Re: Liar Liar

On Jun 18, 7:35 pm, Seanpit <sean...@xxxxxxxxx> wrote:
On Jun 18, 12:05 pm, hersheyh <hershe...@xxxxxxxxx> wrote:

< snip >

It isn't very far about systems
that can and do evolve rapidly at the level of a few hundred
residues.  I'm also not asking you to start from scratch, but from any
system that is already in the gene pool.

Liar.  For cytochrome c, which is your ONLY real example, your own
math shows that you think that *evolution* must assemble it from
random aa's or a maximally distant sequence.  Every other sequence you
talk about is merely a scaling up of the bogus cytochrome c math.

You are the liar here - deliberately so.  The minimum size requirement

Define "minimum size requirement" for cytochrome c and how you
calculate it.

is not the same as the likely gap distance

Define "likely gap distance" for cytochrome c and how you calculate
it.

and my calculations reflect
that.  

The only calculation you made came up with a number that is nothing
but the number of aa sites in cytochrome c (which is not an 'average'
protein in this regard) that would need to be specified if all aa's in
cytochrome c were either freely substitutable or must be absolutely
specified (only one of the 20 possible aa's would work). And the
probability you calcluated was nothing but the probability that
completely random substitution in a protein in which none of those
sites had the right aa would generate a functional cytochrome c
sequence. That probability is essentially the same as you would get
if you randomly assembled proteins from scratch.

Your notion that the minimum likely distance stays at the
minimum possible distance of 1 regardless of the level of functional
complexity is what is utterly contrary to the available facts at
hand.  

No. It is the truth. The minimum possible distance cannot change
regardless of how large the sequence is. I am unconcerned about
"average gap sizes" or perhaps you now call it "minimum likely
distances" from some randomly chosen sequence or maximally distant
sequence. If the 'gap size' or number of mutational steps to produce
selection for a particular function is too large, it won't evolve.
That is, those systems that *have* evolved did so because they had a
pre-existing functional system which could be altered to perform some
(usually) secondary function better or because chance put together two
functional moieties so that a novel function arose (chimeric
duplication which is helped by the exon-intron nature of eucaryotic
genomes).

This notion of yours is utterly ridiculous. You have no
statistical or observational evidence to support this concept
whatsoever.  Yet, you continually spout it off as if it was reality.
It's nothing of the sort.

You haven't made clear that the assumption of your "gap size theory"
involves starting from the maximally distant sequence, just as you did
in cytochrome c.

< snip >

You with your maximally distant notions again.  How many times do I
have to explain to you that the likely gap size

So now it is "likely" gap size rather than "average" gap size?  How do
you calculate the "likely" gap size again?

As I've explained to you dozens of times now, the minimum likely gap
size is related to the average gap size along a Poisson distribution.

And, as I have pointed out, your "average gap size" is not an
"average" in any meaning of the term. Rather, as in cytochrome c, it
is the *maximum* gap size under the assumption that aa's are either
freely substitutable or completely stringent and then the second false
assumption that the ratio seen in cytochrome c applies to all other
protein systems.

What's wrong with your "collective" memory?  Hmmmmm?

My memory is fine. Your terms are bull*** handwaving belied by the
math.

is neither the maximum
possible or your assumption of the minimum possible distance of one?

The minimum possible number of mutations needed to produce a modified
or new function is always one or none.  Regardless of the size of the
starting or ending system.  That is a mathematical fact.

Oh, I know.  The problem is that the minimum possible distance doesn't
stay the *likely* minimum distance as the level of complexity
increases higher and higher. The odds that the minimum possible
distance will be the actual minimum distance drop precipitously along
a Poisson distribution.

The likely minimum gap distance grows in a linear manner with
increasing minimum structural threshold requirements.  It does not
stay at one like you suggest.

The minimum number of mutational steps is all that matters.  The first
one to find that minimum pathway wins the lottery.  But again, I am
telling you  that evolution works by modifying pre-existing sequences
and the sequences that happen to be closest to the goal (wrt number of
mutational steps) will be the likely "winner".

Absolutely true.  It is just that the odds that any sequence will be
close enough to "win" this side of trillions of years of time drop to
practically zero when you are talking about functional systems that
require a minimum number of specifically arranged amino acids to work
that is greater than 1000.

The odds that a functional protein is nearby is quite good. That is
why there are gene families. Unless you have a teleological view of
evolution.

Actually, it is being discovered that the key differences between
humans and apes is not in the genes, but in the non-coding regions of
the genome - quite a bit of which is unique to either humans or
chimps.

http://www.detectingdesign.com/earlyman.html#Key

Micro RNAs (note that "micro") are genes, just not protein coding
genes.  So, what this article tells us is that *most* micro (very
small) RNA sequences in humans are conserved in other organisms (all
but 1%) *except* in the brain, where the frequency of uniquely human
very short RNA sequences increases all the way up to 8%.  And since
these are *micro* (very short) RNAs and don't form large structures,
my guess is that they don't meet your 3000 nt criteria.  But my test
wasn't about new proteins, although it is nice of you to admit that
one can evolve humans without having to generate that which you claim
is impossible.  It was about the rate of change in genomes.  Are there
any of these new micro RNAs that could not be generated in only a few
mutational steps?

It is not so much the genetic information, but the minimum structural
requirements of the resulting system.

microRNAs are the system you pointed to.

To be honest, I don't think we enough yet about the functional
differences between humans and apes to tell if there is an uncrossable
statistical gap or not.  I certainly don't have this information as of
yet.  But, I do have enough information for systems that we do know
much more about.

It's a simple challenge Howard.  Evolution happens quickly and
commonly when no more than a few hundred specified residues are
required at minimum.

Evolution happens quickly *when* there is a selective pressure against
the current w.t. system and a pre-existing system that can be modified
in a few mutational steps to generate a function that is better at
responding to that selective pressure than the present w.t. organism
is.

That's right . . .  and these conditions are met only when the new
function in question requires less than 1000aa at minimum.  These
requirements have never been observed to be met beyond the 1000aa
threshold.

That depends more on the starting point. New systems of 1000aa are
not constructed from scratch. They are the result of modification of
pre-existing functional systems. And, again, the 1000aa is neither
the "average gap size" nor the "likely minimum gap size" you talk
about. It is the *total* size, including both the highly specified aa
sites and the freely substitutable ones. You have no way of
calculating "average gap size". Instead you use "estimated number of
absolutely specified aa sites if sites are either absolutely specified
or freely substitutable in cytochrome c" to calculate an estimate and
extrapolate that % to all other systems. And then you call that
*maximal* number "average gap size". IOW, total bull*** numerology.
And totally irrelevant unless evolution works by essentially building
proteins randomly from scratch or by randomly changing aa's in a
maximally distant protein from your chosen teleologic function. That
is before adding in that cytochrome c is not "average" in any sense.

The reason why there are gene families is precisely because evolution
does not work by the mechanism you are pretending it works by. Your
entire scaffolding is an excellent example of GIGO.

< snip >

It doesn't happen at all in observable time when
more than 1000aa - not even close.  There isn't one single example of
a novel system of function being produced at this level in all of
scientific literature - not one.  Why not?

Because you have ready excuses for all the examples that have been put
forth.  Either the protein is not big enough or the change was a minor
modification or the pre-existing sequence already had that use.

Starting with a sequence that already has the function in question
isn't the evolution of a novel function.  Hello!  Up regulation or
down regulation of a pre-existing functional system is simple.  That's
no problem at all.  Getting a new type of function that wasn't there
before, and that doesn't require that some other functional system be
lost or turned off, is the issue here.

As far as the size requirement, that's always been the point.
Evolution works very well and very quickly below the 1000aa size
threshold, but not beyond it.

That's a simple question.
It isn't difficult and the terms are well defined.

No they aren't.

What don't you understand about the minimum size requirement Howard?

You keep changing it from single proteins to systems. And keep
ignoring that evolution does NOT start building a system from scratch
for some teleologically determined function.

What don't you understand about the likely gap distance as it relates
to the average gap distance

There is no "average" in your "average gap distance". As you
calculate it, it is the *maximal* distance if one were to build a
protein randomly from scratch. That is, when it isn't just a bull***
handwaving number you pull out of yer arse.

as it relates to the minimum structural
size requirements for a system?  Hmmmm?  They aren't the same thing.
I know you are easily confused, but these concepts really aren't that
difficult.

They are simply irrelevant to how evolution actually works.

< snip >

Sean Pitmanwww.DetectingDesign.com


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