Re: The Starting Point Problem - for Howard Hershey

Perplexed in Peoria wrote:
"Seanpit" <seanpitnospam@xxxxxxxxxxxxxxxxxxxxxxxxxxx> wrote in message news:1157907339.445722.3970@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

Perplexed in Peoria wrote:


How could Nature see that it was good even before it had a selectable
function to be passed on over generations? Nature can't see anything
at all unless there is some functional aspect that provides a
reproductive advantage - right? So, where does Nature really come into
the picture here?

I believe that natural selection (i.e. reproduction with heritable variation)
was in existence before genes or ribozymes. The genetic medium was
autocatalytic sets, and a heme-like porphyrin molecule was an important
member of those sets. It bound iron ions - perhaps for cross-membrane
transport or perhaps for some role as a redox cofactor. But it had
some kind of a 'job' contributing to the growth and reproduction of the
organism, and hence Nature is justified in expressing a value judgement.

Sometime later, RNA and ribozymes were developed, and then natural selection
moved into a higher gear. Later yet ribosomes and proteins appeared, and
NS was in the fast lane.

Nice story - Do you have any examples of this sort of thing happening
today? - even one where natural selection is in play without DNA, RNA,
or ribozymes? Where does the notion of the "fittest" come into play
here?

Come on now . . . this is nothing more than pure fantasy. It just
doesn't happen in real life.

What is 'real life'? Things we have witnessed?

Yes . . .

Sean, creation does
not happen in 'real life'.

Creation happens all the time in real life. Don't you create things?
Aren't you capable of designing stuff? - to include higher level
systems of function? Scientists are even capable of manipulating the
very codes of life to produce novel functional changes.

Creation, to include the equivalent creation of higher-level system of
function, especially when it comes to computer programming, happens all
the time. Nothing even remotely close to the scenario you describe for
the evolution without DNA, RNA, or ribozymes, happens at all. Again,
can you even imagine how one system would be more reproductively "fit"
than other in such a scenario?

Abiogenesis does not happen in 'real life'.

You can say that again . . .

If you limit the things you are willing to believe to things that
happen in real life, then you have to believe that things were always
pretty much as they are today. No evidence of a beginning, no prospect
of an end. But you and I both know that that is untenable, both
philosophically and based on the evidence. At least one or the other,
creation or abiogenesis must have happened. Now you have (at least
some) serious interlocutors here who are not gratuitously poking fun
at the more difficult-to-believe parts of creation scenarios. You
might reciprocate the courtesy.

You have to have some basis for your notions here. There simply are
none that I can tell aside from wishful and very imaginative thinking.
Your notions here certainly don't qualify as testable/falsifiable
scientific hypotheses.

My notions of ID in this case is based on the lack of any viable
mechanistic evidence to the contrary. Your story telling certainly
doesn't qualify as having any explanatory value as to how any sort of
mechanism could have actually produced what you claim was produced by a
mindless evolutionary process.

But, as I think hersheyhv also points out, what we are interested in
here is how modern cytochrome c might have come into existence. I claim
that it evolved from earlier, less constrained precursors which did
not perform all of the modern functions.

Every functional system has its own minimum constraints.

I can agree to that.

Well, you're farther along than most in this forum already then.

Regardless of
what you start with, the function of cytochrome c, as a useful part of
the electron transport chain, cannot be realized at all until this
minimum is in place.

I can even buy that, if you emphasize that we are talking about *the*
function of *cytochrome c* and not just any function of a cytochrome
precursor.

That's exactly what I'm talking about.

The odds that your precursor steppingstone
starting point will be within one or two residue changes away from the
cytochrome c minimum just aren't very good - and these odds become
exponentially less good when you start dealing with higher and higher
level functions.

Ah yes! "Within one or two residue changes".

Darwin suggested (at least) two ideas. One is the basic idea of natural
selection - reproduction + variation leads to adaptation. The second
idea was about the nature of the available variation. Darwin insisted
that it must be 'gradual' or 'gradualist'. Today, with modern genetics,
we interpret this second point as meaning change by only one or two
residue changes at a time.

Darwin had some good epistemological and pedagogic reasons for insisting
upon gradualism. The most important was that it placed the causality
with the selection, rather than with the mutation. And indeed, scientific
Darwin critics, from Bateson to Goldschmidt to Gould, have mostly deviated
from Darwin by attacking gradualism (the second idea) rather than by
attacking NS (the first idea).

In a sense, your criticisms can be seen as a variant of scientific attacks
on Darwin's second idea. You claim that complex functionality cannot
arise gradually - that it can only arise by large saltational jumps and
that those jumps are themselves evidence of creation events.

Yes. At higher and higher levels of minimum size and specificity
requirements, novel functions can only be reached by linearly
increasing numbers of specific "jumps" from what already exists. If
these jumps are randomly done, the time involved to achieve the proper
series of jumps grows exponentially.

Well, taking your own psychology as a datum, we can see that Darwin was
right to insist that only a gradualist view of mutation could result
in a totally convincing account of naturalistic evolution. Darwin was
completely correct on the epistemological and pedagogic importance of
gradualism. However, I believe, he was unfortunately incorrect on the
facts.

Really now?! This should be good . . .

We now know that genetic changes of both large and small importance
are happening naturally all the time.

Yep . . .

The small ones happen often enough
so that in a large population they can be considered inevitable, even
in a short period of time.

Sure . . .

But the larger ones, and especially the large
ones that actually 'create' something new and advantageous, are much
more rare.

The problem here is that you don't need "large" mutations involving
many residue changes to achieve large functional changes. Large
functional changes can be achieved with a single point mutation. The
problem here is that the odds against a single point mutation landing
on a novel beneficial island are exponentially reduced with each step
up the ladder of minimum functional complexity.

Now you need both a large population and geological amounts
of time before such mutations become likely, and any specific such mutation
practically never becomes inevitable.

Your problem is that the time required to achieve higher level
functions, functions that require at least a few thousand fairly
specified residues to work at all, is in the trillions upon trillions
of years - on average.

I think you already realize this, but as I try to reconstruct your thinking
from your math, it seems to me that your main failing is in not realizing
that mutations happen on all scales - from the single base to large-scale
insertions and deletions.

And your main failing here is in thinking that multicharacter mutations
are more likely than singe point mutations at finding a novel
beneficial island sequence in sequence space. Mathematically, the odds
are exactly the same. Random walk using small steps is just as likely
to find target sequences in a search space as a random walk that uses
large steps.

And that while the micro-mutations and the
deletions may well be 'random', the large sequence insertions are anything
but random. The inserted sequences frequently already contain bits of
functionality - they fold int alpha helices or beta sheets; they bind
specifically to some other protein sequence within the organism; the contain
the core of some catalytic domain. It is still the case that most such
'macro-mutations' are neutral or harmful, but they turn out to be beneficial
much more frequently than your Yockey-derived estimates suggest.

Really? Do you have even one example of a large mutation like this
producing a novel function that requires at least 1000 fairly specified
residues?

I'm telling you, it just doesn't happen - small or large multicharacter
mutations. Insertions and deletions are most certainly random. That is
why the vast majority of them are either neutral or detrimental - just
like point mutations. Occasionally a multicharacter mutation may end
up producing a truly new and beneficial function, as in the case of
nylonase evolution, but this new function never requires more than a
few hundred fairly specified residues.

Look into it. You'll see that this is true.

Consider the following fictitious conversation between a creationist
and an evolutionist.

C: I don't see how you can believe the human heart evolved. Any simpler
heart just wouldn't pump enough blood for a large ape.

E: But the heart evolved long before the apes. It happened back in
the early days of the vertebrates, in the late Cambrian.

C: But you can't call that a *human* heart. I'm asking how the *human*
heart evolved.

I think that you, as a smart anti-evolutionist, realize that the creationist
above is just being silly. So, I don't see why you don't realize that
you are being equally silly in insisting that unless a protein has all
of the modern cytochrome c functionality, it is just not the real
cytochrome c.

Because, you really haven't achieved the function in question at all -
not even a little bit with your precursor function.

I have achieved little bits of the function in question. I have achieved
heme-wrapping; and later, binding to one redox enzyme; and a little
later, binding to a second redox enzyme.

The problem here is that each of these steppingstone functions, if
actually beneficial to the organism, are separated from each other by a
fair number of non-beneficial residue differences. You really haven't
demonstrated the evolution of any of the steps at all here - much less
the final functional system.

The same thing is true of flagellar evolution scenarios. I'm not
saying that just the final flagellar motility function is impossible.
I'm saying that every step in the proposed pathway of flagellar
motility is impossible. Why? Because each and every one of the
proposed steppingstones is many dozens of residue changes away from the
next closest steppingstone in the proposed pathway. Such gaps cannot
be crossed in trillions of years of time for each and every step in the
pathway at these levels of functional complexity.

You, for some reason, keep
insisting that until I achieve *all* of the functional elements, I
have achieved nothing. Just not so. I am constructing an argument
for how the *machinery* for cytochrome c functionality could have
evolved, even though the full-scale functionality (that you insist on)
arose later as a kind of saltation.

Again, I've never said that you need to achieve all of the functional
elements to have something. There are most certainly subfunctional
elements that would in fact be of some functional benefit. The problem
is that the distance between the closest subfunctional element and a
function like flagellar motility represents almost an eternity in
average time. The cytoc function, being on a much lower level of
functional complexity, would be much closer to it's closest
steppingstone functional system - and therefore, though difficult to
evolve, would be exponentially more evolvable than any step in the
flagellar evolution pathway.

See the difference?

It's just like the
lactase function example I keep bringing up for Howard. The lactase
function cannot be realized, even a little bit, until its minimum of
380 fairly specified residues are in place. Sure, there may be a very
similar sequence, like ebg, that has all but one residue in its proper
place. However, until all are in place to this minimum degree, the
lactase function just won't be realized at all to a selectable
advantage.

Consider the following fictitious discussion:

E: We have several examples of evolution in action - such as the
evolution of improved antibody binding to specific foreign antigens.

C: But, that's not the evolution of a new type of function. That's
simply the refinement of a pre-established function.

That's what you are trying to do here. You are trying to argue that
evolution is nothing more than refining a function that is already
there. That simply isn't true because some functions aren't there at
all until a fairly large minimum sequence size and specificity is in
place.

In
other words, without the electron transport chain in place, in the
beginning, the function of the cytochrome c protein, in this capacity,
doesn't exist. The same protein may work in a different capacity, but
the cytochrome c function, in this capacity, isn't possible.

You refer to '*the* electron transport chain'. But electron transport
chains have also evolved. They have gotten longer, gotten shorter,
duplicated and diverged before rejoining, and done lots of other odd
stuff. You can draw branching phylogenetic trees of electron transport
chains. The one they taught you in pre-med biochemistry involving
mitochondria and starting with the citric acid cycle is not the only
electron transport chain used in the biosphere today. Various bacteria
have a wide variety of electron transport chains. But guess what!
All of these chains seem to have a common ancestor - one which involved
heme-like porphyrins for sure, almost from the beginning, and cytochrome
proteins at a very early stage.

Yes, this is the story you read about in scientific journals. However,
not one step in this story of yours is supported by anything other than
sequence comparisons. There simply are no observable demonstrations of
evolution happening at this level of functional complexity - not one
example.

You mean evolution at this level in the lab of a scientist with a 40 year
working lifetime and a 5 year grant? You really insist that this has
to happen before you will believe? Would you consider someone who insists
on witnessing an act of creation-from-nothingness before they will believe
in God as being simply 'reasonably cautious'?

We aren't talking about changing a dog into a cat or anything like that
here. We are talking about relatively simple biosystem functions
involving no more than a few thousand residues at minimum. Why should
such a relatively simple system take so long to evolve? Hmmmm? Why
is it so easy to evolve a system that requires only a few specified
residues in real time, but exponentially harder and harder to evolve
systems that require a minimum of more and more residues?

Sean Pitman
www.DetectingDesign.com

.