Re: Cascading vs. Specified Systems

On Feb 21, 4:09 pm, Prof Weird <pol...@xxxxxxxxxxxxxxxxxxxxx> wrote:

For 30 years, no bacteria or fungus could digest atrazine; now, they
can.

The proteins involved in this system are :

AtzA - 473 amino acids
AtzB - 481 (or 546) amino acids
AtzC - 403 amino acids

This totals to 1357 amino acids to perform a NOVEL reaction.

Sean initiates standard weaseling :

Yes, but did you not notice the phrase, "working together at the same
time"? A cascading system of different enzymes do not work together
at the same time nor are they required to work in a specific
arrangement with each other.

YES, they are required to work in a specific arrangement with each
other !

AtzA catalyzes the first reaction of converting atrazine to
hydroxyatrazine
AtzB catalyzes the next reaction, AtzC catalyzes the last reaction,
producing products that the bacterium can actually use. The C
reaction cannot occur before the A reaction; thus the temporal
arrangement is specific.

I'm talking about a specific 3D arrangement in space. Not one of
these enzymes is required to be specifically arranged relative to the
other two enzymes in space. The enzymes can do their separate jobs
completely independent of the specific location or relative
orientation of any of the other enzymes in the pathway. This is
unlike a system like the flagellar motility system where each part
must be specifically arranged in space and time relative to all the
other parts in the system - all working together at the same time.

For example, what are the odds of having three specific yet separate 3-
character sequences somewhere in a pool of a million randomly 5-
character sequences? Well, the odds of finding one specific 3-
character sequence are 1 in 26^3 or 1 in 8000. Given a million
randomly generated 3-character sequences, this particular sequence
should be in the pool of options 125 times. The same thing is true
for the other two 3-character sequences. Each of them should appear
in the pool of options 125 times - on average. So, the odds that all
three will be there are 1 - the odds that at least one would not be in
the pool of options - - or 1 - (7997/8000)^333,333 = > 99.9999999%
chance of having all three specific 3-character sequences in the pool
of just 1 million options.

Now, compare this to the odds of having all three specific sequences
in a specific sequential order (like abcdefghi) in the same pool of
options? What would the odds be now that these three specific
sequences would exist in this pool of options in this specific order?
Well, the odds now are only 1 in 5,429,503.

So, you see, overall system specificity makes a BIG difference.

This means the system is IRREDUCIBLY COMPLEX, as well as far beyond
your hallucinatory limit.

It is irreducibly complex, as all systems are, but it is not beyond my
threshold limit because it does not meet the specificity requirement
that all the residues be specifically arranged with each other in
space and work together at the same time.

There are a lot of examples of systems that do meet this requirement.
Cascading systems, such as your enzymatic cascade, simply don't
qualify - unfortunately.

Try again . . .

< snip >

If any one of these parts is removed, the function in
question fails suddenly.

AS DOES THE ABILITY TO DIGEST ATRAZINE IF ANY OF AtzA, B, or C is
removed.

I'm not talking about complete removal, but any alteration of relative
position. Alter the relative position of any of the parts in the
flagellar system and the motility function fails. This is not true
for your enzymatic cascade, which can tolerate any relative position
in space of one enzyme relative to the other two.

< snip >

2) but, but - that NOVEL ability isn't complex enough !!11!!!1!!!

That's true, because you haven't met the specificity requirement.

Actually, I have - you just refuse to accept it. The reaction cycle
MUST BE AtzA to AtzB to Atz C. No other configuration works.

You don't seem to understand the concept of specificity. It isn't the
order of function, it is the relative order of the parts themselves
relative to themselves. Each part must be specifically arranged
relative to all the other parts in the system. That's what sequence
specificity means. Enzymatic cascades do not have the requirement
that each part be specifically arranged in space relative to all the
other parts in the system.

How does a flagella rotate ? A CASCADE of reactions alter protein
shapes which move other proteins.

Flagellar motility works because all the proteins are required to be
in a specific position in space relative to all the other proteins in
the system. Beyond this, they all work together at the same time for
the overall function to work. One doesn't work first, then the other,
and then the last part. Not at all. They all work together at the
very same time. This is not true of your enzymatic cascade where one
protein works while the others do nothing, then the next works while
the others do nothing, and finally the last one works while the others
do nothing. This isn't remotely close to how a flagellar system
works. The motor doesn't stop working while the whip proteins are
doing their job spinning. Hello! They all work at the very same
time.

The individual parts of the rotor and stator are not much larger than
the Atz proteins; if you have no problem with the Atz system evolving,
why, EXACTLY, is a Magical Sky Pixie 'required' to 'explain' the
evolution of the flagellum again ?

Oh, right - it's too complex for YOU to figure out, so an Intelligence
greater than yours simply MUST have done it !

As described above, a fully specified system is far more statistically
complex than a system were none of its parts are actually required to
be in a specific arrangement relative to each other.

3) but, but - you haven't shown that this NOVEL ability isn't due to
the loss of a function in some undefined protein !!

This cascading function is not the result of a loss of any other
system.

Which means IT IS A GAIN. Something you bellowed simply cannot exist.

If you would read just one more sentence, you'd know that this
statement simply isn't true. Such systems do exist and can evolve -
just not beyond the 1000aa threshold level where all the parts of the
system are specified and work together at the same time.

It is a fairly high example of evolution in action. However,
it is not significantly higher in complexity than its largest fairly
specified subpart - i.e., less than 500aa in this case.

Nope - all three components MUST work together to get enzymatic
activity. AtzA must work before AtzB which must work before AtzC.
All three MUST be present - AtzA cannot do all the needed reactions
alone; nor can AtzB or AtzC.

And, as AtzA is a tetramer (no function until all four parts -
representing 1892 aa - get together), your 'specification' whine thus
be skewered.

It is a matter of coded positions, not the total number of residues
repetitively coded (that again does not meet the specificity
requirement). For example, the flagellar system requires about 30
different structural proteins at minimum, coded for by at least 10,000
codons of genetic real estate. However, many many more than 30
proteins are actually used in the system because hundreds and
thousands of copies of some of these proteins are used to build the
overall system. It isn't the copies that count for system complexity.
It is the minimum number of coded residue positions that counts -
i.e., about 10,000 at minimum in this case.

< snip rest until you grasp at least this much >

Sean Pitman
www.DetectingDesign.com

.

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