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://ww