The protein takeover -- a challenge for abiogenesis

[pnyikos]

It has been well over half a century since the Urey-Miller experiment
which produced amino acids of all sorts starting with what they
believed to be a simulation of early earth conditions. It has also
been very close to half a century since the genetic code for
translation of proteins was decoded. And yet, as far as I know:

1. No nucleotide has ever been synthesized by simulating pre-earth
conditions and

2. We still lack a detailed scenario of how the various polypeptides
and strings of nucleotides MIGHT have "evolved" to produce the first
prokaryote.

In re 1: do not confuse purines and pyrimidines [which *have* been
produced under prebiotic conditions] with nucleotides.

In one of the later chapters in the much-maligned _Darwin's Black
Box_, Behe goes through the way one nucleotide is synthesized in
living cells starting with a purine and a number of other molecules.
It is quite complicated.

in re 2: Although there has been a lot of speculation, including
detailed scenarios for hypothetical bits of the grand march towards
the first prokaryotes, I have never seen even a speculative detailed
account of the last phase in the process.

The last phase starts with a "RNA world" in which most of the non-
protein players are already in place: DNA, ribosomes lacking
polypeptides, mRNA, aminoacyl-tRNA, and various ribozymes doing what
is nowadays done with protein enzymes. Especially crucial are
ribozymes for DNA replication, transcription, and reverse
transcription.

It may not be too difficult, given this apparatus, for proto-cells to
crank out some simple structural and "helper" proteins using a
translation scheme with a genetic code approximating the present one.

But how do we get to the "protein takeover" wherein ribosomes are
augmented with polypeptides, and virtually all other ribozymes are
replaced by sophisticated and very high fidelity protein enzymes?

A low fidelity enzyme could be worse than useless, hampering the
action of the ribozyme. So what could be a path that leads to the
immensely thorough and successful protein takeover whose results we
see today?

Never mind if a speculative path is the one that was actually taken;
that we can leave for future centuries of research.

[John Harshman]

pnyikos wrote:

> But how do we get to the "protein takeover" wherein ribosomes are
> augmented with polypeptides, and virtually all other ribozymes are
> replaced by sophisticated and very high fidelity protein enzymes?
>
> A low fidelity enzyme could be worse than useless, hampering the
> action of the ribozyme. So what could be a path that leads to the
> immensely thorough and successful protein takeover whose results we
> see today?

Here's a simple hypothesis: what if the proteins originally started out
as ribozyme-helpers, stabilizing them and increasing their specificity?
And so we get ribozyme-protein complexes. Then, gradually, the protein
could have taken on more of the function and the ribozyme less of the
function in the complex, until finally the ribozyme is redundant.

> Never mind if a speculative path is the one that was actually taken;
> that we can leave for future centuries of research.

So why is this important? If we can't think of a plausible scenario,
does that mean that the origin of life is improbable? I can't think of
scenario for the evolution of many things. Are those things all
improbable, or is it just a failure of imagination?

[pnyikos]

On Mar 19, 1:45 pm, John Harshman <jharsh...@pacbell.net> wrote:
> pnyikos wrote:
> > But how do we get to the "protein takeover" wherein ribosomes are
> > augmented with polypeptides, and virtually all other ribozymes are
> > replaced by sophisticated and very high fidelity protein enzymes?
>
> > A low fidelity enzyme could be worse than useless, hampering the
> > action of the ribozyme.  So what could be a path that leads to the
> > immensely thorough and successful protein takeover whose results we
> > see today?
>
> Here's a simple hypothesis: what if the proteins originally started out
> as ribozyme-helpers, stabilizing them and increasing their specificity?

Can you find a published article, or even a website, which goes into
detail about this hypothesis?

Your hypothesis is far from simple: how does a protein get specific
enough to *enhance* a ribozyme's specificity?

Do even the polypeptides in ribosomes do that? IIRC you once told me
that ribosomes are pretty dumb about identifying the right tRNA to fit
to a codon: they wait passively until one settles for a longer than
average amount of time on the next codon, and then they go to work
adding its amino acid to the growing polypeptide chain.

So where is there any specificity here?

> And so we get ribozyme-protein complexes. Then, gradually, the protein
> could have taken on more of the function and the ribozyme less of the
> function in the complex, until finally the ribozyme is redundant.

That might happen in some cases, but there is a big difference between
enhancing specificity (or stabilizing an enzyme), and taking over the
whole function of an enzyme; the polypeptide chain involved in the
main function might have no resemblance to the one that the "helper"
uses for its functions.

> > Never mind if a speculative path is the one that was actually taken;
> > that we can leave for future centuries of research.
>
> So why is this important?

As to the first clause, it is most unreasonable to expect researchers,
no matter how good, to figure out what actually happened when all
direct data about it is long gone. That was something I kept telling
Julie Thomas, an otherwise superb arguer against homegrown
abiogenesis.

> If we can't think of a plausible scenario,
> does that mean that the origin of life is improbable?

With my directed panspermia hypotheses competing, I think it would
give my favorite "Intelligent Design" hypothesis preference over
"Mother Earth Did It."

This is the hypothesis that an intelligent life form evolved whose
cells were as described in what I said was the starting point for "the
last phase" (the protein takeover), and designed a protein-enzyme-
based life which it then distributed far and wide, one of its targets
being earth.

Quoting from the post to which you are replying:

The last phase starts with a "RNA world" in which most of the non-
protein players are already in place: DNA, ribosomes lacking
polypeptides, mRNA, aminoacyl-tRNA, and various ribozymes doing what
is nowadays done with protein enzymes. Especially crucial are
ribozymes for DNA replication, transcription, and reverse
transcription.

It may not be too difficult, given this apparatus, for proto-cells to
crank out some simple structural and "helper" proteins using a
translation scheme with a genetic code approximating the present one.

========== end of excerpt

Proto-cells like this would be like the actual cells of this
hypothesized intelligent life form.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://www.math.sc.edu/~nyikos/
nyikos @ math.sc.edu

[Richard Norman]

I really don't see how directed panspermia solves anything. If the
extraterrestrial source of our life arose through natural chemical
processes on some distance site, that just multiplies the time
available by about a factor of three, from the time of the big bang
and it just puts the location of the original abiogenesis somewhere
else. A solar system site is terribly unlikely in the time frame and
a site outside the solar system has no shred of evidence to support
such an interaction. On the other hand, if the source is some
extraterrestrial intelligence you have just substituted "God did it"
with "The little green men that I prefer not to call God did it" and
there is still no shred of evidence to support such a notion.

[John Harshman]

pnyikos wrote:
> On Mar 19, 1:45 pm, John Harshman <jharsh...@pacbell.net> wrote:
>> pnyikos wrote:
>>> But how do we get to the "protein takeover" wherein ribosomes are
>>> augmented with polypeptides, and virtually all other ribozymes are
>>> replaced by sophisticated and very high fidelity protein enzymes?
>>> A low fidelity enzyme could be worse than useless, hampering the
>>> action of the ribozyme. So what could be a path that leads to the
>>> immensely thorough and successful protein takeover whose results we
>>> see today?
>> Here's a simple hypothesis: what if the proteins originally started out
>> as ribozyme-helpers, stabilizing them and increasing their specificity?
>
> Can you find a published article, or even a website, which goes into
> detail about this hypothesis?

I don't know. I haven't tried. You asked for a hypothesis, not a guide
to the scientific literature.

> Your hypothesis is far from simple: how does a protein get specific
> enough to *enhance* a ribozyme's specificity?

Mutation and selection?

> Do even the polypeptides in ribosomes do that?

What do you mean by "even"? And no, as far as I know the specificity is
all in the mRNA.

> IIRC you once told me
> that ribosomes are pretty dumb about identifying the right tRNA to fit
> to a codon: they wait passively until one settles for a longer than
> average amount of time on the next codon, and then they go to work
> adding its amino acid to the growing polypeptide chain.
>
> So where is there any specificity here?

It's highly specific. Whatever do you imagine specificity is? It's just
better binding to what you want than to what you don't want. This is
exactly what ribosomes do.

>> And so we get ribozyme-protein complexes. Then, gradually, the protein
>> could have taken on more of the function and the ribozyme less of the
>> function in the complex, until finally the ribozyme is redundant.
>
> That might happen in some cases, but there is a big difference between
> enhancing specificity (or stabilizing an enzyme), and taking over the
> whole function of an enzyme; the polypeptide chain involved in the
> main function might have no resemblance to the one that the "helper"
> uses for its functions.

It might, or it might not. The question is whether my scenario is
plausible. You have presented cases in which it wouldn't happen. But all
we need are cases in which it would.

>>> Never mind if a speculative path is the one that was actually taken;
>>> that we can leave for future centuries of research.
>> So why is this important?
>
> As to the first clause, it is most unreasonable to expect researchers,
> no matter how good, to figure out what actually happened when all
> direct data about it is long gone. That was something I kept telling
> Julie Thomas, an otherwise superb arguer against homegrown
> abiogenesis.

I had no interest in the first clause, or the sentence at all, for that
matter. I was asking about the entire subject of your post.

>> If we can't think of a plausible scenario,
>> does that mean that the origin of life is improbable?
>
> With my directed panspermia hypotheses competing, I think it would
> give my favorite "Intelligent Design" hypothesis preference over
> "Mother Earth Did It."

Only if "we don't know the mechanism" translates into "it's unlikely to
have happened". Do you think it does?

> This is the hypothesis that an intelligent life form evolved whose
> cells were as described in what I said was the starting point for "the
> last phase" (the protein takeover), and designed a protein-enzyme-
> based life which it then distributed far and wide, one of its targets
> being earth.
>
> Quoting from the post to which you are replying:
>
> The last phase starts with a "RNA world" in which most of the non-
> protein players are already in place: DNA, ribosomes lacking
> polypeptides, mRNA, aminoacyl-tRNA, and various ribozymes doing what
> is nowadays done with protein enzymes. Especially crucial are
> ribozymes for DNA replication, transcription, and reverse
> transcription.
>
> It may not be too difficult, given this apparatus, for proto-cells to
> crank out some simple structural and "helper" proteins using a
> translation scheme with a genetic code approximating the present one.
> ========== end of excerpt
>
> Proto-cells like this would be like the actual cells of this
> hypothesized intelligent life form.

You're just making up stories and supposing that the ones you like are
more probable than the ones you don't like. That doesn't strike me as
useful.

[pnyikos]

It might solve the question of how the protein takeover can take place
in more than one place in the galaxy (maybe the universe, depending on
the odds). I'm referring to the odds against a protein takeover
resulting in "life as we know it".

Sufficiently intelligent creatures can make all kinds of things that
cannot evolve naturally, like (to use Hoyle's famous example) a Boeing
747 from the ingredients in a junkyard.

> If the
> extraterrestrial source of our life arose through natural chemical
> processes on some distance site, that just multiplies the time
> available by about a factor of three, from the time of the big bang
> and it just puts the location of the original abiogenesis somewhere
> else.

But it changes the kind of abiogenesis that takes place, to something
demonstrably simpler.

Of course, there is a trade-off: the resulting "life as we don't
exactly know it" may have a harder time evolving into an intelligent
life form than the first prokaryotes did. But then again, maybe not.

Back in the late 1990's, a short-time talk.origins participant with
the unusual name of Wolfram Dachs asked me just how RNA could
substitute for polypeptides in the lining of pores of cell membranes.
When I couldn't give him a good answer, he lost interest and quit.

That got me to thinking: RNA world could incorporate some simple,
repetitive polypeptides without the odds being too long against it,
nothing like the odds against coming up with a highly specific protein
enzyme. Unfortunately it took Wolfram's disappearance to galvanize me
to this realization, and no one else seemed to be interested enough in
this RNA world hypothesis.

> A solar system site is terribly unlikely in the time frame

Of course. My pleasure over seeing directed panspermia mentioned in
an SF film about an expedition to Mars ("They seeded earth" was said
close to the end) was tempered by the great unlikelihood of an
intelligent species evolving on Mars in the short time frame.

> and
> a site outside the solar system has no shred of evidence to support
> such an interaction.

...except for reasoning such as that already used by Crick and Orgel
in the article where they advanced the hypothesis of directed
panspermia:

Icarus 19 (1973) 341-346:
http://profiles.nlm.nih.gov/ps/access/SCBCCP.pdf

>  On the other hand, if the source is some
> extraterrestrial intelligence you have just substituted "God did it"
> with "The little green men that I prefer not to call God did it"

I certainly wouldn't dream of calling my hypothesized RNA-based
intelligent species "little green men," much less "God". After all,
it would be improper to try to put any physical descriptions of them
in the hypothesis.

Anyway, someone who likes to bring God into the picture might prefer
to do it right about where so-called "theistic evolutionists" [read:
neo-deistic evolutionists] bring God in: at the time (or somewhat
later) the first species with a technological potential arose.

The Christians among them have God acting as depicted in whatever part
of the Bible they want to take seriously. Similarly, they could
hypothesize God interacting with the RNA-based species.

I've mentioned this possibility to Ray Martinez, who calls himself a
Christian, but his C. S. Lewis-admiring blinders are too restrictive
for him to even countenance the possibility that God (or an Oyarsa, as
in Lewis's space trilogy) inspired some RNA-world scientists to spread
life throughout the galaxy, the way the human being Ransom was
inspired to intervene in Mars and Venus to save some intelligent
creatures in both places from disaster.

Peter Nyikos

[Alan Kleinman MD PhD]

The “RNA world” concept is not a physically realistic concept. Not
only is it extremely difficult to synthesize ribose without enzymes,
ribose has a very short half life and is unstable. It is nonsense to
think that there was an ocean of ribose for billions of years
simmering until life popped out. Read about the chemical behavior of
ribose in the following paper co-authored by Stanley Miller.

Rates of decomposition of ribose and other sugars: Implications for
chemical evolution http://www.pnas.org/content/92/18/8158.full.pdf

[Paul J Gans]

I'd leave the origin of life to the chemists. The problem is
ultra-hard, mainly because we do not know the conditions
prevailing on earth back when life began. We don't even know
*where* life began, though most feel that it was in water.

But what kind of water? There are a large number of possibilities.

Nevertheless, folks are working on the funadmental chemistry
involved. There is large activity in the synthesis of peptoids
(NOT a misspelling) which are compounds that lie somewhere between
proteins and more mundane polymers. See the rather ancient (2008)
video below:

http://www.youtube.com/watch?v=cUXKA_J13so

Other studies have led to the development of structures that show
chirality even though the molecules lack chiral centers. One such
paper is:

http://pubs.acs.org/doi/abs/10.1021/ja2028684

Here's the abstract:

"We report the isolation of N-aryl peptoid oligomers that adopt
chiral folds, despite the absence of chiral centers. Peptoid
monomers incorporating ortho-substituted N-aryl side chains
are identified that exhibit axial chirality. We observe significant
energy barriers to rotation about the stereogenic carbon-nitrogen
bond, allowing chromatographic purification of stable atropisomeric
forms. We study the atropisomerism of N-aryl peptoid oligomers by
computational modeling, NMR, X-ray crystallography, dynamic HPLC,
and circular dichroism. The results demonstrate a new approach to
promote the conformational ordering of this important class of
foldamer compounds."

Give them another decade and then lets see where we are:

Truth in Posting Notice: Two of my collegues, Bobby Arora
<http://chemistry.fas.nyu.edu/object/paramjitarora.html> and
and Kent Kirschenbaum. <http://www.nyu.edu/projects/kirshenbaum/>,
are working in these areas.
--
--- Paul J. Gans

[Bill]

Uh-Oh. I foresee thousands of posts about how biochemically and
metabolically incompetent evolutionists have produced terrible errors
in the treatment of diabetes.

[Prof Weird]

ONLY IN AQUEOUS SOLUTIONS.

When bound to common borate minerals, it is quite stable.

For instance, the standard, quite easy and abiotically possible way of
making ribose is heating formaldehyde and glycoaldehyde in an alkaline
solution. But this tends to produce a 'browning' reaction as free
radicals generate polymeric mixtures.

HOWEVER, do the reaction in the presence of common borate minerals,
NOT ONLY does the browning reaction not occur, the majority of the
carbon is in the form of pentoses like RIBOSE.

From "Borate minerals stabilize ribose", Ricardo A, Carrigan MA,
Olcott AN, Benner SA, Science (303), 9 Jan 2004, pg 196 !

It turns out that of all the pentose sugars created that way, RIBOSE
IS THE MOST STABLE :

"Theoretical study on the factors controlling the stability of the
borate complexes of ribose, arabinose, lyxose and xylose", Sponer Je,
Sumpter BG, Leszczynski J, Sponer J, Fuentes-Calbrera M, Chemistry
2008, 14(32):9990-8.

Would you care to start screaming your mantras now, or would you like
to pontificate a bit about how special you are first ?

> It is nonsense to
> think that there was an ocean of ribose for billions of years
> simmering until life popped out.

'Billions' of years would not be necessary, given that it seems life
arose within about half a million years after the Earth solidified.

And your 'alternative explanation' is what again ?

Oh, right : you REFUSE to state one ! You seem to ' think' that if
you can just bellow and whine about how 'irrational' evolution is
loudly enough often enough, it will magically go away, and your
unstated 'alternative' will replace it.

> Read about the chemical behavior of
> ribose in the following paper co-authored by Stanley Miller.
>
> Rates of decomposition of ribose and other sugars: Implications for

> chemical evolutionhttp://www.pnas.org/content/92/18/8158.full.pdf- Hide quoted text -
>
> - Show quoted text -

You really SHOULD try reading more up to date material, Dr Dr
Krackpot ! The research SHOWING that borate minerals stabilize ribose
was done less than 8 years ago.

A few more knees to the crotch of your 'argument' :

"Chiral-selective aminoacylation of an RNA minihelix", Tamura K,
Schimmel P, Science 305 (5688): 1253+, August 2004. Seems that not
only can an RNA minihelix load itself with an amino acid, IT IS
CHIROSELECTIVE. D-RNA preferentially loads with L-amino acids, while
S-RNA helixes load with D-amino acids (instead of 50/50, it ends up
75/25). Two problems solved at once !

"Synthesis of activated pyrimidine ribonucleotides in prebiotically
plausible conditions", Powner MW, Gerland B, Sutherland JD, Nature 460
(13 May 2009), 239-242.

It would appear that most people are NOT going for the '*** I ***
can't figure it out, therefore GOD/INTELLIGENT DESIGNER/HYPERADVANCED
ALIENS DIDIT !!1!1!11!1!!1!!' route ... !

[pnyikos]

On Mar 19, 8:52 pm, Prof Weird <pol...@msx.dept-med.pitt.edu> wrote:
> On Mar 19, 8:01 pm, Alan Kleinman MD PhD <klein...@sti.net> wrote:
> > On Mar 19, 8:57 am, pnyikos <nyik...@bellsouth.net> wrote:
>
> > > It has been well over half a century since the Urey-Miller experiment
> > > which produced amino acids of all sorts starting with what they
> > > believed to be a simulation of early earth conditions.  It has also
> > > been very close to half a century since the genetic code for
> > > translation of proteins was decoded.  And yet, as far as I know:

"Prof. Weird" does quite a number on Alan Kleinman, but he leaves the
following untouched:

> > > 1. No nucleotide has ever been synthesized by simulating pre-earth
> > > conditions and

And also this:

> > > 2. We still lack a detailed scenario of how the various polypeptides
> > > and strings of nucleotides  MIGHT have "evolved" to produce the first
> > > prokaryote.
>
> > > In re 1: do not confuse purines and pyrimidines [which *have* been
> > > produced under prebiotic conditions] with nucleotides.
>
> > > In one of the later chapters in the much-maligned _Darwin's Black
> > > Box_, Behe goes through the way one nucleotide is synthesized in
> > > living cells starting with a purine and a number of other molecules.
> > > It is quite complicated.

Ribose, which is the bone of contention below, is part of it, but only
part.

> > > in re 2: Although there has been a lot of speculation, including
> > > detailed scenarios for hypothetical bits of the grand march towards
> > > the first prokaryotes, I have never seen even a speculative detailed
> > > account of the last phase in the process.
>
> > > The last phase starts with a "RNA world" in which most of the non-
> > > protein players are already in place: DNA, ribosomes lacking
> > > polypeptides, mRNA, aminoacyl-tRNA, and various ribozymes doing what
> > > is nowadays done with protein enzymes.  Especially crucial are
> > > ribozymes for DNA replication, transcription, and reverse
> > > transcription.
>
> > The “RNA world” concept is not a physically realistic concept. Not
> > only is it extremely difficult to synthesize ribose without enzymes,
> > ribose has a very short half life and is unstable.
>
> ONLY IN AQUEOUS SOLUTIONS.
>
> When bound to common borate minerals, it is quite stable.

Also, if it is protected by cell membranes, which I assume exist by
the time the protein takeover is supposed to begin in earnest, it
should also be stable, no?

By the way, if anyone wants to argue that cell membranes should only
come *after* the protein takeover is well under way, I'd love to learn
how to keep all the different players mentioned above in harmony with
each other.

> For instance, the standard, quite easy and abiotically possible way of
> making ribose is heating formaldehyde and glycoaldehyde in an alkaline
> solution.  But this tends to produce a 'browning' reaction as free
> radicals generate polymeric mixtures.
>
> HOWEVER, do the reaction in the presence of common borate minerals,
> NOT ONLY does the browning reaction not occur, the majority of the
> carbon is in the form of pentoses like RIBOSE.

Fine, but there are still the phosphate parts of RNA to contend with.
See above.

> From "Borate minerals stabilize ribose", Ricardo A, Carrigan MA,
> Olcott AN, Benner SA, Science (303), 9 Jan 2004, pg 196 !
>
> It turns out that of all the pentose sugars created that way, RIBOSE
> IS THE MOST STABLE :
>
> "Theoretical study on the factors controlling the stability of the
> borate complexes of ribose, arabinose, lyxose and xylose", Sponer Je,
> Sumpter BG, Leszczynski J, Sponer J, Fuentes-Calbrera M, Chemistry
> 2008, 14(32):9990-8.
>
> Would you care to start screaming your mantras now, or would you like
> to pontificate a bit about how special you are first ?
>
> > It is nonsense to
> > think that there was an ocean of ribose for billions of years
> > simmering until life popped out.
>
> 'Billions' of years would not be necessary, given that it seems life
> arose within about half a million years after the Earth solidified.

You misspelled "billion". ["milliard" to Europeans]

> And your 'alternative explanation' is what again ?
>
> Oh, right : you REFUSE to state one !  You seem to ' think' that if
> you can just bellow and whine about how 'irrational' evolution is
> loudly enough often enough, it will magically go away, and your
> unstated 'alternative' will replace it.

The problem is, Kleinman is not talking about ordinary biological
evolution here, but of abiogenesis. That is because Kleinman is mainly
focused on the problems having to do with item 1. up there. That's OK
by me, even though I do hope the protein takeover problem continues to
be actively discussed here.

> > Read about the chemical behavior of
> > ribose in the following paper co-authored by Stanley Miller.
>
> > Rates of decomposition of ribose and other sugars: Implications for
> > chemical evolutionhttp://www.pnas.org/content/92/18/8158.full.pdf
>

> You really SHOULD try reading more up to date material, Dr Dr
> Krackpot !  The research SHOWING that borate minerals stabilize ribose
> was done less than 8 years ago.
>
> A few more knees to the crotch of your 'argument' :
>
> "Chiral-selective aminoacylation of an RNA minihelix", Tamura K,
> Schimmel P, Science 305 (5688): 1253+, August 2004.  Seems that not
> only can an RNA minihelix load itself with an amino acid, IT IS
> CHIROSELECTIVE.  D-RNA preferentially loads with L-amino acids, while
> S-RNA helixes load with D-amino acids (instead of 50/50, it ends up
> 75/25).  Two problems solved at once !

Gans seemed to be all gung-ho about chirality. I assume all that was
ancient history by the time the protein takeover started.

> "Synthesis of activated pyrimidine ribonucleotides in prebiotically
> plausible conditions", Powner MW, Gerland B, Sutherland JD, Nature 460
> (13 May 2009), 239-242.
>
> It would appear that most people are NOT going for the '*** I ***
> can't figure it out, therefore GOD/INTELLIGENT DESIGNER/HYPERADVANCED
> ALIENS DIDIT !!1!1!11!1!!1!!' route ...

I certainly don't think it would take more than one millennium for
humans to produce "pre-protein-takeover" RNA world cells ourselves, so
I don't think the aliens I hypothesize were "hyperadvanced" in any
significant way--they just had a bit more time than we have had so
far.

And no, I don't think humans will produce those ribozyme-rich, protein-
enzyme-poor cells by simulating prebiotic conditions all the way, but
by intelligently designing them. I also think that is how those
hypothesized panspermists did it, and with the extra incentive of a
nanotechnology for more efficiently producing just the polypeptides
they wanted.

[Steven L.]

"Prof Weird" <pol...@msx.dept-med.pitt.edu> wrote in message
news:3558bd45-b148-4aef...@fh22g2000vbb.googlegroups.com:

This is good stuff!
Very informative.

But admit it: You would never have posted it (and I would never have
had the chance to read about it)--if Dr. Kleinman hadn't provoked you
into writing it.


-- Steven L.

[marc.t...@wanadoo.fr]

> nyikos @ math.sc.edu- Masquer le texte des messages précédents -
>
> - Afficher le texte des messages précédents -- Masquer le texte des messages précédents -
>
> - Afficher le texte des messages précédents -- Masquer le texte des messages précédents -
>
> - Afficher le texte des messages précédents -

RNA world was not possible for the reasons you specified. The problem
of the synthesis of genetic polymers within the constraints of the
early Earth chemistry presently remains “a major unanswered
issue” (Shapiro 2006; Lazcano 2010).
Moreover scenarios allowing the emergence of polypeptides (composed of
L-amino acids) before nucleotide emergence are much more plausible.
Actually D-sugar emergence was likely a consequence of the L-amino
acids predominance (Weber & Pizzarello 2006).
According to such scenarios there is no more protein takeover issue.

References:
Lazcano A. Which way to life? Orig.Life Evol.Biosph. 2010;40:161-7.
Shapiro R. Small molecule interactions were central to the origin of
life. Q Rev Biol 2006;81:105-125.
Weber AL, Pizzarello S. The peptide-catalyzed stereospecific synthesis
of tetroses: a possible model for prebiotic molecular evolution. Proc
Natl Acad Sci U S A 2006;103:12713-7.

[pnyikos]

This is a "twofer": I follow up to a post by Harshman on this thread,
and to another one on a thread where we began discussing the protein
takeover.

On Mar 19, 6:34 pm, John Harshman <jharsh...@pacbell.net> wrote:
> pnyikos wrote:
> > On Mar 19, 1:45 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >> pnyikos wrote:
> >>> But how do we get to the "protein takeover" wherein ribosomes are
> >>> augmented with polypeptides, and virtually all other ribozymes are
> >>> replaced by sophisticated and very high fidelity protein enzymes?
> >>> A low fidelity enzyme could be worse than useless, hampering the
> >>> action of the ribozyme.  So what could be a path that leads to the
> >>> immensely thorough and successful protein takeover whose results we
> >>> see today?

John gave a hypothesis, but no pathway:

> >> Here's a simple hypothesis: what if the proteins originally started out
> >> as ribozyme-helpers, stabilizing them and increasing their specificity?
>
> > Can you find a published article, or even a website, which goes into
> > detail about this hypothesis?
>
> I don't know. I haven't tried. You asked for a hypothesis, not a guide
> to the scientific literature.

I asked for a path. Your hypothesis is hardly a sign for a path. You
leave all kinds of natural questions unanswered, like:

> > Your hypothesis is far from simple: how does a protein get specific
> > enough to *enhance* a ribozyme's specificity?
>
> Mutation and selection?

What selection? selection between highly un-specific proteins that
can't help the ribozyme's specificity one whit?

Where's the path I was asking for?

By the way, your "Mutation and selection" harks back to something you
said on Panda's Thumb. We were discussing it on another thread:

Newsgroups: talk.origins, alt.agnosticism
Subject: Re: Evidence for a creator Re: Ray Martinez and denial in the
face

On Mar 16, 5:32 pm, John Harshman <jharsh...@pacbell.net> wrote:
> pnyikos wrote:

> > On Mar 16, 12:34 am, John Harshman <jharsh...@pacbell.net> wrote:

> >> Remember that you are claiming that the probability of abiogenesis is
> >> very, very low. What's your basis for that claim? If you have no basis,
> >> you should also have no claim.
>
> > My basis goes back to something you wrote a short while ago in Panda's
> > Thumb. Since you didn't seem to like my talking about abiogenesis
> > there in the first place, I didn't reply to your naive (IMO) claim
> > that the protein takeover was an example of Darwinian evolution.
>
> Don't think I said that.

Sorry, I was too general: you said it about what is arguably the most
important feature of the protein takeover, because it impinges
directly on the protein translation mechanism itself:

There are reasons to suppose that aminoacyl
synthetases likewise are later additions
that merely improve the fidelity of translation.
Once again, we can see pathways by which
irreducible complexity can evolve through standard Darwinian
mechanisms.
==================== end of excerpt from Panel 5
in: http://pandasthumb.org/archives/2012/02/springer-gets-s.html#comment-panels

Note to other readers: aminoacyl synthetases are the biggest single
factor in making the genetic code what it is, because they are
responsible for matching each tRNA with one AND ONLY ONE amino acid.

John, if you really think these evolved by standard Darwinian
mechanisms once translation was an ongoing thing, you need to come up
with a *pathway*, not just some handwaving as in "Mutation and
selection?"

Heck, you even used the word "pathway" when you said what you did on
the Panda's Thumb.

> > Were you assuming that there was a genetic code in place, except that
> > instead of protein enzymes connecting amino acids to tRNA (as
> > aminoacyl-tRNA synthetases do) there were ribozymes doing the job? If
> > so, just what do you imagine the evolutionary precursors to those
> > synthetases might have been? A synthetase that does a poor job of
> > connecting the right amino acid to the right tRNA is worse than
> > useless--it messes up the job the ribozyme is currently doing.
>
> A simpler scenario would be that the tRNAs originally had binding sites
> for specific amino acids, since lost as redundant.

You'd have to give me details before you could sell me on that
"simpler" bit.

Has anyone ever modified a tRNA in the lab to have a binding site for
the specific amino acid it is paired with today, and only that amino
acid?

The binding sites would have to be configured in such a way that a
ribosome would be able to break the bond and to produce a peptide bond
between the new amino acid and the growing polypeptide string.

And even if that problem is solved, you still have the problem of
getting some protein configured to catalyze the reaction between the
amino acid and the tRNA, a protein enzyme that avoids all other
possible compounds that could also be attached to the tRNA via that
bond.

Has anyone any idea of how such a protein can arise by a "Darwinian
mechanism" one mutation at a time? What would be a starting point?
what would be a pathway?

> > For the benefit of other readers: this is a description of part of
> > what goes on when a cell produces proteins, including enzymes. My
> > first question has to do with proteins already being cranked out
> > assembly-line fashion as they are today, except that the enzymes
> > responsible are made of RNA instead of amino acids.
>
> Let me point out that some of those enzymes are still RNA.
>

The ribosomes are part rRNA. Apart from them, are any of the known
ribozymes involved in the translation of mRNA into polypeptides?

[pnyikos]

Here is another reply to the same post by Harshman that I was replying
to in my "twofer" a few minutes ago.

On Mar 16, 5:32 pm, John Harshman <jharsh...@pacbell.net> wrote

in http://groups.google.com/group/talk.origins/msg/1411ed52be76245d:

> pnyikos wrote:

Repeating a bit from my first reply, for continuity:

> > For the benefit of other readers: this is a description of part of
> > what goes on when a cell produces proteins, including enzymes. My
> > first question has to do with proteins already being cranked out
> > assembly-line fashion as they are today, except that the enzymes
> > responsible are made of RNA instead of amino acids.

[...]
> > And what could
> > get the "computer tape" consisting of mRNA to be coding for really
> > sophisticated proteins?
>
> I don't understand that question.

Does my informal label of "computer tape" for a mRNA molecule bother
you? I was thinking especially of a Turing machine, which is built
around a tape giving instructions. The "instructions" on the mRNA are
the codons, which just happen to correspond to amino acids because of
the genetic code embodied in the aminoacyl-tRNAs.

And the question is a very natural one. At the beginning, before a
genetic code is in place, it's a pretty wild setup, no telling what
polypeptide a mRNA is going to be interpreted as coding for.

But even after there is a genetic code, the mRNA are not likely to
code for anything useful without a LOT of preliminary mutation and
selection.

But even "useful" is way too general: for a protein takeover to
happen, we need specific enzymes to do the work that ribozymes have
done heretofore. And those ribozymes aren't even mRNA.

> > As Karl Popper put it before the "RNA world" hypothesis that I am
> > working with was formulated:
>
> > “What makes the origin of life and of the genetic code a disturbing
> > riddle is this: the genetic code is without any biological function
> > unless it is translated; that is, unless it leads to the synthesis of
> > the proteins whose structure is laid down by the code. But … the
> > machinery by which the cell (at least the non-primitive cell, which is
> > the only one we know) translates the code consists of at least fifty
> > macromolecular components which are themselves coded in the DNA.

In Panda's Thumb, John, you evidently interpreted these "at least
fifty macromolecular components" to be ONLY the polypeptide end
results of translation. But the tRNA, and ribosomes are also coded
into the DNA, and more directly at that.

> >Thus
> > the code can not be translated except by using certain products of its
> > translation.

I think the "Thus" led you to believe this. But one could also
interpret the "Thus" to be referring to the subset of the "at least
fifty" that are actual products of translation.

Are there at least fifty different proteins involved in translation?
I know of the 20 aminoacyl-tRNA synthetases, and the polypeptide
portions of the ribosomes. What else? [I think Ef-Tu was one of
them; I'll have to look that up.]

Anyway, with that nitpicky detail out of the way, the rest of what
Popper wrote was right on target in his day:

> >This constitutes a baffling circle; a really vicious
> > circle, it seems, for any attempt to form a model or theory of the
> > genesis of the genetic code. Thus we may be faced with the possibility
> > that the origin of life (like the origin of physics) becomes an
> > impenetrable barrier to science, and a residue to all attempts to
> > reduce biology to chemistry and physics.”
>
> As I have pointed out, Popper is wrong.

By your interpretation of "Thus," yes.

> Smart guy, limited understanding
> even of the science of his time.

Did they already know in 1974 that the ribosome could still do its
part in translation if the polypeptides are removed?

> Karl Popper, 1974. “Scientific Reduction and the Essential
> > Incompleteness of All Science,” in: Ayala, F. and Dobzhansky, T.,
> > eds., Studies in the Philosophy of Biology, University of California
> > Press, Berkeley, p. 270.

Peter Nyikos

[John Harshman]

Who says they can't? You seem to be implicitly claiming that evolution
in general is impossible, and that no protein can evolve a new function.
Random proteins can often catalyze many reactions a little bit, just
enough that the function can be selected.

> Where's the path I was asking for?

You are apparently looking for a detailed scenario in which every step
of the way is laid out. I don't know what that would look like.
Creationists often ask for a description of each and every amino acid
change. Is that what you're trying for here?

> By the way, your "Mutation and selection" harks back to something you
> said on Panda's Thumb. We were discussing it on another thread:
>
> Newsgroups: talk.origins, alt.agnosticism
> Subject: Re: Evidence for a creator Re: Ray Martinez and denial in the
> face
>
> On Mar 16, 5:32 pm, John Harshman <jharsh...@pacbell.net> wrote:
>> pnyikos wrote:
>>> On Mar 16, 12:34 am, John Harshman <jharsh...@pacbell.net> wrote:
>
>>>> Remember that you are claiming that the probability of abiogenesis is
>>>> very, very low. What's your basis for that claim? If you have no basis,
>>>> you should also have no claim.
>>> My basis goes back to something you wrote a short while ago in Panda's
>>> Thumb. Since you didn't seem to like my talking about abiogenesis
>>> there in the first place, I didn't reply to your naive (IMO) claim
>>> that the protein takeover was an example of Darwinian evolution.
>> Don't think I said that.
>
> Sorry, I was too general: you said it about what is arguably the most
> important feature of the protein takeover, because it impinges
> directly on the protein translation mechanism itself:

Nope, didn't say that either. I said that there were pathways by which
it could happen, and that there was evidence for such a pathway. Do you
disagree?

> There are reasons to suppose that aminoacyl
> synthetases likewise are later additions
> that merely improve the fidelity of translation.
> Once again, we can see pathways by which
> irreducible complexity can evolve through standard Darwinian
> mechanisms.
> ==================== end of excerpt from Panel 5
> in: http://pandasthumb.org/archives/2012/02/springer-gets-s.html#comment-panels
>
> Note to other readers: aminoacyl synthetases are the biggest single
> factor in making the genetic code what it is, because they are
> responsible for matching each tRNA with one AND ONLY ONE amino acid.
>
> John, if you really think these evolved by standard Darwinian
> mechanisms once translation was an ongoing thing, you need to come up
> with a *pathway*, not just some handwaving as in "Mutation and
> selection?"

That wasn't a question. What do you require?

> Heck, you even used the word "pathway" when you said what you did on
> the Panda's Thumb.

OK, it's a rough outline of a pathway. I really don't see why more is
needed when all you're asking for is a plausible notion. Think, for
example, of the transition in vertebrate jaws from cartilages/cartilage
replacement bones -- palatoquadrate and mandibular -- to the dermal
bones dentary, premaxilla, and maxilla. By what pathway could that
possibly have happened? No, the dentary would have been useless for the
purpose of supporting the jaw, because originally it was just a little
scale-like plate on the surface of the face. And in mammals the
mandibular cartilage is just a tiny thing that disappears in the early
embryo. Why, there's no way the ancestor could have had a jaw at all!

>>> Were you assuming that there was a genetic code in place, except that
>>> instead of protein enzymes connecting amino acids to tRNA (as
>>> aminoacyl-tRNA synthetases do) there were ribozymes doing the job? If
>>> so, just what do you imagine the evolutionary precursors to those
>>> synthetases might have been? A synthetase that does a poor job of
>>> connecting the right amino acid to the right tRNA is worse than
>>> useless--it messes up the job the ribozyme is currently doing.
>> A simpler scenario would be that the tRNAs originally had binding sites
>> for specific amino acids, since lost as redundant.
>
> You'd have to give me details before you could sell me on that
> "simpler" bit.
>
> Has anyone ever modified a tRNA in the lab to have a binding site for
> the specific amino acid it is paired with today, and only that amino
> acid?

I don't know why you would demand a laboratory experiment of that sort,
but here's a review:

http://www.ncbi.nlm.nih.gov/pubmed/15952885

I found this in about 20 seconds by googling "rna affinity for amino
acids". How is it that you are incapable of searching?

> The binding sites would have to be configured in such a way that a
> ribosome would be able to break the bond and to produce a peptide bond
> between the new amino acid and the growing polypeptide string.

You mean just like happens with tRNAs today?

> And even if that problem is solved, you still have the problem of
> getting some protein configured to catalyze the reaction between the
> amino acid and the tRNA, a protein enzyme that avoids all other
> possible compounds that could also be attached to the tRNA via that
> bond.

No, no, no. The tRNA is hypothesized to bind directly to the amino acid
all by itself. You don't need a separate enzyme.

> Has anyone any idea of how such a protein can arise by a "Darwinian
> mechanism" one mutation at a time? What would be a starting point?
> what would be a pathway?

No such enzyme is necessary. The tRNA does its own binding.

>>> For the benefit of other readers: this is a description of part of
>>> what goes on when a cell produces proteins, including enzymes. My
>>> first question has to do with proteins already being cranked out
>>> assembly-line fashion as they are today, except that the enzymes
>>> responsible are made of RNA instead of amino acids.
>> Let me point out that some of those enzymes are still RNA.
>
> The ribosomes are part rRNA.

Yes. The part that actually performs the translation.

> Apart from them, are any of the known
> ribozymes involved in the translation of mRNA into polypeptides?

Not to my knowledge. Why should we care? You seem determined to reject
this simple hypothesis, which is fairly common in the literature and yet
which you seem entirely unaware of.

[John Harshman]

pnyikos wrote:
> Here is another reply to the same post by Harshman that I was replying
> to in my "twofer" a few minutes ago.
>
> On Mar 16, 5:32 pm, John Harshman <jharsh...@pacbell.net> wrote
> in http://groups.google.com/group/talk.origins/msg/1411ed52be76245d:
>
>> pnyikos wrote:
>
> Repeating a bit from my first reply, for continuity:
>
>>> For the benefit of other readers: this is a description of part of
>>> what goes on when a cell produces proteins, including enzymes. My
>>> first question has to do with proteins already being cranked out
>>> assembly-line fashion as they are today, except that the enzymes
>>> responsible are made of RNA instead of amino acids.
> [...]
>>> And what could
>>> get the "computer tape" consisting of mRNA to be coding for really
>>> sophisticated proteins?
>> I don't understand that question.
>
> Does my informal label of "computer tape" for a mRNA molecule bother
> you?

Yes, but that isn't why I don't understand the question.

> I was thinking especially of a Turing machine, which is built
> around a tape giving instructions. The "instructions" on the mRNA are
> the codons, which just happen to correspond to amino acids because of
> the genetic code embodied in the aminoacyl-tRNAs.
>
> And the question is a very natural one. At the beginning, before a
> genetic code is in place, it's a pretty wild setup, no telling what
> polypeptide a mRNA is going to be interpreted as coding for.

Who says there is no genetic code in place? It would have to evolve in
tandem with any protein-making machinery. Of course it could have begun,
as many suppose, as a much simpler code, possibly a two-base code, with
fewer amino acids.

> But even after there is a genetic code, the mRNA are not likely to
> code for anything useful without a LOT of preliminary mutation and
> selection.

Actually, it's been shown that random polypeptides often have useful
functions.

> But even "useful" is way too general: for a protein takeover to
> happen, we need specific enzymes to do the work that ribozymes have
> done heretofore.

No problem if there's a gradual replacement.

> And those ribozymes aren't even mRNA.

Why should that matter at all? You're just tossing off objections at
random; perhaps you need an objection code.

>>> As Karl Popper put it before the "RNA world" hypothesis that I am
>>> working with was formulated:
>>> “What makes the origin of life and of the genetic code a disturbing
>>> riddle is this: the genetic code is without any biological function
>>> unless it is translated; that is, unless it leads to the synthesis of
>>> the proteins whose structure is laid down by the code. But … the
>>> machinery by which the cell (at least the non-primitive cell, which is
>>> the only one we know) translates the code consists of at least fifty
>>> macromolecular components which are themselves coded in the DNA.
>
> In Panda's Thumb, John, you evidently interpreted these "at least
> fifty macromolecular components" to be ONLY the polypeptide end
> results of translation.

> But the tRNA, and ribosomes are also coded
> into the DNA, and more directly at that.

That would require a bizarre definition of "coded", which I'm going to
assume Popper at least was clever enough not to use. RNAs are coded;
they're just direct transcriptions. (Of course in the RNA world they
wouldn't even be transcriptions of DNA, merely copies of RNAs.)

>>> Thus
>>> the code can not be translated except by using certain products of its
>>> translation.
>
> I think the "Thus" led you to believe this. But one could also
> interpret the "Thus" to be referring to the subset of the "at least
> fifty" that are actual products of translation.

Yes, that's what "coded" means. You are really reaching. Any component
that doesn't have to be translated presents no problem.

> Are there at least fifty different proteins involved in translation?
> I know of the 20 aminoacyl-tRNA synthetases, and the polypeptide
> portions of the ribosomes. What else? [I think Ef-Tu was one of
> them; I'll have to look that up.]

I don't know where Popper got his numbers. Eukaryotes have 79 ribosomal
proteins, prokaryotes 52.

> Anyway, with that nitpicky detail out of the way, the rest of what
> Popper wrote was right on target in his day:
>
>>> This constitutes a baffling circle; a really vicious
>>> circle, it seems, for any attempt to form a model or theory of the
>>> genesis of the genetic code. Thus we may be faced with the possibility
>>> that the origin of life (like the origin of physics) becomes an
>>> impenetrable barrier to science, and a residue to all attempts to
>>> reduce biology to chemistry and physics.”
>> As I have pointed out, Popper is wrong.
>
> By your interpretation of "Thus," yes.

No, by the fact that Popper is just wrong.

>> Smart guy, limited understanding
>> even of the science of his time.
>
> Did they already know in 1974 that the ribosome could still do its
> part in translation if the polypeptides are removed?

I don't know. I would guess so, since all you have to do is carefully
digest the protein out of purified ribosomes, and that would have been
possible in 1974. But I don't know.

[pnyikos]

Fox showed long ago how some proteinoids (some of which formed what he
called "microspheres") could easily form spontaneously under early
earth conditions, but these weren't really polypeptides. That is, the
amino acids weren't generally linked together by the peptide bonds
that characterize proteins.

Has any of the articles you cite go into how polypeptides might have
been produced under prebiotic conditions?

> Actually D-sugar emergence was likely a consequence of the L-amino
> acids predominance (Weber & Pizzarello 2006).
> According to such scenarios there is no more protein takeover issue.

That creates an issue in the opposite direction: a nucleotide-poor
start instead of a protein-poor start. You have the "nuclear molecule
takeover" problem.

In fact, the protein takeover issue is still there, in a slightly
different form: how is mRNA to be gotten to code for the right kinds
of proteins? Because the mRNA-coded proteins are the ones we see, not
the original hypothetical abiotically produced proteins.

There is something with a name like "basic doctrine" which says
information flows from DNA, RNA etc. to polypeptides, not the
reverse. I know they've come up with exceptions to that, but has any
of your references tackled the general issue of getting an arbitrary
polypeptide to stimulate the formation of a mRNA sequence that codes
for it?

> References:
> Lazcano A. Which way to life? Orig.Life Evol.Biosph. 2010;40:161-7.
> Shapiro R. Small molecule interactions were central to the origin of
> life. Q Rev Biol 2006;81:105-125.
> Weber AL, Pizzarello S. The peptide-catalyzed stereospecific synthesis
> of tetroses: a possible model for prebiotic molecular evolution. Proc
> Natl Acad Sci U S A 2006;103:12713-7.

The title of the latter sounds promising, but isn't it just a PNAS
research announcement? Where is the research paper that gives the
details?

Peter Nyikos

[marc.t...@wanadoo.fr]

Yes, my article "Origin of Evolution versus Origin of Life: A Shift of
Paradigm" Int. J. Mol. Sci. 2011, 12, 3445-3458 (it is in open
access).
In summary:
- The model is a lipid vesicle-based one.
- The solution is in the heterogenous membrane of the vesicles which
is composed of many different types of amphiphiles.
- The hypothesis is that simple carbon-based molecule/membrane site
couples can emerge.
- For each carbon-based molecule/membrane site couple the site
catalyzes the synthesis of the molecule and the molecule stabilizes
the membrane site.
- The outcome is the generation and the accumulation of more complex
enantiomeric carbon-based molecules and thus possibly of enantiomeric
amino acids.
- The model allows the polymerisation of these enantiomeric carbon-
based molecules.

[pnyikos]

You want to START your pathway with one that already can????

>You seem to be implicitly claiming that evolution
> in general is impossible,

What on earth gave you such a bizarre idea??? You know me better than
to think I would implicitly claim such a thing -- I, who have
criticized your cladophile systematics partly because it calls last
common ancestors "fictitious."

>and that no protein can evolve a new function.

Ah. I see. You are opting for an Exaptor of the Gaps Argument

> Random proteins can often catalyze many reactions a little bit, just
> enough that the function can be selected.

"A random protein A, catalyzing reactions z1, ...zn [don't ask me
what n is] whose nature I cannot begin to guess, was exapted via a
string of mutations, while still serving some of these functions
[don't ask me which ones it was still serving at the end of the
string],

"exapted, I say, to give us a protein B, catalyzing reactions y1, ...
y_m [don't ask me what m is] whose nature I cannot begin to guess,
which in turn was exapted, via a string of mutations...

"...which in turn was exapted to give us a protein Z, catalyzing the
replacement of U with C that corrects any ribozyme transcribing DNA
into mRNA but erroneously putting a U where C belongs."

That's the way the Exaptor of the Gaps works, in perfect analogy with
the God of the Gaps.

> > Where's the path I was asking for?
>
> You are apparently looking for a detailed scenario in which every step
> of the way is laid out.

Not really. Some general steps, reasonably close together, like the
fossils we now have linking fishes with mammals, would do very nicely.

Let's begin with this kind of question: what sort of functions might
the individual exapted precursors of the 20 aminoacyl-tRNA synthetases
have performed?

To take just one example: did the one exapted to produce the one that
matches UC_ with Serine have the same function as the one that matches
CC_ with Proline?

Remember, I quoted Voet and Voet as saying that these synthetases are
a highly varied bunch of enzymes. "el cid" countered with the claim
that at least one small fraction matches rather well, and that stands
to reason because tRNA molecules aren't configured all that
differently from each other.

But do the portions that grab the RIGHT amino acids also resemble each
other a great deal? And what about the other portions that defy
comparison? Did the exapted precursors lack these portions? If so,
where were THOSE portions exapted from?

We seem to be nowhere near the argument that Behe was confronted with
at Dover, namely that the bacterial flagellum was the result of an
exapted pump being married to an exapted strand of filament. Behe
rather weakly countered that there is no evidence that it wasn't the
other way around, the pump being exapted from the bacterial flagellum
thru loss of the filament and some other molecules that went with it.

I'm not that picky, I'm just seeing whether we can even get to an
analogous stage here. You haven't advanced one iota beyond the
Exaptor of the Gaps here.

[John Harshman]

Sure. Why not? Of course it might also help the ribozyme's stability or
some other handy thing. It doesn't have to help much.

>> You seem to be implicitly claiming that evolution
>> in general is impossible,
>
> What on earth gave you such a bizarre idea??? You know me better than
> to think I would implicitly claim such a thing -- I, who have
> criticized your cladophile systematics partly because it calls last
> common ancestors "fictitious."

You often appear not to understand the implications of what you say. As
in the example you give of my (=pretty much everyone's) systematics.

>> and that no protein can evolve a new function.
>
> Ah. I see. You are opting for an Exaptor of the Gaps Argument

Wherever do you think new proteins come from?

>> Random proteins can often catalyze many reactions a little bit, just
>> enough that the function can be selected.
>
> "A random protein A, catalyzing reactions z1, ...zn [don't ask me
> what n is] whose nature I cannot begin to guess, was exapted via a
> string of mutations, while still serving some of these functions
> [don't ask me which ones it was still serving at the end of the
> string],
>
> "exapted, I say, to give us a protein B, catalyzing reactions y1, ...
> y_m [don't ask me what m is] whose nature I cannot begin to guess,
> which in turn was exapted, via a string of mutations...
>
> "...which in turn was exapted to give us a protein Z, catalyzing the
> replacement of U with C that corrects any ribozyme transcribing DNA
> into mRNA but erroneously putting a U where C belongs."
>
> That's the way the Exaptor of the Gaps works, in perfect analogy with
> the God of the Gaps.

I didn't even know we were talking about transcription. I thought this
was all about translation. If you want me to go into great detail about
exactly what reactions were catalyzed how, I can't. If that's what you
need for a plausible scenario, nobody is going to come up with one any
time soon.

>>> Where's the path I was asking for?
>> You are apparently looking for a detailed scenario in which every step
>> of the way is laid out.
>
> Not really. Some general steps, reasonably close together, like the
> fossils we now have linking fishes with mammals, would do very nicely.

The problem is that your general steps seem to be intermediate molecules
with particular sequences.

> Let's begin with this kind of question: what sort of functions might
> the individual exapted precursors of the 20 aminoacyl-tRNA synthetases
> have performed?

I have no idea. But don't you have the same problem with any novel
protein? Again, your logic seems to imply an objection to all new
proteins. Is evolution impotent at the molecular level? Michael Behe
thinks so, but I thought you were limiting our designer to very early
interventions, not continuous intervention throughout the history of life.

> To take just one example: did the one exapted to produce the one that
> matches UC_ with Serine have the same function as the one that matches
> CC_ with Proline?

Could be. This isn't something I can come up with.

> Remember, I quoted Voet and Voet as saying that these synthetases are
> a highly varied bunch of enzymes. "el cid" countered with the claim
> that at least one small fraction matches rather well, and that stands
> to reason because tRNA molecules aren't configured all that
> differently from each other.
>
> But do the portions that grab the RIGHT amino acids also resemble each
> other a great deal? And what about the other portions that defy
> comparison? Did the exapted precursors lack these portions? If so,
> where were THOSE portions exapted from?

All interesting questions. But you seem to think they're questions that
preclude answers, rather than just questions I don't know the answer to.
Why?

> We seem to be nowhere near the argument that Behe was confronted with
> at Dover, namely that the bacterial flagellum was the result of an
> exapted pump being married to an exapted strand of filament. Behe
> rather weakly countered that there is no evidence that it wasn't the
> other way around, the pump being exapted from the bacterial flagellum
> thru loss of the filament and some other molecules that went with it.
>
> I'm not that picky, I'm just seeing whether we can even get to an
> analogous stage here. You haven't advanced one iota beyond the
> Exaptor of the Gaps here.

No, we can't very easily get to that stage, since we have no samples of
any prior condition. By the time of the last common ancestor of life,
the whole protein translation system was already in place. Anything
before the UCA is hard to study, and is impossible to study
comparatively. The only possible clues are in paralogs, which some of
the synthetases probably are.

[pnyikos]

I need to cut back on my posting for a while, but I do plan to do at
least one post to this thread each weekday. This might be my only one
for today, but I think it is an important one.

On Mar 20, 6:26 pm, Marc Tessera marc.tess...@wanadoo.fr wrote:
> On 20 mar, 22:18, pnyikos <nyik...@bellsouth.net> wrote:

> > On Mar 20, 1:03 pm, marc.tess...@wanadoo.fr wrote:
> > > RNA world was not possible for the reasons you specified. The problem
> > > of the synthesis of genetic polymers within the constraints of the
> > > early Earth chemistry presently remains “a major unanswered
> > > issue” (Shapiro 2006; Lazcano 2010).
> > > Moreover scenarios allowing the emergence of polypeptides (composed of
> > > L-amino acids) before nucleotide emergence are much more plausible.
>
> > Fox showed long ago how some proteinoids (some of which formed what he
> > called "microspheres") could easily form spontaneously under early
> > earth conditions, but these weren't really polypeptides.  That is, the
> > amino acids weren't generally linked together by the peptide bonds
> > that characterize proteins.
>
> > Has any of the articles you cite go into how polypeptides might have
> > been produced under prebiotic conditions?

Below, Marc, you actually cite an article you have published, but I
could find no mention of peptide bonds there.

What is your background in biochemistry? I've been bereft of a good
biochemist here in talk.origins since the unfortunate death of "el
cid." It would be great if you could pick up where he left off, at the
same level of expertise.

> > > Actually D-sugar emergence was likely a consequence of the L-amino
> > > acids predominance (Weber & Pizzarello 2006).
> > > According to such scenarios there is no more protein takeover issue.
>
> > That creates an issue in the opposite direction: a nucleotide-poor
> > start instead of a protein-poor start.  You have the "nuclear molecule
> > takeover" problem.
>
> > In fact, the protein takeover issue is still there, in a slightly
> > different form: how is mRNA to be gotten to code for the right kinds
> > of proteins?  Because the mRNA-coded proteins are the ones we see, not
> > the original hypothetical abiotically produced proteins.

It would be great if you could give some answers here, at least in the
form of suggested references.

> > There is something with a name like "basic doctrine" which says
> > information flows from DNA, RNA etc. to polypeptides, not the
> > reverse.  I know they've come up with exceptions to that, but has any
> > of your references tackled the general issue of getting an arbitrary
> > polypeptide to stimulate the formation of a mRNA sequence that codes
> > for it?
> > > References:
> > > Lazcano A. Which way to life? Orig.Life Evol.Biosph. 2010;40:161-7.
> > > Shapiro R. Small molecule interactions were central to the origin of
> > > life. Q Rev Biol

> "Has any of the articles you cite go into how polypeptides might have
> been produced under prebiotic conditions?"

You did not cite your article on this thread until now. Is there
another thread where you have cited it and (better yet) discussed it?

> Yes, my article "Origin of Evolution versus Origin of Life: A Shift of
> Paradigm" Int. J. Mol. Sci. 2011, 12, 3445-3458 (it is in open
> access).

Thanks, I've started to read it.

> In summary:
> - The model is a lipid vesicle-based one.

Those vesicles have properties reminiscent of Fox's microspheres. In
particular, they "reproduce" (split in two) under the right conditions
and grow, under conditions I haven't been able to ascertain from your
article. Is there an article that goes into detail on this?

> - The solution is in the heterogenous membrane of the vesicles which
> is composed of  many different types of amphiphiles.

In the first sentence of 3.3 you seem to suggest that this kind of
membrane is yet to be developed experimentally. Correct?

> - The hypothesis is that simple carbon-based molecule/membrane site
> couples can emerge.

OK. Why are amino acids favored over nucleic acids in this model? I
could see no clear indication of this in your paper.

> - For each carbon-based molecule/membrane site couple the site
> catalyzes the synthesis of the molecule and the molecule stabilizes
> the membrane site.

Interesting feedback concept, apparently relevant to mutation and
selection. Has any of this been observed experimentally?

> - The outcome is the generation and the accumulation of more complex
> enantiomeric carbon-based molecules and thus possibly of  enantiomeric
> amino acids.
> - The model allows the polymerisation of these enantiomeric carbon-
> based molecules.

This is the chirality theme that several people here are enthusiastic
about.

Hoping to hear more from you,

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

[marc.t...@wanadoo.fr]

On 21 mar, 21:51, pnyikos <nyik...@bellsouth.net> wrote:
> I need to cut back on my posting for a while, but I do plan to do at
> least one post to this thread each weekday. This might be my only one
> for today, but I think it is an important one.

> In summary:
> - The model is a lipid vesicle-based one.
“Those vesicles have properties reminiscent of Fox's microspheres. In
particular, they "reproduce" (split in two) under the right conditions
and grow, under conditions I haven't been able to ascertain from your

article. Is there an article that goes into detail on this?”
Yes (Szostak 2011, see references).

> - The solution is in the heterogenous membrane of the vesicles which is composed of many different types of amphiphiles.
“In the first sentence of 3.3 you seem to suggest that this kind of

membrane is yet to be developed experimentally. Correct?”
There are some preliminary experiments (Maurer et al. 2009; Namani et
al. 2008; Szostak 2011).

> - The hypothesis is that simple carbon-based molecule/membrane site couples can emerge.
“OK. Why are amino acids favored over nucleic acids in this model? I

could see no clear indication of this in your paper.”
There are several reasons:
- in such a lipid vesicle-based model only small size carbon-based
molecules can enter the vesicle through the membrane;
- amino acids are relatively simple carbon-based molecules which are
relatively easy to synthesize from small size carbon-based molecules.
This is not true for nucleic acids made of bases, sugars and
phosphorus;
- local conditions (i.e. the ones of hydrothermal vents which are the
best locations for the emergence of lipid vesicles) are not favourable
to the survival of RNA-like molecules because of the high temperature
and of the fact that such hydrothermal vents are not a source but
instead a sink of phosphorus (Albarede & Blichert-Toft 2009).

> - For each carbon-based molecule/membrane site couple the site catalyzes the synthesis of the molecule and the molecule stabilizes the membrane site.
“Interesting feedback concept, apparently relevant to mutation and

selection. Has any of this been observed experimentally?”
Not presently because more studies on vesicles with an heterogenous
membrane have to be performed experimentally.

References:
Albarede, F. & Blichert-Toft, J. 2009. The terrestrial cradle of life.
In M. Gerin & M. C. Maurel (Eds.), Origins of Life: Self-Organization
and/or Biological Evolution?: 1-12. EDP Sciences: Paris, France, 2009.
Maurer SE, Deamer DW, Boncella JM, Monnard PA. Chemical evolution of
amphiphiles: glycerol monoacyl derivatives stabilize plausible
prebiotic membranes. Astrobiology. 2009;9:979-87.
Namani T, Deamer DW. Stability of model membranes in extreme
environments. Orig.Life Evol.Biosph. 2008;38:329-41.
Szostak JW. An optimal degree of physical and chemical heterogeneity
for the origin of life? Phil Trans R Soc B 2011;366:2894-2901.

[pnyikos]

Well, Marc, you've certainly given me a lot of interesting reading to
do, but I would also like to make some connection between the rather
early stage of abiogenesis that you have been referring to and later
developments.

Do you see these lipid vesicles as evolving naturally and gradually
into prokaryotic cells? If so, how would nucleic acids enter the
picture?

Peter Nyikos

[marc.t...@wanadoo.fr]

On Mar 23, 3:51 am, pnyikos <nyik...@bellsouth.net> wrote:
> Well, Marc, you've certainly given me a lot of interesting reading to
> do, but I would also like to make some connection between the rather
> early stage of abiogenesis that you have been referring to and later
> developments.
>
> Do you see these lipid vesicles as evolving naturally and gradually
> into prokaryotic cells?  If so, how would nucleic acids enter the
> picture?

O course I have no obvious answer to your challenging question.
However my model is simple and rather heuristic because it explains
major emergences:
1. Heritability and variations (mutations) leading to numerous
distinct lineages and thus to what I call "type 2 evolution".
Actually I think that a clear distinction must be made between the
following two types of evolution:
a) Common evolution or type 1 evolution:
It is in accordance with the second law of thermodynamics which states
that an isolated system (i.e., a system which does not exchange any
heat, work, or matter with the surroundings) can only increase its
entropy over time. It means that its organization will disappear over
time (e.g., the sun which had a certain mass of hydrogen at the
beginning of its history will evolve to a white dwarf when its fuel,
hydrogen, runs out, a kind of stellar death).

b) Evolution which all the terrestrial so-called ‘living’ systems,
viruses and prions stem from or type 2 evolution:
It emerged on the primitive Earth about 4 billion years ago and
involves open dissipative far-from-equilibrium systems which exchange
heat, work, or matter with the surroundings.
Such an evolution has the striking property of not only maintaining
the systems far from their thermodynamic equilibrium but in addition
of leading to the emergence of new systems with a higher level of
organization by the mechanisms of reproduction, heritability and
selection.
Such a process is nevertheless still in accordance with the second law
of thermodynamics because the entropy of what can be considered as an
'isolated system' (which is composed of all the involved systems and
their local surroundings) increases.
2. Enantioselectivity;
3. Polymerization of the enantiomers;
4. A possible way to L-amino-acids (L-AAs);
5. Polymerization of L-AAs leading to possible catalytic dipeptides
and even polypeptides;
6. D-tetroses secondary to the emergence of dipeptides composed of L-
AAs and then D-pentoses thanks to the emergence of catalytic
polypeptides (composed of L-AAs);
7. The next steps towards the emergence of the genetic code is much
more comprehensible once all these previous steps were passed.

[pnyikos]

On Mar 23, 8:46 am, marc.tess...@wanadoo.fr wrote:
> On Mar 23, 3:51 am, pnyikos <nyik...@bellsouth.net> wrote:
>
> > Well, Marc, you've certainly given me a lot of interesting reading to
> > do, but I would also like to make some connection between the rather
> > early stage of abiogenesis that you have been referring to and later
> > developments.
>
> > Do you see these lipid vesicles as evolving naturally and gradually
> > into prokaryotic cells?  If so, how would nucleic acids enter the
> > picture?
>
> O course I have no obvious answer to your challenging question.

Thank you for being so frank. Do you at least hope that the answer to
my first question is Yes?

I ask this because there is an abiogenesis FAQ by Ian Musgrave in
which he talks about HypUrCells (which he also calls "protobionts")
which are quite reminiscent of your lipid vesicles, except that they
are single layered rather than bilayered. He explicitly conjectures
that they are directly ancestral to bacteria:

http://www.talkorigins.org/faqs/abioprob/abioprob.html

I haven't chased down the references he gives yet. Perhaps you would
like to do so.

It's this 7. that I am really curious about: how are abiotically
produced polypeptides going to lead to a genetic code which has to do
with codons and anticodons in nucleic acids?

I won't be posting to talk.origins during weekends unless something
truly extraordinary comes up, but I will be participating on this
thread on Monday. Hope you stick around.

[marc.t...@wanadoo.fr]

On 24 mar, 04:07, pnyikos <nyik...@bellsouth.net> wrote:
> On Mar 23, 8:46 am, marc.tess...@wanadoo.fr wrote:
> > O course I have no obvious answer to your challenging question.
>
> Thank you for being so frank.  Do you at least hope that the answer to my first question is Yes?
>
> I ask this because there is an abiogenesis FAQ by Ian Musgrave in
> which he talks about HypUrCells (which he also calls "protobionts")
> which are quite reminiscent of your lipid vesicles, except that they
> are single layered rather than bilayered.  He explicitly conjectures
> that they are directly ancestral to bacteria:
>
> http://www.talkorigins.org/faqs/abioprob/abioprob.html
>
> I haven't chased down the references he gives yet.  Perhaps you would
> like to do so.

> > 7. The next steps towards the emergence of the genetic code is much
> > more comprehensible once all these previous steps were passed.
>
> It's this 7. that I am really curious about: how are abiotically
> produced polypeptides going to lead to a genetic code which has to do
> with codons and anticodons in nucleic acids?

Once type 2 evolution has emerged and then with the presence of
specific and potent catalysts (i.e. polypeptides composed of L-AAs)
and of D-tetroses an infinite number of plausible scenarios towards
nucleic acids and then to the genetic code may be imagined.
Moreover I think, in the same manner as Stephen Jay Gould, that, once
type 2 evolution has emerged, the probability that the genetic code
emerged was very low because it was likely a historical accident.
Actually I am not very much interested in this issue. What seem to me
much more interesting are plausible scenarios of the emergence of type
2 evolution.
Then my obsession is to provide a proof-of-principle that my model can
be based on science experiments.
Regarding the FAQ by Ian Musgrave I don't think it is update enough as
it dates from 1998.

[pnyikos]

On Mar 24, 4:10 pm, marc.tess...@wanadoo.fr wrote:
> On 24 mar, 04:07, pnyikos <nyik...@bellsouth.net> wrote:

> > On Mar 23, 8:46 am, marc.tess...@wanadoo.fr wrote:
> > > O course I have no obvious answer to your challenging question.
>
> > Thank you for being so frank.  Do you at least hope that the answer to my first question is Yes?
>
> > I ask this because there is an abiogenesis FAQ by Ian Musgrave in
> > which he talks about HypUrCells (which he also calls "protobionts")
> > which are quite reminiscent of your lipid vesicles, except that they
> > are single layered rather than bilayered.  He explicitly conjectures
> > that they are directly ancestral to bacteria:
>
> >http://www.talkorigins.org/faqs/abioprob/abioprob.html
>
> > I haven't chased down the references he gives yet.  Perhaps you would
> > like to do so.
> > > 7. The next steps towards the emergence of the genetic code is much
> > > more comprehensible once all these previous steps were passed.
>
> > It's this 7. that I am really curious about: how are abiotically
> > produced polypeptides going to lead to a genetic code which has to do
> > with codons and anticodons in nucleic acids?
>
> Once type 2 evolution has emerged and then with the presence of
> specific and potent catalysts (i.e. polypeptides composed of L-AAs)
> and of D-tetroses an infinite number of plausible scenarios towards
> nucleic acids and then to the genetic code may be imagined.

So far, I haven't seen a single one that takes us past the stage I
mentioned in my lead article. And that stage already assumed a
genetic code using nucleic acids including mRNA, tRNA, and lots of
ribozymes. From that stage on, we seem to be stuck with Harshman's
"Exaptor of the Gaps" argument right now, but I'm planning to prod him
a bit about this.

> Moreover I think, in the same manner as Stephen Jay Gould, that, once
> type 2 evolution has emerged, the probability that the genetic code
> emerged was very low because it was likely a historical accident.

Note, I said "a genetic code" not "the genetic code." The form a
genetic code takes is of tertiary interest; but without any kind of
genetic code, we are far away from "life as we know it". Even the
stage where the protein takeover began in earnest must have had a
genetic code of some sort.

> Actually I am not very much interested in this issue. What seem to me
> much more interesting are plausible scenarios of the emergence of type
> 2 evolution.

Yes, I have had a chance to read your article more carefully now, and
I see that you are focusing not on the emergence of "life as we know
it" but of type 2 evolution.

> Then my obsession is to provide a proof-of-principle that my model can
> be based on science experiments.

> Regarding the FAQ by Ian Musgrave I don't think it is update enough as
> it dates from 1998.

More importantly, it has a rather naive idea of what constitutes
"life", as far as suitability for evolution is concerned. It only
incorporates the second of the ones you give in your article:

"(1) Local conditions that allow the emergence of open non-equilibrium
structural systems, organizedon a macroscopic level, generated by a
flow of matter and energy that is continuously supplied. These
open far-from-equilibrium systems can maintain themselves far-from-
equilibrium because they are
able to use the matter and energy supplied by the favourable local
environment;

"(2) The systems must be able to self-replicate;

"(3) The systems must be capable of acquiring heritable structure/
function
properties that are relatively independent from the local environment,
i.e., the fact that they belong to a
specific lineage should not depend on the nature of the nutriments
they receive from the local
environment [9]. This last condition is required for the emergence of
distinct lineages allowing
Darwinian natural selection."
-- available by download
from http://www.mdpi.com/1422-0067/12/6/3445/

Even condition (2) is rather poorly illustrated by example Musgrave
gives of a peptide molecule that is able to make a copy of itself from
two halves of itself. Yet he seems to think that with this, and a few
similar examples, he has "put paid" [as they say in the British
Commonwealth] to the creationist idea of how astronomically difficult
it is to produce the proteins of "life as we know it."

And (1) and (3) are conspicuously missing from the Musgrave FAQ. (3)
even suggests that the nutrients should be a whole lot less
complicated than the lineage itself, and that is violated by the "Lee
et al peptide" given by Musgrave:

http://www.talkorigins.org/faqs/abioprob/abioprob.html


Peter Nyikos

[pnyikos]

Google LeComte du Nuoy. :-)

Seriously, you need to invoke the Exaptor of the Gaps [see below] a
good lot just to get something specific enough.

>Of course it might also help the ribozyme's stability or
> some other handy thing. It doesn't have to help much.

Whatever floats your boat. Just make sure it isn't a rock. :-)

> >> You seem to be implicitly claiming that evolution
> >> in general is impossible,
>
> > What on earth gave you such a bizarre idea???  You know me better than
> > to think I would implicitly claim such a thing -- I, who have
> > criticized your cladophile systematics partly because it calls last
> > common ancestors "fictitious."
>
> You often appear not to understand the implications of what you say.

The "example" you give next has got to be one of the worst I have ever
seen.

> As
> in the example you give of my (=pretty much everyone's) systematics.

I have said it plays into the hands of the creationists to say that
LCA's are "fictitious", even more so than the Gould "dirty little
secret" quote of which they are so fond. It's lucky for you they are
so clueless that hardly any of them knows about this "fictitious"
jargon which you cheerfully use.

In short:
Just WHO doesn't understand the implications of what he says?

> >> and that no protein can evolve a new function.
>
> > Ah.  I see.   You are opting for an Exaptor of the Gaps Argument
>
> Wherever do you think new proteins come from?

From mRNA codes that are mutated in a non-silent way. With the help
of the genetic code and over 50 enzymes/ribozymes, etc.

> >> Random proteins can often catalyze many reactions a little bit, just
> >> enough that the function can be selected.
>
> > "A random protein A, catalyzing reactions  z1, ...zn [don't ask me
> > what n is] whose nature I cannot begin to guess, was exapted via a
> > string of mutations, while still serving some of these functions
> > [don't ask me which ones it was still serving at the end of the
> > string],
>
> > "exapted, I say, to give us a protein B, catalyzing reactions y1, ...
> > y_m [don't ask me what m is] whose nature I cannot begin to guess,
> > which in turn was exapted, via a string of mutations...
>
> > "...which in turn was exapted to give us a protein Z, catalyzing the
> > replacement of U with C that corrects any ribozyme transcribing DNA
> > into mRNA but erroneously putting a U where C belongs."
>
> > That's the way the Exaptor of the Gaps works, in perfect analogy with
> > the God of the Gaps.
>
> I didn't even know we were talking about transcription. I thought this
> was all about translation.

I was talking about the protein takeover, period. It may have started
with translation in the Panda's Thumb, but for this thread I decided
to open up the topic.

Continued in next reply, which may not be for a few hours or even
today--but nlt tomorrow. Duty calls.

Peter Nyikos

[John Harshman]

You like to use the phrase "[blank] of the gaps" a lot, but does it
actually say anything? It's been shown by many experiments that random
sequences can produce measurable effects on specific reactions often
enough that we can suppose such things.

>> Of course it might also help the ribozyme's stability or
>> some other handy thing. It doesn't have to help much.
>
> Whatever floats your boat. Just make sure it isn't a rock. :-)
>
>>>> You seem to be implicitly claiming that evolution
>>>> in general is impossible,
>>> What on earth gave you such a bizarre idea??? You know me better than
>>> to think I would implicitly claim such a thing -- I, who have
>>> criticized your cladophile systematics partly because it calls last
>>> common ancestors "fictitious."
>> You often appear not to understand the implications of what you say.
>
> The "example" you give next has got to be one of the worst I have ever
> seen.
>
>> As
>> in the example you give of my (=pretty much everyone's) systematics.
>
> I have said it plays into the hands of the creationists to say that
> LCA's are "fictitious", even more so than the Gould "dirty little
> secret" quote of which they are so fond. It's lucky for you they are
> so clueless that hardly any of them knows about this "fictitious"
> jargon which you cheerfully use.

Apparently you don't understand the difference between "hypothetical"
and "fictitious". Unfortunate. For the record, I have never said that
LCAs are fictitious.

> In short:
> Just WHO doesn't understand the implications of what he says?

As I said, you don't.

>>>> and that no protein can evolve a new function.
>>> Ah. I see. You are opting for an Exaptor of the Gaps Argument
>> Wherever do you think new proteins come from?
>
> From mRNA codes that are mutated in a non-silent way. With the help
> of the genetic code and over 50 enzymes/ribozymes, etc.

Not always. Sometimes they actually do come from random sequences, or
effectively random ones like frame-shifted bits. And of course they
often come from proteins that perform quite different functions, which I
think you might consider also effectively random.

>>>> Random proteins can often catalyze many reactions a little bit, just
>>>> enough that the function can be selected.
>>> "A random protein A, catalyzing reactions z1, ...zn [don't ask me
>>> what n is] whose nature I cannot begin to guess, was exapted via a
>>> string of mutations, while still serving some of these functions
>>> [don't ask me which ones it was still serving at the end of the
>>> string],
>>> "exapted, I say, to give us a protein B, catalyzing reactions y1, ...
>>> y_m [don't ask me what m is] whose nature I cannot begin to guess,
>>> which in turn was exapted, via a string of mutations...
>>> "...which in turn was exapted to give us a protein Z, catalyzing the
>>> replacement of U with C that corrects any ribozyme transcribing DNA
>>> into mRNA but erroneously putting a U where C belongs."
>>> That's the way the Exaptor of the Gaps works, in perfect analogy with
>>> the God of the Gaps.
>> I didn't even know we were talking about transcription. I thought this
>> was all about translation.
>
> I was talking about the protein takeover, period. It may have started
> with translation in the Panda's Thumb, but for this thread I decided
> to open up the topic.

You should say so up front, to prevent confusion. After all, in the RNA
world there's no need for transcription, since we already have RNA.

[pnyikos]

On Mar 20, 7:56 pm, John Harshman <jharsh...@pacbell.net> wrote:
> pnyikos wrote:
> > On Mar 20, 2:59 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >> pnyikos wrote:

Picking up essentially where I left off:

> >>> Where's the path I was asking for?
> >> You are apparently looking for a detailed scenario in which every step
> >> of the way is laid out.
>
> > Not really.  Some general steps, reasonably close together, like the
> > fossils we now have linking fishes with mammals, would do very nicely.
>
> The problem is that your general steps seem to be intermediate molecules
> with particular sequences.

No. They would be classes of intermediate molecules, with similar
sequences, with some function appropriate to them.

Remember, I'm the one who has no problem saying that some member of
Rhipidistra gave rise to tetrapods. Your cladophilia seems to be
what is making you say "particular sequences".

> > Let's begin with this kind of question: what sort of functions might
> > the individual exapted precursors of the 20 aminoacyl-tRNA synthetases
> > have performed?
>
> I have no idea. But don't you have the same problem with any novel
> protein?

Of course not, unless you lay a lot of stress on "novel". I have no
problem with most of the factors in the blood clotting cascade or the
immune system cascade evolving the way Robison and Miller showed they
might have.

> Again, your logic seems to imply an objection to all new
> proteins. Is evolution impotent at the molecular level?

No, otherwise I would have problems with evolution from the first
prokaryote. The problem before that is getting the takeover off the
ground.

> Michael Behe
> thinks so, but I thought you were limiting our designer to very early
> interventions, not continuous intervention throughout the history of life.

Yes, and that is why I was delighted by the Robison-Miller solution to
the problem of those long cascades. The remaining favorites of Behe
look a lot more promising where the "Throomian" panspermists are
concerned.

> > To take just one example: did the one exapted to produce the one that
> > matches UC_ with Serine have the same function as the one that matches
> > CC_ with Proline?

One reason I chose these is that they belong to two different classes
of the four main classes of amino acids.

> Could be. This isn't something I can come up with.
>
> > Remember, I quoted Voet and Voet as saying that these synthetases are
> > a highly varied bunch of enzymes.  "el cid" countered with the claim
> > that at least one small fraction matches rather well, and that stands
> > to reason because tRNA molecules aren't configured all that
> > differently from each other.
>
> > But do the portions that grab the RIGHT amino acids also resemble each
> > other a great deal?  And what about the other portions that defy
> > comparison?  Did the exapted precursors lack these portions?  If so,
> > where were THOSE portions exapted from?
>
> All interesting questions. But you seem to think they're questions that
> preclude answers, rather than just questions I don't know the answer to.

You really need to stop trying to figure out my motivations for my
questions. You are not good at it. I'm involved in a disinterested
search for the truth, and will be glad to acknowledge good answers,
like I did for Robison.

You might already be guessing differently, had you seen the thread I
began on Tiktaalik. My first post started as follows:

Subject: A successful prediction of evolutionary theory: Tiktaalik

For a long time I have been a critic of people who are too ready to
claim that this and that discovery was "predicted by evolutionary
theory," but even I cannot deny the appropriateness of applying that
to the discovery of *Tiktaalik*, a transitional form between lobefin
fish and tetrapods of the Devonian.
-- http://groups.google.com/group/talk.origins/msg/d21b1306e1250405

> > We seem to be nowhere near the argument that Behe was confronted with
> > at Dover, namely that the bacterial flagellum was the result of an
> > exapted pump being married to an exapted strand of filament.  Behe
> > rather weakly countered that there is no evidence that it wasn't the
> > other way around, the pump being exapted from the bacterial flagellum
> > thru loss of the filament and some other molecules that went with it.
>
> > I'm not that picky, I'm just seeing whether we can even get to an
> > analogous stage here.  You haven't advanced one iota beyond the
> > Exaptor of the Gaps here.
>
> No, we can't very easily get to that stage, since we have no samples of
> any prior condition. By the time of the last common ancestor of life,
> the whole protein translation system was already in place. Anything
> before the UCA is hard to study, and is impossible to study
> comparatively.

That sounds a tad pessimistic, coming from a dyed-in-the-wool cladist
like you. Someone could try doing a cladogram of all the genes of
some prokaryote, and then using it to try and guess what the LCAs of
various classes of genes might have looked like.

Of course, if my Throomian sub-hypothesis is correct, this would be
about as meaningful as a cladogram of mountains, [with the fanciful
idea that the sister taxon of the Matterhorn might be some mountain in
the Himalayas] but if some of those reconstructed LCAs, when
synthesized in a lab, are found to perform some useful function, that
would make at least some parts of the cladogram as persuasive as the
ones we have for large parts of the Tree of Life.

>The only possible clues are in paralogs, which some of
> the synthetases probably are.

Explain, please.

By the way, if you read my first post to this thread carefully, you
will see that I use the term "RNA world" quite loosely, to include
DNA. The point was that all the sophisticated enzymes at the start of
the protein takeover were ribozymes. You seem to have missed out on
that in one or two posts, where you say a DNA replicator was not
needed. It was, because cells as sophisticated as the ones I wrote
about need the extra genetic stability DNA provides.

[John Harshman]

pnyikos wrote:
> On Mar 20, 7:56 pm, John Harshman <jharsh...@pacbell.net> wrote:
>> pnyikos wrote:
>>> On Mar 20, 2:59 pm, John Harshman <jharsh...@pacbell.net> wrote:
>>>> pnyikos wrote:
>
> Picking up essentially where I left off:
>
>>>>> Where's the path I was asking for?
>>>> You are apparently looking for a detailed scenario in which every step
>>>> of the way is laid out.
>>> Not really. Some general steps, reasonably close together, like the
>>> fossils we now have linking fishes with mammals, would do very nicely.
>> The problem is that your general steps seem to be intermediate molecules
>> with particular sequences.
>
> No. They would be classes of intermediate molecules, with similar
> sequences, with some function appropriate to them.
>
> Remember, I'm the one who has no problem saying that some member of
> Rhipidistra gave rise to tetrapods. Your cladophilia seems to be
> what is making you say "particular sequences".

But I already mentioned a class of intermediate molecule, two of them:
those that bound to the RNA and aided its function, and those that bound
to it and stabilized it. Not clear what you want here.

>>> Let's begin with this kind of question: what sort of functions might
>>> the individual exapted precursors of the 20 aminoacyl-tRNA synthetases
>>> have performed?
>> I have no idea. But don't you have the same problem with any novel
>> protein?
>
> Of course not, unless you lay a lot of stress on "novel". I have no
> problem with most of the factors in the blood clotting cascade or the
> immune system cascade evolving the way Robison and Miller showed they
> might have.

So you agree that exaptation is common enough.

>> Again, your logic seems to imply an objection to all new
>> proteins. Is evolution impotent at the molecular level?
>
> No, otherwise I would have problems with evolution from the first
> prokaryote. The problem before that is getting the takeover off the
> ground.

Well, obviously I'm not going to present a detailed scenario. We have
very little (approximately no) evidence to go on, and I can't make up
nonexistent protein or RNA structures on spec, even if I were good at
biochemistry, which I'm not. Studies of evolution in which this sort of
thing is done have the advantage that there are paralogs and/or
intermediate conditions in evidence, on which to work.

>> Michael Behe
>> thinks so, but I thought you were limiting our designer to very early
>> interventions, not continuous intervention throughout the history of life.
>
> Yes, and that is why I was delighted by the Robison-Miller solution to
> the problem of those long cascades. The remaining favorites of Behe
> look a lot more promising where the "Throomian" panspermists are
> concerned.

That just shows that your default hypothesis is that evolution doesn't
work; you need a scenario before you can be dislodged from that. Why
should you have such a default?

>>> To take just one example: did the one exapted to produce the one that
>>> matches UC_ with Serine have the same function as the one that matches
>>> CC_ with Proline?
>
> One reason I chose these is that they belong to two different classes
> of the four main classes of amino acids.

Same answer, regardless of your reasons for bringing them up:

>> Could be. This isn't something I can come up with.
>>
>>> Remember, I quoted Voet and Voet as saying that these synthetases are
>>> a highly varied bunch of enzymes. "el cid" countered with the claim
>>> that at least one small fraction matches rather well, and that stands
>>> to reason because tRNA molecules aren't configured all that
>>> differently from each other.
>>> But do the portions that grab the RIGHT amino acids also resemble each
>>> other a great deal? And what about the other portions that defy
>>> comparison? Did the exapted precursors lack these portions? If so,
>>> where were THOSE portions exapted from?
>> All interesting questions. But you seem to think they're questions that
>> preclude answers, rather than just questions I don't know the answer to.
>
> You really need to stop trying to figure out my motivations for my
> questions. You are not good at it. I'm involved in a disinterested
> search for the truth, and will be glad to acknowledge good answers,
> like I did for Robison.

Your disinterested search appears to have a default position, though. If
there is no scenario at present, you suppose that something is unlikely.
Why?

> You might already be guessing differently, had you seen the thread I
> began on Tiktaalik. My first post started as follows:
>
> Subject: A successful prediction of evolutionary theory: Tiktaalik
>
> For a long time I have been a critic of people who are too ready to
> claim that this and that discovery was "predicted by evolutionary
> theory," but even I cannot deny the appropriateness of applying that
> to the discovery of *Tiktaalik*, a transitional form between lobefin
> fish and tetrapods of the Devonian.
> -- http://groups.google.com/group/talk.origins/msg/d21b1306e1250405

Don't actually see the relevance here.

>>> We seem to be nowhere near the argument that Behe was confronted with
>>> at Dover, namely that the bacterial flagellum was the result of an
>>> exapted pump being married to an exapted strand of filament. Behe
>>> rather weakly countered that there is no evidence that it wasn't the
>>> other way around, the pump being exapted from the bacterial flagellum
>>> thru loss of the filament and some other molecules that went with it.
>>> I'm not that picky, I'm just seeing whether we can even get to an
>>> analogous stage here. You haven't advanced one iota beyond the
>>> Exaptor of the Gaps here.
>> No, we can't very easily get to that stage, since we have no samples of
>> any prior condition. By the time of the last common ancestor of life,
>> the whole protein translation system was already in place. Anything
>> before the UCA is hard to study, and is impossible to study
>> comparatively.
>
> That sounds a tad pessimistic, coming from a dyed-in-the-wool cladist
> like you. Someone could try doing a cladogram of all the genes of
> some prokaryote, and then using it to try and guess what the LCAs of
> various classes of genes might have looked like.

Yes, I mentioned that. Those are the paralogs mentioned below. It's the
only hope, but I don't think it's a very strong one.

> Of course, if my Throomian sub-hypothesis is correct, this would be
> about as meaningful as a cladogram of mountains, [with the fanciful
> idea that the sister taxon of the Matterhorn might be some mountain in
> the Himalayas] but if some of those reconstructed LCAs, when
> synthesized in a lab, are found to perform some useful function, that
> would make at least some parts of the cladogram as persuasive as the
> ones we have for large parts of the Tree of Life.

Would evidence of relationships among synthetases be evidence against
your hypothesis?

>> The only possible clues are in paralogs, which some of
>> the synthetases probably are.
>
> Explain, please.

I think we've covered that. Paralogs are different genes that are
descended from a common single gene. Commonly they arise through gene
duplication and divergence.

> By the way, if you read my first post to this thread carefully, you
> will see that I use the term "RNA world" quite loosely, to include
> DNA. The point was that all the sophisticated enzymes at the start of
> the protein takeover were ribozymes. You seem to have missed out on
> that in one or two posts, where you say a DNA replicator was not
> needed. It was, because cells as sophisticated as the ones I wrote
> about need the extra genetic stability DNA provides.

Could be, though I don't see why that's clearly necessary.

[marc.t...@wanadoo.fr]

>    fromhttp://www.mdpi.com/1422-0067/12/6/3445/

>
> Even condition (2) is rather poorly illustrated by example Musgrave
> gives of a peptide molecule that is able to make a copy of itself from
> two halves of itself.  Yet he seems to think that with this, and a few
> similar examples,  he has "put paid" [as they say in the British
> Commonwealth] to the creationist idea of how astronomically difficult
> it is to produce the proteins of "life as we know it."
>
> And (1) and (3) are conspicuously missing from the Musgrave FAQ.  (3)
> even suggests that the nutrients should be a whole lot less
> complicated than the lineage itself, and that is violated by the "Lee
> et al peptide" given by Musgrave:
>
> http://www.talkorigins.org/faqs/abioprob/abioprob.html
>

> Peter Nyikos- Hide quoted text -

>
> - Show quoted text -

Thank you for your comments.
Are you interested in two documents (Word text and Powerpoint
illustrations) that go further in the description of the model? I
would appreciate your comments on these.

[pnyikos]

"specific" is ambiguous. If you've ever watched how Kleinman uses it,
you know what I mean.

Tell me whether *here* it means anything more than "a few [unspecified
in advance] reactions to the exclusion of all others".

If that's all it means, you've got a highly un-specified string of
exaptations to hope for, before you can hope to get a protein that is
specific for the activity that a particular ribozyme is producing.

> >> Of course it might also help the ribozyme's stability or
> >> some other handy thing. It doesn't have to help much.
>
> > Whatever floats your boat.  Just make sure it isn't a rock.  :-)
>
> >>>> You seem to be implicitly claiming that evolution
> >>>> in general is impossible,
> >>> What on earth gave you such a bizarre idea???  You know me better than
> >>> to think I would implicitly claim such a thing -- I, who have
> >>> criticized your cladophile systematics partly because it calls last
> >>> common ancestors "fictitious."
> >> You often appear not to understand the implications of what you say.

You have yet to even begin to make a case for this claim, and without
it, your bizarre idea remains as bizarre as ever.

> > The "example" you give next has got to be one of the worst I have ever
> > seen.
>
> >> As
> >> in the example you give of my (=pretty much everyone's) systematics.
>
> > I have said it plays into the hands of the creationists to say that
> > LCA's are "fictitious", even more so than the Gould "dirty little
> > secret" quote of which they are so fond.  It's lucky for you they are
> > so clueless that hardly any of them knows about this "fictitious"
> > jargon which you cheerfully use.
>
> Apparently you don't understand the difference between "hypothetical"
> and "fictitious".

No, what happened was that I conflated two things: your expression
"purely hypothetical" [yes, you gilded the lily that way] applied to
LCA's and your "fictitious" applied to traditional paraphyletic taxa
(Dinosauria, etc.).

Mea culpa. I'm old enough to where I can tell an old joke on myself
from time to time: "They say the memory is the first thing to go, and
I forget what the second thing is."

>Unfortunate. For the record, I have never said that
> LCAs are fictitious.

Even so, the basic point stands: I am no less zealous for biological
evolution than you are, only my zeal takes on different forms. And
one minor one is, I dislike terms like "purely hypothetical" applied
to very real creatures.

During our 2011 exchange about "purely hypothetical," I used the term
"very REAL organisms" for them, and you responded with:

"Any organism we have not found can't be real to us, even if it must
have
existed. Your idea that ancestors don't exist unless we name them is
silly."
http://groups.google.com/group/talk.origins/msg/5684ce7b859d2453

What WAS silly, incidentally, was your notion that I ever entertained
such an idea. How could anyone calling them "very REAL organisms"
possibly think they don't exist?

> > In short:
> > Just WHO doesn't understand the implications of what he says?
>
> As I said, you don't.

Repeating this mantra is no substitute for giving a valid example.

> >>>> and that no protein can evolve a new function.
> >>> Ah.  I see.   You are opting for an Exaptor of the Gaps Argument
> >> Wherever do you think new proteins come from?
>
> > From mRNA codes that are mutated in a non-silent way.  With the help
> > of the genetic code and over 50 enzymes/ribozymes, etc.
>
> Not always. Sometimes they actually do come from random sequences,

Not by translation? What is it that produces all those peptide bonds?

> or
> effectively random ones like frame-shifted bits. And of course they
> often come from proteins that perform quite different functions, which I
> think you might consider also effectively random.

I wouldn't, not necessarily. Functions could be "quite different" as
far as the molecules acted on are concerned, and yet the mechanisms
whereby this is done could be quite similar.

> >>>> Random proteins can often catalyze many reactions a little bit, just
> >>>> enough that the function can be selected.
> >>> "A random protein A, catalyzing reactions  z1, ...zn [don't ask me
> >>> what n is] whose nature I cannot begin to guess, was exapted via a
> >>> string of mutations, while still serving some of these functions
> >>> [don't ask me which ones it was still serving at the end of the
> >>> string],
> >>> "exapted, I say, to give us a protein B, catalyzing reactions y1, ...
> >>> y_m [don't ask me what m is] whose nature I cannot begin to guess,
> >>> which in turn was exapted, via a string of mutations...
> >>> "...which in turn was exapted to give us a protein Z, catalyzing the
> >>> replacement of U with C that corrects any ribozyme transcribing DNA
> >>> into mRNA but erroneously putting a U where C belongs."
> >>> That's the way the Exaptor of the Gaps works, in perfect analogy with
> >>> the God of the Gaps.
> >> I didn't even know we were talking about transcription. I thought this
> >> was all about translation.
>
> > I was talking about the protein takeover, period.  It may have started
> > with translation in the Panda's Thumb, but for this thread I decided
> > to open up the topic.
>
> You should say so up front, to prevent confusion.

I did, right in my first post. [I didn't say I was opening up a
previously restricted topic, but I did give the topic in opened-up
form.]

>After all, in the RNA
> world there's no need for transcription, since we already have RNA.

As I told you yesterday [and also everyone in the first post to this
thread] I was assuming the presence of DNA, so there is need for
transcription, and also for reverse transcription to code the RNA into
the DNA. Here is how I put it in the first post:

"The last phase starts with a "RNA world" in which most of the non-
protein players are already in place: DNA, ribosomes lacking
polypeptides, mRNA, aminoacyl-tRNA, and various ribozymes doing what
is nowadays done with protein enzymes. Especially crucial are
ribozymes for DNA replication, transcription, and reverse
transcription."

By the way, retroviruses may be the descendants of viruses that
escaped eons ago from protocells that still had reverse transcriptase.

Peter Nyikos

[pnyikos]

> Thank you for your comments.
> Are you interested in two documents (Word text and Powerpoint
> illustrations) that go further in the description of the model? I
> would appreciate your comments on these.

Yes, I would be glad to do so. Please bear with me if I take a month
or more, though. This is a very busy time of year for me.

Peter Nyikos

[John Harshman]

It doesn't. Generally, experiments of that sort began with a particular
target reaction. Obviously, the target varied depending on the
experiment. It was usually some easily assayed enzymatic reaction.

> If that's all it means, you've got a highly un-specified string of
> exaptations to hope for, before you can hope to get a protein that is
> specific for the activity that a particular ribozyme is producing.

That isn't all it means.

>>>> Of course it might also help the ribozyme's stability or
>>>> some other handy thing. It doesn't have to help much.
>>> Whatever floats your boat. Just make sure it isn't a rock. :-)
>>>>>> You seem to be implicitly claiming that evolution
>>>>>> in general is impossible,
>>>>> What on earth gave you such a bizarre idea??? You know me better than
>>>>> to think I would implicitly claim such a thing -- I, who have
>>>>> criticized your cladophile systematics partly because it calls last
>>>>> common ancestors "fictitious."
>>>> You often appear not to understand the implications of what you say.
>
> You have yet to even begin to make a case for this claim, and without
> it, your bizarre idea remains as bizarre as ever.

I have no interest in making a case for what's just a personal
observation. You are free to disagree.

>>> The "example" you give next has got to be one of the worst I have ever
>>> seen.
>>>> As
>>>> in the example you give of my (=pretty much everyone's) systematics.
>>> I have said it plays into the hands of the creationists to say that
>>> LCA's are "fictitious", even more so than the Gould "dirty little
>>> secret" quote of which they are so fond. It's lucky for you they are
>>> so clueless that hardly any of them knows about this "fictitious"
>>> jargon which you cheerfully use.
>> Apparently you don't understand the difference between "hypothetical"
>> and "fictitious".
>
> No, what happened was that I conflated two things: your expression
> "purely hypothetical" [yes, you gilded the lily that way] applied to
> LCA's and your "fictitious" applied to traditional paraphyletic taxa
> (Dinosauria, etc.).
>
> Mea culpa. I'm old enough to where I can tell an old joke on myself
> from time to time: "They say the memory is the first thing to go, and
> I forget what the second thing is."

Congratulations: you are qualified to be governor of Texas.

>> Unfortunate. For the record, I have never said that
>> LCAs are fictitious.
>
> Even so, the basic point stands: I am no less zealous for biological
> evolution than you are, only my zeal takes on different forms. And
> one minor one is, I dislike terms like "purely hypothetical" applied
> to very real creatures.

You appear still not to understand what "hypothetical" means.
Hypothetical entities can be real; they just stop being hypothetical
when we find that they are real. Now if you know that some particular
fossil is the ancestral species that belongs at some node of a
phylogenetic tree, then that ancestor is no longer hypothetical. If,
however, you can't point to that fossil, the ancestor is hypothetical.
What else can it be?

Notice that what's hypothetical is not the existence of such an
ancestor, but just its identity.

> During our 2011 exchange about "purely hypothetical," I used the term
> "very REAL organisms" for them, and you responded with:
>
> "Any organism we have not found can't be real to us, even if it must
> have
> existed. Your idea that ancestors don't exist unless we name them is
> silly."
> http://groups.google.com/group/talk.origins/msg/5684ce7b859d2453
>
> What WAS silly, incidentally, was your notion that I ever entertained
> such an idea. How could anyone calling them "very REAL organisms"
> possibly think they don't exist?

I believe it was in the context of our ability to identify ancestors,
which you claimed at the time we could do.

>>> In short:
>>> Just WHO doesn't understand the implications of what he says?
>> As I said, you don't.
>
> Repeating this mantra is no substitute for giving a valid example.

Agreed. (But please don't say "mantra". It has insulting connotations
here. You know who I'm talking about.) I don't intend to contest the
point, at least not right now.

>>>>>> and that no protein can evolve a new function.
>>>>> Ah. I see. You are opting for an Exaptor of the Gaps Argument
>>>> Wherever do you think new proteins come from?
>>> From mRNA codes that are mutated in a non-silent way. With the help
>>> of the genetic code and over 50 enzymes/ribozymes, etc.
>> Not always. Sometimes they actually do come from random sequences,
>
> Not by translation? What is it that produces all those peptide bonds?

I was focusing on "from mRNA codes". New proteins do have mRNAs, but the
DNA sequences that are transcribed to make those mRNAs may not be
descended from DNA sequences that are mutated versions of sequences that
were transcribed to previous mRNAs. They may come from prior non-coding
sequences. This is by far less common than what you say, but it happens.

>> or
>> effectively random ones like frame-shifted bits. And of course they
>> often come from proteins that perform quite different functions, which I
>> think you might consider also effectively random.
>
> I wouldn't, not necessarily. Functions could be "quite different" as
> far as the molecules acted on are concerned, and yet the mechanisms
> whereby this is done could be quite similar.

Could, yes. Or could be quite different, and indeed the active sites may
be in quite different locations between the two proteins.

>>>>>> Random proteins can often catalyze many reactions a little bit, just
>>>>>> enough that the function can be selected.
>>>>> "A random protein A, catalyzing reactions z1, ...zn [don't ask me
>>>>> what n is] whose nature I cannot begin to guess, was exapted via a
>>>>> string of mutations, while still serving some of these functions
>>>>> [don't ask me which ones it was still serving at the end of the
>>>>> string],
>>>>> "exapted, I say, to give us a protein B, catalyzing reactions y1, ...
>>>>> y_m [don't ask me what m is] whose nature I cannot begin to guess,
>>>>> which in turn was exapted, via a string of mutations...
>>>>> "...which in turn was exapted to give us a protein Z, catalyzing the
>>>>> replacement of U with C that corrects any ribozyme transcribing DNA
>>>>> into mRNA but erroneously putting a U where C belongs."
>>>>> That's the way the Exaptor of the Gaps works, in perfect analogy with
>>>>> the God of the Gaps.
>>>> I didn't even know we were talking about transcription. I thought this
>>>> was all about translation.
>>> I was talking about the protein takeover, period. It may have started
>>> with translation in the Panda's Thumb, but for this thread I decided
>>> to open up the topic.
>> You should say so up front, to prevent confusion.
>
> I did, right in my first post. [I didn't say I was opening up a
> previously restricted topic, but I did give the topic in opened-up
> form.]

If so, my apologies, but I didn't see it.

>> After all, in the RNA
>> world there's no need for transcription, since we already have RNA.
>
> As I told you yesterday [and also everyone in the first post to this
> thread] I was assuming the presence of DNA, so there is need for
> transcription, and also for reverse transcription to code the RNA into
> the DNA. Here is how I put it in the first post:
>
> "The last phase starts with a "RNA world" in which most of the non-
> protein players are already in place: DNA, ribosomes lacking
> polypeptides, mRNA, aminoacyl-tRNA, and various ribozymes doing what
> is nowadays done with protein enzymes. Especially crucial are
> ribozymes for DNA replication, transcription, and reverse
> transcription."

This is not an RNA world, is it? If DNA is the carrier of heredity, we
have already left the RNA world. We might ask which came first, DNA or
protein, but I don't think you can dictate the answer.

> By the way, retroviruses may be the descendants of viruses that
> escaped eons ago from protocells that still had reverse transcriptase.

It's certainly a conceivable hypothesis. I'm not sure how you would test it.

[pnyikos]

Could you be more, er, specific? Musgrave makes a big deal of
abtarget as general as "a ligase that puts together two halves of
itself to make a copy of itself," but what we are really after is a
protein that can take over the extremely demanding job of catalyzing
the replication of DNA.

> > If that's all it means, you've got a highly un-specified string of
> > exaptations to hope for, before you can hope to get a protein that is
> > specific for the activity that a particular ribozyme is producing.
>
> That isn't all it means.
>
> >>>> Of course it might also help the ribozyme's stability or
> >>>> some other handy thing. It doesn't have to help much.

Is that the role of the 50-plus proteins in ribosomes? I have to
wonder why the rRNA in ribosomes did not get replaced in the > 3.5
billion years after the protein takeover was supposedly nearly
complete.

"el cid" claimed that he could find proteins that adequately
substitute for the rRNA if he were given five years.

Having no inkling that he was soon to die, I countered with "You and
what team of Nobel Laureates?" I would have gone a little easier on
him if I had known he was in the last stages of pancreatic cancer, but
I would have been just as skeptical.

You seemed to think it could be done in five years, but if so, why
didn't it happen by natural selection?

By the way, I'm pretty sure I've figured out who "el cid" was, but I
won't say it publicly. I'd much rather he be remembered the way he
was in his final year, rather than the way he was a decade earlier.

Peter Nyikos

[John Harshman]

Keeping in mind that I don't keep up with this field and so don't have a
big list of references handy, try this. It's not the one I was thinking
of (and my files need more organization, certainly) but it should do.

http://www.nature.com/nature/journal/v410/n6829/abs/410715a0.html

>>> If that's all it means, you've got a highly un-specified string of
>>> exaptations to hope for, before you can hope to get a protein that is
>>> specific for the activity that a particular ribozyme is producing.
>> That isn't all it means.
>>
>>>>>> Of course it might also help the ribozyme's stability or
>>>>>> some other handy thing. It doesn't have to help much.
>
> Is that the role of the 50-plus proteins in ribosomes? I have to
> wonder why the rRNA in ribosomes did not get replaced in the > 3.5
> billion years after the protein takeover was supposedly nearly
> complete.

Do we care? What does this have to do with what we're talking about? Are
you claiming that because some RNAs were not replaced by proteins,
therefore no scenario in which RNAs are replaced by proteins can be valid?

If the RNA does the job better than any associated protein, selection
won't favor replacement. Not all conceivable evolutionary paths are
followed.

> "el cid" claimed that he could find proteins that adequately
> substitute for the rRNA if he were given five years.
>
> Having no inkling that he was soon to die, I countered with "You and
> what team of Nobel Laureates?" I would have gone a little easier on
> him if I had known he was in the last stages of pancreatic cancer, but
> I would have been just as skeptical.
>
> You seemed to think it could be done in five years, but if so, why
> didn't it happen by natural selection?

This is in the line of "If we come from monkeys, why are there still
monkeys?"; I had thought more of you than that.

> By the way, I'm pretty sure I've figured out who "el cid" was, but I
> won't say it publicly. I'd much rather he be remembered the way he
> was in his final year, rather than the way he was a decade earlier.

Again, don't care.

[pnyikos]

Returning to this thread after more than a month's absence...

Each one says something, and no two of the following say the same
thing:

Exaptor of the Gaps

Darwin of the Gaps

Randy of the Gaps

Nobody of the Gaps

The last one tickles my funny bone the most: "Nobody said that this is
the way evolution works"--without any effort at an alternative
explanation for the phenomenon under discussion.

I was reminded of this today when seeing your complaints about what
Meyer said on that 700 Club interview.

> >>>> It's been shown by many experiments that random
> >>>> sequences can produce measurable effects on specific reactions often
> >>>> enough that we can suppose such things.
> >>> "specific" is ambiguous.  If you've ever watched how Kleinman uses it,
> >>> you know what I mean.
> >>> Tell me whether *here* it means anything more than "a few [unspecified
> >>> in advance] reactions to the exclusion of all others".
> >> It doesn't. Generally, experiments of that sort began with a particular
> >> target reaction. Obviously, the target varied depending on the
> >> experiment. It was usually some easily assayed enzymatic reaction.
>
> > Could you be more, er, specific?  Musgrave makes a big deal of
> > abtarget as  general as "a ligase that puts together two halves of
> > itself to make a copy of itself," but what we are really after is a
> > protein that can take over the extremely demanding job of catalyzing
> > the replication of DNA.
>
> Keeping in mind that I don't keep up with this field and so don't have a
> big list of references handy, try this. It's not the one I was thinking
> of (and my files need more organization, certainly) but it should do.
>
> http://www.nature.com/nature/journal/v410/n6829/abs/410715a0.html

The abstract certainly looks promising. A pity _Nature_'s paywall now
includes the computer I work from in my university office. I'll have
to look up the hard copy of the article in our library, and I don't
have time for that today.

In fact, I need to sign off now.

[snip of rest, to be replied to when time permits]

Peter Nyikos

[pnyikos]

On Apr 3, 6:39 pm, John Harshman <jharsh...@pacbell.net> wrote:
> pnyikos wrote:
> > On Mar 27, 8:49 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >> pnyikos wrote:
> >>> On Mar 26, 7:38 pm, John Harshman <jharsh...@pacbell.net> wrote:

Picking up where I left off yesterday.

> >>>>>> Of course it might also help the ribozyme's stability or
> >>>>>> some other handy thing. It doesn't have to help much.
>
> > Is that the role of the 50-plus proteins in ribosomes?  I have to
> > wonder why the rRNA in ribosomes did not get replaced in the > 3.5
> > billion years after the protein takeover was supposedly nearly
> > complete.
>
> Do we care? What does this have to do with what we're talking about? Are
> you claiming that because some RNAs were not replaced by proteins,
> therefore no scenario in which RNAs are replaced by proteins can be valid?

Why even ask your third question before getting a reply to the first
two? It treats me the way you would treat a run-of-the-mill
creationist.

I deal in probabilities like a scientist. I suppose you think
mathematicians are not only not scientists, but they cannot be assumed
to have any idea of how a scientist thinks, even after years of
posting in sci.bio.paleontology with lots of "shop talk."

Datum 1: "el cid," who knew more about biochemistry than either of us
is likely to learn in the rest of his lifetime, was convinced that,
given five years, it would be possible to design a protein replacement
for the ribosome.

Datum 2: bacteria and archae, which apparently diverged close to 3.5
bya, both have ribosomes in which the big chunks of rRNA have NOT been
replaced in all that time.

Datum 3: virtually all ribozymes besides the ribosomes were replaced
in a mere half a billion years according to the prevailing hypothesis.

Conclusion: those who cling to the prevailing hypothesis need to
seriously ask whether the replacement in Datum 3 was done by
intelligent agents.

But you are so far from seriously asking it, that on this very thread
you counted your chickens before they were hatched, in the form of a
taunt that I don't realize where my reasoning is taking me -- to a
denial that evolution is possible at all.

The context, after all, was the protein takeover, which may have never
happened in the first place, except in the form of nanotechnology by
an intelligent, ribozyme-based species of panspermists.

> If the RNA does the job better than any associated protein, selection
> won't favor replacement. Not all conceivable evolutionary paths are
> followed.

That's a huge assumption right there, that the RNA does the job better
in the ribosome [see Datum 1 again] but not in the hundreds of
ribozymes that presumably did NOT do the job as well as the associated
proteins which somehow [Exaptor of the Gaps again] arose to take their
places

> > "el cid" claimed that he could find proteins that adequately
> > substitute for the rRNA if he were given five years.
>
> > Having no inkling that he was soon to die, I countered with "You and
> > what team of Nobel Laureates?"  I would have gone a little easier on
> > him if I had known he was in the last stages of pancreatic cancer, but
> > I would have been just as skeptical.
>
> > You seemed to think it could be done in five years, but if so, why
> > didn't it happen by natural selection?
>
> This is in the line of "If we come from monkeys, why are there still
> monkeys?"; I had thought more of you than that.

I thought more of you than to expect such a cheap shot. It assumes
that what I wrote was very far along the line, rather than only a few
little steps along the line that it really is, and with far more
reasoning behind it.

> > By the way, I'm pretty sure I've figured out who "el cid" was, but I
> > won't say it publicly.  I'd much rather he be remembered the way he
> > was in his final year, rather than the way he was a decade earlier.
>
> Again, don't care.

This last crack makes me wonder whether I remember "el cid" with more
affection than you do.

Peter Nyikos

[pnyikos]

The following May 11 post is reposted because John Harshman missed it
and can no longer easily reply to it.

It includes a comment from an earlier post, a comment which John
ignored back then, about something the late el cid said shortly before
his death. Instead of voicing skepticism about what el cid had said,
he issued a cheap shot which you can read below.

Later on, in another thread, he even seemed skeptical about el cid
having said any such thing, and claimed that if he had known about it,
he would have disagreed strongly with it.

'nuff said about that for now. Here's the repost:

=========== end of repost

[John Harshman]

Just trying to save time. Do you intend to answer any of those questions?

> It treats me the way you would treat a run-of-the-mill
> creationist.
>
> I deal in probabilities like a scientist. I suppose you think
> mathematicians are not only not scientists, but they cannot be assumed
> to have any idea of how a scientist thinks, even after years of
> posting in sci.bio.paleontology with lots of "shop talk."

Agreed. Mathematicians are not scientists, and there's no particular
reason to suppose you know how scientists think.

> Datum 1: "el cid," who knew more about biochemistry than either of us
> is likely to learn in the rest of his lifetime, was convinced that,
> given five years, it would be possible to design a protein replacement
> for the ribosome.

If this is anything more than an appeal to authority, what is it?

> Datum 2: bacteria and archae, which apparently diverged close to 3.5
> bya, both have ribosomes in which the big chunks of rRNA have NOT been
> replaced in all that time.
>
> Datum 3: virtually all ribozymes besides the ribosomes were replaced
> in a mere half a billion years according to the prevailing hypothesis.
>
> Conclusion: those who cling to the prevailing hypothesis need to
> seriously ask whether the replacement in Datum 3 was done by
> intelligent agents.

An interesting conclusion, but I can't for the life of me see how it
follows from the premises. Perhaps you will explain.

> But you are so far from seriously asking it, that on this very thread
> you counted your chickens before they were hatched, in the form of a
> taunt that I don't realize where my reasoning is taking me -- to a
> denial that evolution is possible at all.
>
> The context, after all, was the protein takeover, which may have never
> happened in the first place, except in the form of nanotechnology by
> an intelligent, ribozyme-based species of panspermists.
>
>> If the RNA does the job better than any associated protein, selection
>> won't favor replacement. Not all conceivable evolutionary paths are
>> followed.
>
> That's a huge assumption right there, that the RNA does the job better
> in the ribosome [see Datum 1 again] but not in the hundreds of
> ribozymes that presumably did NOT do the job as well as the associated
> proteins which somehow [Exaptor of the Gaps again] arose to take their
> places

That isn't an assumption. It's a hypothesis that would explain the data,
if true. But let's suppose the designers did all this. Why did they
leave one ribozyme in place rather than making a clean sweep? Same
problem, or non-problem, either way.

[snip a few irrelevant bits]

[pnyikos]

On Jun 26, 5:24�pm, John Harshman <jharsh...@pacbell.net> wrote:
> pnyikos wrote:
> > The following May 11 post is reposted because John Harshman missed it
> > and can no longer easily reply to it.
>
> > It includes a comment from an earlier post, a comment which John
> > ignored back then, about something the late el cid said shortly before
> > his death. �Instead of voicing skepticism about what el cid had said,
> > he issued a cheap shot which you can read below.
>
> > Later on, in another thread, he even seemed skeptical about el cid
> > having said any such thing, and claimed that if he had known about it,
> > he would have disagreed strongly with it.
>
> > 'nuff said about that for now.

But more needs to be said about that, and I'll say it now since
Harshman snipped the evidence for what I am saying.

And that is, that the overall evidence, including his more recent
behavior, strongly suggests that Harshman is dissembling about what he
believes and what he does not believe.

In other words, he is insincere.

He might also be so amoral that this does not seem like a reprimand
against him, but a "complaint about how" I've "been wronged" by him.
He's pulled that "wronged" stunt already in response to other evidence
that he is dishonest/insincere.


> >�Here's the repost:

>
> > On Apr 3, 6:39 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >> pnyikos wrote:
> >>> On Mar 27, 8:49 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >>>> pnyikos wrote:
> >>>>> On Mar 26, 7:38 pm, John Harshman <jharsh...@pacbell.net> wrote:
>
> > Picking up where I left off yesterday.
>
> >>>>>>>> Of course it might also help the ribozyme's stability or
> >>>>>>>> some other handy thing. It doesn't have to help much.
>
> >>> Is that the role of the 50-plus proteins in ribosomes? �I have to
> >>> wonder why the rRNA in ribosomes did not get replaced in the > 3.5
> >>> billion years after the protein takeover was supposedly nearly
> >>> complete.
>
> >> Do we care? What does this have to do with what we're talking about? Are
> >> you claiming that because some RNAs were not replaced by proteins,
> >> therefore no scenario in which RNAs are replaced by proteins can be valid?
>
> > Why even ask your third question before getting a reply to the first
> > two?
>
> Just trying to save time. Do you intend to answer any of those questions?

More insincerity on your part? I answered them below in reverse
order.

> > It treats me the way you would treat a run-of-the-mill
> > creationist.
>
> > I deal in probabilities like a scientist. �I suppose you think
> > mathematicians are not only not scientists, but they cannot be assumed
> > to have any idea of how a scientist thinks, even after years of
> > posting in sci.bio.paleontology with lots of "shop talk."
>
> Agreed. Mathematicians are not scientists, and there's no particular
> reason to suppose you know how scientists think.

But you have also (insincerely?) claimed to have actual doubts about
me being able to think like a scientist.

Neither there nor here have you given any basis for your claim, hence
the suspicion of insincerity.

[That may be your cue to say that I'm entitled to suspect anything,
and to continue to avoid giving any basis.]

> > Datum 1: "el cid," who knew more about biochemistry than either of us
> > is likely to learn in the rest of his lifetime, was convinced that,
> > given five years, it would be possible to design a protein replacement
> > for the ribosome.
>
> If this is anything more than an appeal to authority, what is it?

In hindsight, it is a demonstration that you may have been insincere
in claiming to disbelieve what el cid claimed. See above.

> > Datum 2: bacteria and archae, which apparently diverged close to 3.5
> > bya, both have ribosomes in which the big chunks of rRNA have NOT been
> > replaced in all that time.
>
> > Datum 3: virtually all ribozymes besides the ribosomes were replaced
> > in a mere half a billion years according to the prevailing hypothesis.
>
> > Conclusion: those who cling to the prevailing hypothesis need to
> > seriously ask whether the replacement in Datum 3 was done by
> > intelligent agents.

Note the words, "seriously ask whether," and then ask yourself how far
you intend to retreat towards the impregnable fortress I mention
below.

> An interesting conclusion, but I can't for the life of me see how it
> follows from the premises.

Feigning the 'tard again? or just misapplying the Socratic method?
There is one more alternative that comes to mind...

>Perhaps you will explain.

Perhaps you will retreat further towards complete epistemological
nihilism if I do.

Bright university students quickly pick up on the fact that nihilism
is an impregnable fortress. And so they feel quite safe in retreating
as far towards that fortress as they deem necessary to avoid
confronting the opponent's point of view. Perhaps you are behaving in
conformity to this insight.

Remainder deleted, to be dealt with later. Duty calls.

Peter Nyikos

[John Harshman]

pnyikos wrote:

I really don't want to discuss your intuitions about my moral failings.
If you have something relevant to say about the subject we're supposedly
discussing, I'll be glad to respond.

[Ray Martinez]

http://people.maths.ox.ac.uk/dusautoy/newdetails.htm

Charles Simonyi Professor for the Public Understanding of Science is
Professor of Mathematics Marcus du Sautoy; he took the place of
Richard Dawkins.

Carry on....

Ray

PS for Peter: When are you going to get to the point (aliens-did-
it)....LOL!

In case anyone does not know: Peter Nyikos is a Directed Panspermist.

Your Friend,

RM

[*Hemidactylus*]

We had no idea until you clued us in. Thanks.

[Ray Martinez]

Your welcome.

I was actually speaking to marc.tess and others who might not know.

Ray

[John Harshman]

As usual, you mistake the map for the territory. What evidence is there
that DuSautoy knows how scientists think? As far as I can tell, he's
never published anything in any field of science. While science makes
plenty of use of math, math isn't science. You will have to ask the
administration of Oxford why they made that choice.

And one example doesn't make a general case at any rate.

>
> PS for Peter: When are you going to get to the point (aliens-did-
> it)....LOL!
>
> In case anyone does not know: Peter Nyikos is a Directed Panspermist.
>
> Your Friend,

Pretty sure you're nobody's friend.

[Ray Martinez]

Since he was chosen, his scientific peers disagree with your opinion.
I actually happen to agree with you that math isn't science. Math is
an uncertain representation of reality; anyone can support anything
with numbers, statistics and probabilities.

> And one example doesn't make a general case at any rate.
>

Your opinions are noted. Again, DuSautoy was appointed to be the
Charles Simonyi Professor of Public Understanding of Science at
Oxford. So there are some scientists who disagree with you, my only
point. We should also assume that Richard Dawkins supports the
selection of DuSautoy, yes or no?

The larger point here is that I have seen Dembski supporters use the
DuSautoy title as evidence that their boy is a scientist. Dembski, of
course, has an advanced degree in Mathematics. In England (c.1830)
almost all naturalists were ordained Ministers. One was not qualified
to speak about nature until he first earned a degree in Theology
(which had to be a Masters degree). My how things have changed! Of
course Dembski has an advanced degree in Theology too.

Ray

[Robert Camp]

On Jun 26, 4:49 pm, pnyikos <nyik...@bellsouth.net> wrote:
> On Jun 26, 5:24 pm, John Harshman <jharsh...@pacbell.net> wrote:
>
> > pnyikos wrote:

<snip>

> > > Datum 2: bacteria and archae, which apparently diverged close to 3.5
> > > bya, both have ribosomes in which the big chunks of rRNA have NOT been
> > > replaced in all that time.
>
> > > Datum 3: virtually all ribozymes besides the ribosomes were replaced
> > > in a mere half a billion years according to the prevailing hypothesis.
>
> > > Conclusion: those who cling to the prevailing hypothesis need to
> > > seriously ask whether the replacement in Datum 3 was done by
> > > intelligent agents.
>
> Note the words, "seriously ask whether," and then ask yourself how far
> you intend to retreat towards the impregnable fortress I mention
> below.

The words, "those who cling to the prevailing hypothesis need to
seriously ask whether..." do not change - in fact they emphasize - the
obvious implication that *you* think consideration of intervention by
intelligent agents follows from your proposed data.

This connection would seem to be an important, if not critical,
component of your thesis. Why would you choose not to expound upon it,
instead descending once again into imagined victimization and
accusations?

Perhaps you'd like to give it another, more substantive, shot? I'm
interested to hear your answer.

RLC

[John Harshman]

That would be true if he were appointed by his scientific peers. Do you
know how he got the job?

> I actually happen to agree with you that math isn't science. Math is
> an uncertain representation of reality; anyone can support anything
> with numbers, statistics and probabilities.

Yeah, you can use math to support anything that's even remotely true. As
is generally the case when you think you agree with me, you fail to
understand my point.

>> And one example doesn't make a general case at any rate.
>
> Your opinions are noted. Again, DuSautoy was appointed to be the
> Charles Simonyi Professor of Public Understanding of Science at
> Oxford. So there are some scientists who disagree with you, my only
> point.

Was he appointed by scientists?

> We should also assume that Richard Dawkins supports the
> selection of DuSautoy, yes or no?

We should not assume in the absence of evidence. Do you have evidence
for that claim?

> The larger point here is that I have seen Dembski supporters use the
> DuSautoy title as evidence that their boy is a scientist. Dembski, of
> course, has an advanced degree in Mathematics. In England (c.1830)
> almost all naturalists were ordained Ministers. One was not qualified
> to speak about nature until he first earned a degree in Theology
> (which had to be a Masters degree). My how things have changed! Of
> course Dembski has an advanced degree in Theology too.

That bit of meandering doesn't seem to have a point attached. Now of
course someone trained in math can be a scientist, just as someone
"trained" in theology can be. But this apparently isn't so for DuSautoy,
as his CV shows no scientific publications.

[Rolf]

Dembski is an advanced case of creationism gone wild.

[Roger Shrubber]

pnyikos wrote:
> On Jun 26, 5:24 pm, John Harshman<jharsh...@pacbell.net> wrote:
>> pnyikos wrote:
>>> The following May 11 post is reposted because John Harshman missed it
>>> and can no longer easily reply to it.
>>
>>> It includes a comment from an earlier post, a comment which John
>>> ignored back then, about something the late el cid said shortly before
>>> his death. Instead of voicing skepticism about what el cid had said,
>>> he issued a cheap shot which you can read below.
>>
>>> Later on, in another thread, he even seemed skeptical about el cid
>>> having said any such thing, and claimed that if he had known about it,
>>> he would have disagreed strongly with it.
>>
>>> 'nuff said about that for now.
>
> But more needs to be said about that, and I'll say it now since
> Harshman snipped the evidence for what I am saying.
>
> And that is, that the overall evidence, including his more recent
> behavior, strongly suggests that Harshman is dissembling about what he
> believes and what he does not believe.
>
> In other words, he is insincere.
>
> He might also be so amoral that this does not seem like a reprimand
> against him, but a "complaint about how" I've "been wronged" by him.
> He's pulled that "wronged" stunt already in response to other evidence
> that he is dishonest/insincere.

That addition did nothing to get to any protein takeover issue
and that makes it useless noise.

>>> Here's the repost:
>>
>>> On Apr 3, 6:39 pm, John Harshman<jharsh...@pacbell.net> wrote:
>>>> pnyikos wrote:
>>>>> On Mar 27, 8:49 pm, John Harshman<jharsh...@pacbell.net> wrote:
>>>>>> pnyikos wrote:
>>>>>>> On Mar 26, 7:38 pm, John Harshman<jharsh...@pacbell.net> wrote:
>>
>>> Picking up where I left off yesterday.
>>
>>>>>>>>>> Of course it might also help the ribozyme's stability or
>>>>>>>>>> some other handy thing. It doesn't have to help much.
>>
>>>>> Is that the role of the 50-plus proteins in ribosomes? I have to
>>>>> wonder why the rRNA in ribosomes did not get replaced in the> 3.5
>>>>> billion years after the protein takeover was supposedly nearly
>>>>> complete.
>>
>>>> Do we care? What does this have to do with what we're talking about? Are
>>>> you claiming that because some RNAs were not replaced by proteins,
>>>> therefore no scenario in which RNAs are replaced by proteins can be valid?
>>
>>> Why even ask your third question before getting a reply to the first
>>> two?
>>
>> Just trying to save time. Do you intend to answer any of those questions?
>
> More insincerity on your part? I answered them below in reverse
> order.

I don't see clear answers. I see question that seem ill-informed.

>>> It treats me the way you would treat a run-of-the-mill
>>> creationist.
>>
>>> I deal in probabilities like a scientist. I suppose you think
>>> mathematicians are not only not scientists, but they cannot be assumed
>>> to have any idea of how a scientist thinks, even after years of
>>> posting in sci.bio.paleontology with lots of "shop talk."
>>
>> Agreed. Mathematicians are not scientists, and there's no particular
>> reason to suppose you know how scientists think.
>
> But you have also (insincerely?) claimed to have actual doubts about
> me being able to think like a scientist.
>
> Neither there nor here have you given any basis for your claim, hence
> the suspicion of insincerity.
>
> [That may be your cue to say that I'm entitled to suspect anything,
> and to continue to avoid giving any basis.]

Again, banter that is all about personalities and not about moving
from an RNA world to a mostly Protein World.

>>> Datum 1: "el cid," who knew more about biochemistry than either of us
>>> is likely to learn in the rest of his lifetime, was convinced that,
>>> given five years, it would be possible to design a protein replacement
>>> for the ribosome.
>>
>> If this is anything more than an appeal to authority, what is it?
>
> In hindsight, it is a demonstration that you may have been insincere
> in claiming to disbelieve what el cid claimed. See above.

It looks like an appeal to authority to me. That seems to be the
only aspect relevant to RNA to protein.

>>> Datum 2: bacteria and archae, which apparently diverged close to 3.5
>>> bya, both have ribosomes in which the big chunks of rRNA have NOT been
>>> replaced in all that time.
>>
>>> Datum 3: virtually all ribozymes besides the ribosomes were replaced
>>> in a mere half a billion years according to the prevailing hypothesis.
>>
>>> Conclusion: those who cling to the prevailing hypothesis need to
>>> seriously ask whether the replacement in Datum 3 was done by
>>> intelligent agents.
>
> Note the words, "seriously ask whether," and then ask yourself how far
> you intend to retreat towards the impregnable fortress I mention
> below.

More uninteresting meta-discussion.

>> An interesting conclusion, but I can't for the life of me see how it
>> follows from the premises.
>
> Feigning the 'tard again? or just misapplying the Socratic method?
> There is one more alternative that comes to mind...

Pointless and evasive. The specific problem is that "intelligent agents"
comes in out of left field. There must be some unstated premise about
intelligent agents that you take as obvious. Unstated premises are
often a source of miscommunication. Why don't you go ahead and show
exactly how "intelligent agents" winds up in the conclusion.

I anticipate that the unstated premise will be a point of contention
and that is an even better reason for it to be made explicit.

>> Perhaps you will explain.
>
> Perhaps you will retreat further towards complete epistemological
> nihilism if I do.
>
> Bright university students quickly pick up on the fact that nihilism
> is an impregnable fortress. And so they feel quite safe in retreating
> as far towards that fortress as they deem necessary to avoid
> confronting the opponent's point of view. Perhaps you are behaving in
> conformity to this insight.
>
> Remainder deleted, to be dealt with later. Duty calls.

I don't see anything I would consider content of relevance in
your post.

The question that's buried up there is why didn't ribosomal RNA
get replaced by proteins. The commonly accepted answer is that
the ribosome is a trapped artifact. Why don't you accept that
answer? It isn't considered much of a mystery to most biologists.

If you think it is more of a mystery than most biologists do,
maybe you should lay out a full argument instead of calling
people 'Tards' if they can't see your point.

[pnyikos]

On Jun 26, 11:18 pm, Robert Camp <robertlc...@hotmail.com> wrote:
> On Jun 26, 4:49 pm, pnyikos <nyik...@bellsouth.net> wrote:
>
> > On Jun 26, 5:24 pm, John Harshman <jharsh...@pacbell.net> wrote:
>
> > > pnyikos wrote:
>
> <snip>

You snipped something highly embarrassing to Harshman, from which he
ran away.

But in another way, you have helped me, by demonstrating (along with
Martinez and Hemidactylus) that just because a thread has been a back-
and-forth between two people for a long time, it does NOT mean that
those are the only two people following the thread.

This is something else that does not occur naturally to Harshman. On
one occasion, when I was making a comment about him in the third
person by way of introducing the topic under discussion, he asked me
whom I was addressing.

My reply went about like this "Isn't it obvious? I'm addressing
anyone who happens to be reading the post." His reply was that he
thought it was just the two of us.

> > > > Datum 2: bacteria and archae, which apparently diverged close to 3.5
> > > > bya, both have ribosomes in which the big chunks of rRNA have NOT been
> > > > replaced in all that time.
>
> > > > Datum 3: virtually all ribozymes besides the ribosomes were replaced
> > > > in a mere half a billion years according to the prevailing hypothesis.
>
> > > > Conclusion: those who cling to the prevailing hypothesis need to
> > > > seriously ask whether the replacement in Datum 3 was done by
> > > > intelligent agents.

> > Note the words, "seriously ask whether," and then ask yourself how far
> > you intend to retreat towards the impregnable fortress I mention
> > below.
>
> The words, "those who cling to the prevailing hypothesis need to
> seriously ask whether..." do not change - in fact they emphasize - the
> obvious implication that *you* think consideration of intervention by
> intelligent agents follows from your proposed data.

Yes, and the operative word is "consideration." Not agreement--
consideration.

> This connection would seem to be an important, if not critical,
> component of your thesis. Why would you choose not to expound upon it,

Thank you for this new demonstration of how you think like a
polemicist rather than a scientist. I caught you at it yesterday, in
another thread that featured a bizarre treatment by you of a paragraph
from an old (1918) paper by Muller.

I asked you there whether you considered yourself to be at least as
rational as the average YEC. The presence of Martinez on this thread,
and this new demonstration of irrationality, leads me to ask it again.

> instead descending once again into imagined victimization and
> accusations?
>
> Perhaps you'd like to give it another, more substantive, shot? I'm
> interested to hear your answer.

Your snipping of Datum 1 suggests just WHY you are interested, and
it's not for substantive reasons, apparently.

But fear not -- I will give it another shot, and then you can judge
for yourself whether it meets your standards for "substantive".

But I'll do it in response to Harshman, who DID behave reasonably from
time to time on this thread.


Peter Nyikos

[Robert Camp]

On Jun 27, 10:47 am, pnyikos <nyik...@bellsouth.net> wrote:
> On Jun 26, 11:18 pm, Robert Camp <robertlc...@hotmail.com> wrote:
>
> > On Jun 26, 4:49 pm, pnyikos <nyik...@bellsouth.net> wrote:
>
> > > On Jun 26, 5:24 pm, John Harshman <jharsh...@pacbell.net> wrote:
>
> > > > pnyikos wrote:
>
> > <snip>

<snipped for irrelevance>

>  But in another way, you have helped me, by demonstrating (along with
> Martinez and Hemidactylus) that just because a thread has been a back-
> and-forth between two people for a long time, it does NOT mean that
> those are the only two people following the thread.

No one thinks that. Since we discussed related issues elsewhere, I've
checked in on this thread now and then. I don't see the revelation
here.

<snipped for irrelevance>

> > > > > Datum 2: bacteria and archae, which apparently diverged close to 3.5
> > > > > bya, both have ribosomes in which the big chunks of rRNA have NOT been
> > > > > replaced in all that time.
>
> > > > > Datum 3: virtually all ribozymes besides the ribosomes were replaced
> > > > > in a mere half a billion years according to the prevailing hypothesis.
>
> > > > > Conclusion: those who cling to the prevailing hypothesis need to
> > > > > seriously ask whether the replacement in Datum 3 was done by
> > > > > intelligent agents.

> > > Note the words, "seriously ask whether," and then ask yourself how far
> > > you intend to retreat towards the impregnable fortress I mention
> > > below.
>
> > The words, "those who cling to the prevailing hypothesis need to
> > seriously ask whether..." do not change - in fact they emphasize - the
> > obvious implication that *you* think consideration of intervention by
> > intelligent agents follows from your proposed data.
>
> Yes, and the operative word is "consideration."  Not agreement--
> consideration.

Nor was "agreement" a word anyone else used.

> > This connection would seem to be an important, if not critical,
> > component of your thesis. Why would you choose not to expound upon it,

<snipped for continued evasion and irrelevance>

> > instead descending once again into imagined victimization and
> > accusations?
>
> > Perhaps you'd like to give it another, more substantive, shot? I'm
> > interested to hear your answer.
>
> Your snipping of Datum 1 suggests just WHY you are interested, and
> it's not for substantive reasons, apparently.

I snipped "Datum 1" because it was second-hand chatter that was
immaterial to how your thesis follows from the empirical data. Can you
please try to focus on the issues?

<snipped for irrelevance>

RLC

[Ray Martinez]

Very astute observation, Peter. You just described Robert Camp to a
tee! He's a pretty good polemicist.

As a quick aside, regarding thread topic. Have you read Meyer's
"Signature In The Cell"? His treatment of abiogenesis is masterly. The
proposition, as he has shown, is simply impossible.
Too many paradoxes to overcome (and all is needed is one). Life MUST
have had an Intelligent origin. The material assumptions of the ToE
are falsified.

Ray

[pnyikos]

I think it's more appropriate to call it a case of a person sellling
his scientific birthright for a mess of pottage, when he cravenly
capitulated to his YEC employers..

Until that point, he seemed to be as levelheaded and objective as
Behe.

Before you rip into Behe, let me tell you that I am correcting lots
of dubious and outright false claims about him on the thread I
referred to in reply to Camp.

I was referring specifically to the following post, but my replies to
"Prof. Weird" show many more.

http://groups.google.com/group/talk.origins/msg/f01285f76f2b4d6a

I'd appreciate it if you would take a look at my posts to that thread
before duplicating some of those dubious and false claims.

Peter Nyikos

[pnyikos]

On Jun 27, 2:06 pm, Robert Camp <robertlc...@hotmail.com> wrote:
> On Jun 27, 10:47 am, pnyikos <nyik...@bellsouth.net> wrote:
>
> > On Jun 26, 11:18 pm, Robert Camp <robertlc...@hotmail.com> wrote:
>
> > > On Jun 26, 4:49 pm, pnyikos <nyik...@bellsouth.net> wrote:
>
> > > > On Jun 26, 5:24 pm, John Harshman <jharsh...@pacbell.net> wrote:
>
> > > > > pnyikos wrote:
>
> > > <snip>
>
> <snipped for irrelevance>
>
> >  But in another way, you have helped me, by demonstrating (along with
> > Martinez and Hemidactylus) that just because a thread has been a back-
> > and-forth between two people for a long time, it does NOT mean that
> > those are the only two people following the thread.
>
> No one thinks that.

Actions speak louder than words. Case in point: the action you label
as follows:

> <snipped for irrelevance>

Reposted to show what astronomical standards you have for
"relevance". [Harshman shares them, by the way. I'm sure he approves
of your characterization of your snip.]

_______________ begin repost________

This is something else that does not occur naturally to Harshman. On
one occasion, when I was making a comment about him in the third
person by way of introducing the topic under discussion, he asked me
whom I was addressing.

My reply went about like this "Isn't it obvious? I'm addressing
anyone who happens to be reading the post." His reply was that he
thought it was just the two of us.

===================== end of repost

Peter Nyikos

[John Harshman]

Robert Camp wrote:
> On Jun 27, 10:47 am, pnyikos <nyik...@bellsouth.net> wrote:
>> On Jun 26, 11:18 pm, Robert Camp <robertlc...@hotmail.com> wrote:
>>
>>> On Jun 26, 4:49 pm, pnyikos <nyik...@bellsouth.net> wrote:
>>>> On Jun 26, 5:24 pm, John Harshman <jharsh...@pacbell.net> wrote:
>>>>> pnyikos wrote:
>>> <snip>
>
> <snipped for irrelevance>
>
>> But in another way, you have helped me, by demonstrating (along with
>> Martinez and Hemidactylus) that just because a thread has been a back-
>> and-forth between two people for a long time, it does NOT mean that
>> those are the only two people following the thread.
>
> No one thinks that. Since we discussed related issues elsewhere, I've
> checked in on this thread now and then. I don't see the revelation
> here.

I will admit to being surprised that anyone was reading.

[Rolf]

Just a quick aside? You are talking about hot news, News of the Century!

In view of your qualifications, I am convinced. Case settled once and for
all. You are right, no one can deny that. No need for more books, Meyer
solved the problem How could that have been kept secret for so long? I had
no clue. What took you so long?

[Mark Isaak]

On 6/27/12 10:47 AM, pnyikos wrote:
> <snip>
>

> You snipped something highly embarrassing to ____ .
> [other examples snipped]

In case you did not know, Peter, your obsessive rudeness reflect poorly
on you, not on anyone else.

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"It is certain, from experience, that the smallest grain of natural
honesty and benevolence has more effect on men's conduct, than the most
pompous views suggested by theological theories and systems." - D. Hume

[Robert Camp]

What good is it having minions if you don't expect them to hang on
every word?

RLC

[John Harshman]

I believe in treating minions well. Expecting them to read this thread
is too cruel.

[Robert Camp]

I know that DVD! They advertise it late at night on TBN.

RLC

[Ray Martinez]

The title of his chair says otherwise.

There is no reason to believe the selection jury was not comprised of
scientists.

Ray

[John Harshman]

The title of his chair says nothing about his scientific publications.
But his CV is up there for you to look at. It's all math.

> There is no reason to believe the selection jury was not comprised of
> scientists.

There is no reason to suppose there was a selection jury at all, unless
you know something I don't.

[Burkhard]

You are by now discussing a mere issue of semantics, but treat it as
if it is a point of substance -though this time round it is more
John's fault than yours. John started with a perfectly sensible and
arguably true point of content: being a mathematician does not
automatically imply that you know how a biologist, chemist or
physicist thinks.

Unfortunately, he expressed it extremely badly, either because he
suddenly forgot everything he had ever learned about nested
hierarchies ( laboratory sciences<natural sciences<quantitative
sciences<sciences) or because he uses an extremely parochial
definition of "science" which may have currency in small parts of the
US academy, but is by and large ignored everywhere else. What makes it
a bit tragic/funny is of course that those chemists and physicist who
also favour a parochial, exclusive definition of science tend to draw
the line in such a way tha much of biology, and especially
evolutionary biology of the type John does, also fall outside the
"science label".

So for his definition of science, he is right, and your example of the
Simonyi chair is a data point that his word usage is not universally
shared (to put it mildly) Simonyi was of course a computer scientists
himself, and in his endowment of the chair used an extremely wide (and
in the words of Dawkins, "enlightened") concept of "science":

"Finally,' science' here means not only the natural and mathematical
sciences but also the history of science and the philosophy of science
as well. However, preference should be given to specialties which
express or achieve their results mainly by symbolic manipulation, such
as Particle physics, Molecular biology, Cosmology, Genetics, Computer
science, Linguistics, Brain research, and, of course Mathematics. The
reason for this is more than a personal predilection. Symbolic
expression enables the highest degree of abstraction and thence the
utilization of powerful mathematical and data processing tools ensure
tremendous progress. At the same time the very means of success tends
to isolate the scientists from the lay audience and prevents the
communication of the results. Considering the profoundly vital
interdependence between the society at large and the scientific world,
the dearth of effective information flow is positively dangerous."

So "mathematics" counts definitely as science for the purpose of the
job, and that is how people at Oxford would understand it anyway.
Doesn't mean that John's definition of science is wrong, definitions
never are, just not widely shared or helpful. Why he thinks he has to
defend a question of definitions with factual claims about the
appointment process at Oxford (_of course_ the appointment is by a
panel made from his peers at Oxford, including scientists from a
variety of disciplines, and a significant number of external referees)
heaven knowns, apart maybe from goading you.

So he is right on the point of substance, but increasingly strange in
defending his somewhat idiosyncratic word use to express it.

[Roger Shrubber]

In a rather bemused spirit, I'm forced to nominate this as a POTM.

[pnyikos]

Since you seem to be on good terms with Burkhard, perhaps you would be
willing to ask him about a reference he gave to a 2007 paper about
which I am keenly interested. I told you about it on another thread,
as follows:

_______________begin excerpt__________
Just last night, on another thread, Burkhard made a claim about Behe
that many others have made but NOBODY has documented to my knowledge.
He gave as a reference a 2007 paper, and ended his sentence with a
colon.

Then there was a big blank space in his post, 7-10 lines deep, at the
end of which was a passage from several posts earlier, on a totally
different topic.

In the intervening days before I got to it NOBODY showed any curiosity
about how that 2007 paper supposedly established this general claim
about Behe.

I requested someone to post a summary last night, and we'll see what
happens.
================== end of excerpt

The Burkhard reference is in this post of his:
http://groups.google.com/group/talk.origins/msg/c6c8a5637f666c36

Here is how he introduced it:

"The problem with the flagellum is that it is not even IC,
as defined by Behe.
Parts can be removed, and it keeps functioning. See Rajagopala et al.
(2007). "The protein network of bacterial motility". Molecular Systems
Biology 3:"

Which parts, I'd like to know, and in what bacteria?

Peter Nyikos

[Ernest Major]

In message
<a269f4f2-219f-4083...@t8g2000yqd.googlegroups.com>,
pnyikos <nyi...@bellsouth.net> writes

>On Jun 28, 9:04 am, Roger Shrubber <rog.shrubb...@gmail.com> wrote:
>> Burkhard wrote:
>> > On Jun 28, 12:56 am, Ray Martinez<pyramid...@yahoo.com>  wrote:
>> >> On Jun 26, 9:04 pm, John Harshman<jharsh...@pacbell.net>  wrote:
>>
>> >>> Ray Martinez wrote:
>> >>>> On Jun 26, 6:03 pm, John Harshman<jharsh...@pacbell.net>  wrote:
>> >>>>> Ray Martinez wrote:
>> >>>>>> On Jun 26, 2:24 pm, John Harshman<jharsh...@pacbell.net>  wrote:
>> >>>>>>> pnyikos wrote:
>> >>>>>>>> The following May 11 post is reposted because John Harshman
>> >>>>>>>>

>> >>>>>>>> and can no longer easily reply to it.
>> >>>>>>>> It includes a comment from an earlier post, a comment which John
>> >>>>>>>> ignored back then, about something the late el cid said
>> >>>>>>>>shortly before
>> >>>>>>>> his death.  Instead of voicing skepticism about what el cid
>> >>>>>>>>

>> >>>>>>>> he issued a cheap shot which you can read below.
>> >>>>>>>> Later on, in another thread, he even seemed skeptical about el cid
>> >>>>>>>> having said any such thing, and claimed that if he had known
>> >>>>>>>>

That paper is open access.
>
>Peter Nyikos
>
--
alias Ernest Major

[pnyikos]

I forgot to mention that Burkhard has me killfiled, and the way that
other thread is going, he'll never see the request unless someone else
calls it to his attention.

> Since you seem to be on good terms with Burkhard, perhaps you would be
> willing to ask him about a reference he gave to a 2007 paper about
> which I am keenly interested. I told you about it on another thread,
> as follows:

.

[pnyikos]

On Jun 27, 5:18 pm, Mark Isaak <eci...@curioustaxonomyNOSPAM.net>
wrote:

> On 6/27/12 10:47 AM, pnyikos wrote:
>
> > <snip>
>
> > You snipped something highly embarrassing to ____ .
> > [other examples snipped]
>
> In case you did not know, Peter, your obsessive rudeness reflect poorly
> on you, not on anyone else.

With Harshman, it's hard to tell what is more likely to elicit a
meaningful response. Here is a good example, from two days ago. I
thought I was being quite restrained in the following post, but it was
the preceding post that got a meaningful reply from him, not the more
polite one:

______________first included post_____

Newsgroups: talk.origins, alt.agnosticism
From: pnyikos <nyik...@bellsouth.net>
Date: Tue, 26 Jun 2012 11:19:34 -0700 (PDT)
Local: Tues, Jun 26 2012 2:19 pm
Subject: Re: The atheism of J. Coyne Re: Intelligent Design Book Meets
Obstacle

On Jun 13, 2:41 pm, John Harshman <jharsh...@pacbell.net> wrote:

> pnyikos wrote:

> > On Jun 12, 12:30 am, John Harshman <jharsh...@pacbell.net> wrote:
> >> pnyikos wrote:

> >>> On May 31, 1:20 am, John Harshman <jharsh...@pacbell.net> wrote:
> >>>> pnyikos wrote:

...and so on, back and forth, beginning with Harshman saying:

> >>>>>>>>>> For
> >>>>>>>>>> another, you would have to make your chain of probabilities complete.

> >>>>>>>>> What's lacking now, in your estimation?

> >>>>>>>> The stuff I mentioned above.

> >>>>>>> Not all of it surely, not even in your eyes; not the crack about
> >>>>>>> Jesus, for instance.

Before we go on, I'd like to mention that I have reposted that May 11
post on the ribosome, etc. on the protein takeover thread, along with
a few preliminary remarks:

http://groups.google.com/group/talk.origins/msg/daee74b80a2b009b

Now, on to your reply to the sentence about Jesus above:

> >>>>>> You seem oddly sensitive to cracks about Jesus given your professed
> >>>>>> pessimistic agnosticism.

> >>>>> Funny you should acknowledge the validity of the only word ("crack")
> >>>>> that could plausibly lead to this naive conclusion by you.

> >>>> You sure attach bizarre importance to chance phrasing, which wasn't even
> >>>> mine.

> >>> The phrasing "You seem oddly sensitive to cracks about Jesus given
> >>> your professed pessimistic agnosticism." was yours, and yours alone.
> >>> Am I not entitled to attach some importance to it, and to refute it as
> >>> I did above?

I have a hard time making sense of how *I* rather than YOU was
supposed to be attaching bizarre importance to the one word "crack":

> >> The word "crack" was taken from you. You are entitled to refute anything
> >> I say. When do you intend to start?

If you are trying to apply the Socratic method here, you are going
about it all wrong. Let me see whether I can do a better job of it
below.

> > I'm already finished, and you are in denial over the way you made a
> > federal case out of the word "crack" while implicitly acknowledging
> > its appropriateness.
> You are not very good at reading implicit statements, and should
> probably taper off.

Is there anything about my reaction to your remark about Jesus that
led you to think that I was being oddly sensitive to it, besides my
labeling your remark a "crack"?

If not, do you ordinarily think anyone who labels a remark like the
following a "crack" is exhibiting an odd degree of sensitivity to it?

"Jesus wants us to seed the universe? Is this part of
being fruitful and multiplying?"

> > Now, you could re-open the case with a counter-argument, but then you
> > should do me the courtesy of waiting for my counter-counter argument
> > before crowing victory.

> Wait -- you can crow victory any time you want, but I have to wait for
> your counter-argument?

What could possibly have made you think I have such an attitude?

> Just how much does the world revolve around you?

The world of talk.origins probably revolves more around you than it
does around me. After all, you are on the "correct" side of every on-
topic dispute, so your words carry more weight than mine. Do you
disagree?:

Peter Nyikos
======================= end of post

Note how much more aggressive I had been in my preceding post, yet
John was quite up to answering it. In contrast, here is his curt
reply to the above post:

_____________ second included post_____________
Newsgroups: talk.origins, alt.agnosticism
From: John Harshman <jharsh...@pacbell.net>
Date: Tue, 26 Jun 2012 14:15:27 -0700
Local: Tues, Jun 26 2012 5:15 pm
Subject: Re: The atheism of J. Coyne Re: Intelligent Design Book Meets
Obstacle

pnyikos wrote:

This is a placeholder for a reply, just to let you know I saw this
post.
But it contains nothing that needs a reply.

================ end of second included post

[Nashton]

On 06-28-12 1:26 AM, John Harshman wrote:

> Ray Martinez wrote:

>
> There is no reason to suppose there was a selection jury at all, unless
> you know something I don't.
>

"A mathematician is a device for turning coffee into theorems."

[Roger Shrubber]

http://bit.ly/MYxLrE

[pnyikos]

But I've seen his kind enough to know how to handle them after a few
exchanges. Note, by the way, how he is afraid to answer the question
you left in below your sig.

You should like the following post, with which I sent him packing from
another thread:

http://groups.google.com/group/talk.origins/msg/680932ba1943a802

It's the same thread where that exchange took place which I've
reposted in reply to Mark Isaak earlier today.

> As a quick aside, regarding thread topic. Have you read Meyer's
> "Signature In The Cell"?

No, but I've been meaning to do so for some time.

> His treatment of abiogenesis is masterly. The
> proposition, as he has shown, is simply impossible.

I wouldn't say that. But here is something that should interest you:
I've been challenging the talk.origins crowd since 1996 to come up
with even a hypothetical description of how the first bacterium could
have come to be once in a googol of universes like ours, and there
have never been anyone who tried, nor anyone who could cite a book or
a pile of articles or whatever for me where it is done.

> Too many paradoxes to overcome (and all is needed is one). Life MUST
> have had an Intelligent origin. The material assumptions of the ToE
> are falsified.
>
> Ray
>
>

Here is the question Camp won't answer:

> > I asked you there whether you considered yourself to be at least as
> > rational as the average YEC.  The presence of Martinez on this thread,
> > and this new demonstration of irrationality, leads me to ask it again.

Reason is definitely his weak point.

Peter Nyikos

> > > instead descending once again into imagined victimization and
> > > accusations?
>
> > > Perhaps you'd like to give it another, more substantive, shot? I'm
> > > interested to hear your answer.
>
> > Your snipping of Datum 1 suggests just WHY you are interested, and
> > it's not for substantive reasons, apparently.
>
> > But fear not -- I will give it another shot, and then you can judge
> > for yourself whether it meets your standards for "substantive".
>
> > But I'll do it in response to Harshman, who DID behave reasonably from
> > time to time on this  thread.
>

> > Peter Nyikos- Hide quoted text -
>
> - Show quoted text -- Hide quoted text -
>
> - Show quoted text -

[Ray Martinez]

To be quite frank: I don't understand these comments.

> Reason is definitely his weak point.
>

Yes, Robert can be quite unreasonable.

I am an OEC, Peter.

And yes I was following this thread with great interest since the OP
was posted. I don't understand a great deal of the jargon, but to see
evos argue about abiogenesis, among themselves, I find very
entertaining.

Peter: If you have the time and interest may I request that you create
a summary post that outlines your disagreement with John Harshman and
Robert Camp in this thread?

Ray

[pnyikos]

On Jun 26, 5:24 pm, John Harshman <jharsh...@pacbell.net> wrote:
> pnyikos wrote:
>

> > On Apr 3, 6:39 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >> pnyikos wrote:

> >>> On Mar 27, 8:49 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >>>> pnyikos wrote:

> >>>>> On Mar 26, 7:38 pm, John Harshman <jharsh...@pacbell.net> wrote:
>
> > Picking up where I left off yesterday.
>
> >>>>>>>> Of course it might also help the ribozyme's stability or
> >>>>>>>> some other handy thing. It doesn't have to help much.
>
> >>> Is that the role of the 50-plus proteins in ribosomes?  I have to
> >>> wonder why the rRNA in ribosomes did not get replaced in the > 3.5
> >>> billion years after the protein takeover was supposedly nearly
> >>> complete.
>
> >> Do we care? What does this have to do with what we're talking about?

[snip side topic which is the ongoing subject of discussion between us
in sci.bio.paleontology, in a thread I set up this week on cladists,
cladistic systematists, cladophiles, and cladomaniacs, to get to my
original answer:]

> > Datum 1: "el cid," who knew more about biochemistry than either of us
> > is likely to learn in the rest of his lifetime, was convinced that,
> > given five years, it would be possible to design a protein replacement
> > for the ribosome.
>
> If this is anything more than an appeal to authority, what is it?

It's turning out to be a lot of other things, the most recent of which
is a gauge of how astronomical your standards are for the word
"relevant". See the end of this post for why.

> > Datum 2: bacteria and archae, which apparently diverged close to 3.5
> > bya, both have ribosomes in which the big chunks of rRNA have NOT been
> > replaced in all that time.
>
> > Datum 3: virtually all ribozymes besides the ribosomes were replaced
> > in a mere half a billion years according to the prevailing hypothesis.
>
> > Conclusion: those who cling to the prevailing hypothesis need to
> > seriously ask whether the replacement in Datum 3 was done by
> > intelligent agents.

[snip]

> > But you are so far from seriously asking it, that on this very thread
> > you counted your chickens before they were hatched, in the form of a
> > taunt that I don't realize where my reasoning is taking me -- to a
> > denial that evolution is possible at all.

What I was talking about were difficulties in getting a variety of
protein enzymes, in life that lacked any, life very different from the
first prokaryote, and you extrapolated back from life as we know it to
life as we don't know it.

> > The context, after all, was the protein takeover, which may have never
> > happened in the first place, except in the form of nanotechnology by
> > an intelligent, ribozyme-based species of panspermists.
>
> >> If the RNA does the job better than any associated protein, selection
> >> won't favor replacement. Not all conceivable evolutionary paths are
> >> followed.
>
> > That's a huge assumption right there, that the RNA does the job better
> > in the ribosome [see Datum 1 again] but not in the hundreds of
> > ribozymes that presumably did NOT do the job as well as the associated
> > proteins which somehow [Exaptor of the Gaps again] arose to take their
> > places
>
> That isn't an assumption. It's a hypothesis that would explain the data,

It's an assumption until you present some reasoning for it. You can't
just take any half-assed guess, one that just happens to favor your
side of the argument, and label it a scientific hypothesis. You of
all people should know this.

> if true. But let's suppose the designers did all this. Why did they
> leave one ribozyme in place rather than making a clean sweep? Same
> problem, or non-problem, either way.

The two problems don't resemble each other at all. You and lots of
other people have stressed in the past that we simply cannot guess the
motivations of alien intelligences; in particular, we can't assume
their motivations resemble any of ours.

In contrast, if the homegrown abiogenesis hypothesis is true, the
blind natural processes that caused almost all the ribozymes to be
replaced in the first half billion years can be presumed to continue
to operate in the remaining 3.5 billion years.

You assumed a far more problematic transition backwards from known
processes of gene duplication and subsequent divergence of highly
specific enzymes, to a world in which there were no protein enzymes to
kick-start the process.

> [snip a few irrelevant bits]

Those bits bore directly on Datum 1, and whether they are relevant or
not depends on whether you cling to your new-found near-certainty that
"el cid" was dead wrong about what he thought he could do, or go back
to not seeming to have any problem with the idea, like in the part
that you snipped:

_________________repost of relevant portion_______

> > "el cid" claimed that he could find proteins that adequately
> > substitute for the rRNA if he were given five years.
> > Having no inkling that he was soon to die, I countered with "You and
> > what team of Nobel Laureates?" I would have gone a little easier on
> > him if I had known he was in the last stages of pancreatic cancer, but
> > I would have been just as skeptical.
>
> > You seemed to think it could be done in five years, but if so, why
> > didn't it happen by natural selection?
>
> This is in the line of "If we come from monkeys, why are there still
> monkeys?"; I had thought more of you than that.
================= end of repost

You not only did not protest me saying "You seemed to think it could
be done in five years," you ridiculed me for what followed.

So, what does the John Harshman of today think of how easy or how hard
the replacement of the ribosome is, whether by blind nature or by
intelligent humans?

Peter Nyikos

[pnyikos]

You'd think from Harshman's reaction, though, that he read it as
"agreement", wouldn't you, Ray?

> > > > > This connection would seem to be an important, if not critical,
> > > > > component of your thesis. Why would you choose not to expound upon it,
>
> > > > Thank you for this new demonstration of how you think like a
> > > > polemicist rather than a scientist.  I caught you at it yesterday, in
> > > > another thread that featured a bizarre treatment by you of a paragraph
> > > > from an old (1918) paper by Muller.

Camp fought back, but I gave him a solid drubbing last night:

http://groups.google.com/group/talk.origins/msg/2b46f2e51ff82ae0

He's putting up a feeble resistance, but he's had to snip most of what
I wrote and feign incomprehension about what I had meant by
"unambiguous"--he chose to perversely interpret it as
"unobjectionable".

You mean in this last paragraph? Look at it this way: since you are
an OEC [I couldn't recall whether you were that or a YEC] you are at
least in that respect more rational than the average YEC.

In other respects? I'd rather not say, but I'll say this much for
you: you do seem more rational most of the time than Camp does all the
time -- at least, in the posts I've seen from the two of you so far.

I gave him a pretty solid drubbing last night, here:

> > Reason is definitely his weak point.
>
> Yes, Robert can be quite unreasonable.

Have you ever seen him reasonable about anything? I may have, but if
so, I can't recall any cases right now.

> I am an OEC, Peter.
>
> And yes I was following this thread with great interest since the OP
> was posted. I don't understand a great deal of the jargon, but to see
> evos argue about abiogenesis, among themselves, I find very
> entertaining.
>
> Peter: If you have the time and interest may I request that you create
> a summary post that outlines your disagreement with John Harshman and
> Robert Camp in this thread?

That would be difficult. Take a look at my last reply to John, only
an hour or so ago, and my reply to Mark Isaak earlier today. John's
been quite inconsistent, and apt to run away from me at unpredictable
times.

In contrast, Camp is on the way to becoming a "useful idiot" to the
anti-ID zealots. He's hardly worth more of a summary than I already
gave in the post with which I sent him packing from one thread,
mentioned above last time around.

Peter Nyikos

[John Harshman]

Nope, just an appeal to authority. I don't consider appeals to authority
to be relevant.

>>> Datum 2: bacteria and archae, which apparently diverged close to 3.5
>>> bya, both have ribosomes in which the big chunks of rRNA have NOT been
>>> replaced in all that time.
>>> Datum 3: virtually all ribozymes besides the ribosomes were replaced
>>> in a mere half a billion years according to the prevailing hypothesis.
>>> Conclusion: those who cling to the prevailing hypothesis need to
>>> seriously ask whether the replacement in Datum 3 was done by
>>> intelligent agents.
>
> [snip]
>
>>> But you are so far from seriously asking it, that on this very thread
>>> you counted your chickens before they were hatched, in the form of a
>>> taunt that I don't realize where my reasoning is taking me -- to a
>>> denial that evolution is possible at all.
>
> What I was talking about were difficulties in getting a variety of
> protein enzymes, in life that lacked any, life very different from the
> first prokaryote, and you extrapolated back from life as we know it to
> life as we don't know it.

What with all the snippage and rearrangement and such, I've completely
lost what your message may be here.

>>> The context, after all, was the protein takeover, which may have never
>>> happened in the first place, except in the form of nanotechnology by
>>> an intelligent, ribozyme-based species of panspermists.
>>>> If the RNA does the job better than any associated protein, selection
>>>> won't favor replacement. Not all conceivable evolutionary paths are
>>>> followed.
>>> That's a huge assumption right there, that the RNA does the job better
>>> in the ribosome [see Datum 1 again] but not in the hundreds of
>>> ribozymes that presumably did NOT do the job as well as the associated
>>> proteins which somehow [Exaptor of the Gaps again] arose to take their
>>> places
>> That isn't an assumption. It's a hypothesis that would explain the data,
>
> It's an assumption until you present some reasoning for it. You can't
> just take any half-assed guess, one that just happens to favor your
> side of the argument, and label it a scientific hypothesis. You of
> all people should know this.

A hypothesis is just that: a hypothesis. You don't need reasoning in
order to advance a hypothesis. It has the advantage of making sense of
the data, though there are other possible hypotheses with the same
advantage. Testing it would be difficult, of course.

>> if true. But let's suppose the designers did all this. Why did they
>> leave one ribozyme in place rather than making a clean sweep? Same
>> problem, or non-problem, either way.
>
> The two problems don't resemble each other at all. You and lots of
> other people have stressed in the past that we simply cannot guess the
> motivations of alien intelligences; in particular, we can't assume
> their motivations resemble any of ours.

The aliens left the ribosome alone because they're just funny that way?
So you're hiding behind their incomprehensibility? The problem here is
that their inscrutable nature makes them compatible with any data
whatsoever. It's just like goddidit in that respect. You have removed
your aliens from the ability of science to consider. I presume that was
not your intent.

> In contrast, if the homegrown abiogenesis hypothesis is true, the
> blind natural processes that caused almost all the ribozymes to be
> replaced in the first half billion years can be presumed to continue
> to operate in the remaining 3.5 billion years.

Sure. But there could be reasons why the ribosome is entrenched and hard
to replace. First, we shouldn't assume that there is a protein-based
ribosome that would be superior to the RNA one. Second, there is not
guaranteed to be a selectable pathway between every pair of points in
genetic space. So you can't just say that the existence of ribosomes
falsifies recplacement of ribozymes by proteins in other cases.

> You assumed a far more problematic transition backwards from known
> processes of gene duplication and subsequent divergence of highly
> specific enzymes, to a world in which there were no protein enzymes to
> kick-start the process.

I don't understand this last paragraph. Could you explain?

>> [snip a few irrelevant bits]
>
> Those bits bore directly on Datum 1, and whether they are relevant or
> not depends on whether you cling to your new-found near-certainty that
> "el cid" was dead wrong about what he thought he could do, or go back
> to not seeming to have any problem with the idea, like in the part
> that you snipped:
>
> _________________repost of relevant portion_______
>
>>> "el cid" claimed that he could find proteins that adequately
>>> substitute for the rRNA if he were given five years.
>>> Having no inkling that he was soon to die, I countered with "You and
>>> what team of Nobel Laureates?" I would have gone a little easier on
>>> him if I had known he was in the last stages of pancreatic cancer, but
>>> I would have been just as skeptical.
>>> You seemed to think it could be done in five years, but if so, why
>>> didn't it happen by natural selection?
>> This is in the line of "If we come from monkeys, why are there still
>> monkeys?"; I had thought more of you than that.
> ================= end of repost
>
> You not only did not protest me saying "You seemed to think it could
> be done in five years," you ridiculed me for what followed.

Just because I choose not to ridicule some of the things you say doesn't
mean I agree with them. Sometimes I ignore your statements. Ridiculing
everything would waste time. But no, since you ask, I don't agree with
that statement, and never have agreed.

If it's any consolation, I can't make sense of my comment about the
monkeys based on the bit you have quoted here. Perhaps I was talking
about something else, something you haven't quoted.

> So, what does the John Harshman of today think of how easy or how hard
> the replacement of the ribosome is, whether by blind nature or by
> intelligent humans?

I have no strong opinion on how hard it would be for nature to do, given
time. I do strongly doubt that intelligent humans could do it at all
with current technology, let alone within 5 years. I could be wrong, but
I don't think anyone has ever designed a working protein from scratch.
There have been in vitro selection experiments that resulting in
function (selectable, though weak) from random sequences, but that's as
close as I know of. What do you know?

[Rolf]

"pnyikos" <nyi...@bellsouth.net> wrote in message
news:195d214a-2524-4bbc...@3g2000vbx.googlegroups.com...

What? abandoned your old earth young biosphere theory?

>> And yes I was following this thread with great interest since the OP
>> was posted. I don't understand a great deal of the jargon, but to see
>> evos argue about abiogenesis, among themselves, I find very
>> entertaining.
>>
>> Peter: If you have the time and interest may I request that you create
>> a summary post that outlines your disagreement with John Harshman and
>> Robert Camp in this thread?
>

Your own disagreeement not sufficient?

[pnyikos]

On Jun 30, 6:53 am, "Rolf" <rolf.aalb...@gmail.com> wrote:
> "pnyikos" <nyik...@bellsouth.net> wrote in message

Rolf, is there some reason why you are piggybacking on my reply to
Martinez instead of replying to him directly?

You haven't replied to the one reply I've made to you on this thread.
I take it we are in agreement that Dembski has sold his scientific
birthright for a mess of pottage, cooked up by some fundie institution
that employs him and insists on a YEC stance and literal
interpretation of Genesis to where the Noahide flood is worldwide,
etc.

Peter Nyikos

[pnyikos]

On Jun 29, 11:44 am, John Harshman <jharsh...@pacbell.net> wrote:
> pnyikos wrote:
> > On Jun 26, 5:24 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >> pnyikos wrote:
>
> >>> On Apr 3, 6:39 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >>>> pnyikos wrote:
> >>>>> On Mar 27, 8:49 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >>>>>> pnyikos wrote:

> >>>>> I have to
> >>>>> wonder why the rRNA in ribosomes did not get replaced in the > 3.5
> >>>>> billion years after the protein takeover was supposedly nearly
> >>>>> complete.
> >>>> Do we care? What does this have to do with what we're talking about?
>
> > [snip side topic which is the ongoing subject of discussion between us
> > in sci.bio.paleontology, in a thread I set up this week on cladists,
> > cladistic systematists, cladophiles, and cladomaniacs, to get to my
> > original answer:]
>
> >>> Datum 1: "el cid," who knew more about biochemistry than either of us
> >>> is likely to learn in the rest of his lifetime, was convinced that,
> >>> given five years, it would be possible to design a protein replacement
> >>> for the ribosome.
> >> If this is anything more than an appeal to authority, what is it?

The following refers to something ("end of this post") that will
appear in the second reply to this post of yours, John.

> > It's turning out to be a lot of other things, the most recent of which
> > is a gauge of how astronomical your standards are for the word
> > "relevant".  See the end of this post for why.
>
> Nope, just an appeal to authority.

All wrong. The part about "el cid" was an introduction to the actual
point, about which I had every reason to believe, at the time I wrote
it, that you were MORE in agreement with him than I was. The actual
point stands or falls regardless of what you, or I, or "el cid"
believes or said he believes.

> I don't consider appeals to authority
> to be relevant.

I wonder about that. Lately you've been coming across as an
opportunist, and this, along with the sentence that preceded it, looks
like an example of that kind of behavior.

> >>> Datum 2: bacteria and archae, which apparently diverged close to 3.5
> >>> bya, both have ribosomes in which the big chunks of rRNA have NOT been
> >>> replaced in all that time.
.
> >>> Datum 3: virtually all ribozymes besides the ribosomes were replaced
> >>> in a mere half a billion years according to the prevailing hypothesis.
.
> >>> Conclusion: those who cling to the prevailing hypothesis need to
> >>> seriously ask whether the replacement in Datum 3 was done by
> >>> intelligent agents.
>
> > [snip]
>
> >>> But you are so far from seriously asking it, that on this very thread
> >>> you counted your chickens before they were hatched, in the form of a
> >>> taunt that I don't realize where my reasoning is taking me -- to a
> >>> denial that evolution is possible at all.
>
> > What I was talking about were difficulties in getting a variety of
> > protein enzymes, in life that lacked any, life very different from the
> > first prokaryote, and you extrapolated back from life as we know it to
> > life as we don't know it.
>
> What with all the snippage and rearrangement and such, I've completely
> lost what your message may be here.

Completely? You ought to remember the gist of your taunt, even though
it was three months ago -- unless that was a particularly crass
example of opportunism.

Anyway, do you disagree with ANYTHING in the two paragraphs of mine
that preceded your "What with all..;."? Once we get that cleared up,
I'll tell you what my message was, if you still haven't figured it
out.

> >>> The context, after all, was the protein takeover, which may have never
> >>> happened in the first place, except in the form of nanotechnology by
> >>> an intelligent, ribozyme-based species of panspermists.
> >>>> If the RNA does the job better than any associated protein, selection
> >>>> won't favor replacement. Not all conceivable evolutionary paths are
> >>>> followed.
> >>> That's a huge assumption right there, that the RNA does the job better
> >>> in the ribosome [see Datum 1 again] but not in the hundreds of
> >>> ribozymes that presumably did NOT do the job as well as the associated
> >>> proteins which somehow [Exaptor of the Gaps again] arose to take their
> >>> places
> >> That isn't an assumption. It's a hypothesis that would explain the data,
>
> > It's an assumption until you present some reasoning for it. You can't
> > just take any half-assed guess, one that just happens to favor your
> > side of the argument, and label it a scientific hypothesis. You of
> > all people should know this.
>
> A hypothesis is just that: a hypothesis. You don't need reasoning in
> order to advance a hypothesis.

Nor anything besides opportunism, it would seem.

> It has the advantage of making sense of
> the data, though there are other possible hypotheses with the same
> advantage. Testing it would be difficult, of course.
>
> >> if true. But let's suppose the designers did all this. Why did they
> >> leave one ribozyme in place rather than making a clean sweep? Same
> >> problem, or non-problem, either way.
>
> > The two problems don't resemble each other at all. You and lots of
> > other people have stressed in the past that we simply cannot guess the
> > motivations of alien intelligences; in particular, we can't assume
> > their motivations resemble any of ours.

Shortly after I posted the above, there occurred to me what is
probably the simplest and most parsimonious explanation, going back to
the distinction between designing an organism from scratch and doing
it piecemeal, and my hypothesis that the panspermists seeded something
on the order of a million planets, over a time span of (very roughly,
give or take one or two orders of magnitude) the same number of
years..

Is that enough of a hint for you, or will you profess that for the
life of you, you can't see what I'm getting at?

[snip something to be addressed in my next reply]

> > In contrast, if the homegrown abiogenesis hypothesis is true, the
> > blind natural processes that caused almost all the ribozymes to be
> > replaced in the first half billion years can be presumed to continue
> > to operate in the remaining 3.5 billion years.
>
> Sure. But there could be reasons why the ribosome is entrenched and hard
> to replace. First, we shouldn't assume that there is a protein-based
> ribosome that would be superior to the RNA one.

The near-ubiquitousness of the protein takeover does seem to favor
that hypothesis, though.

See, I call it a hypothesis because I *DO* provide reasoning for it.
This reasoning might not rise to the exalted status of what you call
"relevant" or "an argument," but at least it is much further along
the line towards these standards of yours than the guess you made up
there.

Concluded in my next reply.

Peter Nyikos

[John Harshman]

pnyikos wrote:

>>>>> But you are so far from seriously asking it, that on this very thread
>>>>> you counted your chickens before they were hatched, in the form of a
>>>>> taunt that I don't realize where my reasoning is taking me -- to a
>>>>> denial that evolution is possible at all.
>>> What I was talking about were difficulties in getting a variety of
>>> protein enzymes, in life that lacked any, life very different from the
>>> first prokaryote, and you extrapolated back from life as we know it to
>>> life as we don't know it.
>> What with all the snippage and rearrangement and such, I've completely
>> lost what your message may be here.
>
> Completely? You ought to remember the gist of your taunt, even though
> it was three months ago -- unless that was a particularly crass
> example of opportunism.
>
> Anyway, do you disagree with ANYTHING in the two paragraphs of mine
> that preceded your "What with all..;."? Once we get that cleared up,
> I'll tell you what my message was, if you still haven't figured it
> out.

The first paragraph is too pointless to discuss. As for the second, I
agree that you were talking about the difficulties of designing life
with proteins when your sort of life lacks them.

>>>> if true. But let's suppose the designers did all this. Why did they
>>>> leave one ribozyme in place rather than making a clean sweep? Same
>>>> problem, or non-problem, either way.
>>> The two problems don't resemble each other at all. You and lots of
>>> other people have stressed in the past that we simply cannot guess the
>>> motivations of alien intelligences; in particular, we can't assume
>>> their motivations resemble any of ours.
>
> Shortly after I posted the above, there occurred to me what is
> probably the simplest and most parsimonious explanation, going back to
> the distinction between designing an organism from scratch and doing
> it piecemeal, and my hypothesis that the panspermists seeded something
> on the order of a million planets, over a time span of (very roughly,
> give or take one or two orders of magnitude) the same number of
> years..
>
> Is that enough of a hint for you, or will you profess that for the
> life of you, you can't see what I'm getting at?

I'm tired of hints. If you have something to say, just say it. Your
little games are boring me here.

> [snip something to be addressed in my next reply]
>
>>> In contrast, if the homegrown abiogenesis hypothesis is true, the
>>> blind natural processes that caused almost all the ribozymes to be
>>> replaced in the first half billion years can be presumed to continue
>>> to operate in the remaining 3.5 billion years.
>> Sure. But there could be reasons why the ribosome is entrenched and hard
>> to replace. First, we shouldn't assume that there is a protein-based
>> ribosome that would be superior to the RNA one.
>
> The near-ubiquitousness of the protein takeover does seem to favor
> that hypothesis, though.

I don't believe it does. RNA still has multiple functions in our
metabolism, especially in those parts that deal with other RNA. The fact
that we have rRNA and tRNA instead of rPeptides and tPeptides might say
something about the usefulness of RNA in processing RNA.

> See, I call it a hypothesis because I *DO* provide reasoning for it.
> This reasoning might not rise to the exalted status of what you call
> "relevant" or "an argument," but at least it is much further along
> the line towards these standards of yours than the guess you made up
> there.

In the near future, I'm going to start snipping all the irrelevant
boasting and accusations, just to see if we can get this focused a bit
better on the point, if any.

[pnyikos]

On Jun 29, 11:44 am, John Harshman <jharsh...@pacbell.net> wrote:
> pnyikos wrote:
> > On Jun 26, 5:24 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >> pnyikos wrote:
>

I am repeating a bit from my first reply to establish continuity.

> >>> On Apr 3, 6:39 pm, John Harshman <jharsh...@pacbell.net> wrote:

> >>>> If the RNA does the job better than any associated protein, selection
> >>>> won't favor replacement. Not all conceivable evolutionary paths are
> >>>> followed.
>
> >>> That's a huge assumption right there, that the RNA does the job better
> >>> in the ribosome [see Datum 1 again] but not in the hundreds of
> >>> ribozymes that presumably did NOT do the job as well as the associated
> >>> proteins which somehow [Exaptor of the Gaps again] arose to take their

> >>> places.

[...]

> >> But let's suppose the designers did all this. Why did they
> >> leave one ribozyme in place rather than making a clean sweep? Same
> >> problem, or non-problem, either way.
>
> > The two problems don't resemble each other at all. You and lots of
> > other people have stressed in the past that we simply cannot guess the
> > motivations of alien intelligences; in particular, we can't assume
> > their motivations resemble any of ours.

>
> The aliens left the ribosome alone because they're just funny that way?

Where do you get that out of what I wrote?

> So you're hiding behind their incomprehensibility?

No, behind various incidents in your past (opportunistic?) behavior.
When (for example) I suggested less than a week after I returned to
talk.origins, that the bacterial flagellum might have a "Kilroy was
here" aspect to it, you took it in the worst possible way, as
suggesting that the panspermists have a character trait that you
loathe in "gods"-- which I suspect includes YOUR concept of the
Christian God.

http://groups.google.com/group/talk.origins/msg/c86de03485525941

But that was just the first thing that popped into my mind, and I was
in a hurry when I wrote the post to which you are replying. See my
first reply, less than an hour ago, for some hints as to an actual
hypothesis that undermines your "Same problem..." assertion.

>The problem here is
> that their inscrutable nature makes them compatible with any data
> whatsoever. It's just like goddidit in that respect. You have removed
> your aliens from the ability of science to consider. I presume that was
> not your intent.

For someone who makes that presumption, you sure made a lot of
contrary noises before announcing it.

> > In contrast, if the homegrown abiogenesis hypothesis is true, the
> > blind natural processes that caused almost all the ribozymes to be
> > replaced in the first half billion years can be presumed to continue
> > to operate in the remaining 3.5 billion years.
>
> Sure. But there could be reasons why the ribosome is entrenched and hard
> to replace.

[snip something dealt with in first reply]

> Second, there is not
> guaranteed to be a selectable pathway between every pair of points in
> genetic space.

This sounds opportunistic, in the light of your "Exaptor of the Gaps"-
style assertions earlier in this thread, and also in light of what
transpired between us in that post whose url I gave up there:

________excerpt from end of post______

> Where is there even a hypothetical pathway to a working gram-negative
> purple bacteria flagellum to be found?

The question was about what research a panspermy hypothesis would
stimulate. I don't see any of that in your post. As for your
question,
arguments from incredulity are no more effective in panspermy than in
creationism.
============== end of excerpt ================

Or was "arguments from incredulity" the real instance of opportunism?
Pick your poison.

>So you can't just say that the existence of ribosomes
> falsifies recplacement of ribozymes by proteins in other cases.

My dear Watson, it wasn't "falsification" that I was aiming at, just
the basic thesis that directed pasnpermia should be taken seriously.

> > You assumed a far more problematic transition backwards from known
> > processes of gene duplication and subsequent divergence of highly
> > specific enzymes, to a world in which there were no protein enzymes to
> > kick-start the process.
>
> I don't understand this last paragraph. Could you explain?

You and "el cid" both have protested against my label of "wild
extrapolation" [or words to that effect] to characterize the bald
assertion that the processes that account for biological evolution
from the first prokaryote on [and especially from the first metazoan
on] probably explain also the stages before the first prokaryote.

My starting point, though, is a time where there were no sophisticated
protein enzymes for an "Exaptor of the Gaps:" argument to work on.
And the thing that really makes those arguments effective is the
phenomenon of gene duplication and subsequent divergence, isn't it?

> >> [snip a few irrelevant bits]
>
> > Those bits bore directly on Datum 1, and whether they are relevant or
> > not depends on whether you cling to your new-found near-certainty that
> > "el cid" was dead wrong about what he thought he could do, or go back
> > to not seeming to have any problem with the idea, like in the part
> > that you snipped:
>
> > _________________repost of relevant portion_______
>
> >>> "el cid" claimed that he could find proteins that adequately
> >>> substitute for the rRNA if he were given five years.
> >>> Having no inkling that he was soon to die, I countered with "You and
> >>> what team of Nobel Laureates?"  I would have gone a little easier on
> >>> him if I had known he was in the last stages of pancreatic cancer, but
> >>> I would have been just as skeptical.
> >>> You seemed to think it could be done in five years, but if so, why
> >>> didn't it happen by natural selection?
> >> This is in the line of "If we come from monkeys, why are there still
> >> monkeys?"; I had thought more of you than that.
> > ================= end of repost
>
> > You not only did not protest me saying "You seemed to think it could
> > be done in five years," you ridiculed me for what followed.
>
> Just because I choose not to ridicule some of the things you say doesn't
> mean I agree with them.

Very funny.

> Sometimes I ignore your statements.

Ignoring such an obviously relevant issue as the ease or difficulty of
producing a protein ribosome, especially after I stated that YOU
seemed to think it was easy, seems totally out of character for you.

> Ridiculing
> everything would waste time. But no, since you ask, I don't agree with
> that statement, and never have agreed.
>
> If it's any consolation, I can't make sense of my comment about the
> monkeys based on the bit you have quoted here. Perhaps I was talking
> about something else, something you haven't quoted.

The whole theme, all through the post from which it is quoted, was the
ease or difficulty of replacing the ribosome by protein enzymes, with
natural selection having failed to do it for 3 billion years or more
after a hypothesized [by anyone who does not take panspermia
seriously] 500 million or fewer years for the protein takeover to be
essentially complete.

And so your "monkeys" crack seems to have been just another example of
opportunism by you.

> > So, what does the John Harshman of today think of how easy or how hard
> > the replacement of the ribosome is, whether by blind nature or by
> > intelligent humans?
>
> I have no strong opinion on how hard it would be for nature to do, given
> time.

Enough time, there's the rub. Evidently it is going to take more time
than it will take for the sun to make it too hot for life on earth.
Funny how it took so little time for the hypothesized "Exaptor of the
Gaps" process to evolve almost all other enzymes.

> I do strongly doubt that intelligent humans could do it at all
> with current technology, let alone within 5 years. I could be wrong, but
> I don't think anyone has ever designed a working protein from scratch.
> There have been in vitro selection experiments that resulting in
> function (selectable, though weak) from random sequences, but that's as
> close as I know of. What do you know?

I've seen claims of some major success in the opposite direction, of
finding a ribozyme that does a very nice function; just a few months
ago. I'm afraid I've mislaid the reference, though.

The point of the article, though, was that it was done by using a very
clever search through the "space" of all possible RNA sequences, no
more "random" than the hypothesized production of the first really
sophisticated enzymes by natural processes.

Peter Nyikos

[pnyikos]

On Jul 3, 9:21 am, John Harshman <jharsh...@pacbell.net> wrote:
> pnyikos wrote:
> >>>>> But you are so far from seriously asking it, that on this very thread
> >>>>> you counted your chickens before they were hatched, in the form of a
> >>>>> taunt that I don't realize where my reasoning is taking me -- to a
> >>>>> denial that evolution is possible at all.
> >>> What I was talking about were difficulties in getting a variety of
> >>> protein enzymes, in life that lacked any, life very different from the
> >>> first prokaryote, and you extrapolated back from life as we know it to
> >>> life as we don't know it.
> >> What with all the snippage and rearrangement and such, I've completely
> >> lost what your message may be here.
>
> > Completely?  You ought to remember the gist of your taunt, even though
> > it was three months ago -- unless that was a particularly crass
> > example of opportunism.
>
> > Anyway, do you disagree with ANYTHING in the two paragraphs of mine
> > that preceded your "What with all..;."?  Once we get that cleared up,
> > I'll tell you what my message was, if you still haven't figured it
> > out.
>
> The first paragraph is too pointless to discuss.

"pointless" looks like another example of opportunism on your part, to
evade responsibility for a particularly destructive game of yours,
described in the selfsame paragraph.

> As for the second, I
> agree that you were talking about the difficulties of designing life
> with proteins when your sort of life lacks them.

For the benefit of almost all readers, "your sort of life" refers to
one of the three main sub-hypotheses I've advanced, viz. the
"Throomian" hypothesis that the first prokaryote was designed by
aliens whose biochemistry resembled ours with this exception, that
their sophisticated enzymes were all RNA based rather than polypeptide-
based.

But that sort of intelligent design was NOT what my second paragraph
was all about, and the first paragraph should have made that clear.
It was about the difficulty of NATURAL SELECTION producing the first
prokaryote from prebiotic systems of molecules that also lacked
sophisticated enzymes.

>
>
>
> >>>> if true. But let's suppose the designers did all this. Why did they
> >>>> leave one ribozyme in place rather than making a clean sweep? Same
> >>>> problem, or non-problem, either way.
> >>> The two problems don't resemble each other at all. You and lots of
> >>> other people have stressed in the past that we simply cannot guess the
> >>> motivations of alien intelligences; in particular, we can't assume
> >>> their motivations resemble any of ours.
>
> > Shortly after I posted the above, there occurred to me what is
> > probably the simplest and most parsimonious explanation, going back to
> > the distinction between designing an organism from scratch and doing
> > it piecemeal, and my hypothesis that the panspermists seeded something
> > on the order of a million planets, over a time span of (very roughly,
> > give or take one or two orders of magnitude) the same number of
> > years..
>
> > Is that enough of a hint for you, or will you profess that for the
> > life of you, you can't see what I'm getting at?
>
> I'm tired of hints. If you have something to say, just say it. Your
> little games are boring me here.

At least I'm not playing destructive games, like the one I refer to up
there, and others you have been playing since the first few days in
December 2010 after my return to talk.origins.

Remember my telling you about my trip down memory lane, in connection
with your exalted concept of "argument"? The hindsight of two and a
half years shed a great deal of light on your *modus operandi* back
there.

Anyway, it should have been obvious: the parsimonious hypothesis is
that the prokaryotes that were sent to earth were an intermediate
stage in the process of replacing ribozymes with polypeptide-based
enzymes. It stands to reason that the RNA-based enzymes that were
easiest to replace were replaced first, and that the ribosome was
itself at an intermediate stage of replacement, with lots of "helper"
proteins already in place.

Besides parsimony, this hypothesis has testability in its favor, at
least in principle: if we ever colonize the galaxy, as you seem to
think is an easy thing to do, and we find life in many stages of
"protein takeover", all with reasonably similar genetic codes, that
would be a big argument in favor of the Throomian sub-hypothesis.

On the other hand, if the takeover is in essentially the same stage as
that of earth, and the genetic code is very similar, that would
strongly support the overall hypothesis of directed panspermia while
all but falsifying the Throomian sub-hypothesis.

A third possible outcome is that we encounter lots of life with
genetic codes all very different from ours. That would all but
falsify all three main sub-hypotheses of directed panspermia,.

And finally, if we find no life after searching a million likely
planets, that would falsify the hypothesis that WE are the result of
evolution from unicellular organisms sent here by directed
panspermists, but would still leave my general hypothesis about the
frequency of directed panspermia largely unscathed.

Does that begin to answer the question I documented in my last reply
to you, of you asking over a year and a half ago, as far as research
suggested by my panspermia hypothesis goes?

> > [snip something to be addressed in my next reply]
>
> >>> In contrast, if the homegrown abiogenesis hypothesis is true, the
> >>> blind natural processes that caused almost all the ribozymes to be
> >>> replaced in the first half billion years can be presumed to continue
> >>> to operate in the remaining 3.5 billion years.
> >> Sure. But there could be reasons why the ribosome is entrenched and hard
> >> to replace. First, we shouldn't assume that there is a protein-based
> >> ribosome that would be superior to the RNA one.
>
> > The near-ubiquitousness of the protein takeover does seem to favor
> > that hypothesis, though.
>
> I don't believe it does. RNA still has multiple functions in our
> metabolism, especially in those parts that deal with other RNA. The fact
> that we have rRNA

What is rRNA used for besides the production of ribosomes and a VERY
few other ribozymes?

> and tRNA instead of rPeptides and tPeptides might say
> something about the usefulness of RNA in processing RNA.

This is so elementary, I don't see why you bother to say it, unless
you are trying to make me look like someone totally ignorant of the
fact that there is no neat match-up between amino acids as there is
between nucleotides, and hence no known way of making polypeptides
play the role of tRNA -- or mRNA or DNA, for that matter.

Or unless you are trying to create a false impression in readers of
what "the protein takeover" is all about.

> > See, I call it a hypothesis because I *DO* provide reasoning for it.
> > This reasoning might not rise to the exalted status of what you call
> > "relevant" or  "an argument," but at least it is much further along
> > the line towards these standards of yours than the guess you made up
> > there.

[snip new paraphrasal of "I, John Harshman, can dish it out, but I
can't take it."]

Peter Nyikos

[John Harshman]

That was not clear to me.

>>>>>> if true. But let's suppose the designers did all this. Why did they
>>>>>> leave one ribozyme in place rather than making a clean sweep? Same
>>>>>> problem, or non-problem, either way.
>>>>> The two problems don't resemble each other at all. You and lots of
>>>>> other people have stressed in the past that we simply cannot guess the
>>>>> motivations of alien intelligences; in particular, we can't assume
>>>>> their motivations resemble any of ours.
>>> Shortly after I posted the above, there occurred to me what is
>>> probably the simplest and most parsimonious explanation, going back to
>>> the distinction between designing an organism from scratch and doing
>>> it piecemeal, and my hypothesis that the panspermists seeded something
>>> on the order of a million planets, over a time span of (very roughly,
>>> give or take one or two orders of magnitude) the same number of
>>> years..

> the parsimonious hypothesis is
> that the prokaryotes that were sent to earth were an intermediate
> stage in the process of replacing ribozymes with polypeptide-based
> enzymes. It stands to reason that the RNA-based enzymes that were
> easiest to replace were replaced first, and that the ribosome was
> itself at an intermediate stage of replacement, with lots of "helper"
> proteins already in place.

Why is this explanation the parsimonious one? What are the alternatives
that you have considered and rejected as less parsiminious?

> Besides parsimony, this hypothesis has testability in its favor, at
> least in principle: if we ever colonize the galaxy, as you seem to
> think is an easy thing to do, and we find life in many stages of
> "protein takeover", all with reasonably similar genetic codes, that
> would be a big argument in favor of the Throomian sub-hypothesis.

Agreed. In fact, sampling a great many planets in various parts of the
galaxy would bear on a lot of what we discuss here. The field of
exobiology, in general, would benefit from data.

> On the other hand, if the takeover is in essentially the same stage as
> that of earth, and the genetic code is very similar, that would
> strongly support the overall hypothesis of directed panspermia while
> all but falsifying the Throomian sub-hypothesis.

Sure.

> A third possible outcome is that we encounter lots of life with
> genetic codes all very different from ours. That would all but
> falsify all three main sub-hypotheses of directed panspermia,.

Yup.

> And finally, if we find no life after searching a million likely
> planets, that would falsify the hypothesis that WE are the result of
> evolution from unicellular organisms sent here by directed
> panspermists, but would still leave my general hypothesis about the
> frequency of directed panspermia largely unscathed.

Not sure about that last one. Haven't you said that this whole
panspermia thing was a long time ago, and the original neighborhood in
which the panspermists worked has been scattered about the galaxy? Are
we likely to find another planet seeded by the same panspermists within
our current local neighborhood, even assuming your hypothesis?

> Does that begin to answer the question I documented in my last reply
> to you, of you asking over a year and a half ago, as far as research
> suggested by my panspermia hypothesis goes?

It would help if you asked intelligible questions. That one has too many
layers. I'm not sure what your last reply is, or what the question you
documented and I asked is. What you should have done is clearly state
the question, and then ask me if it had been answered.

>>> [snip something to be addressed in my next reply]
>>>>> In contrast, if the homegrown abiogenesis hypothesis is true, the
>>>>> blind natural processes that caused almost all the ribozymes to be
>>>>> replaced in the first half billion years can be presumed to continue
>>>>> to operate in the remaining 3.5 billion years.
>>>> Sure. But there could be reasons why the ribosome is entrenched and hard
>>>> to replace. First, we shouldn't assume that there is a protein-based
>>>> ribosome that would be superior to the RNA one.
>>> The near-ubiquitousness of the protein takeover does seem to favor
>>> that hypothesis, though.
>> I don't believe it does. RNA still has multiple functions in our
>> metabolism, especially in those parts that deal with other RNA. The fact
>> that we have rRNA
>
> What is rRNA used for besides the production of ribosomes and a VERY
> few other ribozymes?

rRNA = ribosomal RNA. All it does is make up the main parts of
ribosomes. I don't understand how you could have asked that question, or
where "a very few other ribozymes" comes from. RNA (with no little r in
front), on the other hand, has a number of additional functions, some of
which we aren't sure of, but which seem to involve gene regulation, some
of which is interaction with mRNA.

>> and tRNA instead of rPeptides and tPeptides might say
>> something about the usefulness of RNA in processing RNA.
>
> This is so elementary, I don't see why you bother to say it, unless
> you are trying to make me look like someone totally ignorant of the
> fact that there is no neat match-up between amino acids as there is
> between nucleotides, and hence no known way of making polypeptides
> play the role of tRNA -- or mRNA or DNA, for that matter.

> Or unless you are trying to create a false impression in readers of
> what "the protein takeover" is all about.

I'm trying to suggest that there might be a functional reason why some
RNA-handling functions are handled by RNA rather than by peptides, and
thus why ribosomal RNA has not been replaced by protein.

[John Harshman]

It's just intended to reflect your idea that aliens move in mysterious
ways, their wonders to perform.

Is it too much to ask that you have some concern for the reader (i.e.
me)? I implore you to think about the person you are trying to
communicate with and ask yourself how to make your posts more easily
digested. In this particular case, you have placed a quote here, and
then in another post (where it would have been more appropriate) alluded
to it cryptically. There, I had no idea what you were talking about. You
also tend to create extremely fragmented, not to say atomized, contexts.
And you have a tendency to hint at what you're saying rather than
actually say. All this makes it hard to get your points. If
communication isn't one of your concerns, never mind.

> Or was "arguments from incredulity" the real instance of opportunism?
> Pick your poison.

Again, you hint at what you're saying here rather than actually saying
it. Am I being invited to choose which of two possible sins I have
committed? Or what?

>> So you can't just say that the existence of ribosomes
>> falsifies recplacement of ribozymes by proteins in other cases.
>
> My dear Watson, it wasn't "falsification" that I was aiming at, just
> the basic thesis that directed pasnpermia should be taken seriously.

OK, but I'm not sure why directed panspermia should be taken seriously,
based on anything you've said here. Perhaps you should actually provide
your argument rather than merely alluding to it.

>>> You assumed a far more problematic transition backwards from known
>>> processes of gene duplication and subsequent divergence of highly
>>> specific enzymes, to a world in which there were no protein enzymes to
>>> kick-start the process.
>> I don't understand this last paragraph. Could you explain?
>
> You and "el cid" both have protested against my label of "wild
> extrapolation" [or words to that effect] to characterize the bald
> assertion that the processes that account for biological evolution
> from the first prokaryote on [and especially from the first metazoan
> on] probably explain also the stages before the first prokaryote.

> My starting point, though, is a time where there were no sophisticated
> protein enzymes for an "Exaptor of the Gaps:" argument to work on.
> And the thing that really makes those arguments effective is the
> phenomenon of gene duplication and subsequent divergence, isn't it?

In fact I don't know how the change from an RNA world to modern biology
happened. I don't even know if there was an RNA world, just that we have
what rather look like vestiges of such a world. I don't know how life
arose, and I maintain that we have very few tools for investigating
things that happened before the last common ancestor of extant life. But
I can speculate with the best of them. Can we agree that once there is
at least one protein-coding gene, then the processes of gene duplication
and divergence can happen? I'm still missing the connection between this
and what we're talking about, though.

There you go again, trying to read my mind. Read my mind now, here: I do
not think we could make a functional, protein-based ribosome in 5 years.
Or longer.

>> I have no strong opinion on how hard it would be for nature to do, given
>> time.
>
> Enough time, there's the rub. Evidently it is going to take more time
> than it will take for the sun to make it too hot for life on earth.
> Funny how it took so little time for the hypothesized "Exaptor of the
> Gaps" process to evolve almost all other enzymes.

Perhaps it will never happen because there's no advantage to it
happening, or no pathway by which it could happen. I wish you would stop
with the pejorative "exaptor of the gaps" phrasing. It's pointless.

>> I do strongly doubt that intelligent humans could do it at all
>> with current technology, let alone within 5 years. I could be wrong, but
>> I don't think anyone has ever designed a working protein from scratch.
>> There have been in vitro selection experiments that resulting in
>> function (selectable, though weak) from random sequences, but that's as
>> close as I know of. What do you know?
>
> I've seen claims of some major success in the opposite direction, of
> finding a ribozyme that does a very nice function; just a few months
> ago. I'm afraid I've mislaid the reference, though.
>
> The point of the article, though, was that it was done by using a very
> clever search through the "space" of all possible RNA sequences, no
> more "random" than the hypothesized production of the first really
> sophisticated enzymes by natural processes.

I'd be interested in knowing more about this.

[pnyikos]

On Jul 3, 12:09 pm, John Harshman <jharsh...@pacbell.net

I'm about to embark on a three and a half day weekend, and have only
enough time left for a tiny snippet.

>I wish you would stop
> with the pejorative "exaptor of the gaps" phrasing. It's pointless.

You reap what you sow, Harshman. The phrase is directly linked to
your gratuitous and derogatory crack, earlier in this thread, about my
logic leading me to a denial of evolution.

Until you unambigously retract and disavow that, I will continue to
use the prhrase.

But I won't use it until I've given you a chance to see what you wrote
back then, after my long weekend.

Peter Nyikos

[John Harshman]

pnyikos wrote:
> On Jul 3, 12:09 pm, John Harshman <jharsh...@pacbell.net
>
> I'm about to embark on a three and a half day weekend, and have only
> enough time left for a tiny snippet.
>
>
>> I wish you would stop
>> with the pejorative "exaptor of the gaps" phrasing. It's pointless.
>
> You reap what you sow, Harshman.

> The phrase is directly linked to
> your gratuitous and derogatory crack, earlier in this thread, about my
> logic leading me to a denial of evolution.
>
> Until you unambigously retract and disavow that, I will continue to
> use the prhrase.

So it's a form of childish revenge, then?

[Earle Jones]

In article
<360af163-3722-4034...@v33g2000yqv.googlegroups.com>,

*
What I can't understand, Peter, is why someone like John Harshman would
spend his time arguing with a math major.

earle
*

[nyi...@bellsouth.net]

On Sunday, July 8, 2012 5:00:51 PM UTC-4, Earle Jones wrote:
> In article
> &lt;360af163-3722-4034...@v33g2000yqv.googlegroups.com&gt;,
> pnyikos &lt;nyi...@bellsouth.net&gt; wrote:
>
> &gt; On Jul 3, 9:21�am, John Harshman &lt;jharsh...@pacbell.net&gt; wrote:
> &gt; &gt; pnyikos wrote:
> &gt; &gt; &gt;&gt;&gt;&gt;&gt; But you are so far from seriously asking it, that on this very thread
> &gt; &gt; &gt;&gt;&gt;&gt;&gt; you counted your chickens before they were hatched, in the form of a
> &gt; &gt; &gt;&gt;&gt;&gt;&gt; taunt that I don&#39;t realize where my reasoning is taking me -- to a
> &gt; &gt; &gt;&gt;&gt;&gt;&gt; denial that evolution is possible at all.
> &gt; &gt; &gt;&gt;&gt; What I was talking about were difficulties in getting a variety of
> &gt; &gt; &gt;&gt;&gt; protein enzymes, in life that lacked any, life very different from the
> &gt; &gt; &gt;&gt;&gt; first prokaryote, and you extrapolated back from life as we know it to
> &gt; &gt; &gt;&gt;&gt; life as we don&#39;t know it.
> &gt; &gt; &gt;&gt; What with all the snippage and rearrangement and such, I&#39;ve completely
> &gt; &gt; &gt;&gt; lost what your message may be here.
> &gt; &gt;
> &gt; &gt; &gt; Completely? �You ought to remember the gist of your taunt, even though
> &gt; &gt; &gt; it was three months ago -- unless that was a particularly crass
> &gt; &gt; &gt; example of opportunism.
> &gt; &gt;
> &gt; &gt; &gt; Anyway, do you disagree with ANYTHING in the two paragraphs of mine
> &gt; &gt; &gt; that preceded your &quot;What with all..;.&quot;? �Once we get that cleared up,
> &gt; &gt; &gt; I&#39;ll tell you what my message was, if you still haven&#39;t figured it
> &gt; &gt; &gt; out.
> &gt; &gt;
> &gt; &gt; The first paragraph is too pointless to discuss.
> &gt;
> &gt; &quot;pointless&quot; looks like another example of opportunism on your part, to
> &gt; evade responsibility for a particularly destructive game of yours,
> &gt; described in the selfsame paragraph.
> &gt;
> &gt; &gt; As for the second, I
> &gt; &gt; agree that you were talking about the difficulties of designing life
> &gt; &gt; with proteins when your sort of life lacks them.
> &gt;
> &gt; For the benefit of almost all readers, &quot;your sort of life&quot; refers to
> &gt; one of the three main sub-hypotheses I&#39;ve advanced, viz. the
> &gt; &quot;Throomian&quot; hypothesis that the first prokaryote was designed by
> &gt; aliens whose biochemistry resembled ours with this exception, that
> &gt; their sophisticated enzymes were all RNA based rather than polypeptide-
> &gt; based.
> &gt;
> &gt; But that sort of intelligent design was NOT what my second paragraph
> &gt; was all about, and the first paragraph should have made that clear.
> &gt; It was about the difficulty of NATURAL SELECTION producing the first
> &gt; prokaryote from prebiotic systems of molecules that also lacked
> &gt; sophisticated enzymes.
> &gt;
> &gt; &gt;
> &gt; &gt;
> &gt; &gt;
> &gt; &gt; &gt;&gt;&gt;&gt; if true. But let&#39;s suppose the designers did all this. Why did they
> &gt; &gt; &gt;&gt;&gt;&gt; leave one ribozyme in place rather than making a clean sweep? Same
> &gt; &gt; &gt;&gt;&gt;&gt; problem, or non-problem, either way.
> &gt; &gt; &gt;&gt;&gt; The two problems don&#39;t resemble each other at all. You and lots of
> &gt; &gt; &gt;&gt;&gt; other people have stressed in the past that we simply cannot guess the
> &gt; &gt; &gt;&gt;&gt; motivations of alien intelligences; in particular, we can&#39;t assume
> &gt; &gt; &gt;&gt;&gt; their motivations resemble any of ours.
> &gt; &gt;
> &gt; &gt; &gt; Shortly after I posted the above, there occurred to me what is
> &gt; &gt; &gt; probably the simplest and most parsimonious explanation, going back to
> &gt; &gt; &gt; the distinction between designing an organism from scratch and doing
> &gt; &gt; &gt; it piecemeal, and my hypothesis that the panspermists seeded something
> &gt; &gt; &gt; on the order of a million planets, over a time span of (very roughly,
> &gt; &gt; &gt; give or take one or two orders of magnitude) the same number of
> &gt; &gt; &gt; years..
> &gt; &gt;
> &gt; &gt; &gt; Is that enough of a hint for you, or will you profess that for the
> &gt; &gt; &gt; life of you, you can&#39;t see what I&#39;m getting at?
> &gt; &gt;
> &gt; &gt; I&#39;m tired of hints. If you have something to say, just say it. Your
> &gt; &gt; little games are boring me here.
> &gt;
> &gt; At least I&#39;m not playing destructive games, like the one I refer to up
> &gt; there, and others you have been playing since the first few days in
> &gt; December 2010 after my return to talk.origins.
> &gt;
> &gt; Remember my telling you about my trip down memory lane, in connection
> &gt; with your exalted concept of &quot;argument&quot;? The hindsight of two and a
> &gt; half years shed a great deal of light on your *modus operandi* back
> &gt; there.
> &gt;
> &gt; Anyway, it should have been obvious: the parsimonious hypothesis is
> &gt; that the prokaryotes that were sent to earth were an intermediate
> &gt; stage in the process of replacing ribozymes with polypeptide-based
> &gt; enzymes. It stands to reason that the RNA-based enzymes that were
> &gt; easiest to replace were replaced first, and that the ribosome was
> &gt; itself at an intermediate stage of replacement, with lots of &quot;helper&quot;
> &gt; proteins already in place.
> &gt;
> &gt; Besides parsimony, this hypothesis has testability in its favor, at
> &gt; least in principle: if we ever colonize the galaxy, as you seem to
> &gt; think is an easy thing to do, and we find life in many stages of
> &gt; &quot;protein takeover&quot;, all with reasonably similar genetic codes, that
> &gt; would be a big argument in favor of the Throomian sub-hypothesis.
> &gt;
> &gt; On the other hand, if the takeover is in essentially the same stage as
> &gt; that of earth, and the genetic code is very similar, that would
> &gt; strongly support the overall hypothesis of directed panspermia while
> &gt; all but falsifying the Throomian sub-hypothesis.
> &gt;
> &gt; A third possible outcome is that we encounter lots of life with
> &gt; genetic codes all very different from ours. That would all but
> &gt; falsify all three main sub-hypotheses of directed panspermia,.
> &gt;
> &gt; And finally, if we find no life after searching a million likely
> &gt; planets, that would falsify the hypothesis that WE are the result of
> &gt; evolution from unicellular organisms sent here by directed
> &gt; panspermists, but would still leave my general hypothesis about the
> &gt; frequency of directed panspermia largely unscathed.
> &gt;
> &gt; Does that begin to answer the question I documented in my last reply
> &gt; to you, of you asking over a year and a half ago, as far as research
> &gt; suggested by my panspermia hypothesis goes?
> &gt;
> &gt;
> &gt;
> &gt; &gt; &gt; [snip something to be addressed in my next reply]
> &gt; &gt;
> &gt; &gt; &gt;&gt;&gt; In contrast, if the homegrown abiogenesis hypothesis is true, the
> &gt; &gt; &gt;&gt;&gt; blind natural processes that caused almost all the ribozymes to be
> &gt; &gt; &gt;&gt;&gt; replaced in the first half billion years can be presumed to continue
> &gt; &gt; &gt;&gt;&gt; to operate in the remaining 3.5 billion years.
> &gt; &gt; &gt;&gt; Sure. But there could be reasons why the ribosome is entrenched and hard
> &gt; &gt; &gt;&gt; to replace. First, we shouldn&#39;t assume that there is a protein-based
> &gt; &gt; &gt;&gt; ribosome that would be superior to the RNA one.
> &gt; &gt;
> &gt; &gt; &gt; The near-ubiquitousness of the protein takeover does seem to favor
> &gt; &gt; &gt; that hypothesis, though.
> &gt; &gt;
> &gt; &gt; I don&#39;t believe it does. RNA still has multiple functions in our
> &gt; &gt; metabolism, especially in those parts that deal with other RNA. The fact
> &gt; &gt; that we have rRNA
> &gt;
> &gt; What is rRNA used for besides the production of ribosomes and a VERY
> &gt; few other ribozymes?
> &gt;
> &gt; &gt; and tRNA instead of rPeptides and tPeptides might say
> &gt; &gt; something about the usefulness of RNA in processing RNA.
> &gt;
> &gt; This is so elementary, I don&#39;t see why you bother to say it, unless
> &gt; you are trying to make me look like someone totally ignorant of the
> &gt; fact that there is no neat match-up between amino acids as there is
> &gt; between nucleotides, and hence no known way of making polypeptides
> &gt; play the role of tRNA -- or mRNA or DNA, for that matter.
> &gt;
> &gt; Or unless you are trying to create a false impression in readers of
> &gt; what &quot;the protein takeover&quot; is all about.
> &gt;
> &gt;
> &gt; &gt; &gt; See, I call it a hypothesis because I *DO* provide reasoning for it.
> &gt; &gt; &gt; This reasoning might not rise to the exalted status of what you call
> &gt; &gt; &gt; &quot;relevant&quot; or �&quot;an argument,&quot; but at least it is much further along
> &gt; &gt; &gt; the line towards these standards of yours than the guess you made up
> &gt; &gt; &gt; there.
> &gt;
> &gt; [snip new paraphrasal of &quot;I, John Harshman, can dish it out, but I
> &gt; can&#39;t take it.&quot;]
> &gt;
> &gt; Peter Nyikos
>
> *
> What I can&#39;t understand, Peter, is why someone like John Harshman would

> spend his time arguing with a math major.
>
> earle
> *

Number one, I'm not a math major, and haven't been for over four decades. See my virtual .sig below.

Number two, this topic involves both math and biology, and John knows more about biology than I do, while I know a hell of a lot more math than he does.

Why are you interested in this issue?

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://www.math.sc.edu/~nyikos/
nyikos @ math.sc.edu
Specialty: set-theoretic topology
Ph.D. Carnegie-Mellon University, 1971

[nyi...@bellsouth.net]

Sorry to keep you waiting for so long, John. I'd hoped Gans or Shrubber might provide me with fresh ideas for this thread, but so far it's been a complete bust.

On Thursday, July 5, 2012 12:39:12 PM UTC-4, John Harshman wrote:
> pnyikos wrote:
> &gt; On Jul 3, 12:09 pm, John Harshman &lt;jharsh...@pacbell.net
> &gt;
> &gt; I&#39;m about to embark on a three and a half day weekend, and have only
> &gt; enough time left for a tiny snippet.
> &gt;
> &gt;
> &gt;&gt; I wish you would stop
> &gt;&gt; with the pejorative &quot;exaptor of the gaps&quot; phrasing. It&#39;s pointless.
> &gt;
> &gt; You reap what you sow, Harshman.
>
> &gt; The phrase is directly linked to
> &gt; your gratuitous and derogatory crack, earlier in this thread, about my
> &gt; logic leading me to a denial of evolution.
> &gt;
> &gt; Until you unambigously retract and disavow that, I will continue to
> &gt; use the prhrase.
>
> So it&#39;s a form of childish revenge, then?

On the contrary: your "denial of evolution" was a childish extrapolation from what I wrote about the replacement of ribozymes by intricate polypeptide-based enzymes: there is not even a hint of any evolutionary path that has been presented by anyone that it could have happened in the 500 million years that it supposedly happened. My saying this was what elicited this childish extrapolation from you.

Your sole defense of that wild extrapolation was what I call the Exaptor of the Gaps argument: you haven't the foggiest idea of what *could* have been exapted for what in this hypothetical natural process, and neither does anyone else under the sun. Never mind "was exapted."

The situation is very different for evolution once we are at the prokaryote level. Here, we actually have structures and sequences that we can analyze. And the situation gets better and better the further up the evolutionary hierarchy we go, because the modifications are proportionately far less, and the ideas for what caused them clearer and clearer.

What's more, the further up we go in the evolutionary hierarchy, the less likely the hypothesis of directed panspermia is as a way of explanation. With the Throomian sub-hypothesis, we are back before the protein takeover, with hypothetical beings whose cells use ribozymes instead of protein enzymes, and thus the hypothesis of a "Darwinian" protein takeover becomes unnecessary.

Don't confuse "unnecessary" with "untrue."

[J.J. O'Shea]

On Wed, 27 Jun 2012 17:18:22 -0400, Mark Isaak wrote
(in article <jsftar$o7r$1...@speranza.aioe.org>):

> On 6/27/12 10:47 AM, pnyikos wrote:
>> <snip>
>>

>> You snipped something highly embarrassing to ____ .
>> [other examples snipped]
>
> In case you did not know, Peter, your obsessive rudeness reflect poorly
> on you, not on anyone else.
>
>

Ooh, you shouldn't have said that. Rig for thermonuclear explosion, close
aboard, when Peter sees that...

--
email to oshea dot j dot j at gmail dot com.

[J.J. O'Shea]

On Thu, 28 Jun 2012 14:30:51 -0400, pnyikos wrote
(in article
<21bef83d-de8d-4664...@l32g2000yqc.googlegroups.com>):

> On Jun 27, 5:18ï¿œpm, Mark Isaak <eci...@curioustaxonomyNOSPAM.net>

And, yep, confirmed.

[pnyikos]

On Jul 18, 9:30�am, "J.J. O'Shea" <try.not...@but.see.sig> wrote:
> On Wed, 27 Jun 2012 17:18:22 -0400, Mark Isaak wrote

> (in article <jsftar$o7...@speranza.aioe.org>):

>
> > On 6/27/12 10:47 AM, pnyikos wrote:
> >> <snip>
>
> >> You snipped something highly embarrassing to ____ .
> >> [other examples snipped]
>
> > In case you did not know, Peter, your obsessive rudeness reflect poorly
> > on you, not on anyone else.
>
> Ooh, you shouldn't have said that. Rig for thermonuclear explosion, close
> aboard, when Peter sees that...

I saw it long ago, Rip van O'Shea, and I responded to it too. And
Mark now has his own troubles on the threads involving UC, where he
has compromised his integrity for you and "jillery."

I'm sure the two of you are proud of the extremism you have stimulated
in him and Paul Gans; probably in Mitchell Coffey as well.

Peter Nyikos

[J.J. O'Shea]

On Wed, 18 Jul 2012 13:39:11 -0400, pnyikos wrote
(in article
<345d8318-5ef4-45c0...@t20g2000yqn.googlegroups.com>):

> On Jul 18, 9:30ï¿œam, "J.J. O'Shea" <try.not...@but.see.sig> wrote:
>> On Wed, 27 Jun 2012 17:18:22 -0400, Mark Isaak wrote
>> (in article <jsftar$o7...@speranza.aioe.org>):
>>
>>> On 6/27/12 10:47 AM, pnyikos wrote:
>>>> <snip>
>>
>>>> You snipped something highly embarrassing to ____ .
>>>> [other examples snipped]
>>
>>> In case you did not know, Peter, your obsessive rudeness reflect poorly
>>> on you, not on anyone else.
>>
>> Ooh, you shouldn't have said that. Rig for thermonuclear explosion, close
>> aboard, when Peter sees that...
>
> I saw it long ago, Rip van O'Shea, and I responded to it too. And
> Mark now has his own troubles on the threads involving UC, where he
> has compromised his integrity for you and "jillery."

And here we go again. Another whopper.

>
> I'm sure the two of you are proud of the extremism you have stimulated
> in him and Paul Gans; probably in Mitchell Coffey as well.

'Extremism'? Extremism in the defense of truth is no vice, you silly boy.

>
> Peter Nyikos

[pnyikos]

On Jul 18, 9:30�am, "J.J. O'Shea" <try.not...@but.see.sig> wrote:
> On Thu, 28 Jun 2012 14:30:51 -0400, pnyikos wrote
> (in article

> <21bef83d-de8d-4664-87a2-5cdaa8bbd...@l32g2000yqc.googlegroups.com>):
>
>
>
>
>
> > On Jun 27, 5:18�pm, Mark Isaak <eci...@curioustaxonomyNOSPAM.net>

Said the kangaroo in her pouch,
"Me too!"
-- _Horton Hears a Who_, by Dr. Seuss


Peter Nyikos

[pnyikos]

On Jul 18, 1:50�pm, "J.J. O'Shea" <try.not...@but.see.sig> wrote:
> On Wed, 18 Jul 2012 13:39:11 -0400, pnyikos wrote
> (in article

> <345d8318-5ef4-45c0-9a0e-5b389dc9a...@t20g2000yqn.googlegroups.com>):

>
>
>
>
>
> > On Jul 18, 9:30 am, "J.J. O'Shea" <try.not...@but.see.sig> wrote:
> >> On Wed, 27 Jun 2012 17:18:22 -0400, Mark Isaak wrote
> >> (in article <jsftar$o7...@speranza.aioe.org>):
>
> >>> On 6/27/12 10:47 AM, pnyikos wrote:
> >>>> <snip>
>
> >>>> You snipped something highly embarrassing to ____ .
> >>>> [other examples snipped]
>
> >>> In case you did not know, Peter, your obsessive rudeness reflect poorly
> >>> on you, not on anyone else.
>
> >> Ooh, you shouldn't have said that. Rig for thermonuclear explosion, close
> >> aboard, when Peter sees that...
>
> > I saw it long ago, Rip van O'Shea, and I responded to it too. �And
> > Mark now has his own troubles on the threads involving UC, where he
> > has compromised his integrity for you and "jillery."
>
> And here we go again. Another whopper.
>
>
>
> > I'm sure the two of you are proud of the extremism you have stimulated
> > in him and Paul Gans; probably in Mitchell Coffey as well.
>
> 'Extremism'? Extremism in the defense of truth is no vice,

Y'all's extremism is in the service of falsehood--the falsehoods
uttered by Gans and Ron O especially.

Y'all were so extreme, jillery tripped over your rationale for
callling me "paranoid" and showed her/himself to be even more paranoid
by y'all's standards, probably because of y'all's determination to
stop all agreement between me and "UC" on anything, at all costs.

Peter Nyikos