Hydrogen Cyanide and the Origin

[TomHendricks474]

Hydrogen Cyanide seem to be a key ingredient in origin scenarios

"When hydrogen cyanide condenses under the conditions described... for the syunthesis or amino
acids, it also yields purines and pyrimidines."

If we need hydrogen cyanide then that is a clue to the history of the origin of life. In order for
life to begin the conditions must have been right for making and accumlating HCN.

"The concentration of cyanide may have existed shortly after the oceans first formed, when their
volume was low and the amount of hydrogen cyanide was high owing to a high rate of impact of comets
and meteorites. The HCN may have been concentrated in certain areas as a result of a high frequency
of electrical storms."

This would suggest the origin came at the earlier and hotter period of the earth.

Also note that" HCN is more volatile than water, a concentration mechanism based on the evaporation
to near dryness of a lake that contains small amounts of HCN wold not give concentrated cyanide
solutions."

quotes from Zubay's Biochemistry.

Tom

 

[Jim Menegay]

[email protected] wrote in message news:<[email protected]>...
> Hydrogen Cyanide seem to be a key ingredient in origin scenarios
[snip]
> Also note that" HCN is more volatile than water, a concentration mechanism based on the
> evaporation to near dryness of a lake that contains small amounts of HCN wold not give
> concentrated cyanide solutions."

The usual concentration mechanism proposed for cyanide is freezing rather than evaporation. Freeze
the H2O and the HCN is left in solution. If, for some reason, you want both hot and cold, imagine a
volcano poking its way thru the Greenland icepack.

But, I believe that a better way to provide cyanide to early life is as a ligand to transition metal
ions. CN- is much more stable as a ligand than in solution - and it is more tightly bound than
competing ligands such as OH- and NH2-. Thus, most of the pre-biosphere's HCN will be ligated rather
than dissolved. The same applies to CO. The metals were mostly Fe++, with Ni++, Co++, Cu++, and Mo++
also around to provide some variety.

If you believe that geochemically (or astro-chemically) formed HCN polymers took part in some kind
of order-out-of-chaos heterotrophic origin of life, then we are in disagreement. More likely, IMHO,
is that HCN was first essential as a feedstock for lipid production. That was the origin of life, as
I define life. Much later, HCN and CO may have been feedstocks for sugar and then nucleotide
production, leading to an RNA world, but life was probably already ancient by that time. Life did
not begin with the ribosome, and it didn't begin with an RNA replicase either. Both were, no doubt,
important steps in the pre-common-ancestor evolution of life, but both are far too complex to have
arisen pre-biotically.

A pre-RNA biochemistry was probably based on interactions among lipid head groups and complex ions.
Perhaps mineral surfaces were also involved. You should read Wachtershauser (sp?) Much of his stuff
is probably wrong, but it is a better approach than basing theories of life's origin on a "soup"
idea that was generated back when people thought that there was something magical about colloids.
Throw out the old soup. Throw out the newer idea that genetics can only come from informational
polymers. Throw out the prejudice that interesting stuff only takes place INSIDE the bag of enzymes.
Notice that it is the bag itself that reproduces. Ask how a bag can make more bag material. Notice
that interesting things need to happen on both the inside and the outside leaflets of the bag. Also
notice that the proton-motive force (PMF) is probably the ancestral energy pool and reaction
coupling mechanism. Phosphate esters, diesters, and anhydrides came later. The PMF may even antedate
DeDuve's beloved thioesters. (IMHO)

Westheimer wrote a beautiful paper back in the 70s entitled "Why Nature Chose Phosphates". To my
mind, the more interesting question is "When Did Nature Choose Phosphates?". Or, perhaps more
interesting, "Where Did Nature Find Phosphates?" My guess is that She found them in deposits of
calcium metaphosphate minerals (deposited, of course by one of your drying cycles). But, notice that
in my theory, organisms already exist to use the energy stored by the drying. Your theory(s) seem to
suggest that the organisms were in some sense created (or at least refined) by the drying.
Personally, I doubt it.

 

[Tomhendricks474]

<< The usual concentration mechanism proposed for cyanide is freezing rather than evaporation.
Freeze the H2O and the HCN is left in solution. If, for some reason, you want both hot and cold,
imagine a volcano poking its way thru the Greenland icepack.

TH I tend to think that when life began it was hot and hotter. Freezing would answer the HCN
question but not much else. We are stuck with the liquid water range mostly. I tend to think to have
drying and to have the hydrogen bonded variants that seem so important - that the steam end is more
likely than the ice end. (I have suggested that before RNA world came a h-bond world where variants
of h-bonding were selected)

But, I believe that a better way to provide cyanide to early life is as a ligand to transition metal
ions. CN- is much more stable as a ligand than in solution - and it is more tightly bound than
competing ligands such as OH- and NH2-. Thus, most of the pre-biosphere's HCN will be ligated rather
than dissolved. The same applies to CO. The metals were mostly Fe++, with Ni++, Co++, Cu++, and Mo++
also around to provide some variety.

If you believe that geochemically (or astro-chemically) formed HCN polymers took part in some kind
of order-out-of-chaos heterotrophic origin of life, then we are in disagreement. More likely, IMHO,
is that HCN was first essential as a feedstock for lipid production. That was the origin of life, as
I define life.

TH There seems to me to be problems with having each of the following develop separately; then
somehow magically come together - aa, nucleic acids, lipid production, etc. I think more likely it
was some symbiosis of all these under similar circumstances. Thus in a wet/dry hot/cold cycle we
could have symbiotic molecules according to temp, wet/dry, pH conditions. And every part of the day
would favor certain symbiants at that temp. I think lipids was a part of that. But the bigger issue
is this. "Feed and breed" (or whatever your def. of life is) is an adaptive respone to what?

Much later, HCN and CO may have been feedstocks for sugar and then nucleotide production, leading
to an RNA world, but life was probably already ancient by that time. Life did not begin with the
ribosome, and it didn't begin with an RNA replicase either. Both were, no doubt, important steps in
the pre-common-ancestor evolution of life, but both are far too complex to have arisen pre-
biotically.

TH I agree. I think first there was the production of assorted monomers, then came the h-bond world.
H-bonds could easily have many variants. Covalent bonds with their high activation energy would
hardly be selected for if it takes endless energy to jump that fence.

A pre-RNA biochemistry was probably based on interactions among lipid head groups and complex ions.
Perhaps mineral surfaces were also involved. You should read Wachtershauser (sp?) Much of his stuff
is probably wrong, but it is a better approach than basing theories of life's origin on a "soup"
idea that was generated back when people thought that there was something magical about colloids.
Throw out the old soup. Throw out the newer idea that genetics can only come from informational
polymers. Throw out the prejudice that interesting stuff only takes place INSIDE the bag of enzymes.
Notice that it is the bag itself that reproduces.

TH The bag and nucleic acids. I think both are a response to heat. (and most likely other
environment cycles of wet/dry and perhaps pH) . If the bag alone, then why would nucleic acids
divide at all.

Ask how a bag can make more bag material.

TH Ask why that would better allow it to survive in its immediate environment. What force is it
trying to survive. And how does this ploy help it survive that force.

Notice that interesting things need to happen on both the inside and the outside leaflets of the
bag. Also notice that the proton-motive force (PMF) is probably the ancestral energy pool and
reaction coupling mechanism. Phosphate esters, diesters, and anhydrides came later. The PMF may
even antedate DeDuve's beloved thioesters. (IMHO)

Westheimer wrote a beautiful paper back in the 70s entitled "Why Nature Chose Phosphates". To my
mind, the more interesting question is "When Did Nature Choose Phosphates?".

TH Let's go one step further. If life was such an advantage why didn't salt, gold, or water 'feed
and breed'? I'm not being facetious. We are taking so much for granted in first life scenarios that
upon closer investigation, make no sense whatsoever. Life had specific chemical properties that best
adapted to specific variants in a specific environment. We need to know all of those specifics to
even begin to approach a good scenario.

Or, perhaps more interesting, "Where Did Nature Find Phosphates?" My guess is that She found them
in deposits of calcium metaphosphate minerals (deposited, of course by one of your drying cycles).
But, notice that in my theory, organisms already exist to use the energy stored by the drying. Your
theory(s) seem to suggest that the organisms were in some sense created (or at least refined) by
the drying. Personally, I doubt it.

>>
TH This is a fascinating topic that I think is ripe for a big discovery. Tom Hendricks

 

[Jim Menegay]

A correction concerning your characterization of my theory, plus some
quibbles regarding the language you use in describing your own theory:

> TH There seems to me to be problems with having each of the following develop separately; then
> somehow magically come together - aa, nucleic acids, lipid production, etc.

But in my theory they DON'T develop separately. Pre-RNA world lipid organisms "invent" nucleic
acids. Then later, RNA world organisms produce amino acids and "invent" proteins. No magic. Just
ordinary garden-variety natural selection pushed back to an earlier era than most people think is
possible. The not-yet-understood "magic" is in the origin of pre-RNA world lipid organisms that can
evolve under natural selection without the benefit of nucleic acids. (Plus, I need to come up with
credible "just-so stories" for why evolution would have taken this particular path.) My theory has
lots of problems, but not the one you mention.

> TH I think more likely it was some symbiosis of all these under similar circumstances.

I've noticed that you use the word "symbiosis" loosely. Properly, you should only speak of a
symbiosis between tRNAs and amino acids if you believe that both are, in some sense, alive. I'll
concede the point for tRNAs, but if you are suggesting that amino acids were somehow alive, then
your theory is MUCH more interesting (if somewhat less credible). It IS conceivable that you could
have an evolving "species" consisting of all the amino acids that reproduce themselves by some kind
of autocatalytic cycle. Then the species consisting of all such living aas might co-evolve with
tRNAs, by adding the arginine trait, for example, and extinguishing the ornithine. That would INDEED
be interesting. But I don't think that is what you are saying. So, I repeat, you really shouldn't
use the word symbiosis.

But, I notice, you seem to assign biological attributes to non-living entities in other cases, too.

> TH "Feed and "breed" (or whatever your def. of life is) is an adaptive respone to what?

> TH Let's go one step further. If life was such an advantage why didn't salt, gold, or water 'feed
> and breed'? I'm not being facetious. ...

> TH (from a different thread) That means when the first proto tRNA hooked up to the first Amino
> Acid - there was a benefit for both THEN, not a million years later. And when two Amino Acids
> formed a peptide bond it was a benefit to those amino acids THEN, not a million years later
> and when RNA folded into a tRNA shape it was a benefit to that RNA strand THEN, not a million
> years later.

No biologist (that I am aware of) claims that life is an "advantage", nor that an inanimate glob of
organic chemicals evolved to the living state in order to reap those advantages. An atom, molecule,
or rock does not have a "will to survive". It is a category error to even talk of non-living things
having interests. Purists might claim that it is a category error to even talk of non-human things
having interests, but evolutionists have (justifiably) expanded the concept to include all living
things. Living things, because they have evolved under natural selection, BEHAVE AS IF they had
interests - specifically, they seem to have an interest in extending and broadening their tree of
descendents.

The word "selection" is sometimes applied to inanimate objects, but this should not be seen as a
evolution-causing process. Living things undergo r-selection (for ability to reproduce) and K-
selection (for ability to survive so as to eventually reproduce). All living things are reasonably
proficient at both.

When you talk about an aa or a rock undergoing "selection" for survival, that is not meaningful in
evolutionary terms. Survival without reproduction is pretty useless. Yes, an aa that is good at
surviving will indeed probably survive and may become relatively more plentiful as a result. But
only slightly. The population of aas is continually replenished by "spontaneous generation". And
THAT is the key difference between the living and the non-living. Inanimate objects can be
spontaneously

to achieve reproduction. (Well, some of them do, anyways.) The fact of reproduction creates a
positive feedback loop. Selected characters can become fixed in a population ONLY IF the population
is amplified by reproduction and is not significantly diluted by spontaneous generation.

Again, if you have a theory that somehow justifies the use of final causation language for
inanimate objects, then you are onto something VERY interesting. But, I suspect that you are not
proposing such a theory. You are merely using language in a slightly sloppy way. There are those
who claim that sloppy language breeds sloppy thinking - just in case those spoil-sports happen to
be right, you might consider revising the language you use. We would hate to lose you to
poetry.bio.evolution ;-)

 

[Jim Menegay]

tomhendricks474 writes:
> Well there is a lot there to consider. And I really don't know enough about it to comment except
> on two things. 1 I think any scenario must consider the environment. The chemical processes can't
> hide from the sun. Thus any system of chemicals must in the end react to and find ways to adapt to
> that environment at that moment in time.
> 2. My other point is that it is much much more likely that a chem system driven by an energy
> source (like the sun) would start life and continue to force it to adapt, than one that depends
> solely on its own single resources. In the former
> - the entire earth is under selection - in the latter a single event must lead to all life and it
> must do so without a single break or mishap over millions of years in a hostile environment.
>

1. But OF COURSE they can hide from the sun. There are kilometers of ocean depths and more
kilometers of porous rock. Many current OOL theories claim that life originated far from the
surface. Some of these theories fear your sun so much that they want to wait until there is an
ozone layer in place before they colonize the surface. That doesn't mean that you are wrong. Your
heat-cycle drying idea is in a long and proud tradition containing many distinguished
researchers. (Personally, I want my lipid organisms to face the sun early and develop
photosynthesis even before they invent RNA.) But you shouldn't claim that your desicated mud-
flats are the ONLY place on the planet where things might happen, or where chemicals might be
challenged. Carl Woese, one of the recent giants of biology, has seriously suggested that it
could have happened in the clouds! He makes a pretty good case for it, too.

2. Regarding "without a single break or mishap over millions of years": Long odds don't frighten me.
I am a very lucky person. Genetically lucky. I've been researching my family tree and I have
discovered something fascinating. As you probably know, in past centuries, infant and child
mortality was much higher than today. Well, I'll have you know that not a single one of my
ancestors, in over three hundred years, has died in childhood. Not a single break or mishap. What
do you think are the odds of that? Three hundred years! Well, of course millions of years without
a break or mishap would probably be much more unlikely - at least a 50:1 shot - I'm not sure how
to do the math. But, still, with my luck, it seems possible. ;-)

 

[RobertMaas]

http://www.google.com/groups?selm=bqee5k%244dv%241%40darwin.ediacara.org
> From: [email protected] (Jim Menegay) The usual
> concentration mechanism proposed for cyanide is freezing
> rather than evaporation. Freeze the H2O and the HCN is
> left in solution. ... But, I believe that a better way to
> provide cyanide to early life is as a ligand to transition
> metal ions. CN- is much more stable as a ligand than in
> solution - and it is more tightly bound than competing
> ligands such as OH- and NH2-. Thus, most of the pre-
> biosphere's HCN will be ligated rather than dissolved. The
> same applies to CO. The metals were mostly Fe++, with
> Ni++, Co++, Cu++, and Mo++ also around to provide some
> variety. ... If you believe that geochemically (or astro-
> chemically) formed HCN polymers took part in some kind of
> order-out-of-chaos heterotrophic origin of life, then we
> are in disagreement. More likely, IMHO, is that HCN was
> first essential as a feedstock for lipid production. That
> was the origin of life, as I define life. ... A pre-RNA
> biochemistry was probably based on interactions among
> lipid head groups and complex ions. Perhaps mineral
> surfaces were also involved. ... Throw out the newer idea
> that genetics can only come from informational polymers.
> Throw out the prejudice that interesting stuff only takes
> place INSIDE the bag of enzymes. Notice that it is the bag
> itself that reproduces. Ask how a bag can make more bag
> material.

Fascinating speculations to remember and ponder! I generally
define life to have fecundity greater than one in absense of
competition or exhaustion of available resources, and having
sufficient genetic stability that heritable traits maintain
fecundity greater than one over many generations, but
sufficient instability that lots of mutations happen over
the course Earth history. So the question is how your idea
fits with that definition. Well, the lipid-bag surface may
have a mixture of chemicals in auto-catalytic cycles, each
reproducing its own kind, and the total mixture on any given
bag could be considered the genome of that bag. If too much
or too little of any given cycle occurs, due to random
fluctuations in the reaction rates, that bag would cease
reproducing so well, allowing other bags with the original
mix, or with an even better mix, to out-reproduce it and
therefore hog most of the resources. Whereas the current
DNA/RNA genomic situation involves a single mechanism for
encoding the gemone, and only variation in the words written
with that alphabet, the original lipid-bag-of-enzymes
mechanism may involve several totally independent auto-
catalytic cycles which happened to be more effective
together than separately so once accidently combined in a
single bag they reproduced better than the separate
originals thus took over the biosphere.

So now you need to work out the details of your speculation:
Which concentrations of high-energy chemicals might have
been produced just by geothermal processes, with hydrogen
sulfide being the most obvious. Then which auto-catalytic
cycles might have occurred just by chance to feed off these
chemical concentrations as a source of energy. Then how
lipid bags might have occurred naturally, perhaps as a waste
product of one of these auto-catalytic cycles. Then how one
of the auto-catalytic cycles might have joined with a lipid
bag in a way that works better than either alone. After
that, it's pretty easy to imagine single-cycle successfully-
reproducing lipid bags accidently merging to combine their
genomes and either succeed or fail compared to the
originals.

But, as I began speculating in 1988, between the first two
steps listed above, after large concentrations of high-
energy chemicals naturally accumulate, before any auto-
catalytic cycle develops, there must have been lots of
simple catalyzed reactions going on, with some chance
occurance of a catalyst meeting with some chemicals it can
catalyze a reaction to produce a lot more of one particular
possible product than would occur without the catalyst. This
would result in an accumulation of that particular catalyzed
reaction product replacing the natural mix that occurred
before. Some really simple catalyst would be involved, such
as some particular metal ion which as you seem to suggest
met with cyanide to form a ligand, a chance mixing of two
rich environments, one producing large amounts of the metal
ion, another producing large concentrations of cyanide such
as by freezing of water, but suddenly by chance some natural
geologic/tektonic/meteorological process brings these two
concentrations together to create a concentration of the
ligand, and by chance a while later that mess meets some
chemicals that can be catalyzed by the ligand.

With asteroids and comets striking Earth at great frequency,
and lots of volcanos opening up all over the ocean floor,
jostling up the ocean all the time, chance meetings would be
the norm. But with some volcanic vents running for long
periods of time between the previous major jostling and the
next, building up large amounts of high-energy chemicals in
the vicinity would also be the norm. So all we need now is
the details, many specific catalyzed reactions that would be
likely to have occurred naturally, and somewhere in that
search space at least one closed-loop. We need to run
computer software that simulates all sorts of chance
chemicals likely to have formed, in high local
concentrations, see which particular reactions might occur
between them, which might be enhanced by which catalyist,
and which catalyzed reaction products might then have been
produced in sufficient quantity to feed into subsequent
reactions. Is the state-of-art in computer simulations of
chemistry up to the task yet? If so, somebody should run
such simulations to build up a list of all the likely
original chemical compositions and likely catalysts and
likely reaction-product concentrations, and keep iterating
until either a closed loop catalytic cycle is discovered or
"the well runs dry" with no closed loop yet and no new
reaction products likely in sufficient quantity to continue
the search.

If that search is successful, then of course we can
proceed to the next step of considering your lipid bags
merging with my auto-catalytic cycle to form the first
reproducing "cell".

Alternately, we could from the start restrict our search to
only those catalyzed reactions that occur on the surface of
lipid bags.

> Date: Mon, 1 Dec 2003 03:56:36 +0000 (UTC)
(I didn't see your article when it first appeared, because I
didn't have any efficient method for finding all followups
(to stuff I had posted) until just a few nights ago when I
finally found your article and put it in the queue to
compose a followup myself. Sorry for very belated response.)

 

[Jim Menegay]

[email protected] wrote in message news:<[email protected]>...
> http://www.google.com/groups?selm=bqee5k%244dv%241%40darw-
> in.ediacara.org
> > From: [email protected] (Jim Menegay) ... A pre-
> > RNA biochemistry was probably based on interactions
> > among lipid head groups and complex ions. Perhaps
> > mineral surfaces were also involved. ... Throw out the
> > idea that genetics can only come from informational
> > polymers. Throw out the prejudice that interesting stuff
> > only takes place INSIDE the bag of enzymes. Notice that
> > it is the bag itself that reproduces. Ask how a bag can
> > make more bag material.
>
> I generally define life to have fecundity greater than one
> in absense of competition or exhaustion of available
> resources, and having sufficient genetic stability that
> heritable traits maintain fecundity greater than one over
> many generations, but sufficient instability that lots of
> mutations happen over the course Earth history.

A perfectly acceptable definition.

> So the question is how your idea fits with that
> definition. Well, the lipid-bag surface may have a mixture
> of chemicals in auto-catalytic cycles, each reproducing
> its own kind, and the total mixture on any given bag could
> be considered the genome of that bag.

Close, but not exactly right. For heredity, you need
two things:
1. The genome of the children is (usually) the same as the
genome of the parent.
2. The genome of an adult organism is (usually) the same as
the genome of that organism when it was a child.

If you define the genome to be the relative proportions of
various chemicals, then reproduction by fission may satisfy
the first requirement, but it is unlikely to satisfy the
second. The reason is that the environment fluctuates.

So, I define the genetic information, not as a point in a
manifold of chemical concentrations, but as an attractor in
the dynamics on that manifold. Although fluctuations in the
environment may change the exact location of the attractor,
the basins of attraction tend to be persistent. An
environmental fluctuation large enough to destroy a basin of
attraction, or to create a new one, would be a catastrophe
in Thom's sense, and a possible cause of mutation in our
hypothetical genetics.

> If too much or too little of any given cycle occurs, due
> to random fluctuations in the reaction rates, that bag
> would cease reproducing so well, allowing other bags with
> the original mix, or with an even better mix, to out-
> reproduce it and therefore hog most of the resources.
> Whereas the current DNA/RNA genomic situation involves a
> single mechanism for encoding the gemone, and only
> variation in the words written with that alphabet, the
> original lipid-bag-of-enzymes mechanism may involve
> several totally independent auto-catalytic cycles which
> happened to be more effective together than separately so
> once accidently combined in a single bag they reproduced
> better than the separate originals thus took over the
> biosphere.

Yes, you seem to understand. However, there are a few points
you may have missed.
3. Membranes have two sides - each with its own "genome".
4. Lipid "rafts" are currently a hot topic in cellular
biology. Extrapolating from this, you can see that a
single side of a membrane might be composed of several
regions, each with its own genome.
5. Membranes can nest. The notion of organelles may not be a
post-LUCA invention.
6. Thus, we can have several different species of
"organisms" living together in an "ecosystem". Unlike
modern ecosystems, these "ecosystems" reproduce. It is
possible that the "genome" of such an ecosystem could be
richer than the sum of its parts. In fact, it is not
completely clear that the lowest level parts even need to
have heritable variation. All they absolutely need to be
able to do is to grow and reproduce.

 

[RobertMaas]

> From: [email protected] (TomHendricks474) Rocks are
> better adapted to the environment than prebiotic life or
> first life - so why would there be any advantage in life?

Rocks have no ability to reproduce their kind, fecundity
near zero. If they sit there for a thousand years, then
deteriorate, still they never reproduce their own kind.
Actually there's no such thing as a rock, in the sense of a
thing that continues unabated. Rather there are pieces of
rocky material of various sizes, which get formed by
breaking off larger accumulations of rocky material, and
which cease to exact as "the same rock" whenever they
themselves break apart or erode to produce one or more
lesser pieces of rocky material. They don't have any pattern
that defines them, which continues over time, through these
breakings. By comparison, living things have a genome which
is replicated and which continues through many generations
even as the individual cells grow and split.

The very first time a living thing reproduced, so there were
now two of the same kind of thing, with the same genome, it
beat out any rock because there was at most only one of any
particular kind of rock.

> Why would it last one day, let alone one year or millions
> of years until it was safely adapted to the environment
> and changes in it.

There's no reason why anything would last one day. But when
living things began to exist as such, i.e. when something
was first able to reproduce its pattern (genome), faster
than various copies of that pattern would randomly be
killed, then the number of such copies grew exponentially
until they filled all places with sufficient facilities for
life, and overflowed into other places, and so long as there
was at least one locale where they survived that way, they
continued indefinitely as a series of successive generations
of one pattern.

> You are accepting without proof that life is more
> survivable than other forms - you've given no reason why.

Well nowadays the answer is simple: There's a big reservoir
of raw materials out of which to form biomass, and a big
supply of free energy to be used by life, and life has
sufficient chemical processing facilities to harness that
energy to use those materials to form more of itself, faster
than it naturally dies out by random events. It looks like
this process will continue for about another billion years,
until the Sun gets so hot the oceans boil away.

How did it originally develop those chemical processing
facilities is the question we're debating.

Note it's not just surviving in the sense of decaying more
slowly, which is the essence of life. It's actually
manufacturing more of oneself so as to increase one's total
biomass. Mere surviving with fecundity less than one is what
pieces of rocky material do. Growing more and more of
oneself is what living things do. Masses of volcanic rock
grow not by replicating themselves, but by more magma coming
up and cooling, and the kind of rock produced is dependent
on the physical and chemical properties of the magna rather
than the properties of the mass of rock previously laid out.
By comparison, living things take in food and make more, not
of whatever is like the food they eat, but of their own
personal pattern. Living things break down their food into
pieces that are common building blocks of all living things,
then re-assemble them per their own pattern, or start from
inorganic chemicals and assemble them into building blocks
from scratch. Rocky material does nothing of the sort,
except in trivial cases such as chemicals that can form two
shapes of crystals, such as alum, where the pre-existing
alum forms a sort of template that guides crystallization of
more of it. If you want to consider alum crystals to satisfy
the definition of life, I won't debate you on that point.

 

[Tim Tyler]

Jim Menegay <[email protected]> wrote or quoted:
> [email protected] wrote in message
> news:<[email protected]>...

> > So the question is how your idea fits with that
> > definition. Well, the lipid-bag surface may have a
> > mixture of chemicals in auto-catalytic cycles, each
> > reproducing its own kind, and the total mixture on any
> > given bag could be considered the genome of that bag.
>
> Close, but not exactly right. For heredity, you need
> two things:
> 1. The genome of the children is (usually) the same as the
> genome of the parent.
> 2. The genome of an adult organism is (usually) the same
> as the genome of that organism when it was a child.
>
> If you define the genome to be the relative proportions of
> various chemicals, then reproduction by fission may
> satisfy the first requirement, but it is unlikely to
> satisfy the second. The reason is that the environment
> fluctuates.

If you are talking "relative proportions" then the first
condition being met is *extremely* unlikely as well.

The problem is that membranous bags splitting is a
stochastic process - with no guarantee that the contents are
divided equally between any offspring. Consequently any
information stored as "proportions" will be subject to a
good deal of drift.

Maynard-Smith (or more to the point, E. Szathmary) attempted
to address this issue by using particular (discrete)
replicators as the entities involved - and by having a small
number of them.

In this way is is possible to make a semi-plausible story
about deviations from even assortment between offspring
being compensated for by selection among the offspring.

However, without this the whole idea is a disaster zone -
and even with it the quantity of selection required to
maintain things soon goes through the roof.

The usual way out for the autocatalytic folk is to say that
proportions don't matter much - it's the presense (or
absense) of particular chemicals that matters - not their
relative proportions.

This doesn't rescue the idea - it just means that problems
with the inheritance medium not being very discrete is not
the cause of its demise.

> So, I define the genetic information, not as a point in a
> manifold of chemical concentrations, but as an attractor
> in the dynamics on that manifold. Although fluctuations in
> the environment may change the exact location of the
> attractor, the basins of attraction tend to be persistent.

***If*** such a thing can happen at all - without template
replication - this would be the most coherent picture.

However - without template replication - the premise is very
questionable.

Without template replication, the landscape looks a lot like
a single big basin with "tars" written on it.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.

 

[Jim Menegay]

Tim Tyler <[email protected]> wrote in message news:<[email protected]>...
> The problem is that membranous bags splitting is a
> stochastic process - with no guarantee that the contents
> are divided equally between any offspring. Consequently
> any information stored as "proportions" will be subject to
> a good deal of drift.
>
> Maynard-Smith (or more to the point, E. Szathmary)
> attempted to address this issue by using particular
> (discrete) replicators as the entities involved - and by
> having a small number of them.
>
> In this way is is possible to make a semi-plausible story
> about deviations from even assortment between offspring
> being compensated for by selection among the offspring.

I believe that you have partially misunderstood Szathmary.
Having a small number of instances of a replicator type is
not part of the solution, it is the variant of the problem
that is most troublesome. Szathmary considered this case to
show that selection solve the problem even in the more
difficult cases.

If there are many instances of each replicator type, the
amount of drift is less severe (proportional to SQRT(N)/N),
and milder selection against deviations from the
optimalproportions can maintain the status quo.

 

[RobertMaas]

> From: [email protected] (Jim Menegay)
> For heredity, you need two things:
> 1. The genome of the children is (usually) the same as the
> genome of the parent.

When meiosis occurs, this premise is invalidated. Also when
a horizontal/lateral gene transfer happens, the very same
individual cell suddenly has a somewhat different genome
from what it had before.

Also, usually related to meiosis, plants and animals
generally follow an alternation between haploid and diploid
genomes, and fungi often have an indeterminate number of
nuclei within each cell, each with possibly quite different
genome, so the genome of the overall cell may be meaningless
for our purpose here.

However if we trace the lineage of each individual piece of
genome, we see that except for mutations and where the
piece overlaps a splice, the piece is exactly the same as
it was before.

In the early/pre-life we're imaginaging, with no solid
linkage between adjacent replicators (auto-catalysts), we
may need to speak only of those individual replicators
rather than any segment or region thereof.

Yes, I'm carrying the "selfish gene" viewpoint to the
extreme. The genome of the whole cell or lipid bubble isn't
what's essential, only the individual "genes" (in some
sense) are essential.

> 2. The genome of an adult organism is (usually) the same
> as the genome of that organism when it was a child.

Some bases may be methylated at some times during
development, making the genome not exactly the same one time
as another. If we allow equivalence classes modulo such
modifications, we might as well allow statistical variations
in numbers of each "gene" (in some sense) within the genome.
But I think the crucial thing that makes this different from
non-living processes is that the genome at any moment is
determined *more* by the genome of that same individual in
the recent past, or the genome of its parent(s), than it is
determined by environmental or developmental factors. That's
what separates a true individual, with its own genome which
is (relatively) fixed, from an ecology which simply is the
mix of all its parts where that mix can drastically change
its stistics based on environmental factors. (For a trivial
example, in a sealed system with a cat, while the cat is
alive most of thd genome in the capsule is cat DNA, with
just a little bit of various kinds of endosymbiotic bacteria
etc., but after the cat dies and the flesh starts to rot,
there is less and less cat DNA and more and more bacterial
DNA in that closed ecosystem as time goes on.)

I suspect the earliest lipid-bubble genome-sets were merely
ecosystems of individual replicators, whose genomic
statistics were determined more by recent environmental
factors than by long-lived maintenance of ancestral genome.
If two lipid bubbles with different statistics (because they
had recently lived in different environments) happened to
come close together in virtually the same environent, they
would gradually adjust their statistics to be more and more
adapted for that environent, thus more and more like each
other, until they became indistinguishable. Accordingly it
wouldn't be correct to say that either had its own genome.
One exception: If one or the other was totally devoid of one
of the various replicators, and it was rare that a
replicator moved from one bubble to another nearby, then
that difference might be permanently (or for a long time)
maintained despite the two bubbles currently residing in the
same environent. In that case it really would be correct to
say the two maintained different genomes over time, i.e. the
two are of different species/strain.

> If you define the genome to be the relative proportions of
> various chemicals, then reproduction by fission may
> satisfy the first requirement, but it is unlikely to
> satisfy the second. The reason is that the environment
> fluctuates.

It won't satisfy the first either, because the fission won't
exactly partition the pieces of genome (the various
individual replicators) half-and-half two-halves-the-same-
statistics. With small numbers of replicators in a single
bubble, statistical sampling virtually guarantees a not-exact-
split. But even with large numbers, one kind of replicator
is more likely to be located on one side of the bubble close
to its source of food, and another kind on another side, and
the split is unlikely to split each region down the middle,
more likely split diagonally so that one daughter bubble
gets a lot more of one kind and the other gets a lot more of
the other kind, and only later does the lesser kind within
one bubble replicate more (because of better food supply due
to "fewer hungry mouths" competing for same food).

> So, I define the genetic information, not as a point in a
> manifold of chemical concentrations, but as an attractor
> in the dynamics on that manifold.

I like that idea. The question is whether a given set
(ignoring statistics) of replicators (auto-catalysts) has
only one attractor, or several attractors with barriers
between them. If the former, we have only one species. If
the latter, we may have more than one species, with true
evolution occurring whenever a species spills over a
barrier to cluster around an attractors that wasn't clustered-
around before.

In modern life, biochemical pathways appropriate for one
species would be disadvantageous in a very distantly related
species that had no need for that particular pathway. For
example, if somehow an insect gene for spending a good
fraction of total energy growing and maintaining and
manipulating wings, were somehow to get into the genome of
an elephant and be effective there, the elephant would waste
a lot of energy trying to do wing stuff and probably die
within one or two generations. Perhaps similar factors
played a role in early lipid-bubble life. Maybe a lipid
bubble adapted for one kind of life, such as using H2S and
some other chemical to derive energy, wasn't compatible with
some other kind of lipid bubble, to where a mixture of the
two genomes wouldn't be good enough at either kind of
respiration, and would die regardless of where it happened
to find itself. So that would be a barrier to replicators
from one kind of bubble accidently moving to another and
equalizing the genome. So a species barrier might have
formed early and be maintained over many generations, even
if there wasn't any really good physical barrier to a
replicator accidently moving from one bubble to another that
happened to touch the first. (The bubble with the new
repliator might allow it to make several copies of itself,
but after the bubble divided the daughter with fewest copies
of the new replicator would survive best due to least
disruption in normal respiration, and over time the
daughters with the most of the new replicator would be
weeded out until none at all remained.)

> An environmental fluctuation large enough to destroy a
> basin of attraction, or to create a new one, would be a
> catastrophe in Thom's sense, and a possible cause of
> mutation in our hypothetical genetics.

These lipid bubbles are very tiny, drifting around in water
currents, some surviving because they happen to find a nice
place to grow, some dying because they drift into
inhospitable territory. Although the physical location of
survival would change due to largescale climate changes,
forcing "migration" to stay within a habitable zone,
generally one or another set of daughters would find a
habitat enough like the old home to be able to survive in
the same basin of attraction as before, with neighbors
living up the edges of the basin where they must change
their statistics somewhat to achieve optimum survival.
(Translating that Lamarkian-sounding wording into true
Darwinian wording: Up the edges, those bubbles that happen
to accidently have more of the right kinds of replicators
will survive better and their numbers will increase relative
to others, but also due to the independent nature of the
replicators whichever replicators have the best food supply
will reproduce most rapidly, so any whole lipid bubble will
in fact perform a somewhat Lamarkian adapation to achieve
the mix of replicators that best utilizes the available food
in that locale.
I.e. statistical-ecosystem-like things, unlike fixed-true-
genome things, really do undergo some kinds of
Lamarkian adaption.)

> 1. Membranes have two sides - each with its own "genome".

Or even more complicated, some replicators may reside on one
or the other side, while some may reside burrowed across the
membrane. Some may also float freely in the interior of the
bubble, or be attached to fibers or other debris within the
interior, either floating freely as if rafts, or hanging
attached to the membrane at the other end of the fiber. Lots
of room for speculation here...

> 2. Lipid "rafts" are currently a hot topic in cellular
> biology. Extrapolating from this, you can see that a
> single side of a membrane might be composed of several
> regions, each with its own genome.

That situation would make it quite unlikely for daughter
bubbles to have all the same kinds of replicators as the
parent do as to retain the capability of equalizing the
statistics eventually to be the same as the parent had
before the split. In this case, the whole bubble would be a
true ecosystem with no pretense of being an individual,
while a single raft would be maybe an ecosystem and maybe an
individual.

> 3. Membranes can nest. The notion of organelles may not be
> a post-LUCA invention.

One problem: If the inner one, due to less stressful
environent, grows faster than the outer one, eventually they
merge. But if due to lack of sufficient food input inside a
membrane, the inner ones all starve to death, the nesting
may not persist if it ever happens in the first place. I
believe the latter is more likely, sigh.

> 4. Thus, we can have several different species of
> "organisms" living together in an "ecosystem". Unlike
> modern ecosystems, these "ecosystems" reproduce. It is
> possible that the "genome" of such an ecosystem could
> be richer than the sum of its parts. In fact, it is not
> completely clear that the lowest level parts even need
> to have heritable variation. All they absolutely need
> to be able to do is to grow and reproduce.

I agree! In these early catalytic cycles (the first
replicators), before polypeptides or anything like them
existed, before there was a generic replication machine
which read a sequence of several different kinds of
something (4 kinds of DNA or RNA currently, but perhaps ten
or so different amino acids copied in an earlier system) and
manufactured a new copy of the same (AA) or complementary
(DNA/RNA) sequence, there was no way a mutated replicator
could itself be a replicator: Almost surely a single
mutation in one of these caused it to no longer catalyze
itself, but instead catalyze nothing at all, or catalyze its
former non-mutated kind, making almost all mutations
immediately fatal.

Speculation: How did the first generic replication machinery
come to be? Before that, I speculate that one of these ecosystem-
like lipid bubble lifeforms got so very good at respiring
and reproducing that it developed extremely high fecundity,
so much so that it filled the oceans with accidental
variants of its form, most of which died and decomposed and
provided food for the survivors, but with such a very large
number of deformed individuals being created minute by
minute around the ocean, every once in a while one of them
was viable to fill a different respiratory niche from its
parent, immediately creating a new "species". In this way
many many different versions of the original replicators
came into existance. Eventually one of these replicators
(catalytic cycles) happened to involve an amino acid, and
then a variant of it produced a slightly different amino
acid. Then these two different variants got together in the
same ecosystem-bubble and by chance they worked more
efficiently on the endpoints of polypeptides than they did
on isolated amino acids, so what would happen is that a
sequence of amino acids would encounter one of these or
another at various times, and whichever was appropriate to
replicate that end amino acid would do it while the other
would do nothing. Then when the appropriate one encountered
the next amino acid in sequence that would replicate, and so
on down the chain to the end. (Note that each replicator is
a cycle of catalysts, for example letting A and B denote the
two amino acids, one cycle might be A->Q->R->S->A and the
other cycle might be B->W->X->B, so with S and X floating
around, if S encounters A at the active end of a polypeptide
it immediately replicates A (as soon as it gets the
necessary food ingrediants), while if X encounters B
likewise.) (Note: Normally X catalyzes the production of B
without any help, whenever it gets the right input food, but
I'm speculating that having another B already sitting at the
active replication point along a polypeptide happens to
enhance that reaction a lot.)

 

[Jim Menegay]

[email protected] wrote in message news:<[email protected]>...
> > From: [email protected] (Jim Menegay)

There are many interesting ideas and speculations in your
post. I will respond to just one of them.

> > 3. Membranes can nest. The notion of organelles may not
> > be a post-LUCA invention.
>
> One problem: If the inner one, due to less stressful
> environent, grows faster than the outer one, eventually
> they merge.

Actually, merger of membranes, like the reverse process of
fission, does not occur easily. Modern membranes have
elaborate mechanisms to "catalyze" and control this. One
consequence of this is that gaining "control" over its own
reproduction will be one of the first and most important
selectable traits that a proto-cell will achieve.

But, in response to your point, growth of an inner membrane
may create tension in the outer membrane, promoting its
growth. At the same time, it may create compression in the
inner membrane, which may either inhibit growth, or perhaps
promote invaginations. The invaginations may lead to
fission. Then, further growth of the pair of inner membranes
may promote dumbbelling of the outer membrane, thus
promoting ITS fission. The scope for interaction and
feedback cycles is not all bio-chemical here. Some of it is
electrostatic, some of it is osmotic, and some of it is
mechanical. There is a lot going on. Not all of the stages
of autocatalytic cycles and hypercycles need to be
molecular.

> But if due to lack of sufficient food input inside a
> membrane, the inner ones all starve to death, the nesting
> may not persist if it ever happens in the first place.

Another thing to consider is that CO, CO2, HCN, NH3, and H2S
readily diffuse across membranes, though their hydrated
forms are ionized and do not. I consider these five "gasses"
to be the main nutrients for membrane growth, (and/or waste
products) so I don't expect inner membranes to be starved.

However, it is necessary to move catalytic quantities of
metal ions and eventually phosphate across the membranes, so
ionophores and perhaps transfer vesicles are additional
selectable traits that will evolve early.

Another point. Different growth rates of inner and outer
sheets of a membrane can cause amphiphilic membrane
molecules to flip sides, possibly carrying a charged head
group with them. So membrane potentials can be created and
discharged without requiring complex enzymes.

Redox potentials can be moved across membranes using either
CO/CO2 disproportionation, lipid soluble disulfides (R-S-S-
R), or H2.

 

[RobertMaas]

> From: Tim Tyler <[email protected]>
>>> 1. The genome of the children is (usually) the same as
>>> the genome of the parent.
> If you are talking "relative proportions" then the first
> condition being met is *extremely* unlikely as well.

If the individual replicators are spread uniformly over the
surface of the lipid bag, possibly because clumping too
close together tends to make them "starve" each other so
there's no natural selection favors those which do not take
any actions to prevent dispersion by simple diffusion
(brownian motion), and there are very large numbers of each
successful "species" of catalytic loop, then on the average
any split of the bag would yield approximately the same
proportions in each daughter bag. Not the exact same
proportions, but close enough that they'd be in the vicinity
of the same "attractor" distribution and remain close to it
over time. That's why I'm willing to stipulate that point
and spend my energy debating other more contested points.

> any information stored as "proportions" will be subject to
> a good deal of drift.

In the absense of an "attractor" distribution, I agree. But
somebody else presented that idea and I accept it as
reasonable. Summary of argument in favor: There's a mix of
nutrients available, which varies with location. In any
particular such mix, any replicator (catalytic loop) which
appears in numbers more than there's food for, will
"starve", and fail to reproduce as rapidly as another
replicator which appears in smaller numbers relative to its
food supply, so discrepancies from an exact match to food
available tend to be damped out, i.e. the proportions of
"species" of catalytic cycles tends to drift back toward
exact match with nutrients available.

But we're talking about very early pre-life that has just
barely managed to achieve fecundity greater than one in the
most optimal nutrient situation. Accordingly, only where the
nutrient mix is very close to optimum will these lipid bags
full of catalytic cycles be able to increase their numbers
and fill up that niche and overflow into neighboring less
optimal niches where they'l have fecundity less than 1 and
die out to be replaced by more overflow from the optimal
place. So not only will mix of replicators track mix of
nutrients, but only one particular mix of nutrients will
produce "life" in the sense of fecundity greater than one,
so only this one mix of nutrients will dominate the replicator-track-
nutrients process, so only one mix of replicators will
dominate the "gene pool", i.e. the combination of natural
selection of nutrient locales and tracking-the-food within
each locale is an attractor in this phase space.

I think it would be neat if somebody (perhaps a beginning
computer-software student wishing to tackle his/her first
nontrivial program) would run a simulation of this:
(1) Unspecified catalytic loops which are specified as to
their food (source of energy and chemicals) and
byproducts, with numbers as to how much of each
byproduct and how much of each of the catalysts
themselves are produced in each individual cycle through
the loop, and overall reaction rate as function of food
availability; No need in this initial simulation to
separate out the individual links in the cycle and
simulate how differences of food available make one of
the links dominate causing build-up of its products
followed by bottleneck (starved for food) for the next
link; Keep it simple this first time around;
(2) Statistical model of semi-turbulent ocean waters, with
shear (analagous to the more well known "wind shear"
experienced by airplanes) due to opposing
eddies/currents in close proximity, such that the longer
a bag is the more shear it's likely to experience from
end to end, and the skinnier a bag is the weaker it is
at the waist hence the more likely to pull apart with a
fixed amount of shear, and the instability whereby once
it starts to stretch out the waist gets thinner making
it easier to stretch, making it get skinnier faster,
causing a break-up in a very short time;
(3) Hypothetical source of various nutrients coming in from
fixed points around the boundary of the simulation, such
as from volcanic vents or exposure to sunlight, which
then get diffused via the semi-turbulent water model;
(4) Simulation of brownian motion of individual molecules
around surface of bag, or just a statistical
approximation to that to keep the simulation of
reasonable size;
(5) Direct calculation of statistics of replicators in each
daughter bag after it's pulled apart by shear;
(6) Reporting detailed statistics, listing for each
individual bag (of perhaps a few hundred) the replicator
statistics, and the physical location, and the nutrient
mix in that location, as a function of time;
(7) Reporting overall statistics, showing what clusters (in
phase space) of replicator-statistics exist
hierarchially, producing some sort of cluster diagram
such as dendogram or nearest-neighbor graph etc.
visually, whereby it's easy to see if there's an
attractor or not or maybe even two different attractors.
(Maybe we'll actually observe speciation of the bag
types, whereby one of the replicators in one of the bags
goes extinct but that bag without that nuisance
replicator is better than the complete bag in some micro-
niche, so that new reduced type of bag fills a niche not
occupied by the all-replicators type of bag. Or maybe
*all* bags suffer extinction of one or another
replicator, just by statistical drift, and those which
have lost one replicator occupy a different niche from
those which have lost another. Maybe we should
deliberately introduce bags missing one or another
replicator just to see if they can survive while all-
replicator bags are competing with them. Or maybe
deliberately modify *EVERY* bag to have some randomly-
chosen replicant go extinct, and see what happens.)

As for the "food" used by the replicants (catalytic loops)
in the above simulation, I imagine simple inorganic
chemicals, and a few single-carbon chemicals, all produced
or present in large quantities in presumed early-Earth
oceans/atmospheres: H2, H2S, H2O, CO2, CO, HCN, Na+, Cl-,
Fe++, Fe+++, SO3--, SO4--, H2C:O, HC:OOH, CH4, NH3, etc. and
dissolved&ionized forms of the gasses above such as NH3 ->
NH4+ + OH- and CO2 -> CO3-- + 2*H+. Does anybody have enough
chemical expertise to work out the redox potentials and
entropy of all these various ions/radicals at various pH, or
at least the redox&entropy difference where meaningful, or
know where the data is online, and thereby "predict" what
combinations of "food" could theoretically drive a catalytic
cycle at least, being driven forward by increase in entropy
while having either positive heat generation (exothermic) or
at least not too negative heat generation (just barely
endothermic)? Alternately, does anybody know where there's a
database for all Chemoautotrophic Bacteria (the ones that
can synthesize all the organic chemicals they need from truly-
inorganic and single-carbon-"pseudo-inorganic" chemicals)
listing precisely what the food requirements are for each
species? It would be nice if each species of hypothetical
catalyst-loop in our simulation would either be proven
theoretically possible from first principles, or be observed
as actually a valid food source by present-day
Chemoautotrophs. (There's another term for them, something
like Chemolithotroph or Lithoautotroph, I forget exactly,
which is a more accurate term.)

> Maynard-Smith (or more to the point, E. Szathmary)
> attempted to address this issue by using particular
> (discrete) replicators as the entities involved - and by
> having a small number of them.

With actual catalytic-loops known, or just hypothesized ones
that process a given kind of food to produce a given kind of
waste? (Just curious, not germain to the current debate at
the moment.)

Did they consider my argument for distribution tracking
nutrients available, due to fecundity of individual
replicant being directly proportional to food available per
unit replicant, and only one narrow range of nutrient-mix
yielding fecundity greater than zero, hence an attractor?

> In this way is is possible to make a semi-plausible story
> about deviations from even assortment between offspring
> being compensated for by selection among the offspring.

It may take a long while for differences in replicant
distribution from one bag to another to make one bag survive
much better or grow much faster than the other, and
meanwhile differential reproduction of individual replicants
within each single bag should damp out the distribution
differences, so I don't think differential growth on a whole-
bag basis will have much of an effect, so long as no bag has
totally lost one or another of the replicants.

> However, without this the whole idea is a disaster zone -
> and even with it the quantity of selection required to
> maintain things soon goes through the roof.

With my model, I don't see any need for selection at all,
merely growth of individual replicants tracking available
food supply, to maintain "things" (optimal mix of replicants
in each bag). Please explain your argument better, unless
you are abandoning that line of argument now.

> The usual way out for the autocatalytic folk is to say
> that proportions don't matter much - it's the presense (or
> absense) of particular chemicals that matters - not their
> relative proportions.

In the very short term, a deficiency in quantity of one
particular replicant might slow down growth of that
particular bag, but over medium-time that replicant has so
much food it grows faster than the rest of its bagmates, so
after a while this bag is doing just as well as others. So I
agree with them, and disagree with you. In the long term
it's the presense or absense, not the initial quantity after
a bag-splitting, that is important.

> Without template replication, the landscape looks a lot
> like a single big basin with "tars" written on it.

And how would this, if true, prevent a single "species" of
bag, i.e. all bags with exactly the same *set* of
replicators in it, where the statistics of those replicators
track available food, from surviving a very long time by
repeatedly growing then tearing apart due to shear then
having statistics of replicators drift back toward optimum
by tracking food available?

An idea that came to me just now: Initially the production
of lipids, which stick together to form bags, would be
totally natural, unrelated to any catalytic loops. So the
growth of the bags physically, by new lipids bumping into
them and sticking, and the replication of the various
catalytic loops residing on the inner and outer surfaces of
the bags, would be essentially independent processes. If the
replicants breed too quickly, they might fill up all
available space on the lipid bag and be too cramped to breed
any more, waiting for the bag to grow before then can once
again breed. But if the bag grows more quickly than the
replicants, there'd be lots of empty space available for
replicants to breed. So maybe the replicants (catalytic
loops) actually track both available food and available
space on the bag, achieving both an optimum total density on
the bags and an optimum relative distribution among the
various species of replicants. Note that cramping can be two
factors: Too cramped and even if a catalytic loop reproduces
there's no place to put the result so one result or another
is physically dislodged from the bag; Food diffusing into
the bag is probably fixed per unit surface area of bag, so
crowding of replicants along surface results in less food
per molecule of replicant. If the diffusion rate of food is
very large, dislodging would be the dominant effect, whereas
if the food is scarse then food per unit surface area
divided by density of replicants per unit surface area would
be the dominant effect. If dislodging is dominant, then this
would cause direct compeition between different replicators
even where they use different food so aren't competing for
available food. If food scarcity is dominant, then any two
species of replicator that have even one of their several
nutritional requirements in common, or at least have their
single limiting nutrient in common, would compete with each
other for that common nutrient, and probably one or the
other go extinct within a given bag. So I expect such common-scarce-
nutrient situations to be short-lived, so in the long run
each scarce nutrient will be required by exactly one species
of replicant. But over *very* long times, the scarcity of
nutrients will change, so what wasn't scarce at one time,
will become scarce, so then any replicants which share this
newly-scarce nutrient will compete and one or other go
extinct. So over very long times, the various replicants
will weed out nearly all shared-nutrient problems. But over
such very long times, new replicators should randomly come
into being and join the lipid-bag ecosystems, so maybe
nutrients that were scarce but aren't any more will once
again have multiple replicants consuming them.

It seems at this point in our discussion that the status quo
will be a single species of lipid bag, containing several
species of individual replicants, and whenever speciation at
the bag level occurs, due to extinction of one or another
replicant in different environments, as soon as these
differing bag-species happen to get into an environment
where their union survives better than either alone, they
will in fact accidently merge and then breed better than non-
merged originals, so all speciation at the bag level will be
only temporary. So really there'll be only a single
permanent species of bag for all the millenia until template
replication starts happening. So maybe we have the answer to
how single-species lipid-bag ecosystem-of-catalytic-loops
life came into being, and how template replication evolved
to our present-day life, and the only "missing link" in our
abiogenesis "just so story" is how lipid-bag life ever
acquired template replication?

 

[RobertMaas]

> From: [email protected] (Jim Menegay) Having a
> small number of instances of a replicator type is not part
> of the solution, it is the variant of the problem that is
> most troublesome.

Yes. The problem I see is that if there are **very** few
copies of each replicator, there's a significant chance the
actual number of copies of one or another replicator will be
zero in one or another of the daughter cells after a
splitting of the lipid bag, rendering that one of the
daughters deficient in that respect, so if the replicators
enhances the survival of the lipid bag then that one
daughter will probably die soon. Also, often both daughters
would be deficient, one in some replicator and the other in
another replicator, so both daughters would die shortly. If
the average number of viable offspring is less than 1, the
whole species of lipid-bags-with-replicators is doomed to
extinction.

> Szathmary considered this case to show that selection
> solve the problem even in the more difficult cases.

Not if viable fecundity is less than one. I assume he puts
some lower bound on the average number of copies of the least-
copied replicator to avoid that problem?

> If there are many instances of each replicator type, the
> amount of drift is less severe (proportional to
> SQRT(N)/N), and milder selection against deviations from
> the optimalproportions can maintain the status quo.

And even with severe selection against bags that have zero
copies of one type of replicator, the viable fecundity isn't
affected hardly at all. I've been envisioning each bag
growing by bits of lipid randomly colliding with it, so it
grows larger and larger, and the only thing that ever breaks
it into daughters is when it's so immensely large that it
suffers shear in water currents. So it might grow as large
as a centimeter or larger before it finally suffers a tear-
apart. In such a large bag, with only five or ten different
kinds of replicators, there would be immense numbers of each
kind, and complete lost of one kind of replicator would
never happen except when that particular replicator was
replicating slower than the others so it couldn't maintain a
large number of copies and its fraction shrunk to zero until
its absolute number of copies also shrunk to a tiny number
at which point one daughter cell would likely have zero
copies of it. Any replicator that survives a long time would
presumably be able, given sufficient food, to replicate
faster than the lipid bag could grow to accomodate it, so
would be limited by food available and/or crowding by other
replicators. Tracking available food in that way would be
enough to restore the proportions of each kind of replicator
(each of which needs a different short-supply nutrient) back
to the food-tracking norm after each splitting of the bag,
even without any selection at the bag level. Selection at
the bag level would tend to pull the proportions away from
the food-tracking distribution partway toward a best-survival-of-
bag distribution.

During the very early times, when bags grow by purely
chemical/physical means of bits of lipid randomly sticking
to them, no catalytic activity to manage the lipid bag in
any way, what kind of bag-level selection could occur caused
by variations in replicators residing on them? Well, any
replicator that actually used lipids for food would be
pretty destructive to the bag of course. Any replicator that
emitted chemicals that damaged the bag, and any replicator
that disrupted the physical integrity of the bag such as
cutting away links between adjacent lipids, likewise. On the
other hand, the first time a replicator occurs that actually
manufactures lipids from other components, that would be a
great benefit, and such newly endowed bags would probably
out-compete the original kind of bag and make the original
kind go extinct, or maybe just merge with all the old-style
bags one by one until none are left unmerged. Bags would now
be a "biological" artifact rather than naturally occurring.
(But note the new replicator must not manufacture lipids too
fast, or the bag it's in will grow faster than the
replicators can replicate, causing there to be bags that are
nearly empty of replicators. But I guess in the case of the
lipid-making replicator, that's a self-limiting process,
because if there aren't very many such replicators per unit
area of bag, then they can't make much lipid per unit area,
so the lipid growth rate slows. But any replicator which
replicates slower than the lipid-maker would decline in
proportion toward zero and start suffing zero-count-in-a-
daughter.)

By the way, for our brainstorming pre-life "just so"
stories, we've been concentrating on lipid bags. What if
instead we have solid globs of tarry stuff such as what was
made in the Miller-Urey experiment? Tar tends to be sticky,
stick to itself, and stick to other stuff. So maybe
replicators would stick to the surface of a glob of tar, or
even consume such tar for nutrition, or maybe manufacture
specific kinds of tarry stuff and deposit it on the glob to
make it grow, maybe both the tar-eating replicators and the
tar-making replicators on a single glob of tar.

 

[Tim Tyler]

Jim Menegay <[email protected]> wrote or quoted:
> Tim Tyler <[email protected]> wrote in message
> news:<[email protected]>...

> > The problem is that membranous bags splitting is a
> > stochastic process - with no guarantee that the contents
> > are divided equally between any offspring. Consequently
> > any information stored as "proportions" will be subject
> > to a good deal of drift.
> >
> > Maynard-Smith (or more to the point, E. Szathmary)
> > attempted to address this issue by using particular
> > (discrete) replicators as the entities involved - and by
> > having a small number of them.
> >
> > In this way is is possible to make a semi-plausible
> > story about deviations from even assortment between
> > offspring being compensated for by selection among the
> > offspring.
>
> I believe that you have partially misunderstood Szathmary.
> Having a small number of instances of a replicator type is
> not part of the solution, it is the variant of the problem
> that is most troublesome. Szathmary considered this case
> to show that selection solve the problem even in the more
> difficult cases.
>
> If there are many instances of each replicator type, the
> amount of drift is less severe (proportional to
> SQRT(N)/N), and milder selection against deviations from
> the optimalproportions can maintain the status quo.

As I said, I was talking about information stored as
"proportions".

This contrasts with information being stored as merely the
presence or absence of particular replicators in the cells.

If information is stored as a ratio of the numbers of
replicators, then greater selection is needed to resist
stochastic perturbations of the proportions of each
replicator as the number of replicators involved in making
up each cell rises - since the mutation rate goes up as the
chances of each daughter cell receiving exactly the same
proportion as the parents goes down.

As the mutation rate rises - so the selection needed to
combat it increases.

Inheritance with stochastic correction is better
fidelity than without it - but there's still a "low
information ceiling".

The bigger the organisms' genome, the more selection is
required to maintain it intact across generations.

This rapidly runs into the problem of needing to have a
hundred offspring just to ensure one of them is viable. That
might work for elm trees - but near the origin of life
having 99% of one's offspring die would have been a big
problem - since by the time an organism has had that many
offspring it is likely to be long-dead itself.

Szathmary's model used molecular template replicators to
function - and *they* acted as the primary means of
inheritance in the model.

The model was intended to show how numerous small
replicators could pool their efforts - without being
physically connected as chromosomes; or suffering an error
catastrophe.

Invoking Szathmary's stochastic corrector in a model of
autocatalys /without/ template replicators would stretch it
to near breaking point.

Once there is one replicator, I see no problem with it
forming a community with others - with or without a
membrane.

The membrane is rather superfluous - complex ecosystems can
be formed from simple replicators in a big pool - as is
described on:

http://originoflife.net/complexity/

Such scenarios apparently address the development of
cooperative, composite structures from ecosystems composed
of small replicators - without the need for invoking
Szathmary's stochastic corrector.

The /main/ problem in the OOL is not one of existing
replicators failing to club together - but rather is one of
forming the first replicators.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.

 

[Perplexed In Pe]

<[email protected]> wrote in message
news:[email protected]...
> > From: [email protected] (Jim Menegay)
[snip]
> I've been envisioning each bag growing by bits of lipid
> randomly colliding with it, so it grows larger and larger,
> and the only thing that ever breaks it into daughters is
> when it's so immensely large that it suffers shear in
> water currents. So it might grow as large as a centimeter
> or larger before it finally suffers a tear-apart.

Many lipid fans believe, as you do, that prebiotic chemistry
can provide enough lipid molecules so that membranes can be
self- assembling. I doubt it. Clearly, the FIRST membrane
had to self-assemble somehow, but after that I want my
membranes to be fully autotrophic for lipid molecules.

Lipids are not easy materials for prebiotic chemistry to
make. There are no good syntheses of long chain
hydrocarbons. If there were, and they provided some
hydrophilic groups with the hydrophobic, there is no reason
why the hydrophilic parts would be concentrated at one end
to produce ambiphiles.

The biggest problem, though, with any possible prebiotic
source of lipids is that the lipids have to be fairly
uniform in length to form a membrane. Ambiphilic lipids of
mixed length tend to form micelles rather than two-sheet
membranes. Furthermore, there are issues related to the
ratio of the cross-sectional area of the tail to the "area"
of the head group. And, the area of the head depends on the
whole population of head groups. A mix of positively and
negatively charged heads packs more tightly than a
population of all negative charges, which must balance
itself with positively charged ions from the solution.

It is fairly easy (for me) to imagine that an autotrophic
cycle of lipid construction in the membrane would continue
adding carbons until the length of the tail was "just
right". It is easy to imagine that the dynamics of the
process would lead naturally to the right kind of balance of
head groups. It is harder for me to imagine that the
prebiotic chemistry of the environment would provide exactly
the kinds of nutritious "foods" that a heterotrophic lipid
organism would need. It is next to impossible for me to
imagine that my primitive lipid organisms would be fussy
eaters who know good food from bad. It is easier for me to
imagine that the only foods available are inorganic.

(However, there is one interesting idea out there that might
provide a source of ambiphiles to our aqueous membranes.
Ambiphiles that might have a standard length. This is the
idea that atmospheric aerosols might develop single-layer
lipid envelopes - tails out, heads in. One nice thing about
this idea is that it may be much easier to get the CO and
HCN needed for chain growth directly from the atmosphere
rather than from the oceans. Eventually, the aerosols might
grow into water droplets and fall into the oceans where some
of the ambiphiles are picked up by growing lipid organisms.
The wind then turns what is left into more aerosols. Woese
once suggested that atmospheric water droplets could have
been the original cells. The only problem with this is that
water droplets rarely reproduce - in your terms, fecundity
is probably less than one. Aerosols are smaller than
droplets, and they live much longer. They almost never
reproduce, though they may fuse.)

> During the very early times, when bags grow by purely
> chemical/physical means of bits of lipid randomly sticking
> to them, no catalytic activity to manage the lipid bag in
> any way, what kind of bag-level selection could occur
> caused by variations in replicators residing on them?
> Well, any replicator that actually used lipids for food
> would be pretty destructive to the bag of course. Any
> replicator that emitted chemicals that damaged the bag,
> and any replicator that disrupted the physical integrity
> of the bag such as cutting away links between adjacent
> lipids, likewise. On the other hand, the first time a
> replicator occurs that actually manufactures lipids from
> other components, that would be a great benefit, and such
> newly endowed bags would probably out-compete the original
> kind of bag and make the original kind go extinct, or
> maybe just merge with all the old-style bags one by one
> until none are left unmerged. Bags would now be a
> "biological" artifact rather than naturally occurring.
> (But note the new replicator must not manufacture lipids
> too fast, or the bag it's in will grow faster than the
> replicators can replicate, causing there to be bags that
> are nearly empty of replicators. But I guess in the case
> of the lipid-making replicator, that's a self-limiting
> process, because if there aren't very many such
> replicators per unit area of bag, then they can't make
> much lipid per unit area, so the lipid growth rate slows.
> But any replicator which replicates slower than the lipid-
> maker would decline in proportion toward zero and start
> suffing zero-count-in-a-daughter.)

Good thinking. As Dyson points out, "living" cycles need to
have an S-shaped growth curve - exponential replicator
growth when the population is low, but which tapers off when
the population is high. For "individualistic", selfish
cycles, it is probably good enough to focus on the
replication and let the environment do the tapering due to
resource shortages. But, if we want our cycle to function as
part of a coherent ecosystem of co-operating cycles, we need
to evolve some kind of self-regulation or collective
regulation.

 

[Perplexed In Pe]

"Tim Tyler" <[email protected]> wrote in message
news:[email protected]...
> Jim Menegay <[email protected]> wrote or quoted:
> > Tim Tyler <[email protected]> wrote in message
news:<[email protected]>...
>
> > > The problem is that membranous bags splitting is a
> > > stochastic
process -
> > > with no guarantee that the contents are divided
> > > equally between any offspring. Consequently any
> > > information stored as "proportions" will be subject to
> > > a good deal of drift.
> > >
> > > Maynard-Smith (or more to the point, E. Szathmary)
> > > attempted to
address
> > > this issue by using particular (discrete) replicators
> > > as the entities involved - and by having a small
> > > number of them.
> > >
> > > In this way is is possible to make a semi-plausible
> > > story about deviations from even assortment between
> > > offspring being compensated for by selection among the
> > > offspring.
> >
> > I believe that you have partially misunderstood
> > Szathmary. Having a small number of instances of a
> > replicator type is not part of the solution, it is the
> > variant of the problem that is most troublesome.
> > Szathmary considered this case to show that selection
> > solve the problem even in the more difficult cases.
> >
> > If there are many instances of each replicator type, the
> > amount of drift is less severe (proportional to
> > SQRT(N)/N), and milder selection against deviations from
> > the optimalproportions can maintain the status quo.
>
> As I said, I was talking about information stored as
> "proportions".
>
> This contrasts with information being stored as merely
> the presence or absence of particular replicators in
> the cells.

There is indeed a big contrast between "analog" information
such as proportions and "digital" information such as
presence/absense or the choice of attractor/basin in a
dynamical system.

I believe that analog information cannot properly be called
"genetic" information at all, precisely for the reasons you
give below.

> If information is stored as a ratio of the numbers of
> replicators, then greater selection is needed to resist
> stochastic perturbations of the proportions of each
> replicator as the number of replicators involved in making
> up each cell rises - since the mutation rate goes up as
> the chances of each daughter cell receiving exactly the
> same proportion as the parents goes down.
>
> As the mutation rate rises - so the selection needed to
> combat it increases.
>
> Inheritance with stochastic correction is better fidelity
> than without it - but there's still a "low information
> ceiling".
[snip]
> Szathmary's model used molecular template replicators to
> function - and *they* acted as the primary means of
> inheritance in the model.
>
> The model was intended to show how numerous small
> replicators could pool their efforts - without being
> physically connected as chromosomes; or suffering an error
> catastrophe.

Regarding my claim that a small number of replicators is
part of the problem rather than part of the solution: I
think I see how, if a 3:2 ratio between replicators A and B
is optimal, then it is easier to maintain that exact ratio
in a balanced fission when the population of A is 6 and that
of B is 4, as opposed to when the population of A is 60 and
that of B is 40.

That is, I see that the information is more digital with
a small number of replicators, and more analog with a
large number. However, when you consider the steps
required in getting a 3:2 population back to 6:4, I think
that my large population of 60:40 and weaker selection
for small deviations from the "exact proportion" is a
more viable approach.

> Invoking Szathmary's stochastic corrector in a model of
> autocatalys /without/ template replicators would stretch
> it to near breaking point.

Hmmm. I thought YOU were the one who invoked this model as
an argument against autocatalysis. But I can see now that
you were simply stating the problem (which is common to
replicators and autocats) and describing the Szathmary
solution to the replicator side of the problem without
suggesting that it might extend to autocats.

Moving on, it seems to me that the issue of analog vs
digital information has been coming up lately on a number
of threads.

*This one. *Tim, Guy, and Jim on what constitutes "heredity"
in complex systems. *John and Jim on whether natural
selection can act on metric traits without invoking "genes".
*Jim's insistence that traits for species selection have to
be emergent at the deme or species level and have to be
maintained as an "ESS" or attractor at that level for
"species selection". *Tim vs Jim on the usefulness of near-
neutral variants.

I also notice an analogy between Szathmary's problem and
Eigen's. Eigen, with the help of selection, maintains a "quasi-
species" near an optimum sequence in the face of variance
introduced by mutation. Szathmary, with the help of
selection, maintains a population near an optimum ratio in
the face of variance introduced by sampling error.

I see both as struggling against the same issue - analog
information is not easily heritable in a long term sense.
(Note that Eigen's information is digital at a reductionist
level, but analog at the level Eigen is interested in - he
talks about a "distance" from the optimal sequence.
Similarly, Szathmary's information is also digital in some
sense, in that he is counting things, but it is also analog
in the "true" sense.)

Maintaining analog information close to an environmentally
specified optimum can be done using selection, but it takes
a huge cut out of the reproductive excess. It is far better
to have digital information that is "usually" reproduced
exactly, and then to only use selection to deal with the
exceptions to that "usually". That seems to take a much
smaller cut.

 

[RobertMaas]

> From: [email protected] (TomHendricks474)
RM> The very first time a living thing reproduced, so there
RM> were now two of the same kind of thing, with the same
RM> genome, it beat out any rock because there was at most
RM> only one of any particular kind of rock.

> 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.

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. 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.

> Where is this place? Is the sun gone?

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.

> No replicator can hide from the sun.

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.

> In the end being a replicator is worth nothing.

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.

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

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.

> b. you have a way of replicating these molecules

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.

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, 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).

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

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, 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&current 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.

> It makes sense that there was an environmentally induced
> replication ions [sic] before any self replicator.

I agree, but open chains of catalytic activity, a big
quantity of naturally-occurring A catalyzes the making of a
small quantity of B, which catalyzes the making of only a
tiny bit of C, which breaks up before it can catalyze
anything new such as D, only enhances the total quantity of
B and C a little bit, compared to the orders of magnitude
enhancement in quantity that a closed loop (with fecundity
greater than one) would achieve.

> You say manufacturing more of oneself. But what is
> oneself?

"it" is a loop of catalytic chemical compounds. Each
chemical in the loop catalyzes the making of the next around
the loop. Given an average quantity of a particular chemical
within the loop, there's a rate of making the next chemical,
and a rate of that next chemical breaking up, and
equilibrium between making and breakup determines the
average quantity of that next chemical. The single-step
fecundity is defined as the quantity of that next chemical
divided by the quantity of the given chemical before it.
Multiplying these single-step fecundities all the way around
the loop gives the closed-loop fecundity. If that is greater
than one, the quantity of each chemical grows exponentially.
If less than one, the quanitty damps down to zero, and only
a natural re-supply of one or more chemicals in the loop
will keep it from actually disappearing totally.

> the only thing a replicator can do is replicate what has
> already been selected as surviving that environment

In the absense of fecundity greater than one, *nothing*
survives in the long term. The meaning of the word "survive"
as you use it depends on what time scale you are talking
about. A chemical that survives a minute might not survive
two minutes. So does that count as "surviving" or not? It
depends on what threshold for time you are using. Without
stating the threshold, your use of the term "surviving" is
meaningless.

> thus the only thing that can be copied is thermally stable
> molecules.

Again, "stable" is like "survive". Do you mean stable for
one minute or two minutes or what?? Without stating your time-
threshold for "stable", your use of the word is meaningless.
No chemical is stable forever. Every chemical is stable for
some, however brief, moment of time.

Anything can be copied if it's stable longer than it takes
to make a copy. Paper that sits in a library for 200 years
decomposes and all the information on it is lost if nobody
bothered to make a copy until it was too late. But paper
that is kept for only a few years before the information
is copied to new paper (or other medium) has survived
"long enough".

So if a chemical is stable (on the average, think
"halflife") for only two days, but every hour it replicates
to make two where there was only one before, then after two
days there would be 2**48 copies around but half have been
destroyed so there are ony 2**47 still around, which is
plenty enough!! Another chemical, with equal stability, but
which took 3 days to replicate, would die out, as would a
chemical that replicated once per hour but was stable for
only a half hour. (With catalytic loops the math gets more
complicated, but the basic idea is the same.)

 

[Tim Tyler]

Perplexed in Peoria <[email protected]> wrote or quoted:
> "Tim Tyler" <[email protected]> wrote in message
> > Jim Menegay <[email protected]> wrote or quoted:
> > > Tim Tyler <[email protected]> wrote in message

> > As I said, I was talking about information stored as
> > "proportions".
> >
> > This contrasts with information being stored as merely
> > the presence or absence of particular replicators in the
> > cells.
>
> There is indeed a big contrast between "analog"
> information such as proportions and "digital" information
> such as presence/absense or the choice of attractor/basin
> in a dynamical system.
>
> I believe that analog information cannot properly be
> called "genetic" information at all, precisely for the
> reasons you give below.

[...]

> Moving on, it seems to me that the issue of analog vs
> digital information has been coming up lately on a number
> of threads.
>
> *This one. [...]

> I also notice an analogy between Szathmary's problem and
> Eigen's [...]

> I see both as struggling against the same issue - analog
> information is not easily heritable in a long term
> sense. [...]

> Maintaining analog information close to an environmentally
> specified optimum can be done using selection, but it
> takes a huge cut out of the reproductive excess. It is far
> better to have digital information that is "usually"
> reproduced exactly, and then to only use selection to deal
> with the exceptions to that "usually". That seems to take
> a much smaller cut.

Dawkins once wrote a pop-sci piece (in River Out Of Eden,
Ch.1, The Digital River) about the wonders of digital
inheritance (vs analog inhertance).

His thesis at the time - IIRC - digital was better than
analog - and that was why we had digital genes, and that was
why we have digital TV, music and movies - and that was why
all organisms everywhere in the universe will use digital
information storage media for their genes.

This is all very well - but analog media are not as bad as
all that - since you can fairly easily use them to simulate
digital media.

It *certainly* doesn't need selection to compensate for the
deficiencies of storing information in analog media - since
you can effectively change an analog medium into a digital
one by simple tricks such as forcing all low values to zero
- and all high values to one.

There *is* a cost in doing this - but it doesn't have to be
paid in terms of selection and dead offspring - it can be
paid by sacrificing some of the information storage capacity
in the device in question.

So: if you have an analog information-storage medium,
don't despair:

Despite Dawkins' warnings about the evils of blending
inheritance - and how organisms everywhere will use digital
storage media - you can still build perfectly good organisms
out of an analog information storage medium.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.

 

[Perplexed In Pe]

"Tim Tyler" <[email protected]> wrote in message
news:[email protected]...
> Perplexed in Peoria <[email protected]> wrote
> or quoted:
> > Maintaining analog information close to an
> > environmentally specified optimum can be done using
> > selection, but it takes a huge cut out of the
> > reproductive excess. It is far better to have digital
information
> > that is "usually" reproduced exactly, and then to only
> > use selection to deal with the exceptions to that
> > "usually". That seems to take a much smaller cut.
>
> Dawkins once wrote a pop-sci piece (in River Out Of Eden,
> Ch.1, The Digital River) about the wonders of digital
> inheritance (vs analog inhertance).
>
> His thesis at the time - IIRC - digital was better than
> analog - and that was why we had digital genes, and that
> was why we have digital TV, music and movies - and that
> was why all organisms everywhere in the universe will use
> digital information storage media for their genes.
>
> This is all very well - but analog media are not as bad as
> all that - since you can fairly easily use them to
> simulate digital media.
>
> It *certainly* doesn't need selection to compensate for
> the deficiencies of storing information in analog media -
> since you can effectively change an analog medium into a
> digital one by simple tricks such as forcing all low
> values to zero - and all high values to one.
>
> There *is* a cost in doing this - but it doesn't have to
> be paid in terms of selection and dead offspring - it can
> be paid by sacrificing some of the information storage
> capacity in the device in question.

The point that you are missing is that this is not a one-
time cost in decreased storage capacity. It is a continuing
cost that must be paid by the organism both in greater
energy usage during its lifetime, and in decreased viability
(selection). There are costs to be paid over time whether
you choose analog or digital, but if you choose analog, you
don't really have the option of paying in energy - you are
pretty much stuck with selection as the currency in which
you will have to pay the price.

For digital information, if you want to put your information
into a long-term storage format, you will have to pay an
energy price each time you read, and a hefty price each time
you write. But simply letting the information sit there can
be fairly cheap, as long as you don't need to consult it or
refresh it. But there is a trade-off - the best long-term
storage media involve a high energy-per-bit, hence they are
expensive to refresh. Furthermore, if you want to use
redundancy to increase long-term accuracy, then you have
just introduced another refresh cycle.

Organisms using the digital medium of DNA are using a
moderately long term medium, so they pay costs for reading
(transcription), writing (replication), and redundancy
(translation and recombination).

Analog information (outside biology) cannot be "resharpened"
by copying. So, the only way to store it long term is to use
a very high energy per bit and then to rarely read it -
because the very act of reading degrades the information.
Furthermore, the kinds of information - time series - that
is sometimes stored in analog format is not the kind of
information that is most useful in biology.

So, AFAIK, the only use of analog information in biology
is short-term. Signal transduction (cyclic AMP and all
that) is analog. Over a shortly longer time frame, plants
store analog information for the lifetime of the organism
- a bonzai remembers how it was tortured and an aspen
grove remembers where on the hillside the competition is
too fierce.

> So: if you have an analog information-storage medium,
> don't despair:
>
> Despite Dawkins' warnings about the evils of blending
> inheritance - and how organisms everywhere will use
> digital storage media - you can still build perfectly good
> organisms out of an analog information storage medium.

I would like to see that design! Presumably you intend to
use homunculi to encode development information in the
egg and sperm? Which of the two homunculi of the zygote
do you use for development? Or, perhaps these organisms
are meant to

This is a stretch, but there is a sense in which each year's
growth in an oak tree is new organism, descended from the
organism of the previous year's growth. This new organism
inherits its shape from its parent. Analog information
transmission between generations - if you want to call it
that! But I wouldn't want to base long term evolution on
something like that.