Re: Experimental basis for the Non-Beneficial Gap Problem

On Jul 12, 9:48 am, Seanpit <sean...@xxxxxxxxx> 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."

And, since the absolute number of sequence differences is a function
of time since divergence and evolutionary constraint, the amount of
*sequence* difference will be primarily affected by those factors.
Size will only play a role if all the *relevant* factors are
controlled for. For example, the absolute amount of *sequence*
difference between yeast cytochrome c and human cytochrome c is much
larger than the absolute amount of *sequence* difference between human
hemoglobin and chimpanzee hemoglobin. That is *despite* the fact that
cytochrome c has greater evolutionary constraint on change than does
hemoglobin.

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!"

Sean, your statement would only make sense if you thought that
evolution teaches that each organism (human and rat, for example) had
to *independently* evolve hemoglobin from some random or other
sequence rather than merely retain that *function* and *structure*
(and *sequence* except for the inevitable neutral drift and perhaps
some minor selective differences) from common ancestors. I can assure
you that evolution only requires that hemoglobin evolve once. All
current living vertebrates have similar hemoglobins by common descent,
not independent evolution. Perhaps that is because *your* preferred
solution (magical poofing by some invisible fairy) would involve
separate independent magical poofings of each and every gene from
nothingness. But perhaps you have some evidence for the model which,
if you were honest, would be the one you support.

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

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.  

No. The *maximum gap size* for a 100 aa system in which one
effectively has the equivalent of 30 completely invariant sites and 70
sites completely free to vary is *effectively* 30, not 100. 100 aa is
the "minimum threshold size" and includes aa's that are completely
free to vary as well as sites with partial variance and sites that are
invariant or close to it. You have *defined* "minimum threshold size"
as being the size of the smallest known protein that performs a
*function* (except when you depart from that, as in the eubacterial
flagella).

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.

And how do you calculate this "average" distance? The only
calculation I have seen is for cytochrome c and the number you came up
with was nothing but the *effective maximal gap size* by the
simplification of the model to ignore partial constraint on specific
aa's.

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?

No. The mathematical error is your conflating "minimum threshold
size" with "maximum gap size" when you know full well that the former
is NOT the latter. And then calculating the real "effective maximum
gap size" and mislabeling it "average" for cytochrome c. But
understanding your own terms does not seem to be a strength of yours.

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.  

No. That is the *effective maximum gap size*. 30 aa's is, if you
simplify cytochrome c and assume that it only has invariant sites and
sites which are sequence irrelevant, a simplification that merely is
simpler to see and does not change "maximum gap size" in the other
intermediate cases, the *total* number of absolutely invariant sites.
Those sites must be one and only one of the 20 possible aa's. All 70
other sites can be any aa. To produce a *functional* cytochrome c by
random changes from the *maximum possible distance*, you would start
with any sequence which differs from the invariant aa at the 30
sites. The 70 sites that can vary freely do so without *any* effect
on *function* and are thus irrelevant. The *effective maximum
possible distance* from a protein with cytochrome c function is *any*
protein that differs from the invariant aa that this model of
cytochrome c requires. Changing the model so that some sites only
have partial constraint rather than the simplified model of invariant
or free to vary does not change the "maximum possible distance", but
merely distributes the functionality among more of the 100 aa's.

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.

Again, I *was* using that ratio. It is just that you have
mischaracterized the 30 aa as representing "average gap distance" when
it is actually the "effective maximum gap distance".

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.

Again, the number you have calculated is NOT the "average" gap
distance. It is the "effective maximum gap distance". You have not
calculated, nor can you calculate, "average gap distance" from the
Yockey data. You have, at best, merely misunderstood what you
calculated from the Yockey data. 100, the "minimum threshold size" is
not the effective maximum gap size precisely because aa sites vary wrt
constraint. 30 is the "effective maximum gap size" because it is
representative of the probability of generating cytochrome c by
completely random assembly of a 100 aa long protein. 30 aa is a
measure of the 'evolutionary constraint' of cytochrome c and, in fact,
the very way that number was calculated tells you that it is a number
that is indicative of the probability of generating cytochrome c from
scratch by random assembly.

I cannot help it if you do not understand what that number means. But
it most certainly is NOT the "average gap size". It is the "effective
maximum gap size" generated by assuming that proteins are randomly
assembled from scratch.

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.

Remember that the only actual *number* you have is the *maximum gap
size* based on the strawman assumption that evolution works by random
assembly. It is no wonder that you cannot give us any Poisson
distribution, since that would have to be based on *actual* data
rather than bogus numerology.

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.  

I notice your continued failure to even tell us what probability level
of this supposed Poisson distribution is so unlikely as to represent a
"minimum likely distance" given that there are millions of species and
millions of years.

Nor do you mention that evolution actually works by testing by
variation of what currently exists for the "shortest available
pathway" to a new useful utility. And that, if there is no reasonably
short pathway, the only consequence is that the new useful utility
will not form. So I can give up hoping to sprout wings on human
backs.

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.

Sean Pitmanwww.DetectingDesign.com


.

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 ...
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  • 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: Most valuable poster
    ... nylonase or lactase evolution examples. ... sequence within an entire genome, one or two, will be within striking ... within striking distance of very low-level functions. ... The gap distance is always much smaller than the size of the next ...
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  • Re: Experimental basis for the Non-Beneficial Gap Problem
    ... unless you think evolution starts from some random sequence maximally ... It is never at the maximum possible distance - ... greater, on average, compared to a collection of smaller proteins." ... If an amino acid is entirely free to vary, it doesn't contribute to any gap size. ...
    (talk.origins)
  • Maximum, Average, and Likely Minimum Gap Distances
    ... That means that the maximum gap size in that sequence ... say was the the maximum gap size is the length of the sequence. ... How is that relevant when determining gap distance? ... In order to know the distance between two islands of unknown position ...
    (talk.origins)
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