting structural change is what determines
the nature of this interaction.

Actually, it *is* sometimes the mutation that determines "beneficial",
"neutral", or "detrimental". *If* the particular mutation is at an
'active' site and causes a change that affects which *particular*
substrate is bound. This can happen *without* any significant change
in structure (which is why, for example, there is no significant
change in the *structure* of embryonic and adult beta globins of
hemoglobin). There is a *quantitative change* in the affinity of the
hemoglobin molecule for O2 that makes the two types of hemoglobin
(embryonic and adult) non-substitutable one for the other.

Sequence change *is* sometimes important, but its importance lies in
cases like the above or like the aldosterone receptor (two aa changes
are sufficient to produce the change between binding cortisol and
binding aldosterone, modifying the receptor so it preferentially binds
one or the other related steroids). Similarly, small changes in
*sequence* can lead to significant changes in terms of binding to
allosteric elements, other proteins, or in the amounts and timing of
synthesis. These are all very important evolutionary mechanisms. In
fact, most evolutionary change involves the amount and timing of
synthesis or the interaction and divergence of duplicate copies to
specialize in related functions.

Again, you keep conflating and misusing the terms "structure" and
"sequence" and "function" as if all three terms were a muddled mess in
what you call a brain.

*Most* evolutionary change that involves a *major* change in
*structure* does so not by single aa changes (other than those that
change function by truncation of a longer protein, where stop codons
can work). *Most* evolutionary change that involves a *major* change
in *structure* is accomplished by the combining of independently
evolved whole structural elements to produce a chimeric structure that
has a novel or combined function. Or it evolves by endoduplication of
structural elements.

That is, searches of *larger* sequence space is not done by starting
with some random sequence of a given size and changing its aa's one at
a time. Rather the space of these larger sequences is explored by
combining smaller *independently funcitonal* elements from proteins
and retaining those that happen to have utility. Like *real* islands,
they typically arose from underneath, not usually by sailing the
oceans in search of a function.

Sean Pitmanwww.DetectingDesign.com


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Relevant Pages

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