Re: Experimental basis for the Non-Beneficial Gap Problem

On Jul 11, 2:20 pm, Seanpit <sean...@xxxxxxxxx> wrote:
On Jul 10, 7:48 pm, hersheyh <hershe...@xxxxxxxxx> wrote:

[snip]

Except that "gap size" is not a function of "minimum threshold size"
unless you think evolution starts from some random sequence maximally
distant from the teleologic endpoint.

Even you now admit, along with John Harshman, that there is a
relationship between the size of systems and the absolute number of
differences between systems.  That's a fact.  The likely minimum gap
distance is always smaller than the minimum structural threshold
requirement - always.  It is never at the maximum possible distance -
never.  I really don't know why I have to repeatedly correct you on
this idea.

I said that "gap size" is NOT a function of "minimum threshold size"
unless Sean is proposing an obvious strawman evolution and Sean claims
that this is *admitting* "a relationship between the size of systems
and the absolute number of differences between systems". How he can
accomplish this completely backassward logic, I don't know.

The "maximum gap size" is what you sometimes call "average gap size".
The only protein for which you actually calculate any kind of "gap
size" from actual data is cytochrome c. All other proteins are merely
cytochrome c writ larger, in your bizarre world. And that calculated
number amounts to nothing but, if you simplify your model protein to
containing only completely invariant and completely free to vary
sites, the effective number of completely invariant sites The same
degree of invariance would hold for model proteins that had fewer
absolutely invariant sites and more partially variable sites. That
is, you assume that the "gap size" is the distance between a protein
that has some non-functional aa at every possible invariant site
(completely variable sites, of course, don't matter). That number
(about 30 for cytochrome c) is the *maximal gap size*, not any kind of
"average gap size".

An *actual* "average gap size" has never been actually calculated by
you for any protein. Not even cytochrome c. Never. Not once. All
you have done is pull a number out of yer arse. "Minimum likely gap
sizes", likewise, has never been calculated for any protein. Not even
cytochrome c. It is simply pulled out of yer arse as well, typically
after waving the term Poisson ratio as if you actually knew that there
was a Poisson distribution from actual data.

[snip]

.

Relevant Pages

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