I'm sorry to be so late in responding, Öö . These last two weeks
were almost completely taken with preparing, and then grading,
final exams, along with some family obligations.
Today is my last day this year for posting, but I hope we can pick up this OOL theme
when I return from my break. It has a timelessness that personal comments lack.
On Thursday, December 7, 2023 at 1:37:02 PM UTC-5, Öö Tiib wrote:
> On Wednesday 6 December 2023 at 22:27:01 UTC+2,
peter2...@gmail.com wrote:
> > On Wednesday, December 6, 2023 at 4:47:00 AM UTC-5, Öö Tiib wrote:
> > > For me the issue is not what words Tour says but what he has done.
> >
> > So, aren't you interested in what we know and do not know about
> > the origins of life? Specifically, life as we know it, based on protein enzymes.
> >
> > This is what makes OOL so fascinating for me: the Central Doctrine
> > of the biochemistry of life as we know it is that information passes from nucleotides
> > to polypeptides (which are either proteins or the main ingredients of proteins)
> > but almost no information passes in the opposite direction.
> >
> Yes, and so all peptides used in life are of rather limited set of possible
> peptide space.
And the ribozymes of which we know are a far more limited set. The ones
I talk about here have vanished, supplanted by protein enzymes,
yet they were indispensable for getting life as we know it started.
>That highly likely makes the choices taken (and solutions
> built from such choices) suboptimal. Proteins are still remarkably better
> than ribozymes even as only rather narrow subset of the full potential is
> used.
What is your basis for this comparison? The ribosome is a ribozyme together with
a lot of "helper" proteins, but it can do its essential work [albeit less efficiently]
without them. As for the others I talk about next, we have no idea where
they lie in "polynucleotide" space.
> > To make a long story short, all paths from simple chemicals to life as we know it
> > seem to have to pass through the bottleneck of a ribozyme RNA replicase.
> > I described this concept to Erik Simpson earlier on this thread, but
> > no one here seems to be interested in trying to find another kind of path.
> RdRp and DdRp are available in protein form. I agree that ribozyme RdRp feels
> most logical to have for to go from RNA world to RNA + protein world.
> Protein RdRp we have and it is likely more efficient and robust than ribozyme
> RdRp but obviously could not be there before proteins themselves.
Yes, it requires a very high fidelity genetic code to produce the necessary protein enzymes.
Before then, a DNA genome is probably indispensable. Without knowing what the RdRp ribozymes
are like, we cannot be sure how easy or how hard it is to have mutations to a transcriptase or
reverse transcriptase or DNA replicase -- all necessarily ribozymes before their protein
counterparts have a chance of being produced in abundance.
> > And now comes the punch line: nobody, not even Lee Cronin, the "opponent" of Tour in the
> > debate, has the foggiest idea what ribozyme replicase (either for RNA or DNA, by the way)
> > might look like. By this I mean: what on earth might the sequence of nucleotides making it up be?
> >
> OK I see the only issue is we now do not have any ribozyme RdRp.
It's a huge one, make no mistake.
> But that is logical as even "more modern" protein RdRp is only yet there in some viruses.
Or lost in organisms, being no longer necessary for them. DNA replicase and transcriptase
to RNA are all that we need now, apparently, with mutations taking place in the DNA genomes
of both nuclei and endosymbionts (including mitochondria and chloroplasts).
> So what is the anticipated barrier to existence of ribozyme RdRp before its
> protein competitor emerged?
It's a bit like "lifting yourself up by the bootstraps." Without high fidelity replicators
to start with, how could any promising nucleotide sequence avoid getting degraded
by mutations to "junk RNA" or, at best, something not on a path towards a true replicase?
> Peptides could evolve with ribozyme RdRp forming protein RdRp that competed ribozyme RdRp out.
How do you replicate a polypeptide? We have nothing that does that directly, not even
in viruses, otherwise some kinds could replicate without host cell ribosomes -- unheard of!
> There must be some
> issue on that trajectory I don't see.
Don't forget the Central Dogma of which I wrote above. Its twin is that genetic
information does not flow from one polypeptide to another.
Below, we revert to talking about James Tour, after which you got speculative about AI.
Due to shortness of time, I'll defer any comment I make to after my break.
Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of So. Carolina at Columbia
http://people.math.sc.edu/nyikos
PS One last question: have you started looking at the 3+ hour video I talked about below?
> > > Tour has record of challenges. With Tour there will be conditions and
> > > inconveniences with such challenges.
> > Why don't you confine yourself to this latest one? This is the
> > one that a mainstream OOL researcher took seriously enough
> > to result in an amazing debate.
> >
> > Who cares about the ones where Tour's opponents were incompetent and/or clowns?
> >
> I did totally disappoint in him when he washed floor with "professor" Dave.
> That proved to me that it is political show only, and that is what is Tour's
> goal.
> > > "Challenges" themselves are for
> > > show, but whoever accepts those just gets nothing, even no right to
> > > record:
> > > “It shall not be recorded or extend beyond the three of us as this is
> > > not for show but for my edification.”
> > This one was not only recorded, the YouTube recording lasts for over
> > three hours, and I haven't had the time yet to go over the final hour.
> > > <
https://uncommondescent.com/intelligent-design/professor-james-tour-accepts-nick-matzkes-offer-to-explain-macroevolution/>
> > >
> > > Why should they then do it if they get nothing? Or what "reward" is that
> > > Tour erases his youtube channel?
> > He won't have the power to erase this one:
> >
> >
https://www.youtube.com/watch?v=6GDv4f2zUus
> >
> > It's part of a prestigious series, with Harvard University hosting.
> >
> I try to find time to listen it at weekend (or to read the subtitles). Thanks.
> > > YouTube is not getting less full of
> > > BS. It is nothing like million of dollars that late James Randi offered
> > > for any paranormal or supernatural evidence whatsoever in his challenge.
> >
> > The origin of life is arguably the most difficult unsolved problem in all the
> > physical sciences. The origin of the cell is far more complicated than the evolution
> > of stars. Astrophysicists have been able to deduce what goes on in stars, depending
> > on where they started on the Herzprung-Russel main sequence.
> > Our sun will leave it before getting any further than carbon in producing heavier elements,
> > and will quickly become a white dwarf after that.
> >
> Oh who knows, we can not even figure out origin of petroleum. It is often located
> twice deeper than any organic sediment is (and so any fossil can be). Or may be
> there was (still is?) some kind of deep underground life? But I am rather
> convinced that manufacturing more potent than our own life-like technologies is
> coming soon anyway or already undergoing. With advance of nanotechnology and
> billions pumped into it each year it is highly likely that we have superior
> to our own biochemistry nanotechnology available soon.
> > The biggest stars can go all the way to iron, then suffer core collapse,
> > then become supernovas, producing all the remaining naturally occurring elements
> > in an unimaginably spectacular chain of reactions, then collapse either into a neutron star or a black hole.
> >
> > Along the way, they will first undergo a "hydrogen flash" while burning helium in earnest, then when
> > the helium is badly depleted, they will undergo a "helium flash". Both happen deep
> > inside, and no one has observed these and many other things
> > which they have deduced simply on well established theoretical grounds.
> >
> > But life is far too complicated for biologists to be good at the theory of its origins to the
> > same spectacular extent -- or even to a much less spectacular extent.
> >
> Issue is that whatever was OOL the result of it advanced in so pitifully sluggish
> pace that the study figuring it out is doomed to bring no economic benefits.
> At same time we have clearly done quite a step ahead in manufacturing
> mental singularities and not even hiding that. We can't yet figure what is economic
> effect of those (besides that it will be extensive).
>
> On worst cases ... within few decades there will be (A) large-scale battle between
> various grey goos controlled by various SkyNets by what current biochemistry including
> ourselves is either (A.1) already thrown aside as worthless or (A.2) kept still in role
> of curiously inferior pets or (B) whatever gods there supposedly exist and sometimes
> intervene stop hiding and (B.1) erase and forbid making SkyNets, (B.2) welcome
> SkyNets and teach them what are the next rules of game.