Re: Of Mice and Straw Men


hersheyhv wrote:
> Seanpit wrote:
> > hersheyhv wrote:
> > > Seanpit wrote:
> > > > Howard,
> > > >
> > > > You obviously don't get my point about cytochrome C at all. I'm not
> > > > saying that CC cannot evolve or that it is not similar to other
> > > > functional sequences within the electron transport chain.
> > >
> > > No. But you claim that it evolved from a random sequence by a random
> > > walk with no possibility of intermediate utility.
> >
> > No, I never did say this.
>
> Your math says it. Your mathematical calculation of probabilities
> explicitly implies that cytorchrome c and *every other system you
> mention* starts out as a random sequence and proceeds in an aimless
> random walk and only reaches *the predetermined* utility by chance
> alone.

Not true. My position is that with increasing minimum size and/or
specificity requirements the average distance to the next closest
beneficial island cluster of beneficial sequences grows in absolute
distance in a rather linear fashion - creating a multicharacter neutral
gap. This increase in absolute distance translates into an exponential
increase in random walk distance/time.

As I've said before, you can start wherever you want and the average
time it takes to find new islands of beneficial sequences will not
change. You might happen to be really lucky and start really close to
a particular beneficial island cluster at a high level, but odds are
evolution will never make it off this island to any other at the same
level or higher.

Functions like lactase, nylonase, cytochrome c, and other such
relatively short single protein functions are not at very high levels
of functional complexity. Their minimum requirements are no more than
a few hundred fairly specified residues at most. The neutral gaps
between what is already in the genome and such functions are on
occasion fairly small and evolution can be and has been successful in
real time. Go beyond this though to those functions requiring a few
thousand fairly specified residues at minimum and evolution just
doesn't happen.

> So, yes. I will keep repeating that you either do not
> understand the meaning of your calculations or you really believe that
> evolution works the way that you propose, despite my pointing out
> repeatedly that it does not. You have not presented a single case
> where evolution ever *had to* produce a protein by a random walk that
> required even 10 selectively neutral non-functional intermediates
> before reaching the 'function'. You have merely *hypothesized* that
> they *might* exist and then acted like you knew that they really do.

Many of the proposed steps in flagellar evolution models require dozens
of such multi-character changes. Not one of them has ever been shown
to occur in real life. We aren't talking about evolving a new species
here or any such major macroevolution change here. We are just talking
about evolving a single step in the flagellar evolution pathway beyond
very low levels, just one. It has never happened and it never will.

> > You continually misrepresent my position like
> > this despite my correcting you about such strawmen caricatures over and
> > over again.
> >
> > For the umpteenth time, evolution can start with any functional or
> > non-functional sequence you want.
>
> And it remains a fact that *you* *never do* start with any functional
> sequence and you object to anyone who starts their evolutionary steps
> with any sequence that doesn't meet your mathematical fantasy of large
> neutral gaps.

Not true. I use the flagellar evolution models proposed by you guys.
These models do start with functional subsystems - which is perfectly
fine. It is just that the next steppingstone function is always too
far away from what there is to start with at such high levels of
functional complexity.

> *You* always start with a random non-functional
> sequence.

Not true. I always start with a functional sequence and see how long
it would take to find the next closest functional sequence at a higher
level of minimum size and/or specificity.

> And when I, or anyone else points out that the 'function'
> that evolves, be it galactosidase 'function' from ebg, or cytochrome c
> 'function' from cytochrome c1 or flagellar 'function' from a chimeric
> fliG connecting the motor and the rotateable pore, you criticize us
> because these do NOT require your mathematical fantasy of long neutral
> (non-functional) walks from random, non-useful sequences.

The minimum requirements for the galactosidase function are less than
400 fairly specified residues. Cytochrome c only requires a minimum of
less than 80aa. Such functions are at a low level of functional
complexity. Flagellar motility, on the other hand, requires many
thousands of fairly specified residues. The problem here is that none
of the proposed steps, to include your chimeric FliG connecting the
motor to a rotatable pore, have ever been shown to actually evolve in
real life. The gaps involved are just too big. In fact, what seems
like such a small jump to you is actually a huge canyon statistically -
not crossable in trillions of years of average time.

> You dismiss
> *real* evolution (descent with modification) in favor of a strawman
> mathematical fantasy that every one agrees would not happen. Your
> fantasy never NEEDS to happen. It is your ignorant idea that evolution
> proceeds by the mechanism ennumerated in your mathematical fantasy that
> I am criticising; evolution does not proceed by the mechanism
> ennumerated in your mathematical fantasy. It proceeds via descent with
> modification and extensive borrowing of pre-existing functional
> moieties.

At higher levels the required moieties simply do not exist in ratios
that are large enough to continue up the ladder of functional
complexity. Evolution starts stalling out at very low levels and never
makes it up the ladder very far. That's what really happens in real
life experiments. It's a fact.

> > It is just that at higher levels of
> > functional complexity, beyond those functions that only require a few
> > hundred fairly specified residues at minimum, the multi-character gaps
> > simply get to large to cross this size of a practical eternity of time.
>
> And, again, what is the relevance of talking about these "higher levels
> of functional complexity" if those higher levels of *functional*
> complexity arose by modification of a pre-existing sequence that both
> *had* useful functional utility and also *had* most of the sequences
> needed for the new 'function'.

You simply assume that if subsystems of a particular function exist
with independent functions that it would be a fairly easy thing to
bring these subsystems together to form a larger more complex united
system of function. Well, it just isn't that easy. At higher levels
such a process would involve trillions of years of average time. I
know this is a bummer for you, but that's the way it is.
Statistically, there's just no way around it.

> Cytochrome c did not have to reinvent
> heme-binding sites for its new 'function'. It *borrowed* them from a
> pre-existing protein (namely cytochrome c1). There is no evolutionary
> event that I am aware of that NEEDS to to cross the multi-character
> gaps you fantasize exist.

Tell me how to get to each of the next steppingstones in flagellar
evolution without any multi-character changes. It just can't be done.
After a while of honestly thinking about it one is simply forced to
recognize the necessity of multi-character changes beyond very low
levels. They are there and they do indeed grow with increasing minimum
requirements of size and/or specificity.

>Your large gaps are a mathematical fantasy
> that no one in his or her right mind would think actually happens.

Not true. Show me where there are no multi-character gaps in flagellar
models.

> You
> *hypothesize* that these large gaps exist because you have an argument
> against *that* particular model of evolution. But you falsely claim
> that that model is what *evolutionary biologists* claim as well. It is
> not.

I know it's not what popular biology claims, but popular biology is
wrong. The multi-character gaps are indeed there. Prove me wrong.

> You have not demonstrated or presented a single *function* that
> did evolve that *required* crossing your large gaps.

That's because functions that do evolve are always at low levels of
functional complexity (requiring no more than a few hundred fairly
specified residues at minimum) where the ratio of beneficial sequences
in sequence space is high enough to be fairly close to what is already
in the gene pool library.

> Hell, I have, and
> I am no genius, presented workable ideas about how a rotateable
> flagella could arise from a single chimeric protein fusion mutation

Not without significant multi-character changes involved you haven't.

> and
> how cytochrome c could arise by a single partial duplication. Neither
> *function* existed before these mutations; but it would exist
> afterward.

Cytochrome C is at a much lower level of complexity than is flagellar
motilty.

> > Cytochrome C, by the way, only requires a minimum of about 80 fairly
> > specified residues.
>
> This number of 80 is only relevant in your mathematical fantasy that
> cytochrome c arose by starting with a random sequence and proceding in
> a non-functional random walk until cytchrome c *function* happens to be
> landed on.

Not true. Show me how you could make cytochrome c smaller or more
flexible and still maintain its function to at least some minimally
selectable degree. You see, it is a fact that the cytochrome c
function requires a minimum size and specificity of arrangement before
its function can be realized - even a little bit. This is not fantasy.
It is fact.

> In my model, the evoluton of cytochome c's unique
> *function* does not require changing any of the amino acids involved in
> heme-binding. That was borrowed from cytochrome c1. It probably does
> not require changing any amino acids involved in interaction with
> cytochrome c1. It may not require changing any amino acids involved in
> the interaction with cytochrome a. It may require a few changes to
> produce a selectable redox between that of cytochrome c1 and cytochrome
> a. Once a selectable utility is obtained, of course, selection will
> rapidly optimize it.

This says nothing about the minimum size and/or specificity
requirements of cytochrome c or the cytochrome island to which it
belongs. Showing that CC is indeed very close to something else in the
genome has nothing to do with its minimum requirements. It only has to
do with suggesting that it may be evolvable given a certain
pre-existing starting point of other cytochromes - which is true.
Getting to this cytochrome island cluster in the first place is another
issue. But, again, CC is at a relatively low level of functional
complexity. At higher levels the steppingstones get more and more
widely spaced.

> > Obviously then, it is not beyond my boundary of
> > evolvability. Its fairly high degree of minimum specificity
> > requirements certainly create sizable gaps around its island cluster of
> > closely related sequences (to include other similar cytochromes in the
> > ETC which are all on the same island cluster), but not sizable enough
> > to stall evolution out given Darwinian time scales.
>
> Again, the number you present only makes sense if your model is that
> all 80 sites have to evolve by a random walk of non-functional
> intermediates.

I never said that all 80 sites have to change by random walk. You
continually assert that this is my position, but I've never said this
and my statistics do not depend on this sort of assertion. This is
just a strawman tactic on your part.

All I'm saying is that there is indeed a minimum requirement for such
functions. For CC this minimum is about 80 fairly specified residues.
Even at this relatively low level, there are gaps. The gaps are not
nearly as large as they are at higher levels, but given the fairly high
minimum specificity requirements of CC and the other cytochromes in the
ETC, this island of closely related sequences does indeed have gaps
between its own island cluster and all other sequences in the average
gene pool. These multi-character gaps may only be a handful of changes
wide and are therefore theoretically crossable in evolutionary time
frames, but they are still there.

> That argument *is* a strawman argument. It is a
> mathematical fantasy that no evolutionary model even considers.

You are arguing against a strawman version of my position of your own
creation. My real model is very much in line with how evolution is
supposed to work.

> > <snip rest of strawman>
>
> I am most certainly NOT making a strawman of your argument.

Yes, you are.

> Your
> argument, the math that you present, *claims* that the only way to
> evolve cytochrome c is to start with a sequence that has NONE of the 80
> "fairly specified residues" and proceeds, by a neutral random walk
> through sequence space that has NO function, until it accidently lands
> on the rare island of cytochrome c function.

Not true. My model actually predicts that at lower levels of
functional complexity, especially below levels involving a minimum of
only a few hundred fairly specified residues, that many if not most of
the required minimum will already exist pre-formed in a given gene
pool. Out of the 80 required minimum 75 may already exist to the
degree of specificity needed, leaving a gap of only 5. Such a gap is
indeed crossable in evolutionary time frames.

However, when you move up to those functions that require a few
thousand fairly specified residues, the gaps grow so that the average
distance to the next closest beneficial island cluster is no longer 5,
but 50. When the required multi-character difference is only 50 out of
thousands, such a small percentage difference may not seem like much at
all. It seems like such a small gap; so small as to be insignificant.
But, it is actually devastating to evolutionary progress, requiring
trillions upon trillions of years of average time for even a huge
genetic pool to cross.

> Either you don't
> understand the math you are using (that is, you are presenting an
> argument without even understanding what you are saying) or you are not
> being truthful. Being generous, I assume your ignorance over your
> perfidity.

Thanks ; )

> And MY point is that such a *hypothetical* mathematical argument is
> irrelevant to the way *real* evolution works. It is nothing but an
> abstract mathematical exercise signifying nothing of importance or
> relevance to real evolutionary pathways. I fully agree that *if*
> evolution worked the way *you* claim it does, in *your* mathematical
> descriptions, evolution would be next to impossible, and that includes
> the evolution of cytochrome c. But your model is not the way that
> evolution has ever been proposed to act. Your model is a strawman. It
> is most certainly not descent with modification.

Evolution has indeed been proposed to act using random mutation and
function based selection over time. Evolution is supposed to change
what is already available with tiny modifications over time to produced
novel functions at higher and higher levels of functional complexity.
That is how evolution is supposed to work. The problem with this
mindless model is that at higher levels the neutral gaps do indeed
outpace the ability of such mindless mechanisms to keep up. This
stalling out of evolutionary progress is demonstrable in real life
experiments. It's a fact.

> Cytochrome c 'function' did not arise by *your* proposed mechanism.

If CC's function did evolve, it most certainly evolved via your
proposed mechanism -which is the same as my proposed mechanism for how
evolution is supposed to work. We are proposing the same mechanism
Howard. We really are. You're painting of my position is nothing more
than a strawman - a caricature that isn't real. The problem is that
this mechanism of yours, your own mechanism mind you, depends upon
closely spaced steppingstones all the way up the ladder. It really
does. These steppingstone pathways just aren't that close anymore as
you move up the ladder. They really do get farther and farther apart
so that the random walk times required to get from one steppingstone
island to the next do indeed move into the trillions upon trillions of
years beyond the few hundred fairly specified residue minimum.

> No
> one thinks it did. Cytochrome c probably arose by the mechanism I
> described, and arose from a molecule that already had the heme-binding
> moiety, already had the cytochrome c1- affinity, may have even already
> had the cytochrome a affinity. And the mutation (as in single
> mutational event; in this case a partial duplication) may have itself
> produced a molecule with the right redox potential (not the *optimal*
> potential of present cytochrome c, but a selectable and useful redox
> potential). In short, I am telling you that your argument against the
> model you propose as the way proteins evolve is correct. But it is
> irrelevant because no one thinks that is the way evolution happened. It
> is, IOW, a strawman argument. It is an argument that you, indeed, have
> a counter to; if evolution worked or had to work that way, it would be
> impossible. But evolution is not (and never was) thought to work that
> way.

The way you propose evolution to "work" only works if the
steppingstones never get very far apart as you go up the ladder. But,
they do start moving apart. The average random walk times do start to
increase, exponentially, beyond very low levels of minimum size and/or
specificity requirements. That's a big problem for *your* ToE.

Sean Pitman
www.DetectingDesign.com

.

Relevant Pages

  • Re: Sean Pitman: definitions wanted
    ... but are claiming and asserting without evidence that this ... gaps) is the only possible mechanism for evolution. ... *regardless* of the size of the sequence or the number of amino acids ...
    (talk.origins)
  • Re: Of Mice and Straw Men
    ... >>> You obviously don't get my point about cytochrome C at all. ... But you claim that it evolved from a random sequence by a random ... evolution works the way that you propose, ... with any sequence that doesn't meet your mathematical fantasy of large ...
    (talk.origins)
  • Re: The Starting Point Problem - for Howard Hershey
    ... sequence space with particular kinds of attached functions. ... I have never said that cytochrome c *function* can be ... Take the lactase function, for example. ... because evolution has no way of sampling total sequence space. ...
    (talk.origins)
  • Re: Most valuable poster
    ... nylonase or lactase evolution examples. ... residues), you have the ability, so you say, to tell us *exactly* what ... the average gap size is based on the size of the end product. ... recognizable sequence homologs or recognizable intermediate functions. ...
    (talk.origins)
  • Re: Most valuable poster
    ... nylonase or lactase evolution examples. ... sequence within an entire genome, one or two, will be within striking ... within striking distance of very low-level functions. ... The gap distance is always much smaller than the size of the next ...
    (talk.origins)
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