Re: PONG (was Re: Thermodynamics, Biological Evolution,andDisorder)

[EMAIL PROTECTED] (charlie wagner) wrote in message news:<[EMAIL PROTECTED]>...
> [EMAIL PROTECTED] (Larry Moran) wrote in message news:<[EMAIL PROTECTED]>...
> > On Wed, 5 Nov 2003 00:27:40 +0000 (UTC), 
> > littleblondgirl <[EMAIL PROTECTED]> wrote:
> > 
> > [snip]
> > 
> > > Those are pathetic examples, if they can be called examples at all.
> > > Did mutation and natural selection create the Krebs Cycle? The immune
> > > response system? The syrinx of the bird? The marvelous adaptation of
> > > structure and process that allows us to hear and see? It has no such
> > > power. If it did, science would have demonstrated it long ago.
> > 
> > I don't know much about the syrinx of the bird. The evolution of eyes
> > and ears have been covered numerous times so I'll leave it to others
> > to spew out the references.
> 
> It has never been demonstrated that variation and selection has the
> power to create the complex structures and biochemical processes found
> in eyes and ears.

One could argue that it has never been demonstrated that *anything*
has the power to have created the complex structures and processes you
describe.  That does not make it reasonable to conclude that they have
never existed, nor that interpreting the available evidence (such as
the fact that the structures actually exist) to mean that they have is
indicative of some sort of "bias"; however, that is exactly the logic
you are using here.

Evidence that something has actually happened is a fortiori evidence
that it is possible.  Hence it is proper to ask:  If these structures
*had* evolved via mutation and selection, what sort of evidence would
we expect to find in nature that we might not expect to find if they
hadn't?  That is what Larry's exposition below is intended to
demonstrate, and I think he does pretty good job of showing that we
see exactly those distinctive traces we would expect common descent
via gradual modification to leave behind, and that no other available
proposal would anticipate.

> 
>  The evolution of the immune system has also
> > been described by many experts in previous posts. Lots of things that
> > Charlie doesn't know about have been demonstrated by science.
> 
> And lots of things that you claim have been demonstrated by science
> actually have not. Unless you mean that someone made up a story to
> explain it. Unfortunately, just-so stories are not science.

But hypotheses that generate testable predictions are.  I know you
have an eccentric concept of scientific methodology, but I do not see
how you can deny this.  At any rate, any account of a specific
sequence events (such as the evolution of the vertebrate immune
system) is going to be a "story", and that is exactly what you -I
mean, littleblondgirl- asked for, so I fail to see why you would
complain about getting exactly what you requested.

> 
> > 
> > I'd like to address the evolution of the Krebs Cycle (Citric Acid Cycle).
> > As it happens, I've just finished writing a brief description of this
> > for introductory biochemistry students. Charlie won't accept the evidence
> > for evolution of the Citric Acid Cycle because it comes from a biochemist
> > and he doesn't trust experts. Nevertheless, I include it for the luckers
> > just to show that we have a pretty good idea of how this pathway evolved.
> 
> Not true. I rely on experts to inform me on subjects that I don't know
> about. However, I never accept what a so-called "expert" says just
> because he's an expert. I expect that the person will give me a
> reasonable explanation, backed by empirical data that makes sense. I
> take very little on "authority", but I'm quite willing to change my
> mind if meaningful arguments are offered and supporting data provided.
> You're saying here that you want me to accept your hypothesis because
> you're an "expert" yet you refuse to take any time to explain it.
> 
> > 
> > There's some jargon, and a thorough understanding requires a knowledge of
> > some basic biochemistry. Charlie will think this is obfuscation. He 
> > will object to what I've written because he can't understand every 
> > sentence and won't make the attempt to learn the basics. I have no 
> > intention of trying to explain it to him since past experience indicates
> > that he is unteachable. I'd be happy to explain it to others if they
> > want more information.
> 
> Anything you can write, I can understand. You don't seem to get that.
> If I reject what you say, it's because you have failed to adequately
> demonstrate it and/or explain it. I am not "unteachable" but I am
> "unindoctrinatable", unlike most of your students.
> 
> > 
> > 
> >      13.9 Evolution of the Citric Acid Cycle
> > 
> >      The reactions of the citric acid cycle were first discovered in 
> >      mammals and many of the key enzymes were purified from liver 
> >      extracts. As we have seen, the citric acid cycle can be viewed as 
> >      the end stage of glycolysis where it results in the oxidation of 
> >      acetyl CoA produced as one of the products of glycolysis. However, 
> >      there are many organisms that do not encounter glucose as a major 
> >      carbon source and the production of ATP equivalents via glycolysis 
> >      and the citric acid cycle may not be a major source of metabolic 
> >      energy in such species.
> 
> OK
> 
> > 
> >      We need to examine the function of the citric acid cycle enzymes 
> >      in bacteria in order to understand their role in simple single-celled 
> >      organisms. These roles might allow us to deduce the pathways that 
> >      could have existed in the primitive cells that eventually gave rise 
> >      to complex eukaryotes. Fortunately, the sequences of over one hundred 
> >      prokaryotic genomes are now available as a result of the huge 
> >      technological advances in recombinant DNA technology and DNA 
> >      sequencing methods. We can now examine the complete complement of 
> >      metabolic enzymes in many diverse species of bacteria and ask whether 
> >      they possess the pathways that we have discussed in this chapter. 
> >      These analyses are greatly aided by developments in the fields of 
> >      comparative genomics, molecular evolution, and bioinformatics.
> 
> You're starting out with a pre-existing bias. You're assuming that
> primitive cells "gave rise" to complex eukaryotes. 

The challenge was to demonstrate how variation and selection might
give rise to complex structures and processes that were not there
before.  The question necessarily presupposes that the classical Krebs
cycle might have arisen gradually from simpler precursors that were
already in place, and imposes the task of demonstrating how this is
feasible.  Larry Moran is simply entertaining the premise of
littleblondgirl's question; if you have a problem with it, I suggest
you take it up with littleblondgirl.


> There's simply no
> justification for that assumption and if you start off with that
> premise, you're bound to go astray. 

The justification is that it is necessarily a premise of any question
about how a particular structure could have evolved that the organisms
that have it today descended from more primitive ones that initially
lacked such structures.  You shouldn't complain so much when people
actually answer the question you asked.

> You believe that this happened,
> therefore you believe that the pathways exist. So when you see
> similarities, you immediately identify that as a pathway of evolution.

That eukaryotes are descended from prokaryotes is not some sort of ad
hoc hypothesis Larry made up to construct his Krebs cycle lineage.  It
is a conclusion long since reached by many other independent lines of
evidence.  That he is able to find simpler versions of the Krebs cycle
exactly where this independently-derived conclusion about eukaryote
lineage suggests he should find them is a major point in favor of his
argument.

I am out of time.  I will answer the rest of this post later.

Von Smith
Fortuna nimis dat multis, satis nulli.