Re: Six Simple And Reasonable Questions ...

On Oct 3, 8:53 pm, Seanpit <sean...@xxxxxxxxx> wrote:
On Oct 3, 1:10 pm, hersheyh <hershe...@xxxxxxxxx> wrote:



Seanpit wrote:
On Oct 2, 9:15 pm, Boikat <boi...@xxxxxxxxxxxxx> wrote:
On Oct 2, 6:06 pm, Seanpit <sean...@xxxxxxxxx> wrote:

[snip]

This Darwinian mechanism is demonstrably limited in creative potential
to the very lowest levels of functional complexity.  It has not and
statistically cannot produce anything that requires a minimum of more
than a few hundred fairly specified amino acid residues working
together at the same time.  That's a demonstrable fact.

http://www.detectingdesign.com/flagellum.html#Calculation

[snip]

Where in this calculation do you get the idea that proteins must
assemble from scratch?  That's not true at all an you know it.  The
calculation always assumes that the actual gap distance is much less
than the maximum possible distance.  You, on the other hand, always
assume, for some very strange reason, that the minimum possible gap
distance is the likely gap distance regardless of the level of
functional complexity.  That's absolute nonsense.

You are the liar here since you continually misrepresent my position
despite the endless number of times I've corrected you on this.  Yet,
you seem to think that misrepresentations are the best you can do
since you can't really argue against my true position on this
issue . . .

I assumed that Sean had not changed what he had written in the past
and I have long since gone over his previous calculation step-by-step
demonstrating what it actually does (I am speaking in the guise of
"St. Thomas the Doubter"). I will include that evisceration of his
previous argument of merely a year ago below. I just went to his
website

http://www.detectingdesign.com/flagellum.html#Calculation

to see if he had changed his argument fundamentally. He hasn't, but
he has made some cosmetic changes that might fool some into thinking
he has made a relevant change.

I will include his so-called 'new' argument and show the problems with
it in a subsequent post. But I just want to remind people of how weak
and shallow his argument was merely a year ago.

******repeat old post****


Thomas: "Do you understand the importance of clearly stating one's
working assumptions and hypotheses or models in scientific analyses
and calculations? Yes or no?"

Sean's answer (Yes or no.):

Thomas: "Do you understand the difference between a mathematical
calculation and a crude hand-waving guess or estimation and why it is
important to explicitly state which is which? Yes or no?"

Sean's answer (Yes or no):

Thomas would then ask Sean to read the following statement:

"Well, first we have to calculate the likely gap size. Using an
average between the calculations of Yockey and Sauer, the ratio of
potential beneficial vs. non-beneficial for 100aa systems is about
1e-40. This creates a ratio for a 1,000aa system of about
1e-40^(1000/100) = 1e-400. So, the average gap size between
potentially beneficial sequences at this level would be about 308
residue differences - i.e., 20^308 = 1e400."

Thomas: "Did you write and post this in your web site? Yes or no."

Sean's reply (yes or no):

Thomas: "Do you use this paragraph to claim that you can and have
mathematically *calculated* a number you call "average gap size" or
"likely gap size". Yes or no?"

Sean's reply (yes or no):

Thomas: "Does this paragraph tell the viewer how to calculate the
value you call "average gap size? Yes or no?"

Sean's reply (yes or no):

Thomas: "Do you not claim, in this paragraph, that Yockey's ratio of
1e-40 is "the ratio of potential beneficial vs. non-beneficial
[sequences] for 100aa systems"? Yes or no?"

Sean's reply (yes or no):

Thomas: "Is, in fact, Yockey's ratio of 1e-40 *actually* "the ratio
of potential beneficial vs. non-beneficial [sequences] for 100aa
systems"? Yes or no?"

Sean's reply (yes or no):

Thomas: "Would it not be accurate to say that Yockey's ratio is an
"estimate of the number of sequences that have modern cytochrome c
function (i.e., a single *specified* function) divided by (roughly,
given the assumption that total sequence space at the 100aa level and
total sequence space minus the sequences that have cytochrome c
activity are about the same number) the number of sequences that lack
modern cytochrome c function? Yes or no?"

Sean's reply (yes or no):

Thomas (assuming that Sean answered the previous question honestly):
"Why, then, are you using and insisting on using an inaccurate
description rather than an accurate one to describe Yockey's ratio?
[Note to Sean: This is where you can blather on about how you *want*
people reading your paragraph to be misled into thinking the number
means one thing when it actually means something else.]

Sean's blather about why his lying about what Yockey's ratio means is
valid here:

Thomas: "Is not your calculation of "average gap size" merely the
taking of the 20th root of the inverse of Yockey's ratio or its
extrapolation to larger proteins? Yes or no?"

Sean's answer (yes or no):

Thomas: "Isn't the inverse of the Yockey ratio the number of
sequences that lack cytochrome c function per each sequence that has
cytochrome c function? Yes or no?"

Sean's answer (yes or no):

Thomas: "Isn't the Yockey ratio a measure of "sequence specificity"
for the particular specified function (cytochrome c in this case)?
That is, the greater the sequence stricture for the specified
function, the smaller the fraction of total sequence space (for a
given length) that would have that function. Yes or no?"

Sean's answer (yes or no):

Thomas: "Since Yockey's ratio or its inverse is a measure of
"sequence specificity" and taking the 20th root of a number is simply
a mathematical transformation, is not the 20th root also just a
measure of the degree of "sequence specificity" of modern cytochrome
c's (the specified function that Yockey examined)? Yes or no?"

Sean's answer (yes or no):

Thomas (assuming that Sean answers the previous question honestly, or
is able to understand his math): "Specifically, is not the 20th root
of the inverse of Yockey's ratio *really* a measure of the 'effective
number of invariant aa residues required for a modern cytochrome c
function', which is mathematically the same as the number of invariant
sites in cytochrome c if one assumes that there are only invariant and
freely variant sites? Yes or no?"

Sean's answer (yes or no):

Thomas: "There are two standard meanings of the the word "average".
When you use the word "average" in the phrase "average gap size",
which of the following meanings are you using?: 1) In math, "average"
is the sum of a series of actual measurements divided by the number of
trials in the series? 2) "Average" can also mean, colloquially,
'typical' and, in this case, might imply that the "gap size" has been
determined for a 'typical' or 'average' protein, namely cytochrome c.
3) Some private non-standard meaning."

Sean's answer (1, 2, or 3):

Depending on Sean's answer to the above, a follow-up question will
allow him to explain his reasoning.

Thomas: "If you answered 1) above, could you please present the
evidence, the series of trials, that produced that "average"? And
explain how an "average" can be computed from the 20th root of the
inverse of Yockey's ratio?"

Sean's answer here:

Thomas: "If you answered 2) above, could you please present the
evidence that cytochrome c is an "average" protein wrt the degree of
sequence specificity as measured by "effective number of invariant
sites"?"

Sean's answer here:

Thomas: "If you answered 3) above, could you explain why you chose to
use the word "average" when you did not mean any of the standard
meanings of "average". Did you do it because it sounded good? Did
you do it because you thought it might fool some innumerate people,
possibly including yourself, into thinking you had actually calculated
an "average"?"

Sean's answer here:

Thomas: "Since the only relevant biological meaning of the 20th root
of the inverse of Yockey's ratio is that it is the "effective number
of invariant aa sites in cytochrome c", isn't saying that this number
is the "gap size" *really* mean that the "gap" that must be crossed
is one that includes *all* and *each* of the effectively invariant
sites in this protein? IOW, rather than an "average" gap size,
doesn't this number represent the *maximum* possible gap size,
representing, as it does, all the aa sites that are relevant to the
specified function? Yes or no?"

Sean's answer here (yes or no):

If Sean answers dishonestly by saying "No.", a follow-up question will
be asked.

Thomas: "Explain why you think this number is not the 'maximum' gap
size -- the largest number of aa's that must be fully specified to
generate the function. All the other aa's are, of course, free to be
any aa."

Sean's answer here (if needed):

Thomas: "Is it not the case that the only models of evolution in
which there is a gap size that is the same as the "total number of
effectively invariant sites" away from a specified function models
where the starting point is either no sequence at all (the sequence
must be built from scratch) or a sequence which differs from the
specified end function at each and every effectively invariant site.
And is it not true, further, that these models assume that the
sequences are built by chance alone either _ab nihilo_ or from a
starting point which is maximally distant from any sequence with the
specified function? Yes or no?"

Sean's answer here (yes or no):

Thomas: "Have you not, elsewhere in your writings, claimed,
specifically, that you recognize that these models do not represent
standard evolutionary models? Yes or no?"

Sean's answer here (yes or no):

Thomas: "So which should we believe, Sean? Your math or your words?"

Sean's answer here (math or words):

*****end repost****
[snip]


The numerology is correct. It matches both the statistical and
observational evidence right on.  You, on the other hand, have
absolutely no statistical or observational evidence to back up your
notion that your mechanism could remotely do the job you say it did
beyond very low levels of functional complexity.

I think, in the above re-post, I had gone over Sean's initial
calculation of what *he* mislabelled "average gap size" or "likely gap
size" step-by-step and reported what he *actually* calculated and how
that differed from what he *claimed* to have calculated. I am pleased
that Sean did recognize how lousy that argument was. Now I will go
over his new numerological bull*** and show the problems with it.
[So much bull***, so little time. It may take a little while. I have
some other things to do. But the basic problem I can initially see is
his false assumption that sequences with a specified function are
randomly scattered in total sequence space which need to be found by
random walks from random sequence space, when even he recognizes that
that isn't true. And his continued refusal to realize that proteins
do not have *a* teleologic function, but have subfunctions and
multiple *functions*, both primary and secondary, allowing the
emergence of new function without drastic change in structure.]


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