Re: Experimental basis for the Non-Beneficial Gap Problem

Seanpit wrote:
On Jul 11, 4:42 pm, hersheyh <hershe...@xxxxxxxxx> wrote:
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.

This is what I originally wrote in a discussion with Harshman:

"What I'm saying is that if you compare a collection of larger
proteins the *absolute number* of sequence differences with be
greater, on average, compared to a collection of smaller proteins."

John Harshman responded with:

"Which makes perfect sense. If two proteins are 5% different,
they will have 5 differences if they're 100 residues long, and 50 if
they're 1000 residues long. Ten times as many!"

You also agreed with this statement. Now you are trying to go back on
it? How is that?

I, for one, apparently misunderstood the vague term "collection" here. I was talking about homologous proteins in pairs of taxa. In retrospect it's not clear what you were talking about. What were you talking about? What pairs of proteins were you comparing?

The "maximum gap size" is what you sometimes call "average gap size".

The maximum gap size for a 100aa system is 100aa differences. That's
the maximum - obviously. The average distance is always smaller than
this maximum when it comes to living things - always. And, the
minimum likely distances is smaller still - always.

How many times do I have to explain it to you before you will give up
on this constant strawman mischaracterization of yours? - this
deliberate lie?

Now that's silly. If an amino acid is entirely free to vary, it doesn't contribute to any gap size. So if you have a 100aa system in which 30 residues are constrained and 70 are free to vary, the maximum gap size is 30. Since you always talk in terms of "fairly specified residues", this must be what you meant. If you're allowing the number of constrained residues to vary within your "fairly specified" count, then nobody has any idea any more what you're trying to say.

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".

You don't understand. The average gap size is a function of the ratio
of potentially beneficial vs. non-beneficial. This ratio is
calculated by the same means used by Yockey and supported by other
more direct experiments like those done by Sauer, Olsen, and the
others listed. This ratio is not, let me repeat NOT, a measure of the
maximum gap size. It is, obviously, a measure of the average gap size
for the function in question in sequence space.

No, it's the maximum effective gap size, because it counts constrained sites and ignores unconstrained sites. Unconstrained sites shouldn't count, since it doesn't matter what's in them.

An *actual* "average gap size" has never been actually calculated by
you for any protein. Not even cytochrome c. Never. Not once.

You don't understand statistics then. The average gap size is a
function of the ratio of potentially beneficial vs. non-beneficial -
which has indeed be estimated for specific functions like CytoC as
well as several other types of unique protein-based functions by
direct experimentation.

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.

The minimum likely distance between target sequences where the ratio
of targets to non-targets is known, but their specific location in
sequence space is unknown, falls along a Poisson distribution. There
is no Poisson ratio. The ratio calculated by those like Yockey is
what is used to calculate the Poisson distribution to estimate the
likelihood of a minimum gap distance.

This doesn't seem to have anything to do with the actual numbers you keep quoting. Why is 100 the maximum gap size of a 100-site sequence? If you're talking about poisson-distributed changes, there should be no actual maximum, since a poisson process could continue infinitely long without attaining a perfect sequence match. You really aren't making sense here.

.

Relevant Pages

  • Re: The Relationship of Gaps to Thresholds
    ... other than a fair degree of sequence similarity. ... Your MATH explicitly says that the size of the gap needed to be ... is roughly 30% of the total size of the end protein. ... start at some average distance away (that distance being a function of ...
    (talk.origins)
  • Re: The Relationship of Gaps to Thresholds
    ... mechanism for retaining *proteins* that lack function. ... to making the protein encoded by the sequence. ... Any sequences in sequence space can be reached by ... linear manner with the increase in the average gap distance. ...
    (talk.origins)
  • Re: Liar Liar
    ... random aa's or a maximally distant sequence. ... Define "likely gap distance" for cytochrome c and how you calculate ... completely random substitution in a protein in which none of those ...
    (talk.origins)
  • Re: Experimental basis for the Non-Beneficial Gap Problem
    ... unless you think evolution starts from some random sequence maximally ... distance is always smaller than the minimum structural threshold ... The maximum gap size for a 100aa system is 100aa differences. ...
    (talk.origins)
  • Re: Tony Raymonds contra-gap argument
    ... certain types of functional systems with smaller proteins. ... fewer number and still have the flagellar motility function. ... increase the number of sequences searched within sequence space. ... likely minimum gap size will not long remain at the minimum possible ...
    (talk.origins)