No it burned up. The best ribozyme in the world can't hide from
> UV/sun - it burned up. The only thing that would survive the uv/sun
> is something that is chemically selected for surviving UV/sun high
> heat.

RM
Per my speculations, my "just so stories", the first living thing, or
replicator, wasn't anything anywhere near as complicated as a ribozyme.
It was just some set of chemicals in a loop each of which catalyzed the
production of the next given available chemicals naturally present. To
form a loop, they must be resistant to whatever the temperature was at
that time. 

TH
I see your point, and it answers my concern. But take it a step further. IF
this replicating loop survived the heat, and if it is such that it replicates -
then what is it replicating? It's replicating itself which is a heat survivor.
Thus what it is coding  is survival in heat or it wouldn't be coding at all -
it would be burned up.
Right? So what we are reproducing with our first replicators - is heat
resistant copies. Agreed?

RM
And I presume they were *not* directly exposed to solar UV.
The solar UV disturbed many chemicals on the surface of the ocean,
creating highly-reactive free radicals, meta-stable states, etc., which
diffused down into the less exposed places where my first life was
getting started.

TH
UV may have been a selection force that was necessary.
Elsewhere on this newsgroup is a study that suggests RNA needed UV. And its
main drawback is dimers, often in T - but no T in RNA - that comes with DNA.


> Where is this place? Is the sun gone?

RM
No, but the Sun's UV light can't penetrate more than just a thin layer
of water.

> Is there no sun/uv heat cycle?

If the atmosphere was filled with water vapor and carbon dioxide, and
lots of dust blasted up by asteroid crashes, and lots of dust raining
down from evaporated incoming comets, maybe there wasn't much direct
sunlight at the surface, like Venus and Titan today although with a
temperature much cooler than Venus and very much warmer than Titan.

TH
Now we are getting somewhere. I contend that this is right. And that when the
temperature lowered to the point where H2O was in a liquid state, and the seas
began to form, that there were tremendous rainstorms. This rain helped take the
CO2 out of the atmosphere, continue to cool it, form the seas, and for the
first time probably - let the Sun shine through. I think this was the window of
opportunity for life. It needed the sun, it needed liquid water, but it needed
the top end of liquid water in order for chemical reactions to work at peak
speed (note the hi Tm of RNA which I think is a clue to how hi the
environmental temp was before and during RNA World)

> No replicator can hide from the sun.

RM
It doesn't have to actively hide. It merely has to be lucky in starting
well below the water's surface on during a Venus/Titan
smoggy-atmosphere time period, and not getting churned up to the more
hostile surface too much, so it can replicate many times before getting
destroyed by solar UV or whatever.

TH
But there is a catch 22 here. You need the sun for energy, but you are
suggesting that life hides from its energy source. You may have  protection but
you've lost your  energy source that powers everything you do. There may be
ways around it, but they stretch credibility for me. Why separate yourself from
what you need most?.

> In the end being a replicator is worth nothing.

RM
Um, I disagree. Being something that successfully replicates many times
before being destroyed by chance, means that its pattern will increase
in frequency among the mix of chemicals in the ocean.

TH
Yes but replicating with none of the replicates dying would be better wouldn't
it? So if you are replicating a thermally stable molecule (and note that every
step in life makes life chemistry more thermally stable - that is not a
coincidence) wouldn't its replicates have the edge?

> What counts is when
> a. you have thermally stable molecules

RM
Thermal stability is one factor in surviving long enough to replicate
lots of times. But being a really good catalyst, to replicate very
quickly, is another factor. It's a race to replicate faster than being
destroyed, a combination of replication speed and resistance to being
destroyed, that a replicator must win.

TH
Again being a thermally stable molecule comes first.
I don't disagree as much as suggest the order is wrong.
First you get thermally stable monomers and such - then they build into the
rest - but all of this is driven by the sun's energy IMO.
Here is something to think of. Being a catalyst helps you replicate - yes. But
it doesn't help you survive or adapt to your environment very quickly. So it is
a rush to win over odds during the short term the building-a-catalyst chemistry
, goes on. I don't think that is the way that things happened.

> b. you have a way of replicating these molecules

RM
Well, a replicator, such as a catalytic loop, by definition replicates
itself, so if such molecules are in the loop, then of course what you
say is true. Alternately, some product of the loop, which is not within
the loop itself, might be something that sticks around and protects the
loop from breakdown.

> THus you have a way of replicating thermally stable molecules that
> have been selected to survive - now they have both survivability and
> descent with modification.

RM
Actually you don't necessarily have descent with modification yet. See
for example my other postings speculating about an earlier form of
replicators residing on a lipid bubble, as an ecosystem, where each
individual replicator had no ability to be modified and remain an
effective replicator. See also my speculations about how such a
non-evolving form of almost-life might develop a mechanism for
variation and modification ("true mutations").

> 1. why does it have to be a SELF replicator.

That's what we're talking about: The very first replicators, which
can't be parasites on some other mechanism that replicates RNA or DNA
or whatever, the way viruses currently rely on cells to do their
replication for them. So they must do the job themselves, all by
themselves, with free food from Solar and geothermal activies,

TH
But that isn't all by themselves is it? You've fudged the facts and said WITH.
why not say it correctly. It is environmentally induced replication.
Then you also see how replication could come from a heat cycle (denaturing
paired or folded strands in high (and dry?) heat, annealing hybrids in low))
Also there is a temperature symbiosis of sorts - same chemical reactions happen
at same temp. So this by itself brings together like minded molecules to
chemically react together always at the same time (temp)


RM
 but
nothing there which will replicate them. Perhaps the term "self replicator"
is confusing you. I don't mean a single molecule that makes copies
of itself directly. I mean a closed loop of catalysts. Each molecule
of A, upon encountering sufficient food for making B, does so, resulting
in gradually increasing quantity of B so long as A hasn't been destroyed.
Each B, upon encountering sufficient food for making C, does so, resulting
in gradually increasing quantity of C so long as that B hasn't been destroyed,
but there are lots of other B's being made, so so long as the total quantity
of B doesn't collapse to zero there will be new C's being made.
Each C, upon encountering sufficient food for making D, does so,
resulting in gradually increasing quantity of D so long as that C
hasn't been destroyed, but there are lots of other C's being made, so
so long as the total quantity of C doesn't collapse to zero there will
be new D's being made. And so on around the loop. Finally any Z's
encountering food for making A's do so. The quantity of A,B,C,...,Z
increase exponentially, until one of the links starts to exhaust all
available food. Let's arbitrarily say it's Z making A that is
food-limited. So just as much A is manufactured to consume all
available food for that link, while all the other links have plenty of
food but are limited by the amount of catalysts going in and the
reaction rate with that catalyst. What I call a self replicator is this
entire loop of catalysts, not just one of the catalysts in the loop.
Each individual catalyst replicates itself indirectly through the chain
of the others. But the whole loop replicates "itself" directly, without
the help of any other catalysts (except naturally-occuring ones that
process food coming in).

TH
OK, that could happen. This is the part that puzzles me too. I strip it down to
this question. Why would RNA need protein? Or the other way around. It is the
toughest question of all for me.

> If there was an environmentally induced replicator for a billion
> years before this would you be upset that it wasn't a SELF induced.

RM
All of the catalysts I proposed were originally created naturally by
the environment producing activated chemicals some of which
spontaneously combine to make new chemicals some of which had catalytic
activity some of which formed the first closed catalytic loop I
hypothesized. But once the loop achieves fecundity greater than one,
and exponentially grows in quantity until all available food is
consumed as fast as it gets created


TH
Stop here. Why does anything need or want food?
We cannot take that for granted.
I suggest nothing needs food. Instead heat is forced on molecules that
gradually prebiotically 'evolve' ways of dumping the mess. then later using it
before dumping - then its food.
Give the food idea a million years to evolve - say I.



RM
, I suspect the quantity of these
catalysts from the cycle itself would be many times larger than the
quantity of these same catalysts created the old non-loop way.

Think of the following metaphor: You turn on your amplifier and put the
microphone close enough to the loudspeakers that some signal goes
around a loop. When you turn up the gain just enough to have net
amplification around the loop greater than one for one particular
frequency, that one frequency increases exponentially until it's
limited by the amplifier voltage¤t limits. That one frequency, as
well as all other frequencies, were previously present already in
"white noise" caused by quantum noise in the circuitry, but now the
closed-loop single-tone is orders of magnitude stronger than the
white-noise component of that same frequency. For practical purposes,
the white-noise component can be ignored.

TH
I think this analogy works best if you say
RNA and amino acids (peptides). Somewhere and in
someway extremely early on, they began in some
prebiotic chemical support system that helped each
better survive - the peptides into novel proteins (that are not denatured) and
the RNA into replication and coding.

Tom

(rest snipped - I see your point, and sorta agree mostly)
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