Re: Experimental basis for the Non-Beneficial Gap Problem

On Jul 10, 4:24 pm, Seanpit <sean...@xxxxxxxxx> wrote:
On Jul 9, 11:51 am, hersheyh <hershe...@xxxxxxxxx> wrote:



On Jul 9, 7:47 am, Seanpit <sean...@xxxxxxxxx> wrote:

On Jul 8, 4:53 pm, Rupert Morrish <rup...@xxxxxxxxxxx> wrote:

[snip]

And, what that means is that the average number of
mutations needed to cross the gap increases exponentially.

And where, exactly, have you actually calculated an "average" anything
from actual data?  To do that, you would first have to show, in
systems that *did* evolve, that there was some sort of correlation
between the size of the end product and the number of mutational steps
from functionally useful precursors.  You have never shown such a
correlation from actual data from actual systems that have evolved.
You have merely *assumed* without evidence that there is such a
correlation.

You don't have it quite right.  All the systems that have been
observed to evolve have had a structural threshold minimum of no more
than a few hundred fairly specified residues.  The vast majority of
these real examples of evolution in action have crossed gaps of only
one or two residue differences.  This true regardless of if the
minimum structural requirements were 40aa or 400aa.   So, according to
your argument you would say that there is no correlation between the
size of the minimum gap distance and the structural threshold
requirement.  That's where you're quite mistaken.

Why is that a mistake? It is, rather, direct evidence that there is
no correlation between "minimum structural requirement" and "gap size"
for SYSTEMS THAT HAVE EVOLVED. My hypothesis is that, for systems
that DO evolve, there is no correlation between the number of
mutational steps required and the structural threshold requirement
(size) of the end result. Rather, my claim is that proteins evolve
when there is a short pathway wrt number of mutational steps and that
is a function of what specific precursor or ancestral sequences exist
in the particular organism. And that is what the data shows.

According to your hypothesis, there should be, on average, a ten-fold
difference in "gap size" for the 40 aa and the 400 aa system. That
is, for systems that have evolved, there is no evidence to support a
model of evolution in which your hypothetical "gap size" plays a
role.

Consider a novel system of function that only requires 40aa.  

Such as the "maximum gap size" of a protein slightly larger than
cytochrome c (which was about 30 aa, according to your math, although
you mislabeled it as "average gap size" rather than what it really is:
"maximum" gap size).

Most
bacterial genomes would have a large number of pre-existing starting
point sequences that would be within a handful of mutations of this
potentially beneficial target.  

Bull***. *Some* bacteria somewhere in space/time would, by chance,
have genomes that have sequence and structure that *could* reach
*some* other structure/sequence that has a modified or different
function within a handful of mutations. Evolution does not require
that *all* bacteria have these sequences. If some bacteria only has
proteins that are, say, 40 mutational steps away from cytochrome c,
that bacteria will not evolve cytochrome c.

Compare this with a 400aa target
system.  There will be exponentially fewer starting points within the
genome that will be within the same handful of mutations from this
higher level system.

That depends on what starting points a specific organism has. No
organism has some reservoir of 400 aa random sequences that are used
as the source of all new functions. Organisms have currently
functioning 400 (and smaller and larger) aa sequences, which have
various functions and subfunctions, some of which may be useful in
some new function. For example, one does not need to change *all* the
sites involved in binding cortisol and transducing evidence of that
binding across the membrane in the evolution of an aldosterone
receptor. In fact, one does not need to change *any* of the
transmembrane subfunctions. Nor most of the aa's involved in binding
generic steroid. Duplication and divergence producing a *gene
family* of steroid receptors, all roughly the same size and with much
of the same structure, is not a process where "average gap size" (if
you could actually calculate it and not the maximal gap size) has any
relevance.

If every new function that ever arose had to arise from scratch or
from some random sequence, you could talk about "average gap size" and
actually make sense. If, for example, some organism has no proteins
that bind to any steroids and no proteins can cross membranes and
transduce a change from one side of a membrane to another, you would
have found a cell in which one would have to generate the protein from
scratch or from some random sequence. That would be a cell that
would not evolve an aldosterone receptor.

Similarly, if there were bacterial cells that completely lacked any
pores that contained extruded whips and/or completely lacked any
transmembrane motor that converted energy into mechanical motion, then
such a cell would be unable to evolve motorized rotation of a pore/
whip. And even most cells with those features may not be able to link
them easily in a few steps. But all that is required is that a cell
have those features *and* be able to link them in a few steps.
Regardless of the size of the end product. IOW, the evolution of a
function is not a function of size. It is a function of specific
structure/sequences that pre-exist in particular arrangements in
particular organisms.

See the correlation?  That is why 1000aa systems don't evolve in real
time - - because, as you extrapolate this pattern while moving up the
ladder of functional complexity, the odds of any pre-existing starting
point being with striking distance of any potentially beneficial
1000aa drop exponentially.

That is based on a hypothetical relationship between "minimum
threshold size" and "gap size" that you *still* have not supported.
In fact, the actual material evidence, even you agree, says that there
is no such correlation. And you keep pretending that evolution works
by starting from some random sequence or maximally distant sequence
rather than, *when* (note the *when*) evolution happens, it is because
there are systems available in a particular organism at a particular
time that can be converted to one with a new added subfunction in
addition to all the subfunctions that already existed in the proteins.

< snip >

The minimum number is related to the average number along a Poisson
distribution.  The odds that the minimum number will stay at the
minimum possible number of 1, as those like Howard Hershey suggest,
drop dramatically along a Poisson distribution as the average number
increases exponentially.

As the "average" gap size increases, assuming you could actually
calculate "average gap size* form total size, the probability that the
minimum *available* pathway at any one time involves a single step
would decrease.

That's right.  That's the only important factor affecting predictive
value here.

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.

But the minimum *possible* pathway will still be one,
regardless of the size of the end result.

That fact, while true, is completely irrelevant as far as predicting
the outcome of evolutionary potential is concerned.  Its an irrelevant
red herring.

No. It is very relevant. It says that *when* evolution has happened,
it has done so in an organism in which there was some pre-existing
structures and functions that could be modified in a few steps.
*When* the gap is large or larger (which is NOT a function of the size
of the end product), then evolution of the novel feature will not
happen in that organism. In fact, that is exactly what your
discussion of ebg and lactase shows. *When* an organism has the pre-
existing ebg, evolution of lactase of 400 aa in length is easy.
*When* an organism lacks all the sequences that have the potential to
easily evolve lactase, the evolution of lactase, still 400 aa in
length, is much more difficult and may be extremely rare in most real
time experiments. That is, the evolution of lactase function is NOT
determined by the end size, NOT correlated to the end size *at all*.
It is a function of what pre-existing functional sequences exist in
particular organisms.

But what those odds are
depends on what the starting system contains and not on the size of
the end product.

The starting points are known.  The target locations are not.  Unknown
target locations are what introduce the random variable into the
equation and necessitate the use of odds to determine the likelihood
that any target will be within striking range of any one of the known
starting points.

Evolution works by searching the nearby sequence and structure space
of the pre-existing genome of that organism. *When* such a search
happens upon a change that is useful, it will be selected for. *When*
such a search does not happen upon a useful change, the organism will
remain unchanged except for neutral drift. If there is some target,
in a particular organism, that requires crossing a large functionless
gap, that target will not be reached and the organism will be
unchanged.

You don't use any calculations nor do you even try to estimate the
odds that any target will be within striking distance of any one of
your known starting points.  That's what makes your position
completely devoid of predictive value and therefore non-scientific.

I certainly can predict consequences of my model of evolution. I
already have. I predicted that one consequence will be that "new"
functions will have evidence of having come from older functions. And
if the new function has arisen in a short time frame, it will show
extensive homology with that ancestor rather than show no correlation
to any other protein. If the 'new' function is actually very old,
then neutral drift and subsequent losses and gains may hide the
ancestral relationship. But often, even then there will be sequence
(and even more structural) evidence of homology with proteins that
perform related but non-identical function.

Naturally, because you do not have a scientific explanation, your
explanation (magical poofing by an invisible fairy) is consistent with
anything one observes. However, what one does NOT observe is any
protein having crossed large functionless gaps. The simplest
explanation for that failure is that there are no such gaps that
evolution has ever had to cross.

Unless, of course, you can actually calculate an
"average gap size" with real data involving things you accept as
having 'evolved' and show us the correlation between total size and
'mutational gap size' without invoking the idea of a maximally distant
starting point and complete randomness.

The pattern is very clear – even with functional systems that have
actually evolved in real time.

That is not even close to a calculation of "average gap size". It is
nothing but hand-waving bull ***. The pattern for *real* functional
systems that have actually evolved in real time is NO correlation of
number of mutational steps with the minimum threshold size. NONE.
ZERO. NADA. NOTHING. There is a correlation between the existence
of precursor proteins that have similar structure and sequence and
subfunction to the end product and the evolvability of that end
product. The closer, in mutational steps, that functional substrate
is to the end product, the easier it is to evolve it in the time
available. But that is not a correlation with size.

If anyone considered that the likelihood of 1000aa protein systems
arising without precursors was an argument in favor of evolution, you
may have a point. But no-one does, so you are simply attacking a straw man.

I never said that one had to start without precursors.

That is what your numerology proclaims while you deny that it does so.

How is that Howard?  Do you not understand basic mathematics?  My
mathematics assume that the likely minimum gap distance is always
smaller than the maximum possible distance.  

Yes. You handwave those smaller numbers into existence. You do NOT
mathematically determine them. And the only gap size you have ever
calculated has been the *maximum gap distance*, the total number of
invariant sites in a model that mathematically assumes that the
protein only has invariant and completely variant sites. And you
assume that the starting point is a sequence that differs from the end
protein at every invariant site (the completely variant sites don't
matter). You mislabeled that *maximum* gap size as the "average" gap
size.

How do you not understand
such a simple concept?

Yes. I recognize how you have utterly failed to present a rational
argument or even mathematically support the bogus argument you made.
The reason why you always come out with that 1000 aa schtick is
because you *cannot* calculate the "average gap size" or demonstrate
that that gap size is related to total size. And then pretend you are
being fair when you pull bogus numbers out yer arse.

Start with
whatever precursor you want in an organism that never had the novel
function in question to begin with.

Like Lenski did?  Like nylonase?

That's right . . .

There are always starting points
that are closer to a potentially beneficial functional system than the
maximum possible distance.  However, the gap that remains is still too
large to cross when it comes to systems with minimum part requirements
beyond 1000aa.

What evidence do you have to support this claim?

It's not been observed to happen . . .

That is not evidence. It is assertion based on your lie that systems
that *have* evolved have done so by crossing some hypothetical large
neutral gap *all at once*.

Sean Pitmanwww.DetectingDesign.com


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