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
On Mar 19, 6:34 pm, John Harshman <jharsh...@pacbell.net
> pnyikos wrote:
> > On Mar 19, 1:45 pm, John Harshman <jharsh...@pacbell.net
> >> 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
> > On Mar 16, 12:34 am, John Harshman <jharsh...@pacbell.net
> >> 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
==================== end of excerpt from Panel 5
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
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
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
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
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?