Re: The possible is likely?

On Nov 18, 7:51 pm, Seanpit <seanpitnos...@naturalselection.
0catch.com> wrote:
On Nov 17, 4:55 pm, hersheyh <hershe...@xxxxxxxxx> wrote:



No you haven't.  You have talked about *average* gap size.  You have
talked about *minimum* gap size.  But the only *honest* description is
that you are talking about *wild-ass guess gap size*.  But if you want
to call something the "likely gap size" leaving off the word *minimum*
(which is always 1) and then describe how you calculate that, go
ahead.  But the use of the word *minimum* when you are not talking
about the number 1 is dishonest propaganda.

The minimum possible gap distance is one.  The minimum actual distance
between a starting point and target sequence is not necessarily one.

And the *actual* minimum distance will be different for each and every
evolved system based on what the starting and ending points are.

Sorry. I should have said *actual* gap size rather than *actual*
minimum distance. The *actual* gap size crossed need not be the
minimum.

The actual minimum distance is not directly known.  

Like I (and many other of the voices passing through your ears and
disappearing in the vacuum inbetween -- sound does not travel well in
vacuums) have pointed out and you have agreed, there are many examples
of what you call "low level" evolution that has occurred. It should
be possible to plot the *actual* gap distance between functional
intermediates against the size of these systems (there is some
significant variation in their size) and come up with a significant
correlation between size and *actual* gap distances to, say, modify a
protein so that it resists an antibiotic or changes primary and
secondary substrate. Shouldn't it? And *actual* gap size is better
than estimated gap size.

I'm talking about
how to estimate what the actual minimum distance is likely to be.  

A good way to estimate something like this would be to plot the curve
in the area where there is *actual* data and extrapolate the curve to
the area in question. Assuming, of course, that there actually is a
correlation between size of the end result and any particular "gap"
that must be crossed to modify or add a function or in which a new
function emerges or a novel function appears (the last will typically
be due to chimera formation, but it can be due to regulation of
amounts like some eye crystallins).

You
do not do this at all.  You just say that evolution happens when the
minimum distance is close to the minimum possible distance.

And the odds of *someone* winning the lottery is actually pretty good
even if the odds of *my* winning it are either poor (if I were to buy
a ticket) or zero (if I don't). That is, winning the lottery is
contingent on buying a ticket.

Evolution is like a biased or rigged lottery rather than an honest
one. Organisms differ in their odds of winning the evolution lottery.
Some organisms effectively do not have any ticket at all. Others have
tickets with only a slim to essentially non-existent chance of
winning. And others have tickets that have a high probability of
winning. The winner will most likely be in that last category.

 That's
not a scientific hypothesis Howard.  That has no predictive value when
it comes to estimating how long evolution should take to evolve a
novel beneficial function at various levels of functional complexity.

That's right. Evolution is a historical science that aims to describe
what *did* happen, not what will happen in the future. The
expectations and predictions of the consequences of organisms having
evolved by common descent and patterns consistent with historical
descent patterns are tested by maximal parsimony and pathway analysis,
not by bogus numerology based on straw man models that are ahistorical
models.

Saying that it will happen when the gaps are small is just silly. It's
true, but it isn't science.  

Saying that a river's course will (nearly) always be affected by
geography either because of the environment *selecting* the river's
course or by meanders when the environment is flat would be just as
silly. The evolutionary novelty that will be the very first occur
will typically not be the one with the longest possible gap, the
average gap, or even a small gap. It will be the most likely that the
first organism that comes up with an evolutionary solution (say,
resistance to a toxin or ability to use a resource others can't) will
be the one in which the gap is the smallest possible gap given
available starting points. That winner will win because it was
already, for entirely other or arbitrary or chance reasons, was
"exapted" for that change.

Again, evolution is a claim of historical process in the past. That
historical process makes specific pattern predictions that are clearly
distinguishable from other patterns (such as random pattern or pattern
that is due solely to functionality or a pattern of using standardized
parts). The pattern has been empirically tested. Evolution won.
Magical poofing, if it occurred, had to have done so, for some obscure
reason, while giving the false appearance of common descent.

It makes no useful prediction.

It makes very useful predictions wrt what pattern one should see in
sequences. That is, if organisms have evolved by common descent
rather than by some mechanism that would produce a different pattern,
we would expect a consistent branching pattern. That is testable, has
been tested, and is consistent with common descent.

The question is, what is the likelihood that the actual minimum
distance will be the minimum possible distance?

That should be "actual gap distance".  To determine *actual* gap
distance you need to look at specific starting and ending
requirements.  

There are lots of potential targets in sequence space Howard.  That
means there are lots of gap distances.  This also means there is an
average gap distance and an actual maximum and an actual minimum
distance - none of which are directly known.  The only distance that
are directly known are the theoretical maximum and minimum distances.

I agree. The maximum gap is the total size of the sequence (or, if
you want, the functionally relevant subset of that size). The minimum
gap is one. The average gap would be half way in between. But the
only way the maximum and average would have any meaning is assuming
that evolution works by the straw man "747 in a tornado" mechanism of
complete randomness.

These are the only distances that are absolutely knowable.  The actual
distances, on the other hand are not directly knowable and are
therefore subject to scientific investigation and estimation.

The *actual* gaps between *functions* is, in fact, quite measureable.
What I see is that the size of the gap that needs to be crossed to a
modified functionality is a function of what *actual* organisms have
in their genomes to start with and the size of the end function system
is irrelevant. I don't know what data you are looking at where all
organisms have the same probability of evolving, say, a lactase
function. In my understanding, the odds of evolving, say, a lactase
function depends on the presence or absence of ebg or some other
protein that can be evolved to that function in a reasonable number of
steps. Not on the size of the lactase at the end.

In other words, what
is the actual minimum distance
likely to be? - i.e., the likely
minimum gap distance.

The "actual distance" in a particular case.  The "likely gap distance"
under certain assumptions and models.

Stop fucking using the word "minimum".  What you mean is the "likely
gap distance", not the "likely minimum gap distance".

You like to talk about the minimum possible distance of one.  That
isn't the actual minimum distance when it comes to the potential
targets at a particular level of sequence/structure space.

How do you know when your argument claims that only the end size tells
us how big the gap is? The *actual* gap size is a function of what is
fortuitously present (or not) in a particular genome. The only way
one could calculate a gap size based on the size of the end product is
if one assumed that evolution worked by the completely random "747 in
a tornado" mechanism and that there was essentially no difference in
the starting genomes of any organism.

BTW, everyone but you apparently recognizes that you have not ever
really talked about *actual* gaps between real *functional* precursors
and real *functional* end points, but talked as if all organisms built
everything in them from scratch by wandering across some total
sequence space that you apparently think has some real relevance.

 Again,
there are a bunch of targets out there.  Some are closer to your
starting point than others.  The question is, which one of them is the
closest?  In other words, what is distance to the closet target?

If the environment is rich in lactose, but I can only use the rarer
glucose, I can stil survive (as I have in the past). That doesn't
mean it would not be a good thing for my future reproductive success
to find some way to use the lactose. If, by chance, I have a protein
that can be duplicated and modified easily (a few steps) to have some
lactase activity, that would increase the odds that I would be the
first to cross that gap. If I did, then likely my progeny would hog
all the environments with lactose and organisms without that advantage
would have to survive in other environments. Because my particular
lactase would be optimized quickly, I would probably prevent even the
evolution of other organisms that could produce a different lactase
fairly easily. If I don't have the necessary existing sequence that
is easy to modify to lactase, I would just have to be satisfied with
environments that have enough glucose, no matter how much lactose they
had. That is, evolution virtually ensures that those organisms with
the pathway with the smallest gaps are the ones that will evolve the
function. Even if doing so results in Rube Goldberg relatively
inefficient mechanisms.

-
i.e., the minimum distance I need to travel through space to reach a
beneficial target?  This distance isn't necessarily the minimum
possible distance of one.

Never said that the *actual* gap size was always the minimum possible
distance of one. But the evolutionary *winner* will almost always be
the organism which has the smallest gap distance that must be
crossed. That is the one that will evolve the function first. And
first is important in evolution. Evolution finds the smallest
available gap size in the same way that a river finds the optimal
channel to the sea.

What do you not understand about this concept?  Why are you trying to
play this silly game of semantics?

You are the one playing silly semantic games. I understand the
difference between bull*** terminology like "likely *minimum* gap
size" when what you mean is something far from the minimum and
actually means something like "average" based on a straw man model of
evolution. If you don't want to play semantic games, leave off the
adjective "minimum". Use terminology like "estimated average or
likely gap size" if evolution works under the assumptions of my
model. Or the upper end of the smallest 10% of possible gap sizes if
evolution actually worked by the "747 in a tornado" model of
completely random synthesis from scratch (or the equivalent of
completely random mutation starting from either a maximally distant or
average distant starting point in total sequence space. Whatever.
Just don't use the dishonest language you are using.

And yes, the likely minimum is in fact related to the average gap
distance along a Poisson distribution.

Under the bogus idea of the "747 in a tornado" straw man model of
evolution.

LOL - The only way the likely minimum distance isn't related to the
average distance along a Poisson distribution is if the targets in
sequence/structure space were nicely clustered close together at all
levels of functional complexity and this clustering effect did not
loosen at all as you moved up the ladder.

That doesn't deny that you are using a "747 in a tornado model" to
estimate "average gap size" as if evolution worked by a random start
in total sequence space. *Any* model of how evolution works that uses
total sequence space has no basis in reality.

This fantastic clustering effect would indeed save the ToE.  The only
problem is that it demonstrably doesn't happen.  The clusters do not
stay as clustered at higher levels as they were at lower levels.  The
island clusters spread apart and fracture as you move up the ladder of
functional complexity.

How far from the "island" of fetal hemoglobin is the "island" of
embryonic hemoglobin? How far is the "island" of myoglobin? This all
assumes that no protein system can ever change size or change function
by linking to some other protein. This is a very bogus model of
reality in more ways than one.

This is a demonstrable fact if you just look at the differences in
sequence requirements for higher and higher-level systems.  There
really is no argument here.

Of course there is. Unless, of course, you actually admit that your
analysis is based on the "747 in a tornado" straw man model of
evolution. Then it would be true but irrelevant.

You can no more be "likely"
minimum than you can be a little bit pregnant.  *Minimum* means
*minimum*.  You only use the term *minimum* as a propaganda tool to
imply that your numbers is a *minimum*.

The actual minimum isn't directly known.  

No.  The actual *minimum* is always the last mutational step in the
process and is always 1.

No.  That's the minimum possible distance.  

Which, when it has been crossed, is the *actual* minimum possible
distance covering the last step.

You don't even estimate the odds that this is likely to be the case
for any level of functional complexity.  You just assert that it was
the case without any demonstration or statistical analysis of the odds
that it is remotely likely to have been the case or to ever be the
case in the future over any period of time.

Such assertions are not science Howard.

You wouldn't know science if it kicked you in the face.

The actual minimum
distance between a starting point and the next closest potential
target is not always one.  

True only if you make additional assumptions like the idea that both
the starting point and target must have some useful function. Without
that assumption, the actual minimal distance is always the last step.

A target is defined as having a novel beneficial function.  Such
targets do not necessarily exist within one step of a starting point
within a chosen pool of starting points.

Never claimed they did. Never claimed that evolution of this or that
function was necessarily even possible. For example, I recognize the
greater difficulty in evolving lactase in E. coli that lack an ebg
gene. I certainly don't claim that something can evolve regardless of
the *actual* starting points.

You can, of course, argue that the starting point is a neutral
sequence that just happens to be one point mutation away from a
target.  Again, what are the odds?  What are the odds that a pool of
starting points, even neutral ones, will be within the minimum
possible distance of one mutation from any target in sequence/
structure space?  You don't even estimate these odds.  You don't use
any statistical analysis at all.

Because evolution means that organisms are not all the same,
calculating the "average" probability of *all* organisms evolving
system a is utterly without meaning.

The actual minimum distance can be a great
deal larger than one.

Depending on the additional assumptions that you place on the starting
and ending points.  

My statement is true *regardless* of the initial assumptions - except
for the definition of targets being functionally beneficial over what
already exists within the starting pool of options.

And the *actual* starting pool of options is idiosyncratically linked
to *actual* genomes and not to "total sequence space." Which is why
one must look at the actual features, sequence, and structure of the
particular system and provide what you call a "just-so" story from
that evidence. Evolution simply does not work by your straw man
model.

In your case, your math says that your starting
point is either a sequence of the same size that is maximally (your
math says this) or randomly placed relative to the teleologic target.
You deny this and say the starting point can be anywhere (unless that
anywhere is one mutational step away of course).

Let's say that there is a universal lottery.  There are a trillion
possible winning numbers in this lottery, but in order to win you have
to line up 100 numbers row to match at least one of these winning 100-
digit numbers.  What are the odds that your chosen staring point will
be just one character off?

Evolution is not a lottery where everyone has an equal ticket. And it
is not taking place in total sequence space.

You see, I'm talking about averages here. You have to at least
consider the odds of successful placement of your original staring
point(s).  You can't just say that because it is possible that it is
remotely likely to start off right next to a winning target in
sequence/structure space.

But, for argument's sake, let's say that you get extremely lucky with
your original starting point at a very high level of complexity - only
one point mutation away from a 1,000aa system that is functional
beneficial.  You will of course quickly find that island via RM.
However, what are the odds that you'll find another one this side of
trillions of years of time?

And all you would get is bull*** numerology that has no relevance.

You see, in order to answer these questions you have to know at least
something about the ratio of targets to non-targets and that targets
do not stay as clustered in sequence space at higher levels as they
were at lower levels.  Both of these features of targets in sequence/
structure space are known.

 That may not be the actual minimum gap size
between functional states.  But since you cannot calculate the actual
minimum gap size, pulling a number out of yer arse does not make that
number the most likely number.

That is exactly what we are trying to estimate - the actual minimum
gap distance.  

No.  You are not trying at all to do that.  Instead you are only
interested in generating large gap numbers using hidden assumptions to
do so.

Not true.  I'm actually trying to estimate the actual likely gap
distance - the actual minimum distance needed to be crossed by RM to
achieve success.  

And doing so based on bogus straw man ideas that imply that all
organisms have an equal chance, but it is small because they have to
search total sequence space.

This is what you need to do in order to have a real
scientific theory to support the mechanism of RM/NS.  

I have actual experimental evidence that the mechanism of RM and NS
both exist.

This is exactly
what you don't have.  All you have is your mantra that evolution
happens when the gap distance is small enough.  That says nothing at
all about when the gap distance is LIKELY to be small enough - don't
you see that?  This means that the mechanism of RM/NS is not
scientifically supported and has no predictive value beyond very very
low levels of functional complexity.

That is what is not directly known and therefore what
is subject to scientific investigation.  Your assertions that what is
possible can always happen is not scientific since it carries with it
no statistical odds analysis whatsoever - - and therefore no
predictive value.

Yes, my idea that evolution works by modifying pre-existing systems to
produce new ones and that subsequent variation in sequence is going to
produce a consilience of patterns has bee statistically verified.

Similarities do not explain the differences.  The pattern can be
explained by RM.  However, the functional differences have not been
explained by RM/NS beyond very low levels of functional complexity.
There is no statistical analysis...

read more »

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