Blind Faith in the Mechanism of the ToE

On Jul 10, 9:42 am, hersheyh <hershe...@xxxxxxxxx> wrote:
One should distinguish between what Yockey and all the other papers
(including the most recent one) that Sean misconstrues actually do say
and what his evolutionary claim is.

These papers, not surprisingly, tell us that modern proteins that
perform named functions have sequence constraints related to those
named functions. That is, not all proteins can perform these named
functions. The degree of sequence constraint for such named functions
varies from protein to protein and within proteins. The mechanism for
estimating the degree of sequence constraint involves taking a large
collection of variant sequences from different organisms (or by
experimentally modifying sequence) and observing what sorts of
sequence changes are allowed without drastically altering the named
function.

So far so good. The higher the sequence constraints the exponentially
rarer the number of such sequences in sequence space – obviously.

Also, not surprisingly, larger proteins (the papers do not discuss
protein systems like the eubacterial flagella) have more subfunctions
that are part of its named function. But the subfunction density of
proteins, although it does vary, is always significantly less than the
maximum possible wrt sequence constraint. Again, because the authors
estimate sequence constraint only for a named function, they are
making no claim that that function arose by a random walk from some
random or maximally distant sequence. Because of this, Sean merely
inserts his strawman evolutionary ideas rather than realistic
evolutionary ideas about how evolution would generate larger multi-
subfunctional proteins with emergent or novel properties and pretends
that they flow from the evidence in these papers. They don't.

As I've pointed out to you over and over again, this maximally distant
starting point notion is yours, not mine. It is your little strawman
mischaracterization of my position. You say that you have to
continually present this mischaracterization, this deliberate lie, in
order to get me to admit that the actual gap distances are not
maximally distant. That's another bogus lie. I shouldn't have to
explain everything every time. Can't you remember anything from one
day to the next?

I've always noted, over and over again, that the average and likely
minimum gap distances are always less than the maximum possible
distance or total size of the system. That's always true. What is
not true is your notion that the minimum possible gap distance of one
is somehow important to the problem. It isn't. It is completely
irrelevant since it says absolutely nothing about the likelihood that
this minimum possible distance will be the actual distance. That's
your number one problem here.

None of these papers make any claim about the *mechanism* of how this
named function arose by evolution. Only claims about the fraction of
total sequence space that is estimated to be occupiable by a specific
named modern function.

That's exactly right. We already know the proposed mechanism – random
mutation and natural selection. The NS part of this equation cannot
work at all in the non-beneficial gaps that exist between potentially
beneficial islands. It can only work once a novel island is reached
by random mutations of some sort. The rarity of these island targets
is what is illustrated by the papers I've presented here. What is
also obvious is that the rarity of these island targets gets
exponentially rarer at higher and higher levels of functional
complexity.

Now, you have tried to propose some sort of clustering effect to
compensate for this exponential decline in the ratio of potentially
beneficial vs. non-beneficial. The problem with this notion is that
the clustering effect becomes less and less clustered at higher and
higher levels. In order to solve your problem, the clustering effect
would have to become exponentially more and more clustered. That
doesn't happen. Just the opposite actually happens (per the paper of
Choi and Kim and per the evaluation of actual minimum sequence
differences for different kinds of higher-level functions).

So, you are basically stuck. The islands do drift farther and farther
apart as one climbs the ladder of functional complexity. That's an
overwhelming fact given the evidence at hand.

And I certainly would concede that any modern named functional system
does indeed occupy only a small fraction of total sequence space.
Most of the reason for this is the difficulty of independent evolution
of a function when the niche is already occupied by the first system
to have evolved. The second is that the sequences of modern named
functions in different species are not *independently* generated
completely separately from each other; they are dependently related
through the process of common descent. In fact, that assumption
underlies all the estimates he used.

An independently derived or completely non-homologous system with a
similar function would still be just as isolated in sequence space at
a given level of functional complexity. You just don't seem to
realize how enormous sequences spaces actually are - - especially
beyond the 1000aa level. This strained argument of yours makes
absolutely no difference whatsoever.

For example, all non-homologous rotary flagellar motility systems are
extremely widely separated in sequence space since they are, obviously
non-homologous, and occupy a very high level of functional complexity
(i.e., all require many thousand specifically coded residue
positions).

Sean's <start sarcasm> 'real contribution' <end sarcasm> is applying
strawman evolution to these numbers. His claim is that
'evolution' (aka, strawman evolution) of any of the modern named
functions in each and every organism had to arise *independently* by a
completely random stepwise process of assembly or change from some
random or maximally distant sequence.

That's your strawman mischaracterization yet again. I've repeated
said just the opposite – that the starting point is never maximally
distant – NEVER. Rather, it is your claim that the minimum possible
distance of "one" is somehow relevant to this issue. That's nonsense.

That is, in essence, what his
claim that the minimum threshold *size* of a functional protein is
correlated with the "gap size" (number of mutational steps, which he
often pretends is due only to point mutation or addition of aa's one
at a time) that must be crossed between some (random?, maximally
distant?) starting protein (which may or may not have any function) of
the same minimum threshold size and the teleologically named
functional protein. The independence of the evolution of the function
in different organisms flows from his idea that organisms are
separately created.

First off, the minimum threshold size of a functional system is
correlated with both the average gap size and the likely minimum gap
size.

Also, I've never pretended that only point mutations can be used.
That's another deliberate lie on your part. If you care to look it
up, I've explained over and over again in this forum that any kind of
random mutation can be used – both single and multicharacter
mutations. It is just that the odds of success are the same
regardless of the type of mutations that are used when searching
randomly for a target sequence with an unknown location.

And again, I've never said that the starting point is a random
starting point. The target positions are what are unknown, not the
starting point(s). The starting points are always functionally
beneficially starting point islands. These starting point islands are
NEVER maximally distant from the next closest potentially beneficial
system in sequence space. I've always said that. So, I don't see why
you continually see the need to misrepresent my position again and
again the way you do?

Yes, I know you argue that my calculations require maximum distance,
but that's also a lie. My calculations always assume a much less than
maximum gap size between potentially beneficial islands in sequence
space. Compare this to your notion that the minimum possible distance
of one, which is indeed the minimum possible distance, is somehow
relevant to how likely the evolutionary mechanism is to explain the
existence of various high-level systems that exist in every living
thing.

So, let's assume a protein of "minimum threshold size" of 300 aa's.
In Sean's world, the evolution of that protein to any new
teleologically named function involves crossing a "gap size" that is
some fraction of those 300 aa's NO MATTER WHAT THE STARTING SEQUENCE
IS.

Not true. At the level of 300aa, the likely minimum gap distance for
most bacterial genomes is only a handful of residue differences wide
at most. For some bacterial gene pools the gap distance is indeed
just one mutation wide at this very low level of functional
complexity.

You know that I've explained this to you dozens of times now. Why
present this deliberate mischaracterization over and over again like
this? What is the purpose to such deliberate strawman
misrepresentation on your part? - - aside from the goldfish-level
memory capabilities of the Howard Hershey collective that is . . .

That is the only way that there can be a consistent correlation
between "gap size" and "minimum threshold size". Otherwise "gap size"
only correlates with how many mutational steps exist between the
starting protein and the end protein and that is idiosyncratically
related to what proteins existed in the ancestor that can act as
starting protein.

You're right. It is certainly true that the actual gap distance does
indeed depend upon what proteins exist or existed in the gene pool of
a given kind of organism. Where you go way off base is in thinking
that the odds of what is likely to exist or have ever existed in any
gene pool of any organism are not at all related to the ratio of
beneficial vs. non-beneficial sequences in sequence space.

This is all about the odds Howard. What are the odds that the gap
distance will be short enough for the evolutionary mechanism to
cross? Hmmm? You have absolutely no idea. You cannot answer this
question at all. The best you can say is that the gap distance must
have been small enough in the past because I know evolution happened.
That sort of thinking is nothing short of blind faith or outright
bravado. It isn't science. It says nothing about the odds of your
faith in the existence of small gap distances at high levels of
complexity actually being true.

Sean then might say that what he really means is that there is an
"average gap size", which is what he *really* means by "gap size".
But the "average gap size" is assuming that evolution works by
starting with some random protein in total sequence space, not the
proteins available in actual organisms.

Not true. The average gap size is the average gap size. It is
calculated based on the ratio of beneficial vs. non-beneficial
sequences in sequence space. By itself, it doesn't say anything about
the actual location of potential targets in sequence space. But, what
it does say is that the likelihood that the minimum gap distance
(which is the really important gap distance by the way) will be small
enough to cross given an entire gene pool of starting points. The
minimum likely gap distance is related to the average gap distance
along a Poisson distribution. That means that a linear increase in
the average gap distance will also result in a linear increase in the
likely minimum gap distance was well.

Is this prediction 100%? Of course not. Nothing in science reaches
perfection. However, at higher and higher levels of complexity this
prediction becomes exponentially more and more reliable.

No evolutionary theory
explanation for any protein assumes that the starting point is some
random protein in total sequence space.

The starting point isn't random. What is unknown, however, is the
target distance. You simply can't say that it is likely to be a small
distance independent of any consideration of the odds provided by the
overall ratio of beneficial vs. non-beneficial.

IOW, Sean's "average gap
size" is an entirely theoretical construct based on the idea of a non-
existent total sequence space not present in any organism and
unrelated to the actual constraints on any real evolutionary model.
It is, in short, bull*** numerology. And that is aside from the fact
that no "average" was actually calculated or harmed in his math.

What is completely BS is your assumption of small gap distances
without any consideration of the odds whatsoever. You have no
calculations at all. You have no method for even estimating the likely
gap distances. You have nothing . . . nothing at all beyond your
extraordinary bravado, bald assertions, and blind faith that evolution
must have done the job. In short, your notions are scientific since
they have absolutely no predictive value at all – none.

Sean Pitman
www.DetectingDesign.com

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