Re: Howard theory - "cannot be computed"

On Mar 3, 8:45 am, hersheyh <hershe...@xxxxxxxxx> wrote:

The only thing you look at is what is possible without considering the
likelihood of what is possible.  That's your problem.  Without
statistical support, your stories about what is possible are just-so
fairytale stories - not science.

Bullshit.  What statistics can do is rule in or rule out particular
explanations with specific honestly stated assumptions.  In this case,
you have presented a probability estimate, but have dishonestly hidden
the underlying assumptions that go into that estimate.  The key hidden
assumption of the hypothesis you are testing is that a protein of a
given size is *necessarily* assembled completely randomly from
scratch, at least for all the aa differences important for function,
with no possible utility for any intermediate structural state (that
is, the only possible function is the teleological goal you asserted
as "the" function).  That is the probability that your *math*
describes even when your 'lips' say otherwise.  You then compare that
probability with the probability that real proteins could arise *by
that specific mechanism* in the time available and conclude that you
can reject the mechanism.  I agree.  The proteins we see in organisms
today were NOT produced by completely random assembly with no
intermediate utility from scratch.

Tell me where in my calculations, specifically, I assume a random
starting point? Also, where do I assume that there are no other
beneficial sequences besides the ending point?

This assertions are simply lies are your part and you know it. I do
not start "from scratch" in my calculations and I do not assume only a
single target in sequence space. My calculations assume a great many
potential targets and a minimum likely distance between targets that
is calculable to at least a useful degree of certainty.

Compare this with your completely baseless assumption that the likely
gap distance is the minimum possible gap distance. While everyone
agrees that the minimum possible distance is always possible, it isn't
remotely likely. That's the problems. Your imagined scenarios are
certainly possible. It is just that they aren't even remotely close
to being a likely representation of reality.

That is why you use no real statistical analyses to consider the
likelihood of your stories. You just assume that it is good enough to
demonstration the possible without having to worry about likelihoods -
i.e., real scientific support.

Let me repeat.  We *both* reject the *real* hypothesis that you
tested: completely random assembly directly from scratch with only the
end teleologic goal function having utility.  We do not disagree on
that.  The problem is that you think that exhausts all possible
natural mechanisms, whereas I *know* that it does not *and* you
repeatedly lie and claim that you are not requiring that the entire
protein be assembled completely randomly from scratch with no possible
function until the teleologic end function is acheived.  [If you
introduce a useful intermediate state, that would mean that the size
of useless gaps is not represented by the functionally minimal protein
size you claim in your math.]

Upon what basis do you assume a closer useful target that I calculate
with my math? You have no mathematical basis for this assumption.
All you have is your argument that it is possible. Yes Howard, it is
possible. But, that doesn't make it remotely likely to have the
targets as close together as you need them to be in sequence space.

In order to support your assertions that was
is possible is also plausible, you need to produce some real
statistical support for your argument. Howard hasn't done this - and
neither has anyone else.

Bullshit. I have to present supporting *evidence*. I have. I have
agreed that your statistics would be valid *if* evolution involved
random assembly from scratch or the mathematical equivalent. So we
both agree that we can rule out that evolution is due to chance
alone. Only you think that is actually how evolution works, however.
In my way of thinking that means we need to look at non-random causal
factors.

The only thing you look at is what is possible without considering the
likelihood of what is possible. That's your problem. Without
statistical support, your stories about what is possible are just-so
fairytale stories - not science.

The actual statistical evidence strongly suggests that each one of
Howard's proposed steppingstones is widely surrounded by very large
Hamming distances (likely much greater than 50 or even 100).

Those are numbers you simply pull out of yer arse. They have no basis
whatsoever. We have rejected the idea that protein sequences are
assembled by chance alone.

That's why you're wrong. Protein sequences are assembled by chance
alone until the next beneficial steppingstone in sequence space is
actually discovered.

At NO point after the current protein synthetic mechanisms first
formed, both phylogenetically and ontologically, were or are protein
sequences ever assembled by chance alone.

Not true. Each step in the proposed evolutionary pathways are only
successful by the chance landing of a randomly taken step on the right
position in sequence space. Only after the random steps are taken and
happen to land on the right sequence, by pure chance, can NS come into
the picture to preferentially select among all the chance discoveries
in sequence space.

If you have no idea as to the odds that the next
steppingstone will be reached in a given amount of time, your position
isn't scientific since it has no predictive power.

To calculate the amount of time between "steppingstones" you have o
have a model in which you know both the starting point for *each*
*specific* steppingstone and the end point that needs to be reached.

No. You have to have a model that produces the odds of distribution.
The actual specific location of each steppingstone need not be known
to have a good model with very good predictive power. In contrast,
your "model" has no predictive power at all.

That is NOT the model you present. I have presented reasonable models
for "steppingstone" start and end points.

No you haven't. You've just presented possible methods. You've
presented nothing showing that your "possibilities" are even remotely
likely or "reasonable" in a scientific sense.

You talk about some airy
fairy "minimum likely distance" that is not any *specific* distance at
all. Just a number you pull out of yer arse that is less than the
total size.

Science isn't about knowing a specific distance. If you could know
the specific distance, you wouldn't need science. Science is about
using limited knowledge about specifics to determine the likely
distances when the actual distances are not directly known or
knowable.

You seem to confuse direct knowledge with science. If direct
knowledge is available, that removes the need for science. Science is
only useful when direct knowledge is not available and one is trying
to determine the most likely "truth" given limited information.
That's science. That's what you do not do. Your just-so stories are
not scientific. They are just wishful thinking.

That means you have NO idea at all about
the size of the Hamming distance (which must be gaps that are non-
functional) that was crossed in those systems that have evolved.

The Hamming distance concerns gaps that are neutral as well as
functionally non-beneficial.

And why the bloody hell are neutral changes included?

NS cannot select amonst neutral differences in a preferential manner.
Therefore, neutral mutations are not guided by NS and are therefore
random.

And yes, this distance can be determined
to a useful degree of certainty.

Then why the bloody hell have you not done so? All you have done is
present the *maximum* gap size and then pull an arbitrary smaller
number out of yer arse and claim that it is the "likely minimum gap
size".

Not true. I've shown very clearly with a number of references and
statistical methods why the actual minimum Hamming distance is far
greater than the number I've actually used - i.e., a gap of 50. The
actual likely minimum HD is far greater than 50 at the 1000 fsaar
level of functional complexity.

Demonstrating that a small Hamming distance exists between a plausible
functional ancestral state (plausible because cell still have those
functions, as do flagella) and the added function is all I need. The
odds of a flagella arising from the linkage of a pre-existing pore and
motor are much higher than the odds of either a magical poofer or
random assembly from scratch.

But you haven't demonstrated any such thing. You've only demonstrated
that the distance could be small if things were set up like you
imagine they could be set up.

Is it my imagination that eubacterial flagella are composed of
rotatable pores and motors that rotate them? Is it my imagination
that a *real* flagella has sequence substructures that already are
'rotatable pores' and 'motors'? Your complaint is merely and only
based on the fact that the system described is similar in *sequence*
to a fully functional flagella, even though it only has the specific
functions I claim would be likely *functional* precursors to the added
function of motorized rotation.

It is only in your imagination that real ppors and motors could easily
link up to produce the next step in your proposed evolutionary
pathway. Such a demonstration is extremely unlikely this side of a
practical eternity of time. That is why it has never been observed
without starting with subsystems that were already part of the fully
formed flagellar system to begin with. I've gone into extensive
detail with you as to why your imagined scenario is very unlikely to
work starting with subsystems that were not already historically part
of the final product to begin with.

That's not the same thing as
demonstrating that this small distance you imagine is remotely likely
to exist in the real world.

Showing that this small mutational step from predicted precursor
function to have the added function of motorized rotation actually
exists in a real experiment is somehow NOT showing that that such a
system cannot exist in the real world?

Again, you used parts that were already ideally suited since they were
already part of the final flagellar motility system to begin with.

Your position is built entirely on
imagining what could exist without any consideration of what is
actually likely to exist.

Like the *functional* systems with the same required properties that
exist in real cells. Face it,Sean, you would not be happy unless I
started from a completely non-functional precursor sequence and
magically poofed 1000 changes all at once.

Try to at least start with subsystems that were not already part of
the final product to begin with for a change. That's what you're
actually claiming is possible - right? Ok, show that it is also
"likely" for once . . .

Let's be clear here. Contrary to your lies, I've never suggested that
the starting point be non-functional. What I have suggested is that
the starting point(s) not have been originally derived from the ending
points to begin with.

But magical poofing of
1000's of aa's in one swell foop is not MY explanation for the added
function of motorized rotation. It's yours.

It's your deliberate lie or mischaracterization of my position and you
know it.

Can you tell me how your
mechanism works in as much detail as I used to explain mine. Since
neither of us are not discussing "random assembly from scratch", we
can both discard that strawman you generate your probability numbers
from and discuss causal mechanisms.

The mechanism is deliberate assembly on a nano-scale. We already know
how humans can do such work. We have absolutely no idea how RM/NS can
come remotely close to doing it. Your mechanism only exists in your
head - not in reality.

Again, demonstrating what is possible is not the same thing as
demonstrating what is likely . . .

And you prefer impossible fairies magically poofing systems into
existence... so you prefer impossible explanations?

Human-level intelligence and its creative capacity isn't impossible or
"magical poofing". It is quite real.

Howard
has presented absolutely nothing to counter this statistical and
observational evidence.

I just did. The odds of a flagella arising from the linkage of a pre-
existing pore and motor are much greater than either of the two models
you present. How *much* greater depends on particulars that cannot be
computed. But greater none-the-less.

LOL - if you can't determine the "how much" part of the problem, your
position isn't scientific. It has absolutely no quantifiable
"advantage".

The *requirement* for calculating a probability number is that the
step involved occur completely by chance. My claim is that the system
has chance elements, but also has *causal factors*. Calculating a
probability number and discovering that something occurs far more
often than would be predicted by that frequency only tells you that
there is some causal factor (e.g., the dice are loaded) distorting the
results. It doesn't tell you that God-did-it even if you are too
ignorant or stupid to think of another explanation. I agree that we
can reject chance alone as an explanation. You present your empirical
evidence for your magical poofer causal explanation and I have already
presented my evidence for how intermediate functional steps can arise
(because they are useful to the organism's reproductive success) and
how, once arisen, small modifications can produce added functions
which also may increase reproductive success.

The supposed advantage of your position is entirely in
your head. It is not quantifiable or determinable in any degree.

Neither is your preferred explanation.

My suggested mechanism is both quantifiable and demonstrable. It
happens every day. Yours doesn't - except in your vivid imagination.

But yours alternative to pure
chance assembly, unlike mine, has no supporting evidence whatsoever.

Your mechanism depends entirely on chance assembly to find the next
steppingstone in your proposed pathway. That is why your mechanism is
called "RM/NS". What do you think the word "random" means here?

It is merely a fall-back explanation used by the ignorant who "think"
that such an explanation explains anything. What is your evidence
that some entity exists who comes down and poofs complex biochemical
systems like flagella into existence all at once?

The system itself is evidence enough - just like artifactual radio
signals would be evidence enough, by themselves, for ETI.

That is why you don't put forward any numbers, calculations, or
statistical analysis of any kind to support your position.

I did. I accepted your numbers for what they are: the probability of
completely random assembly from scratch.

That's not what they are. They don't start from scratch - not even
close. Starting from scratch would be starting at the maximum
possible distance. My numbers assume the minimum *likely* distance -
not the maximum or your prefered minimum possible distance.

And then I rejected that
explanation in favor of one that has causal factors like intermediate
utility and selection. You're just upset that I didn't choose your
evidenceless explaination that something intelligent did something at
some point and place somehow producing whatever you want your fairy to
produce.

You reject anything that indicates the need for intelligent input. In
fact, you reject any such evidence so strongly that you would favor
your fairytale just-so imagined stories instead - regardless of a
complete lack of scientific support for your notions. You simply have
a desire for them to be true, so you just choose to believe them
despite all the evidence to the contrary. That's not science Howard.
That's wishful thinking.

I cannot give a probability number in the absence of knowing exactly
what the start and end points are that must be accomplished by chance
alone.

Yes, you can. That's what science is all about. If you know the
exact starting and ending points, you wouldn't need science to
determine the likely distance. You'd already know directly.

If that mutational distance is the probability of forming a
functional chimeric linker protein, I think I have adequately shown
that the minimum random step can be that of the set of deletion
mutants that have been experimentally observed in the model system.

Anything is possible Howard. That doesn't make it remotely likely.

And that probability is a hell of a lot more likely than complete
random assembly from scratch (or by assembly by magical assembly
fairies, AFAICT).

Some real numbers Howard - and where not starting from "scratch"
here. Start with subsystems that were not already part of the final
system in question this time.

Your
position is simply not falsifiable or testable in any scientific way.
That is why it isn't science. It's just-so story telling.

Supported by *real* evidence rather than by *assertion* that if total
random assembly isn't true the only causal explanation is the magical
fairy causal explanation.

You have no "real evidence" aside from your bald assertions and
stories that what is possible is also likely. That's nonsense
Howard. Put up some real numbers for once - at least some effort to
do some real science.

Sean Pitman
www.DetectingDesign.com

.

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