Hydrogen Cyanide and the Origin

Perplexed in Peoria <[email hidden]> wrote or quoted:

Quoted message said:

"Tim Tyler" <[email hidden]> wrote in message

Quoted message said:

Perplexed in Peoria <[email hidden]> wrote or
quoted:

Quoted message said:

Quoted message said:

Quoted message said:

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.

If you have an analog medium with some degree of noise
present, you can use it as a arbitrarily high-fidelity information-
transmission device - provided you have enough of it.

It's no different from a digital medium in this respect.

The reason it has all the same theoretical properties is
that it can be used to exactly simulate a digital medium.

That's basically what computers and DNA do. They construct a
digital medium out of what are basically analog components -
using techniques such as thresholding.

There is absolutely no need for an organism with an analogue
storage medium to pay any reproductive cost in terms of dead
babies who have been selected out.

They can pay their costs in error correction machinery
instead.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

Quoted message said:

From: [email hidden] (Jim Menegay) There are
many interesting ideas and speculations in your post.

I'm taking that as a compliment on my creative mind.

Quoted message said:

I will respond to just one of them.

Sad, maybe someday you'll have some spare time to revisit
what I posted and respond to some other interesting
speculations.

Quoted message said:

Actually, merger of membranes, like the reverse process of
fission, does not occur easily. Modern membranes have
elaborate mechanisms to "catalyze" and control this.

On the other hand, the very earliest lipid bags which formed
naturally and broke apart naturally and grew by random
deposition of new lipid molecules, surely didn't have any
self-control mechanism at all, not even a way to catalyze
their faster growth. Even second-generation lipid bags,
which contained an enzyme for catalyzing the production of
more lipids, still didn't have elaborate regulatory
mechanisms that current-day cells have for maintaining their
cell walls. (Hmm, when I was in biology in high school, the
teacher emphasized that only plants have cell walls, animals
have cell membranes instead. But nowadays I read the term
"cell wall" used more generally.)

Quoted message said:

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.

With these lipid bags growing all over the place, they would
represent a good food supply for any catalyst that happened
to eat lipids, especially if that catalyst occurs in large
numbers because it is part of a catalytic loop with
fecundity greater than one. Accordingly, a very early
selectable trait of a proto-cell (lipid bag) might be
resistance to any new catalysts coming in from outside, any
one of which might be such a lipid-eating parasite. It would
be good to allow an indruder every once in a while, like
maybe after every hundred or so generations, to allow for
mutations, but not to allow an intruder so often that you
get a parasite more often than you reproduce.

Quoted message said:

... growth of an inner membrane may create tension in the
outer membrane, promoting its growth.

I don't quite see the logical requirement that growth
increases whenever tension increases, although I can see
that tension would cause stretching whereby the
molecules are spaced further apart giving less crowding
in the competition for incoming food. But this
stretching must be very small, probably not significant.
Any significant stretching would simply tear the lipids
apart, rupturing the bag.

Quoted message said:

At the same time, it may create compression in the inner
membrane, which may either inhibit growth, or perhaps
promote invaginations.

Now this makes more sense to me, more likely to be
universally true.

Quoted message said:

The invaginations may lead to fission.

(of the inner membrane)

Quoted message said:

Then, further growth of the pair of inner membranes may
promote dumbbelling of the outer membrane, thus promoting
ITS fission.

OK, I agree, except that after the outer membrane is torn
apart by the too-large inner membrane, it's unlikely to ever
seal back up to form two daughter cells. More likely the
whole outer bag will be disrupted until the inner membranes
escape and finally there's room for the outer membranes to
seal back up. Maybe what will really happen is that the
inner membranes cause a rupture in the outer membrane, and
one of the inner membranes escapes through the rupture, then
the outer membrane seals back with only the other inner
membrane still inside. But the escaped one of the two inner
membranes won't survive long because it's in a hostile
environment now. So I don't see this as anything good toward
survival of the pre-cell. Back to the earlier idea: the
inner membrane is too crowded so it slows its growth rate
and no rupture or invaginations etc. ever happen. (Note that
when an invagination starts, that part of the inner membrane
is further from its incoming food, so it stops growing, and
ceases invaginating any deeper. Or the not invaginated part
continues to grow, pressing on the invaginated part, which
buckles further. The invaginated part, having no food,
naturally decomposes. So analagously to plate tektonics,
there's a cycle of inner-membrane sliding under itself and
decomposing and new plate forming to replace it.)

Quoted message said:

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.

Presumably CO2 is a waste product, but the other four are
foods for some of the catalysts. If the outer membrane is
densely populated with catalysts which gobble any food
getting close, allowing only a small amount to escape either
by passing inside or by moving back away on the outside,
then the inner membrane will have significantly less food
than the outer membrane. Even if the inner membrane has 80%
of the food that the outer membrane has, that's enough
difference that the outer membrane will always grow faster
than the inner membrane, so the inner membrane is unlikely
to grow to press against the outer membrane.

Furthermore, if we watch the random walk of one molecule
that has just passed across the outer membrane into its
interior, it is much more likely to wander back to the outer
membrane, again and again, then it is to ever wander far
enough inside to finally encounter the inner membrane,
except if the inner membrane is already pressing close to
the outer membrane. Therefore even if the outer membrane
isn't very good at capturing incoming food, it'll still have
an immense advantage over the inner membrane in quantity of
food acquired, and the inner membrane will never grow to
press against the outer membrane except by chance at one
point, so the inner membrane will never get a decent food
supply relative to what the outer membrane is getting.

<[email hidden]> wrote in message "]news:[email hidden]...

Quoted message said:

Quoted message said:

From: [email hidden] (Jim Menegay)

Quoted message said:

Quoted message said:

There are many interesting ideas and speculations in
your post.

I'm taking that as a compliment on my creative mind.

That is how I intended it. All OOL discussion involves
speculation, there is nothing wrong with that. Incidentally,
it is nice to have someone with whom to discuss autocats and
lipids. Before you showed up, the active OOL posters were
Tim Tyler, who is into Cairns-Smith, and the Borg fellow
with his heat cycles. (The naked RNA gene people, are
probably a majority, but they maintain a smug silence.)

Quoted message said:

Quoted message said:

I will respond to just one of them.

Sad, maybe someday you'll have some spare time to revisit
what I posted and respond to some other interesting
speculations.

IIRC, I either agreed with what you wrote, or your
speculations were based on assumptions that are reasonable,
they are just not the assumptions I would make. If you have
a pet theory of your own to discuss, post it as another
thread, and I will try to comment.

Quoted message said:

Quoted message said:

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.

On the other hand, the very earliest lipid bags which
formed naturally and broke apart naturally and grew by
random deposition of new lipid molecules, surely didn't
have any self-control mechanism at all, not even a way to
catalyze their faster growth.

Understood, except that I don't believe that your
heterotrophic "first generation bags" ever existed. There is
just no good prebiotic source of lipid molecules. And, if
there were, those molecules would more likely be poisonous
than nutritious.

Quoted message said:

Even second-generation lipid bags, which contained an
enzyme for catalyzing the production of more lipids, still
didn't have elaborate regulatory mechanisms that current-
day cells have for maintaining their cell walls.

Nothing elaborate, but they might have had walls and a
"mechanism" for reproduction better than waiting for
shearing forces - see below.

Quoted message said:

(Hmm, when I was in biology in high school, the teacher
emphasized that only plants have cell walls, animals have
cell membranes instead. But nowadays I read the term "cell
wall" used more generally.)

I remember that too, back in the good old "two kingdoms"
days. Nowadays, we would say that plants, many fungi, some
protists, and most bacteria have various kinds of "cell
walls", though the LUCA quite possibly did not. "Walls" have
been reinvented several times, and lost many times.

One of my speculations is that my early lipid organisms
could have had a "cell wall" made of minerals (perhaps
calcium carbonate, iron oxide, or iron pyrite). Not only
that, but they can gain energy by building a wall. I have
explained elsewhere how this might happen for iron oxide.
If CaCO3 is deposited in conjunction with a
decarboxylation, that might drive reactions. And
Wachtershauser advocates pyrite:

Evolution of the first metabolic cycles. Proc Natl Acad
Sci U S A. 1990 Jan;87(1):200-4.

A similar recent speculation by Martin and Russell has
organisms with iron sulfide cell walls, but no lipids:

On the origins of cells: a hypothesis for the
evolutionary transitions from abiotic geochemistry to
chemoautotrophic prokaryotes, and from prokaryotes to
nucleated cells. Philos Trans R Soc Lond B Biol Sci. 2003
Jan 29;358(1429):59-83

If the first lipid organisms did grow walls and membrane
together, we can speculate what might happen when the wall
has grown to cover about 90% of the surface, leaving a small
"breathing hole". Now, continued growth of the wall is
inward, constricting the living space. But the lipid
continues to grow. Depending on osmotic conditions, we can
imagine that a lipid bubble is extruded by the adult walled
cell through its breathing hole. The bubble breaks loose,
and is a "spore". Since we are assuming that depositing
mineral on an existing mineral surface is needed for growth,
the spore cannot yet grow. But, if it happens to find a
mineral surface to attach to (perhaps the outside of one of
its cousins), then it too can start growing to reproductive
maturity (ie. 90% walled).

Of course, this "cell wall" is not really the "ancestor" of
modern cell walls. It is the "archetype". Nice word, that.
Archetypes abound in my OOL thinking. The Model T was not
the ancestor of modern cars, but it was an archetype. A
necessary archetype, because it led to the infrastructure of
paved roads and gas stations upon which modern cars are
dependent. As in Cairns-Smith's metaphor of the arch,
archetypes can disappear without a trace except the "ghost
of functionality past".

Quoted message said:

[...] With these lipid bags growing all over the place,
they would represent a good food supply for any catalyst
that happened to eat lipids, especially if that catalyst
occurs in large numbers because it is part of a catalytic
loop with fecundity greater than one. Accordingly, a very
early selectable trait of a proto-cell (lipid bag) might
be resistance to any new catalysts coming in from outside,
any one of which might be such a lipid-eating parasite. It
would be good to allow an indruder every once in a while,
like maybe after every hundred or so generations, to allow
for mutations, but not to allow an intruder so often that
you get a parasite more often than you reproduce.

I agree with your assessment of how much mutation is
desirable, but I disagree with your assumption that a
single "catalyst" molecule is likely to ignite a parasitic
cycle. My assumption is that a cycle is fecund only if
several of its member chemical species are present in
sufficient quantity.

The phrase "autocatalytic cycle" is ambiguous. Some people
use the phrase to mean only that you have the sequence of
reactions A -> B -> ... -> Z -> 2A, with nutrients being
added and/or wastes being released at each step. So, for
example, Wachtershauser would say that fumarate is a
catalyst in his reductive citric acid cycle. This may be
technically correct, but it is not what biologists usually
mean by a catalyst when they think of enzymes.

As I use the phrase, there has to be a second kind of
catalysis on top of the first. Perhaps I should use the
phrase "autocatalytic hypercycle". Some (perhaps most) of
the cycle reactions will need some help to proceed rapidly
enough. That help must be provided by members of the cycle
and their side products. So, I expect that biologically
interesting cycles will have multiple members that are
autocatalytic in both senses - both stoichiometrically and
enzymatically. And, for virulence, all of those dual-
function molecular species must be present.

Quoted message said:

Quoted message said:

... growth of an inner membrane may create tension in
the outer membrane, promoting its growth.

I don't quite see the logical requirement that growth
increases whenever tension increases, although I can see
that tension would cause stretching whereby the molecules
are spaced further apart giving less crowding in the
competition for incoming food. [...]

It is fairly easy to come up with a carbon-fixing growth
cycle for lipids, in which a carbon is added, some
reductions occur, and the result after three or four
reactions is a slightly longer lipid. It is more difficult
to come up with a way of producing short lipids to insert
into the membrane so that they can begin to grow.

Assuming that that problem is solved, you can now see how
tension in the membrane might be conducive to growth - it
makes it easier to insert short lipids to begin their
growth cycle.

Quoted message said:

Quoted message said:

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.

Presumably CO2 is a waste product, but the other four are
foods for some of the catalysts.

I tend to agree, but Wachtershauser is more ambitious. He
uses CO2 as a nutrient. He may be right. We can't say right
now whether CO and HCN were available in sufficient quantity
to be a major foodstuff, though I am almost sure that they
were needed as "vitamins".

Also, one of NH3 and HCN is also waste - probably NH3. I
suspect that we also need a waste product corresponding to
H2S. Wachtershauser, of course, would say that it is a solid
waste - pyrite.

Quoted message said:

If the outer membrane is densely populated with catalysts
which gobble any food getting close, allowing only a small
amount to escape either by passing inside or by moving
back away on the outside, then the inner membrane will
have significantly less food than the outer membrane. Even
if the inner membrane has 80% of the food that the outer
membrane has, that's enough difference that the outer
membrane will always grow faster than the inner membrane,
so the inner membrane is unlikely to grow to press against
the outer membrane.

The four or five gasses that we are talking about can
diffuse easily across many membranes. However, minerals
cannot, until ionophores are developed. So my nested
membranes may use a different growth strategy than the outer
one. Not a problem - in fact, it is desirable. We want
several species of organisms to make up an ecosystem. In any
case, nesting is probably not going to be present in the
first lipid organism. It is only suggested as one
possibility for how lipid organisms could have enough of a
genome to evolve by natural selection to an RNA world and
"real" neo-Darwinian evolution.

It is possible that inner membranes draw nutrition from the
"scraps" discarded by enclosing membranes. (I don't call
this "waste" because the discarding in not "intentional".
For example, short lipids may be inserted into the inner
side of the outer membrane with the intention that they be
lengthened by carbon fixation. But, inevitably, they will
sometimes pop out, making their way to the outer side of the
inner membrane. They may serve there as starters, or they
may be oxidized to fuel the reductions needed for the inner
membrane's own carbon fixing cycle.

We have here an archetype for modern salvage pathways in
metabolism. And "salvage" is a wonderful archetype for OOL
thinking. For example, much later, in the RNA world, most
amino acids were synthesized while already attached to their
tRNAs. But after protein synthesis got going really strong,
there was an accumulation of free amino acids in the cell
interior as a result of the hydrolysis of proteins. The
modern aaRSs arose as a salvage pathway. And, once that
pathway was working, it became possible to synthesize amino
acids and release them to the solution, rather than building
them already attached.

Quoted message said:

[...]

The rest of your post is based on the assumption, which I
reject, that nested organisms will inevitably be starved. No
further comment needed.

Tim Tyler <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Perplexed in Peoria <[email hidden]> wrote
or quoted:

Quoted message said:

"Tim Tyler" <[email hidden]> wrote in message

Quoted message said:

Perplexed in Peoria <[email hidden]> wrote
or quoted:

Quoted message said:

Quoted message said:

> 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.

If you have an analog medium with some degree of noise
present, you can use it as a arbitrarily high-fidelity information-
transmission device - provided you have enough of it.

It's no different from a digital medium in this respect.

The reason it has all the same theoretical properties is
that it can be used to exactly simulate a digital medium.

That's basically what computers and DNA do. They construct
a digital medium out of what are basically analog
components - using techniques such as thresholding.

There is absolutely no need for an organism with an
analogue storage medium to pay any reproductive cost in
terms of dead babies who have been selected out.

They can pay their costs in error correction machinery
instead.

Just a commment upon this thread. Would it not be true that
social knowledge is analog data - since it is stored in the
brain, which seems to be an analog device. Hence, the
evolution of social knowledge would be an example of
evolution using analog data storage.

Sincerely

John Hewitt

Tim Tyler <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Perplexed in Peoria <[email hidden]> wrote
or quoted:

Quoted message said:

"Tim Tyler" <[email hidden]> wrote in message

Quoted message said:

Perplexed in Peoria <[email hidden]> wrote
or quoted:

Quoted message said:

Quoted message said:

> 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).

Unfortunately, I don't have access to that Dawkins book at
this time. So, I won't be trying to defend his
oversimplifications. I will defend my own
oversimplifications, thank you. ;-)

Quoted message said:

Quoted message said:

Quoted message said:

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.

If you have an analog medium with some degree of noise
present, you can use it as a arbitrarily high-fidelity information-
transmission device - provided you have enough of it.

It's no different from a digital medium in this respect.

The reason it has all the same theoretical properties is
that it can be used to exactly simulate a digital medium.

That's basically what computers and DNA do. They construct
a digital medium out of what are basically analog
components - using techniques such as thresholding.

There is absolutely no need for an organism with an
analogue storage medium to pay any reproductive cost in
terms of dead babies who have been selected out.

They can pay their costs in error correction machinery
instead.

Thanks for being obstinate on this. You have forced me
to think it through more clearly. Now that I have given
it enough thought, my new opinion is that you are still
dead wrong.

I think that we agree that analog information and digital
information are both, at root, the same thing. We agree that
the two types of information are interconvertible. We agree
that both suffer from degradation due to noise. We agree
that the effects of noise can be reduced in two ways: (1) by
increasing the amount of energy expended in reading,
copying, and transforming information, and
(2) by putting the information into a "long-term storage"
medium which is "insulated" and which has a low
effective noise "temperature". We agree that neither
approach can eliminate errors, they can only reduce
errors. We agree that the "long-term" storage media are
pretty much limited to the lifetime of a cell, and that
copying the information for the next generation requires
a transformation step that must take place at the high
ambient noise levels. We agree that for information to
be accurately transmitted over the long term (millions
of years) there is the need for a final proofreading
step - natural selection (aka dead babies). And,
finally, we agree that a good design will do
proofreading at earlier stages as well, so that instead
of dead babies we have dead cells or dead molecules.

So far, analog and digital seem identical - at least in
principle. But when you start looking at the details, there
are differences.

The error rate for a good digital operation is something
like one error per thousand. That is 0.1% of the time, the
information is changed, whereas 99.9% of the time, it is
unchanged.

The error rate for a good analog operation is something like
one part per thousand. That is, 100% of the time the
information is changed, but it is not changed by much - only
by about 0.1%

If the digital operation is repeated 1000 times, there is a
37% chance that no error has occurred. The errors match a
Poisson distribution. Natural selection can handle this.

If the analog operation is repeated 1000 times, you get
a normal distribution. Natural selection can handle
this as well.

But, suppose you think that dead babies are gross, and you
want to do proofreading, because dead cells and dead
molecules are cool. Easy to do in the digital case. You will
almost always be proofreading against an exact perfect
replica of the original information.

However, in the analog case, you will be proofreading
against an unexact copy of the original. In fact, your
proofreading step will sometimes reject copies that are
closer to the original template than is the current
template. Proofreading does do some good - the normal
distribution that is presented to natural selection is
narrowed, but it is not narrowed as much as it would be in
the digital case. Conclusion, analog kills babies, digital
kills cells and molecules.

There is more. So far, we have been assuming that there is
no bias in the information processing machinery. In the
analog case, we have been assuming that the operation
transforms a normally distributed input to a normally
distributed output with the same mean, but a slightly larger
variance. But what if there is a bias? What if the analog
operation has an output with a slightly higher mean than the
input? That bias will be cumulative over a thousand
operations.

What about digital bias? Suppose that the operation,
including proofreading, tends to change 0 to 1 slightly more
frequently than it changes 1 to 0. This bias is not
cumulative in the same way. Once an error happens, you are
done - it doesn't keep getting worse. If the bias causes one
extra error per million operations, that means one dead baby
per million operations in the digital case. But in the
analog case, the entire population is shifted in the
direction of the bias, so that it is suboptimal. Selection
is the only force pushing back. My tentative conclusion:
more dead babies in the analog case. (Not a proof - just an
intuition).

Even without considering natural selection, there are
reasons to think that the basic information processing steps
for analog will require more energy than digital to achieve
the same level of accuracy. You have not specified how you
intend to represent your analog information, so I will
assume that you intend to use (relative) concentrations of
various chemicals.

Using CCDs (charge coupled devices) as a model, I am willing
to concede that a molecular biological mechanism could be
constructed for the "long term" storage of information, and
its transmission from place to place. A CCD stores charge -
there is minimal leakage. It is possible to force
essentially all of the charge from one compartment to
another. (CCD's are used to form and then process image
information - particularly in astronomy).

Suppose we want to be able to read this information with
an accuracy of 1%. Our molecular machinery cannot directly
sense the concentration of a chemical. All it can do is to
sense the presence or absense of a particular molecule. To
get a 1% accuracy, we need to interact with 10,000
molecules, plus or minus 100. This is because 10,000 =
100^2. The sampling error is roughly the square root of
the sample size. Of course, we don't interact with all of
these molecules at once. We interact over a period of
time, producing some other chemical effect over the same
period of time.

Suppose that we actually have 100 molecules in a
compartment, and that we want to copy this information. That
is, we want to end up with two compartments each containing
100 molecules plus or minus 1 molecule. We insert the probe
end of our allosteric enzyme into the compartment and leave
it there for a predetermined time period so that we can
expect it to have 10,000 interactions. Every hundredth
interaction, we synthesize a molecule in the second
compartment. Voila! it works.

Want proofreading? That can be done too. Our probing enzyme
needs to be able to both synthesize and destroy molecules in
the second compartment, depending on whether there is an
interaction in the first compartment. This is where the
energy cost comes in. We need to reach a steady state in
which the creation and destruction of molecules in the
second compartment is happening at the same rate.
Furthermore, there is a thermodynamic cost in running the
"futile cycle". But, if you are willing to pay the cost, you
have proofreading that is just as accurate as digital
proofreading.

But consider what we have accomplished. We are processing
analog information with 1% accuracy. This corresponds to 6
or 7 digital bits. To do this, we needed a special enzyme
just to handle one step in the processing of this 6 or 7
bits of information. That is, we need a special enzyme for
each channel and a channel can carry only a few bits. But
to build an organism, we need something like a million
channels of this size. That is a million species of
chemicals, each of which can be distinguished from another
by enzymes. And, we need a million special enzymes. How are
they to be produced?

Returning to the model of CCDs, we can see that the key to
their success is two special facts: (1) Each channel is
treated the same - one set of machinery (enzyme) can handle
every channel. (2) The channels are processed sequentially -
each channel is identified to the machinery by position. It
doesn't take a genius to see that these same two special
facts are used by biology in its information processing
machinery. My conclusion: although in theory, the low level
machinery for analog works as well as it does for digital,
in practice the need to economize on machinery (by applying
the same machinery to multiple channels) has caused
evolution to relegate analog to a peripheral role.

Analog works fine for special purpose channels in which time-
responsiveness is at a premium and there is no need for long
term storage. It also works OK for some long term purposes,
as long as you are willing to tolerate a lot of dead babies.

Furthermore, let me point out that the particular form of
digital proofreading that biology uses doesn't result in
dead molecules (let alone cells or babies). It only results
in a dead chemical bond. We don't throw away whole mRNA
strands, or whole proteins. We throw away only a few base
pairs of RNA, or an adenosylated amino acid. It is very
unclear how analog proofreading could be done so
efficiently.

But perhaps you have a different model of analog information
than the one I have supplied. Something different from
concentrations of chemicals. My claim is that digital is
still going to be better for two reasons:

(3) Proofreading is more effective. Hence, less work is left
for natural selection.
(4) Multiple channels can be handled using the same
machinery. If each channel required distinct machinery,
then how could the machinery itself be specified by
analog information?

Quoted message said:

Tim Tyler said:

Perplexed in Peoria <[email hidden]> wrote or
quoted:

Quoted message said:

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

Quoted message said:

> > 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.

It is a mixed and very misleading metaphor. Which is perhaps
why it has largely been ignored since...

Quoted message said:

Quoted message said:

Quoted message said:

>
> 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.

If you have an analog medium with some degree of noise
present, you can use it as a arbitrarily high-fidelity
information-transmission device - provided you have
enough of it.

It's no different from a digital medium in this respect.

The reason it has all the same theoretical properties is
that it can be used to exactly simulate a digital
medium.

That's basically what computers and DNA do. They
construct a digital medium out of what are basically
analog components - using techniques such as
thresholding.

There is absolutely no need for an organism with an
analogue storage medium to pay any reproductive cost in
terms of dead babies who have been selected out.

They can pay their costs in error correction machinery
instead.

Just a commment upon this thread. Would it not be true
that social knowledge is analog data - since it is stored
in the brain, which seems to be an analog device. Hence,
the evolution of social knowledge would be an example of
evolution using analog data storage.

All data storage in the real world is analogue. The only
difference between analogue and digital is the fidelty of
replication. I think that any evolutionary process is going
to maximise the fidelity to the point where further
improvements would be too costly, no matter whether it is
cultural, biological or technological. I completely agree
with Tim, and would say that "digital" is, in the real (as
opposed to abstract) world, a name for "very-high-fidelity
reproduction" over analogue substrates.

That digital media use thresholds to ensure that fidelity is
secondary. And neither genes nor electrical currents routed
via transistors are digital in the strict sense of abstract
bits. We are confusing our abstract representations of
things with the things themselves if we think genes are
digital. Digital objects do not mismatch. Digital objects do
not denature. This is true also in culture.

Scott Atran and others have argued that because culture is
analogue, it must be non-particulate (error 1) and therefore
the only way to explain the persistance of cultural forms is
that they are attractor basins (error 2). Social knowledge
can be high fidelity without being particulate, and there
are other explanations than some vague appeal to attractors
in a space that is not defined.
--
John S Wilkins PhD - www.wilkins.id.au a little emptier, a
little spent as always by that quiver in the self,
subjugated, yes, and obedient. -- Seamus Heaney

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler <[email hidden]> wrote in message
news:<[email hidden]>...

Quoted message said:

Perplexed in Peoria <[email hidden]> wrote or
quoted:

Quoted message said:

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

Quoted message said:

> > Maintaining analog information close to an
> > environmentally specified optimum can be done
> > using selection, but it takes a huge cut out

Quoted message said:

Quoted message said:

Quoted message said:

> > 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).

Unfortunately, I don't have access to that Dawkins book at
this time. So, I won't be trying to defend his
oversimplifications. I will defend my own
oversimplifications, thank you. ;-)

Quoted message said:

Quoted message said:

> 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.

If you have an analog medium with some degree of noise
present, you can use it as a arbitrarily high-fidelity
information-transmission device - provided you have
enough of it.

It's no different from a digital medium in this respect.

The reason it has all the same theoretical properties is
that it can be used to exactly simulate a digital
medium.

That's basically what computers and DNA do. They
construct a digital medium out of what are basically
analog components - using techniques such as
thresholding.

There is absolutely no need for an organism with an
analogue storage medium to pay any reproductive cost in
terms of dead babies who have been selected out.

They can pay their costs in error correction machinery
instead.

Thanks for being obstinate on this. You have forced me
to think it through more clearly. Now that I have given
it enough thought, my new opinion is that you are still
dead wrong.

I think that we agree that analog information and digital
information are both, at root, the same thing. We agree
that the two types of information are interconvertible. We
agree that both suffer from degradation due to noise. We
agree that the effects of noise can be reduced in two
ways: (1) by increasing the amount of energy expended in
reading, copying, and transforming information, and
(2) by putting the information into a "long-term storage"
medium which is "insulated" and which has a low
effective noise "temperature". We agree that neither
approach can eliminate errors, they can only reduce
errors. We agree that the "long-term" storage media
are pretty much limited to the lifetime of a cell, and
that copying the information for the next generation
requires a transformation step that must take place at
the high ambient noise levels. We agree that for
information to be accurately transmitted over the long
term (millions of years) there is the need for a final
proofreading step - natural selection (aka dead
babies). And, finally, we agree that a good design
will do proofreading at earlier stages as well, so
that instead of dead babies we have dead cells or dead
molecules.

Quoted message said:

So far, analog and digital seem identical - at least in
principle. But when you start looking at the details,
there are differences.

The error rate for a good digital operation is something
like one error per thousand. That is 0.1% of the time, the
information is changed, whereas 99.9% of the time, it is
unchanged.

The error rate for a good analog operation is something
like one part per thousand. That is, 100% of the time the
information is changed, but it is not changed by much -
only by about 0.1%

I am not aware of anything about the definition of the
terms "analog" and "digital" that specifies what error
rates they exhibit.

In the real world, both sorts of system are subject to noise
- and neither has perfect fideleity. If you assume that
analog storage media have high error rates, then your
conclusion follows.

However analog media can be accurate and digital media can
be noisy. The degree of nosie is a different idea to
whether a system encodes information in an analogue or a
digital formats.

Quoted message said:

However, in the analog case, you will be proofreading
against an unexact copy of the original. In fact, your
proofreading step will sometimes reject copies that are
closer to the original template than is the current
template. Proofreading does do some good - the normal
distribution that is presented to natural selection is
narrowed, but it is not narrowed as much as it would be in
the digital case. Conclusion, analog kills babies, digital
kills cells and molecules.

No way ;-)

Digital copies are not exact either (since all real systems
are subject to noise).

If you are getting dead babies from using an analogue
storage media, then you can use the sorts of technology
use by the electronic engineers to make a digital medium
out of it.

That should reassure you that no large numbers of dead
babies are logically needed.

Quoted message said:

There is more. So far, we have been assuming that there is
no bias in the information processing machinery. In the
analog case, we have been assuming that the operation
transforms a normally distributed input to a normally
distributed output with the same mean, but a slightly
larger variance. But what if there is a bias? What if the
analog operation has an output with a slightly higher mean
than the input? That bias will be cumulative over a
thousand operations.

What about digital bias? Suppose that the operation,
including proofreading, tends to change 0 to 1 slightly
more frequently than it changes 1 to 0. This bias is not
cumulative in the same way. Once an error happens, you are
done - it doesn't keep getting worse.

It does - if you have more than one bit to store ;-)

The analog medium seemed to have a good deal of storage
capacity. Should not the digital media you are comparing it
with have comparable storage capacity?

Quoted message said:

Even without considering natural selection, there are
reasons to think that the basic information processing
steps for analog will require more energy than digital to
achieve the same level of accuracy. You have not specified
how you intend to represent your analog information, so I
will assume that you intend to use (relative)
concentrations of various chemicals.

Fair enough. The brain seems suitable as a sample analogue
storage medium. At any rate it certainly isn't *completely*
digital - since it uses "neural weights" and "frequency-
dependent activation" to operate.

So - though individual nerve firing is discrete - and
individual nerve cells are discrete - the whole process has
significant analog elements.

How then does it manage to store anything for long periods
of time? It uses many electronic engineering-style tricks to
achive fidelity. Among those tricks is the notion of an
"activation threshold". This is much the same sort of
thresholding that the electronics folk used to damp down
their error terms with.

Quoted message said:

Returning to the model of CCDs, we can see that the key to
their success is two special facts: (1) Each channel is
treated the same - one set of machinery (enzyme) can
handle every channel. (2) The channels are processed
sequentially - each channel is identified to the machinery
by position. It doesn't take a genius to see that these
same two special facts are used by biology in its
information processing machinery. My conclusion: although
in theory, the low level machinery for analog works as
well as it does for digital, in practice the need to
economize on machinery (by applying the same machinery to
multiple channels) has caused evolution to relegate analog
to a peripheral role.

Analog storage is secondary when it comes to genetics
(though issues of methylation of DNA may eventually be
regarded as complex enough to severely mess up the ideal of
DNA as a digital storage medium).

However, it plays a more evidently prominent role when it
comes to storing memories - and that process is still an
important one.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

[email hidden] (John Wilkins) wrote in message news:<[email hidden]>...

Quoted message said:

All data storage in the real world is analogue.

Ah! Reductionism again. But Wolfram and Fredkin might
disagree as to whether the ultimate reduction is to analog
or digital.

In general, I think that it is a bad idea to think of either
analog or digital as the ultimate truth about the "real
world". We don't know enough about reality to make such
judgements. All we have to work with are models of reality.
Analog and digital are two such models. Neither lives in the
"real world". Both are abstract conceptual entities.

Quoted message said:

The only difference between analogue and digital is the
fidelty of replication.

Disagree. See below.

Quoted message said:

I think that any evolutionary process is going to maximise
the fidelity to the point where further improvements would
be too costly, no matter whether it is cultural,
biological or technological.

Agreed.

Quoted message said:

I completely agree with Tim, and would say that "digital"
is, in the real (as opposed to abstract) world, a name for
"very-high-fidelity reproduction" over analogue
substrates. That digital media use thresholds to ensure
that fidelity is secondary.

First, I don't think that Tim said that. Second, I don't
think that thresholding per se is the whole distinction.
Digital involves a "force" that pushes signals that drift
close to the threshold back to nominal values. Analog tries
to avoid such "distortions" of the received signal.

If you Aussies are familiar with the noble sport of bowling,
you may appreciate this analogy. The skilled bowler aims his
ball down the lanes using analog information. The medium,
(the lane) is as flat as possible, to avoid distorting the
bowler's signal. However, an unskilled bowler is producing
digital information. The overwhelming majority of his balls
end up in the "gutter", and the gutters provide forces such
that a variety of inputs will mostly result in one of two
possible outputs.

The ideal digital bowling lane would slope toward the
gutters from the center (the threshold). And it is this
"basin of attraction" feature in the dynamics that
distinguishes digital from analog.

Tim Tyler <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

I think that we agree that analog information and
digital information are both, at root, the same thing.
We agree that the two types of information are
interconvertible. We agree that both suffer from
degradation due to noise. We agree that the effects of
noise can be reduced in two ways: (1) by increasing the
amount of energy expended in reading, copying, and
transforming information, and
(2) by putting the information into a "long-term
storage" medium which is "insulated" and which has a
low effective noise "temperature". We agree that
neither approach can eliminate errors, they can only
reduce errors. We agree that the "long-term" storage
media are pretty much limited to the lifetime of a
cell, and that copying the information for the next
generation requires a transformation step that must
take place at the high ambient noise levels. We
agree that for information to be accurately
transmitted over the long term (millions of years)
there is the need for a final proofreading step -
natural selection (aka dead babies). And, finally,
we agree that a good design will do proofreading at
earlier stages as well, so that instead of dead
babies we have dead cells or dead molecules.

Quoted message said:

So far, analog and digital seem identical - at least in
principle. But when you start looking at the details,
there are differences.

The error rate for a good digital operation is something
like one error per thousand. That is 0.1% of the time,
the information is changed, whereas 99.9% of the time,
it is unchanged.

The error rate for a good analog operation is something
like one part per thousand. That is, 100% of the time
the information is changed, but it is not changed by
much - only by about 0.1%

I am not aware of anything about the definition of the
terms "analog" and "digital" that specifies what error
rates they exhibit.

Perhaps I was unclear. My numbers were intended as an
illustration that both analog and digital are subject to
noise, but that the noise manifests itself in different
ways. I did not mean to suggest the particular error rates
that I used in my example as part of the definition of
digital or analog.

Quoted message said:

In the real world, both sorts of system are subject to
noise - and neither has perfect fideleity. If you assume
that analog storage media have high error rates, then your
conclusion follows.

I made no such assumption. I tried to make the error rates
equivalent.

Quoted message said:

However analog media can be accurate and digital media can
be noisy. The degree of nosie is a different idea to
whether a system encodes information in an analogue or a
digital formats.

I really begin to suspect that you are not reading what I
wrote before responding.

Quoted message said:

Quoted message said:

However, in the analog case, you will be proofreading
against an unexact copy of the original. In fact, your
proofreading step will sometimes reject copies that are
closer to the original template than is the current
template. Proofreading does do some good - the normal
distribution that is presented to natural selection is
narrowed, but it is not narrowed as much as it would be
in the digital case. Conclusion, analog kills babies,
digital kills cells and molecules.

No way ;-)

Digital copies are not exact either (since all real
systems are subject to noise).

And now I know that you are not reading carefully what I
tried to write carefully. I covered the fact that digital
media are not exact all of the time in the paragraph that
you deleted.

Quoted message said:

If you are getting dead babies from using an analogue
storage media, then you can use the sorts of technology
use by the electronic engineers to make a digital medium
out of it.

That should reassure you that no large numbers of dead
babies are logically needed.

I must be missing your point here. It appears that you are
saying that analog doesn't lead to excessive dead babies,
because if it did, then you could switch to digital.

Quoted message said:

Quoted message said:

There is more. So far, we have been assuming that there
is no bias in the information processing machinery. In
the analog case, we have been assuming that the
operation transforms a normally distributed input to a
normally distributed output with the same mean, but a
slightly larger variance. But what if there is a bias?
What if the analog operation has an output with a
slightly higher mean than the input? That bias will be
cumulative over a thousand operations.

What about digital bias? Suppose that the operation,
including proofreading, tends to change 0 to 1 slightly
more frequently than it changes 1 to 0. This bias is not
cumulative in the same way. Once an error happens, you
are done - it doesn't keep getting worse.

It does - if you have more than one bit to store ;-)

The analog medium seemed to have a good deal of storage
capacity. Should not the digital media you are comparing
it with have comparable storage capacity?

Again, it seems you are not paying attention to my argument
and are simply producing a response as a knee-jerk reaction.
A bias simply is not cumulative in digital media. It doesn't
matter whether you have one bit or ten (corresponding to a
0.1% resolution in an analog medium). Errors in any of those
ten bits are treated as fatal, and must be dealt with
eventually by selection.

Quoted message said:

Quoted message said:

Even without considering natural selection, there are
reasons to think that the basic information processing
steps for analog will require more energy than digital
to achieve the same level of accuracy. You have not
specified how you intend to represent your analog
information, so I will assume that you intend to use
(relative) concentrations of various chemicals.

Fair enough. The brain seems suitable as a sample analogue
storage medium. At any rate it certainly isn't
*completely* digital - since it uses "neural weights" and
"frequency-dependent activation" to operate.

Frequencies are analog, to be sure. They are also an
interesting example of an analog medium that can be
transmitted virtually error free, except for occasional
(fatal) disruptions. So, in that sense, they are digital.
But unfortunately, short of rotating media, there is no way
to put frequency data into long-term storage. The brain uses
frequencies to encode light intensities, for example.

Quoted message said:

So - though individual nerve firing is discrete - and
individual nerve cells are discrete - the whole process
has significant analog elements.

How then does it manage to store anything for long periods
of time? It uses many electronic engineering-style tricks
to achive fidelity. Among those tricks is the notion of an
"activation threshold". This is much the same sort of
thresholding that the electronics folk used to damp down
their error terms with.

That is, it uses digital. I would also describe the
formation of long term memories by means of interneural
connection topology as essentially digital.

Quoted message said:

[snip] Analog storage is secondary when it comes to
genetics (though issues of methylation of DNA may
eventually be regarded as complex enough to severely mess
up the ideal of DNA as a digital storage medium).

I assume you are referring to cases in which % of
methylation caries the message, rather than exact location
of methylation. Yes, I would agree that this is analog. This
is analog piggybacking on a basically digital medium. Just
the opposite of DSL. Another interesting hybrid case is
transcription and translation "concensus promoter"
sequences. This is data that is transmitted digitally to
progeny, but is interpreted in an analog fashion.

Quoted message said:

However, it plays a more evidently prominent role when it
comes to storing memories - and that process is still an
important one.

I would say that the information itself is digital, but the
decision as to whether to form or to retain a synapse is
analog. Another interesting hybrid.

[email hidden] (John Wilkins) wrote in
:"]news:[email hidden]:

Quoted message said:

All data storage in the real world is analogue. The only
difference between analogue and digital is the fidelty of
replication. I think that any evolutionary process is
going to maximise the fidelity to the point where further
improvements would be too costly, no matter whether it is
cultural, biological or technological. I completely agree
with Tim, and would say that "digital" is, in the real (as
opposed to abstract) world, a name for "very-high-fidelity
reproduction" over analogue substrates.

Umm - whatever happened to your reductionist stance? Unless
you are denying quantum mechanics, or are arguing for
emergent properties, it would seem that your only logically
consistent argument would be that all data storage in the
real world is digital.

Yours,

Bill Morse

Jim Menegay said:

(John Wilkins) said:

All data storage in the real world is analogue.

Ah! Reductionism again. But Wolfram and Fredkin might
disagree as to whether the ultimate reduction is to analog
or digital.

In general, I think that it is a bad idea to think of
either analog or digital as the ultimate truth about the
"real world". We don't know enough about reality to make
such judgements. All we have to work with are models of
reality. Analog and digital are two such models. Neither
lives in the "real world". Both are abstract conceptual
entities.

Quoted message said:

The only difference between analogue and digital is the
fidelty of replication.

Disagree. See below.

Quoted message said:

I think that any evolutionary process is going to
maximise the fidelity to the point where further
improvements would be too costly, no matter whether it
is cultural, biological or technological.

Agreed.

Quoted message said:

I completely agree with Tim, and would say that
"digital" is, in the real (as opposed to abstract)
world, a name for "very-high-fidelity reproduction" over
analogue substrates. That digital media use thresholds
to ensure that fidelity is secondary.

First, I don't think that Tim said that. Second, I
don't think

No, I added that to what Tim said.

Quoted message said:

that thresholding per se is the whole distinction. Digital
involves a "force" that pushes signals that drift close to
the threshold back to nominal values. Analog tries to
avoid such "distortions" of the received signal.

I don't follow this. Thresholding is how an analog signal
can become a digital one (as in FM v AM). The "trying"
here is done by the sender and receiver, and is imposed,
so to speak, on the analogue signal. What that "force" can
be I have simply no idea. But I am not an engineer so I
would appreciate the education you can give me in making
this clear.

Quoted message said:

If you Aussies are familiar with the noble sport of
bowling, you may appreciate this analogy. The skilled
bowler aims his ball down the lanes using analog
information. The medium, (the lane) is as flat as
possible, to avoid distorting the bowler's signal.
However, an unskilled bowler is producing digital
information. The overwhelming majority of his balls end up
in the "gutter", and the gutters provide forces such that
a variety of inputs will mostly result in one of two
possible outputs.

The ideal digital bowling lane would slope toward the
gutters from the center (the threshold). And it is this
"basin of attraction" feature in the dynamics that
distinguishes digital from analog.

The point and logic of this example escape me entirely, I'm
afraid. And I do bowl. Some of my bowling makes it to the
end of the lane, and I even get a strike occasionally. But I
was unaware of using digital technology or techniques to do
so - it was all analogue...
--
John S Wilkins PhD - www.wilkins.id.au a little emptier, a
little spent as always by that quiver in the self,
subjugated, yes, and obedient. -- Seamus Heaney

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

The ideal digital bowling lane would slope toward the
gutters from the center (the threshold). And it is this
"basin of attraction" feature in the dynamics that
distinguishes digital from analog.

...but surely analog systems can exhibit basins of
attraction as well.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler <[email hidden]> wrote in message
news:<[email hidden]>...

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

[snip agreement]

Quoted message said:

Quoted message said:

Quoted message said:

So far, analog and digital seem identical - at least
in principle. But when you start looking at the
details, there are differences.

The error rate for a good digital operation is
something like one error per thousand. That is 0.1% of
the time, the information is changed, whereas 99.9% of
the time, it is unchanged.

The error rate for a good analog operation is
something like one part per thousand. That is, 100% of
the time the information is changed, but it is not
changed by much - only by about 0.1%

I am not aware of anything about the definition of the
terms "analog" and "digital" that specifies what error
rates they exhibit.

Perhaps I was unclear. My numbers were intended as an
illustration that both analog and digital are subject to
noise, but that the noise manifests itself in different
ways. I did not mean to suggest the particular error rates
that I used in my example as part of the definition of
digital or analog.

Quoted message said:

In the real world, both sorts of system are subject to
noise - and neither has perfect fideleity. If you assume
that analog storage media have high error rates, then
your conclusion follows.

I made no such assumption. I tried to make the error rates
equivalent.

A 1 chance of a bitflip every 1000 bits is roughly
equivalent (in terms of the error rate) to a +/- 1/1000
change in an 0-999 integer value?

It isn't. It isn't anywhere remotely equivalent:

Store 1000 bits of information in both media.

That's 1000 bits of digital information - and about 98
numbers from 0-999.

How much information is needed to store the details of what
errors took place in one generation?

In the digital case a number between 0 and 999 should
normally suffice to describe the location of the error.
Sometimes more will be needed - but sometimes less - so the
error can be described in 10 bits.

In the analog case you need about one bit per value to
encode whether the error is "+" or "-". So that's
about 98 bits.

About ten times much information is needed to describe the
locations of the errors in the analog case.

That's about the same as saying there was ten times as much
error occurring in the analog medium.

No wonder it doesn't make such a good information storage
device, in your example - the error rate is effectively ten
times as big.

This doesn't reflect badly on analog media, though - it just
shows that the error rates you pulled out of the air
happened to heavily favour digital media.

Quoted message said:

Quoted message said:

If you are getting dead babies from using an analogue
storage media, then you can use the sorts of technology
use by the electronic engineers to make a digital medium
out of it.

That should reassure you that no large numbers of dead
babies are logically needed.

I must be missing your point here. It appears that you are
saying that analog doesn't lead to excessive dead babies,
because if it did, then you could switch to digital.

That's about the size of it. Analog media can be used to
simulate digital ones - with whatever fidelity you like - so
their properties can't be all that different.

The only possible variable is how the density of information
storage is traded off against the resulting error rate.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

"Tim Tyler" <[email hidden]> wrote in message
"]news:[email hidden]...

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

The ideal digital bowling lane would slope toward the
gutters from the center (the threshold). And it is this
"basin of attraction" feature in the dynamics that
distinguishes digital from analog.

...but surely analog systems can exhibit basins of
attraction as well.

But surely an IDEAL analog system will not. See my
reply to John.

Quoted message said:

From: [email hidden] (Jim Menegay) If you have a
pet theory of your own to discuss, post it as another
thread, and I will try to comment.

I don't have any full-fledged theory, just the idea of lots
of random catalysts acting on lots of naturally-occurring
and previously-catalyzed chemicals to produce new chemicals
some of which are new catalysts, and by chance among these
many chemicals there's a catalytic loop plus sufficient
"food" for it that it achieves around-the-loop fecundity
greater than one causing it to rapidly grow exponentially
until it's food-limited, and then to persist so long as its
"food" continues to be naturally produced. Thanks to these
recent discussions, I've developed the idea toward colonies
of such catalytic loops sharing a lipid bubble, and I've
adopted the idea of branching chains of catalysts forming a
tree which eventually by chance closes a loop. And with that
in place, it seems obvious that in different locales on
Earth the tree would grow in different directions and form
its first loop in a different place (meaning using a
different set of catalysts to form the loop), so there'd be
at most one such loop in each locale, but where mixing
between different single-catalytic-loop locales occurs two
different already-established catalytic cycles might get
together to form an ecosystem, and such ecosystems could be
the first genetic system. But I'm pretty flexible about the
details, and would like to see lots of research done to
check this kind of theory to see if it would actually work
in nature.

Quoted message said:

I don't believe that your heterotrophic "first generation
bags" ever existed. There is just no good prebiotic source
of lipid molecules.

Oh. In reading about them so much, as "naturally
occurring", I just assumed the lipids would form under
prebiotic conditions. So let me backtrack on that
speculation. As an alternative, could one of the early
catalytic cycles have, by chance, produced some primitive
lipid as a waste product, and diffusion caused it to be
distributed worldwide, and then in some locales it'd be
concentrated enough to form bags?

Quoted message said:

And, if there were, those molecules would more likely be
poisonous than nutritious.

If we assume one of the catalytic cycles produced the first
lipids, and if we accept your speculation that it'd probably
be toxic, then like any moderately-toxic waste product it'd
be a limiting factor against "life", temporarily inhibiting
"life" until it diffused away enough. (This is analagous to
the first H2O -> O2 photosynthesis, where O2 was toxic so it
had to oxidize ferrous iron or bubble away before the
creatures that made it could resume life processes.) Some
replicators (catalytic cycles) would find those lipid bags
less toxic than others. The question is whether any would
find it so infinitesimally toxic that they could hitch a
ride on a lipid bag to gain some survival advantage, such as
resistance to temperature or chemical swings, using the bag
as a buffer, an averaging factor, against extremes. For
example, a very highly active chemical, such as a molecular
fragment directly from a UV photon event or lightning strike
or volcanic vent, striking a bare replicator might disrupt
it, but that same highly active chemical striking a lipid
bag would disrupt that bag instead of the replicator, and be
degraded to something which when it later encounters the
replicator won't disrupt it. Meanwhile the less-active
chemicals coming in would pass right through the lipid bag
without reacting with it, and also pass by other catalysts
that don't consume that particular "food", then nicely react
with the appropriate catalyst at the first chance encounter
with (an instance of) it.

Quoted message said:

Quoted message said:

Even second-generation lipid bags, which contained an
enzyme for catalyzing the production of more lipids,
still didn't have elaborate regulatory mechanisms that
current-day cells have for maintaining their cell walls.

Nothing elaborate, but they might have had walls and a
"mechanism" for reproduction better than waiting for
shearing forces - see below.

Even today some kinds of cells, mostly fungi, don't bother
to split the cells even after the nucleus has already
divided many times. In the early days when there was no
specific nucleus or DNA loop or any other specific
reproductive part that needed to be split into multiple
cells so that if one suffered a disaster not all copies of
DNA would be destroyed, I see no particular advantage to a
lipid bag splitting at all, hence no reason why deliberate
splitting of the bag would evolve at that time. Even after
some kind of linear-strand genome evolved, it might have
been a long time before deliberate cell division was
invented. However I can see some evolution of resistance to
splitting caused by shear forces, namely that if the bag is
too small, due to too many breakings, then random
fluctuations in the frequencies of the various replicants
might drive one or another to zero often enough to be a
source of too many fatal mutations. Also if the main purpose
of the replicators residing in lipid bags is for protection
against extremes of temperature and against too-highly-
active chemicals, then there's an advantage to a lipid bag
holding tight as much as possible, resisting tearing open.
Accordingly there might be a survival advantage in
stretching into a dumbell shape with a narrow neck, and
letting that neck be drawn to a near-zero-diameter thread
whereby a "catastrophe" happens whereby its lipid molecules
at the narrowest point suddenly re-join as two separate
tips. 2-d ASCII diagram of that:

Before: /---\ /---\
| ====== |
\---/ \---/ After: /---\ /---\
| ==><== |
\---/ \---/ That way, at no point would the bag ever
actually be ruptured "open" to where raw chemicals could
leak into the inside or replicators get accidently
dislodged and leak out. So maybe after selection for
individual replicators which can survive residing just
inside a lipid bag, and selection for sets of replicators
which can co-exist in such a bag because no two of them
require the same scarce nutrient, and selection for sets
of replicators that have at least one creating new lipids
as a "waste" product, and selection for not too much nor
too little of lipid production, and selection for
production of and retention of lipids that best intercept
too-highly-active chemicals while allowing medium-reactive
chemicals to get in, the next evolutionary trend might
have been selection for lipids which are best at resisting
tearing apart under shearing forces, doing the dumbell
"catastrophe" kind of cell division instead. Once that's
firmly established, if there would ever be an advantage to
deliberately dividing the cell under conditions of
relatively mild shearing forces, or in total absense of
shear, I can see that evolving as a reasonable next
evolutionary step.

Quoted message said:

One of my speculations is that my early lipid organisms
could have had a "cell wall" made of minerals (perhaps
calcium carbonate, iron oxide, or iron pyrite). Not only
that, but they can gain energy by building a wall. I have
explained elsewhere how this might happen for iron oxide.
If CaCO3 is deposited in conjunction with a
decarboxylation, that might drive reactions. And
Wachtershauser advocates pyrite:

Hmm, I like that idea, not just for your reason (waste
product of metabolism, such as ferrous-iron-electron-donor
pathways), but also because these minerals might offer
additional defense against too-highly-reactive chemicals
coming in, and the bulk mass of these walls might offer
additional damping of thermal variations. With a thick
enough and massive enough wall, I can imagine one of these
"cells" being swept into a geothermal crevice, exposed to
boiling water for a moment then spurted back out into the
open ocean, and survive due to internal temperature swinging
only halfway to the boiling point where only a fraction of
the replicators and lipids are broken apart, and the
surviving replicators quickly consume the pieces of their
disrupted brothers to grow back to near original quantities.

Quoted message said:

A similar recent speculation by Martin and Russell has
organisms with iron sulfide cell walls, but no lipids:

But iron sulfide doesn't spontaneously form strong but
flexible bags, right? So I think I'll stick with some lipids
(or tars etc.) as an essential part of the early replicator-
ecosystem bags.

Quoted message said:

On the origins of cells: a hypothesis for the
evolutionary transitions from abiotic geochemistry to
chemoautotrophic prokaryotes, and from prokaryotes to
nucleated cells.

Um, that's two steps, the second basically sketched by Lynn
Margulis, and we have more recently filled in some of the
details she didn't originally have, such as specific strains
of bacteria very much like what originally formed the
symbiosis, but the first of those two steps is a **huge**
step which we've broken into a succession of smaller steps
in our recent discussions here. If that author/researcher
thinks the two steps are of roughly equal size, and has a
simple single explanation for the first step, I believe him
to be mistaken. Just as most revolutions in DNA-cell
metabolism happened very long ago, and for the past 500
million years almost all the interesting evolution has
happened along two or three very narrow branches of the
evolutionary tree (animals, plants, and maybe fungi),
likewise I tend to believe that the basic DNA-cell metabolic
system itself has been relatively stable for over 3000
million years, with only a small number of medium-size
disruptions (H2O photosynthesis and eukaryotic cell being
the biggest two, end-Permian extinction (caused by asteroid
hitting Australia?) being in distant third place), and not a
single total overhaul (replacement) of the basic system
(although it looks like Humans are starting a whole new
one), but long long ago several total overhauls of the
replicator system occurred before our DNA-based one came
into existance. Any one of these total overhauls would be
much greater a fundamental change in the nature of life than
any change or disaster or extinction event of the past 3000+
million years.

Quoted message said:

If the first lipid organisms did grow walls and membrane
together, we can speculate what might happen when the wall
has grown to cover about 90% of the surface, leaving a
small "breathing hole".

Remember that these primitive "cells" have no way to force
fluid through a narrow passage, the way sponges do for
example. I see no advantage, and lots of disadvantage, to a
primitive cell suffocating itself, compared to a porous cell
wall that intercepts too-highly-active chemicals while
passing just-right-active chemicals needed as "food". (Note
that even a little bit of bias toward intercepting more
active chemicals may be enough to allow a lipid system to
have fecundity just a little bit greater than one in a semi-
hostile environment where it'd die out without that little
bit of protection, thereby allowing it to colonize just a
little bit closer to the raw sources of food (UV surface and
volcanic vents) where there's no competition for food.)

Quoted message said:

I disagree with your assumption that a single "catalyst"
molecule is likely to ignite a parasitic cycle. My
assumption is that a cycle is fecund only if several of
its member chemical species are present in sufficient
quantity.

Here's an argument for my case: Suppose there's a catalytic
chain: A catalyzes production of B. B catalyzes production
of C. etc. to Y catalyzes production of Z. And suppose we
form a loop by Z catalyzing A, and the product of all the
single-step fecundities is greater than one, so indirectly
any chemical in the chain catalyzes itself with exponential
growth to consume all available of the scarcest nutrient.

Now if the product of all the single-step fecundities is
greater than one, then at least one of the individual single-
step fecundities is greater than one, and probably most of
the short sequences (sub-chains) have start-to-end
fecundities greater than one, and for at least one of the
catalysts, probably more than one, the following property is
true: Let M be that particular catalyst: M->N fecundity is
greater than one, and M->N->O fecundity is greater than one,
etc., each chain starting with M has fecundity greater than
one, all the way around the loop back to M. (I'm not totally
sure that's mathematically implied.) So let's examine what
happens when a single molecule of M arrives at a nice food
supply. It makes more than one molecule of N before the
original M is destroyed, and those several N make more than
one O before all the Ns are destroyed, etc. P Q R ... around
back to making more of M. Even though that one M got
destroyed before the loop finished going around, suddenly
there are a whole bunch of M now, ready to start the cycle
again but on a grander scale. It doesn't matter whether this
cycle continues to chase its tail with a gap where a
particular species of catalyst is all gone before the first
of the new batch is created once around the loop, or whether
the random spread of timing of catalytic reactions grows to
where eventually at least one molecule of each kind in the
cycle are all simultaneously present. In either case, from a
single 'M' molecule invading, the total size of this
invading catalytic loop grows exponentially, eating up the
food, in this case the lipid bag that was invaded.

Quoted message said:

The phrase "autocatalytic cycle" is ambiguous. Some people
use the phrase to mean only that you have the sequence of
reactions A -> B -> ... -> Z -> 2A, with nutrients being
added and/or wastes being released at each step.

Including a coefficient of '1' on A, leaving the
coefficients on B..Z undefined, not necessarily greater than
1, and replacing the '2' at the end by any coefficient
greater than 1, yes that's basically what I mean by a
catalytic cycle with overall (once-around-loop) fecundity
greater than one. But your expression there gave me an idea
for a trivial mathematical proof of the claim I made
earlier: 1A -> bB -> cC -> ... -> yY -> zZ -> aA where lower
case letters are coefficients (equilibrium number of
molecules of that corresponding catalyst, assuming
constantly exactly one molecule of A at the left, and 'a' is
greater than 1. (Note the b,c,...,y,z can be any nonzero
values whatsoever. If any are less than one, it just means
you need more than 1 A at the start to have good chance of
getting at least one of that small-coefficient chemical to
avoid the chain totally breaking at that weakest point.) Now
pick the smallest coefficient in the whole chain, say for
example it's 'n'. Multiply all the coefficients by the
inverse of 'n', so now we have 1N in the middle and all the
other coefficients are greater than one:
1/nA -> b/nB -> ... m/nM -> 1N -> o/nO -> ... z/nZ -> a/nA
(Well in case of an exact tie, the other tied
coefficients would now be exactly one. Let's not worry
about that statistically impossible case.) Now cut off
the chain from A to N (duplicating the term 1N) and paste
it onto the end, scaling the coefficient of A by 'a' to
make it match there (unduplicating the a/nA term), and
likewise scaling all other coefficients in the moved
chain by 'a': 1N -> o/nO -> p/nP -> ... -> z/nZ -> a/nA
-> ab/nB -> ... -> am/nM -> aN Now every segment starting
from 1N has end-to-end fecundity (the coefficient on the
last term of it) greater than one. Q.E.D. Therefore a
single molecule of N could invade successfully.

Quoted message said:

We can't say right now whether CO and HCN were available
in sufficient quantity to be a major foodstuff, though I
am almost sure that they were needed as "vitamins". Also,
one of NH3 and HCN is also waste - probably NH3.

I agree about HCN being nutrient and NH3 being waste. Note
that in these very early catalytic cycles, we don't have
sofisticated mechanisms that can directly react ordinary
things together. Instead these early catalytic cycles would
rely on highly active short-lived fragments from UV
radiation or lightning strikes or volcanic vents. Although
the first-generation results of UV radiation etc., such as
free O-- ions, O3+ radicals, H+ protons, atomic nitrogen,
etc., you name it with a monkey at keyboard and it probably
gets created when enough energy strikes a common molecule
such as CO2 or NH3, would get degraded the first time they
strike almost any other molecule, and would disrupt a
catalyst if they happened to strike it, second-generation
fragments after such strikings might survive long enough to
make their way to our lipid bag ecosystems and might be tame
enough not to disrupt them. I imagine free -CN or -NH2
radicals for example (don't know what charge they'd have)
might play a role. Each catalytic loop might require one or
two such second-generation medium-high-energy fragments as
"food". These would be like the big lift at the start of a
roller-coaster ride, and then the rest of the catalytic loop
would mostly coast downhill without any further huge input
of energy. I understand that in particular large quantites
of cyanide are produced by UV radiation under presumed
primitive conditions, correct? The experts among us need to
think mostly about early products of UV radiation etc., and
cascades of reaction products starting from them, rather
than more "normal" chemicals we are used to today. These
cascades from UV etc. events could quickly make whole trees
of chemicals present in significant quantities, causing
catalytic chains to close to form loops rather quickly. Only
after these have been around a long time would, by chance, a
more "normal" catalyst for a more "normal" reaction occur.
(At least that's my intuition.)

Quoted message said:

From: "Perplexed in Peoria" <[email hidden]> In
your writing on this, you use the word "catalyst", but you
don't use the word "precursor". This creates the picture
in my mind that each catalyst in your cycle is producing
its product from food molecules.

Well each catalyst is simply enhancing a reaction so that it
occurs at a fast rate while at reasonable temperatures. Each
such reaction takes a small number of "food" or "reactant"
molecules and rearranges them to form a small number of
"product" molecules. The thing about a catalyst is that it
goes in and comes out basically the same, or that it has a
small number of forms and switches from one form to another
form after each reaction, or that it switches from one form
to another after a reaction then spontaneously reverts to
original form after a while, etc.

You wish to use the word "precursor"? To mean the same thing
as "food" or "reactant", or to mean something else, for
example in some *other* reaction where our friend the
catalyst wasn't playing a role as a catalyst but was in fact
the product of that reaction, which involved some *other*
catalyst to make *that* reaction occur? In that case there
may be more than one precursor to our friend-catalyst in
that other reaction. But in the context of a catalytic loop,
there would be one precursor in the loop, the rest of the
precursors being merely food going into the loop.

Quoted message said:

no large organic molecule can be built from scratch by a
single catalyst.

That's a strawman! Let me rephrase so you understand:
There's this random chemical that happens to have catalytic
capability, that is it enhances a bunch of different
reactions without itself being consumed in those reactions.
One of these reactions happens to take readily available
materials from natural sources, and produce some products,
one of which would virtually never occur except with the
aid of some catalyst. So thanks to the chance occurrance of
this one molecule with catalytic ability, and thanks to the
abundance of the reactants it works on in this one
reaction, this one reaction occurs several times before
that one molecule gets accidently broken apart. (Or if the
catalyst is just a metal ion etc., it might catalyze
gazillions of individual chemical reactions over a period
of millions of years before by chance it gets snagged in a
tektonic plate that is subducting into the mantle and that
metal ion or whatever is taken out of service for hundreds
of millions of years.)

All this catalyst (metal ion, or actual molecule) does is
enable some tiny change such as bonding two molecules or
splitting a molecule or moving a sidechain from one molecule
to another etc. At the small end of the range of reactant
size, there's not much splitting possible, so most reactions
make larger molecules. At slighter larger reactant size,
some reactions make smaller molecules and some make larger
molecules. As long sequences of catalyzed reactions happen,
it's somewhat a random walk how large the molecules get, but
every so often a moderately large molecules is built from a
slightly smaller one or from two pieces totalling the large
size. If it's energetically favorable to polymerize, and if
a suitable catalyst for polymerization is available, very
long polymers might form rather quickly. Otherwise I'd
expect only small to medium-size molecules.

Quoted message said:

But the main point is that to produce anything, you need
both a precursor and a catalyst.

Yes. In most cases the precursors would be abundantly
available, and the product from the catalyzed reaction would
be something new but which builds up in quantity if the
catalyst stays around a while.

Occasionally there'd be a reaction where all but one of the
reactants are common, but one reactant is rare. So that rare
reactant would be all used up to make the product. Not much
of interest there.

Occasionally a long-lived catalyst would catalyze a reaction
from common ingredients, and the reaction product would be
something with catalytic ability, which would then start to
build up in quantity, significantly increasting the rate of
all the reactions it catalyzes (where the reactants are
common), causing large amounts of its reaction products to
occur, among which there might be yet another chemical with
catalytic ability, whose quantity would build up, causing
yet another bloom of catalyzed reactions and build-up of
reaction products, etc.

At this point, the question that needs to be answered is:
For a given catalyst (either long-lived such as metal ion,
or re-generated in great quantity such as product of
reactions using former), of all the reactions it catalyzes,
how many reaction products of them all have catalytic
capability of their own? If on the average each catalyst
causes the production of significant quantities of more than
one other catalyst, then already we have a branching tree of
catalyst-begats-catalyst, and surely we'll get a catalytic
loop within a relatively short time geologically speaking.
Or if polymerization happens readily, then surely among the
various polymers created there would be a whole lot of
different catalysts, and a good chance of completing a loop
somewhere. The Miller-Urey result, lots of tarry stuff,
indicates some sort of polymerization happens readily.
Whether this is just an activated chemical fragment
attaching itself to a molecule and then grabbing another
nearby molecule to glue them together, or an actual
polymerization catalyst that got formed spontaneously, I
don't know. But in either case I belive the tarry stuff was
formed in the early-Earth seas, and wind/wave action sloshed
it around to break it apart to expose inner bonds to fresh
water to allow it to catalyze new reactions, resulting in a
very rich assortment of medium-length molecules, many of
which had catalytic ability (not a large fraction, just a
large number of catalysts among a vastly larger total number
of different kinds of molecules).

Quoted message said:

you need more than one or two chemical species to be
infectuous

Consider seventeen kinds of molecules (a1 a2 b1 b2 b3 c1 ...
g3) naturally occurring in large quantities, which are
reactants in a 7-link catalytic loop (A -> B -> ... -> G ->
A), producing various waste products (m n o ... u): A + a1 +
a2 -> A + B + m B + b1 + b2 + b3 -> B + C + n + o C + c1 +
c2 -> C + D D + d1 + d2 + d3 -> D + E + p E + e1 + e2 -> E +
F + q + r F + f1 + f2 -> F + G + s G + g1 + g2 + g3 -> G + A
+ t + u Suppose e2 is a lipid which is part of some bag that
supports a nice colony. Suppose one molecule of E happens by
and attaches to that bag and grabs a molecule of e2, and
finds an e1 floating by in the water, and does its reaction.
Then it finds another e2 nearby on the bag, grabs it, finds
another e1 floating by, and does its reaction again. q and r
drift away, but some of the molecules of F that are created
do their thing while still nearby, making G which does its
thing, etc. around the loop until a bunch of E are made, any
of which still nearby quickly attach to e2's of the bag.
Before long all the e2 of the bag is eaten away, and the
large quantity of E that was created will now diffuse away
to infect other e2-lipid bags.

Quoted message said:

I agree that growth is more urgent than reproduction.
However, an organism that grows without reproducing leaves
all its eggs in one basket, and natural selection seems to
favor multiple, geographically dispersible, baskets.

I agree. But these lipid-bag colonies are very flexible as
to the size of the bag, not like for example like elephants
which if fifty times as large would crush their lungs and
suffocate. If a lipid bag merely grows as large as possible,
sooner or later shear will stretch it apart, and its "eggs"
will now be in more than one basket. So these lipid-bag
colonies could survive for a nice long time, and have "eggs"
in many baskets, without any explicit mechanism to split.

At such time as any two species of bag have different bag
strengths, caused by differences in their "genome" (set of
replicators in them), then natural selection would favor
whichever is optimum for longterm survival.

Quoted message said:

Quoted message said:

... Also if the main purpose of the replicators residing
in lipid bags is for protection against extremes of
temperature and against too-highly-active chemicals, ...

Quoted message said:

In my viewpoint, the main "purpose" is in residing near
your symbiotes,

Per my idea, in these early lipid-bag colonies of
replicators, each replicator (catalytic loop) originated in
a different environment, and later these came together and
any that consumed the same scarce "food" competed for it and
only one survived, and the set that remained was a set which
happened to all use different foods (except for very common
foods where sharing a food wouldn't be limiting). None of
the waste of one cycle was food for another, so there was no
specific value in being near a different kind of replicator
except maybe that other replicators damped some kinds of
harsh chemicals by reacting with them first.

Quoted message said:

You ought to learn the chemical distinction between ions
and free radicals if you are going to use the word
radical.

In high-school chemistry I learned that an ion is a
single atom which is charged, whereas a radical is more
than one atom but not a whole molecule, which may be
either charged or not. For example Na+ is just an ion
whereas SO4-- is a radical, and -NH2 (the initial -
denoting a dangling place where a covalent bond should
be, not a negative charge) is also a radical, although we
were doing only inorganic chemistry so didn't deal with
covalent bonds explicitly. Please correct my use of
terminology if that's not current usage.

Quoted message said:

In any case, my speculations tend to discount the role of
free radicals from the global environment as a food for my
organisms. I would see such radicals as too dangerous.

In the world before any catalytic cycles existed, free
radicals etc. were the spur that triggered the formation of
a wide variety of really strange molecular species, many of
which were highly reactive. This great variety of molecule,
and great activity, resulted in both molecular catalysts and
reactants for them to catalyze reactions upon. This is how
the first catalytic cycles formed.

In the atmosphere, UV strikes a molecule, such as NH3, and
either knocks an electron off producing a charged molecule,
or severs a bond producing fragements which may or may not
be charged. The free electron sticks to another random
molecule creating an oppositely charged molecule. A fragment
collides with a molecule and grabs a bond and either joins
with it to make a bigger fragment or exchanges something.
Charged molecules collide and stick for a moment to
neutralize their charge, possibly overcoming activation
energy to react during that moment. The variety of new
molecules thereby created rains down to the ocean.

At the surface of the ocean, UV does all those things except
the temporary products have a chance to react with organic
soup before deactivating, increaseing both the destructive
capability and the random-new-molecule-forging capability.

The same argument applies to geothermal vents.

The first catalytic cycles probably occurred very close to
the surface of the ocean or inside a volcanic vent, just
because of the greater variety of things going on there. But
once a stable catalytic cycle formed, if it stayed there it
probably got disrupted whereas if it diffused away it had a
better chance to survive, so among the many copies of each
catalyst in a cycle, some randomly survived by diffusing
slightly away and the rest stayed too close and got
disrupted. Since these catalytic cycles depended on "food"
from the danger zone, any that diffused too far away became
inactive until they randomly wandered back into the food
zone again. (Note that each molecule undergoes random-walk
independently of others in the same cycle. All it takes is
one molecule wandering back into a good-food region to start
the cycle going there again.)

Quoted message said:

You are definitely talking about a heterotrophic theory
here, rather than an autotrophic one.

Well I'm *not* talking about eating food that comes from
some other living being, only eating raw chemicals that
happen to form naturally. So your use of that word might be
misleading.

Quoted message said:

My main objection to heterotrophy is this: any environment
that produces high energy organic chemicals that you can
use will also produce a smorgasbord of high energy organic
chemicals that you can't use - that would be actively
disruptive if you tried to use them.

I agree. That's why the catalytic cycles would have to form
very close to the disruptive zone where a small amount of
very active chemicals, maybe only one or two species in any
significant quantity, drift down (from surface) or out (from
vent). So the early catalytic cycle would be dependent on a
big "roller coaster lift" from that one highly active
chemical, relying on more tame chemicals for the rest of the
cycle. It'd reside in that narrow layer of water where every
so often an active molecule of the right species comes in
and preferentially finds the catalyst that takes it as food,
immediately removing it from the water so other catalysts
that might be damaged by it don't touch it. (Note the one
catalyst that uses it would [censored] it whenever it drifted
nearby, whereas the other catalysts would not [censored] it so
wouldn't be damaged unless they ventured too close.)

Possibly that one highly-active chemical would be scarce in
the zone where the catalytic cycle resides, so there'd be a
build-up of whatever precursors were needed with it, and a
deficiency of whatever was produced from it, until one
molecule of the highly-active species arrived, at which time
it'd immediately react with the appropriate catalyst and the
rest of the cycle would complete in rapid succession
yielding more of that one catalyst again. (All molecular
catalysts decompose naturally, hence decline in quantity
when not renewed, so perhaps most of the catalytic cycle
would nearly disappear while waiting for the highly-active
chemical to appear. For example, if G -> A was the big
roller coaster lift, and A -> B -> ... -> G were the
downward coast, with food for G -> A scarse, A would decay
fastest, and with it mostly gone B would start to decay, and
with B mostly gone C would start to decay, etc. until only
maybe F and G remained, and if still no active chemical then
F would be gone and G would start to decay. With F&G still
around, if the active molecule arrives and hits F it'd
damage it, but if it hits G it'd kick-start the ride again.
Maybe most of the decay is caused by the active chemical
coming in and striking the wrong catalyst anyway.)

The roller coaster metaphor might be a little misleading.
Every step in the catalytic cycle needs a source of
negentropy to drive it. It's just that one of the steps
needs a big kick and would ignore any little nudge, while
the rest of the steps need only a little nudge and would be
damaged by a big kick. So most of the time little-nudge food
is coming in, and the rest of the cycle is building up huge
quantities of G from large quantities of F from medium
quantities of E from small quanties of D from tiny
quantities of C not yet destroyed, all of B and A gone by
now. Then one highly-active module needed by G comes in and
most of the time the first thing it hits is indeed G because
of such large quantities of G built up, making one molecule
of A, which during the next lull makes several molecules of
B, which rebuilds the supply of C, etc.

Quoted message said:

Thermodynamic free energy for driving the cycles has to
come from redox, perhaps with photo-assist.

Indirect photo-assist, from UV making highly-active stuff,
per my "just so story".

Quoted message said:

No "fermentations".

Agreed. There is nothing complex enough to ferment
initially. (The Miller-Urey tar stuff has too much variety
and not enough bound energy to be fermentable, by my guess
anyway.) Fermentation is parasitical/preditory upon products
of other life, mostly large concentrations of specific
sugars, which doesn't yet exist at this point in our
scenerios.

Quoted message said:

... Miller experiments ... They produce soup or tars,
depending on your prejudices. I don't like that direction
- that way lies chaos, ... I want life to start simple and
then slowly add complexity - not to start complex and then
somehow find order in that chaos.

They are not *complex* in the sense of lots of purposeful
order, such as fractally-nested hierarchies of structure, as
current life is. They are merely complex in the sense of
having lots of mathematical entropy in the sense of having
lots of purposeless variety. Each chemical reaction is
simple: A random bunch of chemicals react with the aid of
some random catalyst. The reactants and the catalyst simply
drift in from who knows where, and then the reaction
products and released catalyst simply drift away to who
knows where. That's a very simple system which can be
modeled almost entirely statistically with the whole equal
to the sum of its individual parts, no need to take any
organization of the parts into consideration, only need to
take into account that the statistics vary with geography,
partly due to forcing conditions (UV on surface, geothermal
energy in vents, different temperatures by latitude and
ocean depth) and partly due to sudden accumulations of
particular replicators in one locale which take a long time
to diffuse worldwide due to other replicators that have
consumed almost all available food in other locales.

Before the first replicators (catalytic cycles with
fecundity greater than one) form, a high amount of
purposeless random variety is exactly what is needed to "let
a thousand flowers bloom" and see which "flower" chances
upon a closed loop of catalysts in some locale, then see
which other "flower" chances upon likewise in another
locale, etc.

Each closed loop is very simple, just a chance implication
cycle. No regulatory mechanisms, no very specific catalytic
capability, just general catalytic capability that happens
to form a loop in some locale with such-and-such food
abundantly available. So my "just so story" has the initial
simplicity of mechanism you desire, it just has a lot more
different experiments running in parallel then you can
comfortably imagine.

One feature you might like, if you really like ultra-simple
starts to life on Earth: As soon as a catalytic cycle gets
really going in one locale, it gobbles up much of the
"food" there, reducing input to other dead-end catalytic
chains, reducing the total amount of variety in chemical
species in that locale. Also the particular "foods" it
consumes are probably the most active species of chemicals
around, so actually the amount of reduction in the
"thousand flowers" process is probably immensely starved.
It does produce large quantities of its particular waste
products, but these are limited in variety, and most or all
low-energy chemicals, so they only re-boost the "thousand
flowers" randomness a little bit if any. So the local
region would resemble a very simple ecosystem with a single
species dominating all chemical processes, and that one
species being very simple itself.

Once several catalytic cycles have occupied all the major
niches where lots of negentropy (free energy) is available,
there's no longer any place where new catalytic experiments
can take place, and the Miller-Urey era is all finished
(until the next huge rain of comets or asteroids boils away
the oceans, so there's no liquid water to percolate down
into pores in rock to keep any catalytic cycles going even
there, and later when the oceans re-form all this has to
start over; perhaps this happened several times; but let's
talk now only about the last Miller-Urey era, the one which
didn't get obliterated, the one which evolved to what we
have today, below🙂.

Maybe one of these first catalytic loops had at least one
catalyst which had handedness. Maybe this handedness was
preserved through all the evolutionary transformations
from then to now. Or maybe two different catalytic loops
involved handedness, and one of them eventually yielded
the handedness of amino acids and the other eventually
yielded the opposite handedness of something else that I
forget what.

<[email hidden]> wrote in message
"]news:[email hidden]...

Quoted message said:

Quoted message said:

From: [email hidden] (Jim Menegay) If you have
a pet theory of your own to discuss, post it as another
thread, and I will try to comment.

I don't have any full-fledged theory, just the idea of
lots of random catalysts acting on lots of naturally-
occurring and previously-catalyzed chemicals to produce
new chemicals some of which are new catalysts, and by
chance among these many chemicals there's a catalytic loop
plus sufficient "food" for it that it achieves around-the-
loop fecundity greater than one causing it to rapidly grow
exponentially until it's food-limited, and then to persist
so long as its "food" continues to be naturally produced.

In your writing on this, you use the word "catalyst", but
you don't use the word "precursor". This creates the picture
in my mind that each catalyst in your cycle is producing its
product from food molecules. This idea is of course absurd -
no large organic molecule can be built from scratch by a
single catalyst. The alternative picture is that the
"catalyst" is functioning as both the precursor and the
catalyst for the production of its successor in the cycle.
That is also unlikely.

It seems to me that you have to think of the main cycle in
terms of precursors, and to see the catalytic cycles as
separate. An example: modular arithmetic. Write down the
numbers 0-6 in a cycle. Draw precursor arrows from each
number N to its successor N+1 mod 7. That is the precursor
cycle. Now, using a different color pen, draw catalytic
arrows from each number N to 2N mod 7. These constitute
the catalytic cycles. Each arrow represents the idea that
the source number (representing a chemical species) acts
as a catalyst for the production of the destination number
from its precursor plus food. In this case, we actually
have three catalytic cycles associated with the single
precursor cycle.

You can play around with this idea in a lot of ways. But the
main point is that to produce anything, you need both a
precursor and a catalyst. Also, you can see that you need
more than one or two chemical species to be infectuous, but
you may not need all seven.

Quoted message said:

Thanks to these recent discussions, I've developed the
idea toward colonies of such catalytic loops sharing a
lipid bubble, and I've adopted the idea of branching
chains of catalysts forming a tree which eventually by
chance closes a loop. And with that in place, it seems
obvious that in different locales on Earth the tree would
grow in different directions and form its first loop in a
different place (meaning using a different set of
catalysts to form the loop), so there'd be at most one
such loop in each locale, but where mixing between
different single-catalytic-loop locales occurs two
different already-established catalytic cycles might get
together to form an ecosystem, and such ecosystems could
be the first genetic system. But I'm pretty flexible about
the details, and would like to see lots of research done
to check this kind of theory to see if it would actually
work in nature.

Quoted message said:

I don't believe that your heterotrophic "first
generation bags" ever existed. There is just no good
prebiotic source of lipid molecules.

Oh. In reading about them so much, as "naturally
occurring", I just assumed the lipids would form under
prebiotic conditions. So let me backtrack on that
speculation. As an alternative, could one of the early
catalytic cycles have, by chance, produced some primitive
lipid as a waste product, and diffusion caused it to be
distributed worldwide, and then in some locales it'd be
concentrated enough to form bags?

I would guess that if there were non-bag cycles producing
bag material as a byproduct, then the bags of waste material
would form locally. A possible exception is the idea I
mentioned of autocatalytic aerosols producing single layer
membranes. When these hit the ocean, the result is likely to
be a lipid monolayer forming like an oilslick on the ocean.
Breaking waves might well convert this to closed bags.

Quoted message said:

Quoted message said:

And, if there were, those molecules would more likely be
poisonous than nutritious.

If we assume one of the catalytic cycles produced the
first lipids, and if we accept your speculation that it'd
probably be toxic, then like any moderately-toxic waste
product it'd be a limiting factor against "life",
temporarily inhibiting "life" until it diffused away
enough. (This is analagous to the first H2O -> O2
photosynthesis, where O2 was toxic so it had to oxidize
ferrous iron or bubble away before the creatures that made
it could resume life processes.) Some replicators
(catalytic cycles) would find those lipid bags less toxic
than others. The question is whether any would find it so
infinitesimally toxic that they could hitch a ride on a
lipid bag to gain some survival advantage, such as
resistance to temperature or chemical swings, using the
bag as a buffer, an averaging factor, against extremes.
For example, a very highly active chemical, such as a
molecular fragment directly from a UV photon event or
lightning strike or volcanic vent, striking a bare
replicator might disrupt it, but that same highly active
chemical striking a lipid bag would disrupt that bag
instead of the replicator, and be degraded to something
which when it later encounters the replicator won't
disrupt it. Meanwhile the less-active chemicals coming in
would pass right through the lipid bag without reacting
with it, and also pass by other catalysts that don't
consume that particular "food", then nicely react with the
appropriate catalyst at the first chance encounter with
(an instance of) it.

Quoted message said:

Quoted message said:

Even second-generation lipid bags, which contained an
enzyme for catalyzing the production of more lipids,
still didn't have elaborate regulatory mechanisms that
current-day cells have for maintaining their cell
walls.

Nothing elaborate, but they might have had walls and a
"mechanism" for reproduction better than waiting for
shearing forces - see below.

Even today some kinds of cells, mostly fungi, don't bother
to split the cells even after the nucleus has already
divided many times. In the early days when there was no
specific nucleus or DNA loop or any other specific
reproductive part that needed to be split into multiple
cells so that if one suffered a disaster not all copies of
DNA would be destroyed, I see no particular advantage to a
lipid bag splitting at all,

I agree that growth is more urgent than reproduction.
However, an organism that grows without reproducing leaves
all its eggs in one basket, and natural selection seems to
favor multiple, geographically dispersible, baskets.

Quoted message said:

hence no reason why deliberate splitting of the bag would
evolve at that time. Even after some kind of linear-strand
genome evolved, it might have been a long time before
deliberate cell division was invented. However I can see
some evolution of resistance to splitting caused by shear
forces, namely that if the bag is too small, due to too
many breakings, then random fluctuations in the
frequencies of the various replicants might drive one or
another to zero often enough to be a source of too many
fatal mutations. Also if the main purpose of the
replicators residing in lipid bags is for protection
against extremes of temperature and against too-highly-
active chemicals, then

In my viewpoint, the main "purpose" is in residing near your
symbiotes, and the fact that if you and your symbiotes are
all amphoteric, then the activation entropies are lowered
and you don't have to be such a good catalyst.

Quoted message said:

there's an advantage to a lipid bag holding tight as much
as possible, resisting tearing open. Accordingly there
might be a survival advantage in stretching into a dumbell
shape with a narrow neck, and letting that neck be drawn
to a near-zero-diameter thread whereby a "catastrophe"
happens whereby its lipid molecules at the narrowest point
suddenly re-join as two separate tips. 2-d ASCII diagram
of that:

Before: /---\ /---\
| ====== |
\---/ \---/ After: /---\ /---\
| ==><== |
\---/ \---/ That way, at no point would the bag ever
actually be ruptured "open" to where raw chemicals could
leak into the inside or replicators get accidently
dislodged and leak out. So maybe after selection for
individual replicators which can survive residing just
inside a lipid bag, and selection for sets of
replicators which can co-exist in such a bag because no
two of them require the same scarce nutrient, and
selection for sets of replicators that have at least one
creating new lipids as a "waste" product, and selection
for not too much nor too little of lipid production, and
selection for production of and retention of lipids that
best intercept too-highly-active chemicals while
allowing medium-reactive chemicals to get in, the next
evolutionary trend might have been selection for lipids
which are best at resisting tearing apart under shearing
forces, doing the dumbell "catastrophe" kind of cell
division instead. Once that's firmly established, if
there would ever be an advantage to deliberately
dividing the cell under conditions of relatively mild
shearing forces, or in total absense of shear, I can see
that evolving as a reasonable next evolutionary step.

Quoted message said:

One of my speculations is that my early lipid organisms
could have had a "cell wall" made of minerals (perhaps
calcium carbonate, iron oxide, or iron pyrite). Not only
that, but they can gain energy by building a wall. I
have explained elsewhere how this might happen for iron
oxide. If CaCO3 is deposited in conjunction with a
decarboxylation, that might drive reactions. And
Wachtershauser advocates pyrite:

Hmm, I like that idea, not just for your reason (waste
product of metabolism, such as ferrous-iron-electron-donor
pathways), but also because these minerals might offer
additional defense against too-highly-reactive chemicals
coming in, and the bulk mass of these walls might offer
additional damping of thermal variations. With a thick
enough and massive enough wall, I can imagine one of these
"cells" being swept into a geothermal crevice, exposed to
boiling water for a moment then spurted back out into the
open ocean, and survive due to internal temperature
swinging only halfway to the boiling point where only a
fraction of the replicators and lipids are broken apart,
and the surviving replicators quickly consume the pieces
of their disrupted brothers to grow back to near original
quantities.

Quoted message said:

A similar recent speculation by Martin and Russell has
organisms with iron sulfide cell walls, but no lipids:

But iron sulfide doesn't spontaneously form strong but
flexible bags, right? So I think I'll stick with some
lipids (or tars etc.) as an essential part of the early
replicator-ecosystem bags.

Quoted message said:

On the origins of cells: a hypothesis for the
evolutionary transitions from abiotic geochemistry to
chemoautotrophic prokaryotes, and from prokaryotes to
nucleated cells.

Um, that's two steps, the second basically sketched by
Lynn Margulis,

Yes, two steps which may have been 1.5Gy apart. But perhaps
not as logically distinct as you think. Read the paper, it
is a good one. Margulis was right about mitochondria and
chloroplasts, but is she also right about the nucleus and
kineties? The answers to some of these 2.3 Gya questions
tell us something about the LUCA maybe 2.8Gya, which may
tell us something about the early RNA world maybe 3.3 Gya,
which may tell us something about OOL maybe 3.8Gya. It all
fits together.

Quoted message said:

and we have more recently filled in some of the details
she didn't originally have, such as specific strains of
bacteria very much like what originally formed the
symbiosis, but the first of those two steps is a **huge**
step which we've broken into a succession of smaller steps
in our recent discussions here. If that author/researcher
thinks the two steps are of roughly equal size, and has a
simple single explanation for the first step, I believe
him to be mistaken. Just as most revolutions in DNA-cell
metabolism happened very long ago, and for the past 500
million years almost all the interesting evolution has
happened along two or three very narrow branches of the
evolutionary tree (animals, plants, and maybe fungi),
likewise I tend to believe that the basic DNA-cell
metabolic system itself has been relatively stable for
over 3000 million years, with only a small number of medium-
size disruptions (H2O photosynthesis and eukaryotic cell
being the biggest two, end-Permian extinction (caused by
asteroid hitting Australia?) being in distant third
place), and not a single total overhaul (replacement) of
the basic system (although it looks like Humans are
starting a whole new one), but long long ago several total
overhauls of the replicator system occurred before our DNA-
based one came into existance. Any one of these total
overhauls would be much greater a fundamental change in
the nature of life than any change or disaster or
extinction event of the past 3000+ million years.

Quoted message said:

If the first lipid organisms did grow walls and membrane
together, we can speculate what might happen when the
wall has grown to cover about 90% of the surface,
leaving a small "breathing hole".

Remember that these primitive "cells" have no way to force
fluid through a narrow passage, the way sponges do for
example.

The bubble blowing could be in response to periodic osmotic
oscillations, if they live in a tidal estuary, for example.
Or, they could possibly blow bubbles "deliberately". Control
over osmosis is one of the first functions that a cellular
organism must establish.

Quoted message said:

I see no advantage, and lots of disadvantage, to a
primitive cell suffocating itself, compared to a
porous cell wall that intercepts too-highly-active
chemicals while passing just-right-active chemicals
needed as "food".

Perhaps I misled in calling the reproductive orifice a
breathing hole. Mineral cell walls can be, and probably
will be irregular affairs that contain pores about the
diameter of a bilayer thickness. These will permit entry
and exit of food and waste. The reproductive orifice is
many times larger.

Quoted message said:

(Note that even a little bit of bias toward intercepting
more active chemicals may be enough to allow a lipid
system to have fecundity just a little bit greater than
one in a semi-hostile environment where it'd die out
without that little bit of protection, thereby allowing it
to colonize just a little bit closer to the raw sources of
food (UV surface and volcanic vents) where there's no
competition for food.)

[snip discussion which is based on a neglect of the
distinction between catalysts and precursors]

Quoted message said:

Quoted message said:

We can't say right now whether CO and HCN were available
in sufficient quantity to be a major foodstuff, though I
am almost sure that they were needed as "vitamins".
Also, one of NH3 and HCN is also waste - probably NH3.

I agree about HCN being nutrient and NH3 being waste. Note
that in these very early catalytic cycles, we don't have
sofisticated mechanisms that can directly react ordinary
things together. Instead these early catalytic cycles
would rely on highly active short-lived fragments from UV
radiation or lightning strikes or volcanic vents.

The exhalations of vents are not "highly active". The
atmospheric products of UV and lightning are the things that
produce a "soup". I reject the notion that the soup is
nutritive. HCN and CO, however they are produced, cannot be
called highly active.

Quoted message said:

Although the first-generation results of UV radiation
etc., such as free O-- ions, O3+ radicals, H+ protons,
atomic nitrogen, etc., you name it with a monkey at
keyboard and it probably gets created when enough energy
strikes a common molecule such as CO2 or NH3, would get
degraded the first time they strike almost any other
molecule, and would disrupt a catalyst if they happened to
strike it, second-generation fragments after such
strikings might survive long enough to make their way to
our lipid bag ecosystems and might be tame enough not to
disrupt them. I imagine free -CN or -NH2 radicals for
example (don't know what charge they'd have) might play a
role. Each

You ought to learn the chemical distinction between ions and
free radicals if you are going to use the word radical. In
any case, my speculations tend to discount the role of free
radicals from the global environment as a food for my
organisms. I would see such radicals as too dangerous.

Quoted message said:

catalytic loop might require one or two such second-
generation medium-high-energy fragments as "food". These
would be like the big lift at the start of a roller-
coaster ride, and then the rest of the catalytic loop
would mostly coast downhill without any further huge input
of energy.

You are definitely talking about a heterotrophic theory
here, rather than an autotrophic one. My main objection to
heterotrophy is this: any environment that produces high
energy organic chemicals that you can use will also produce
a smorgasbord of high energy organic chemicals that you
can't use - that would be actively disruptive if you tried
to use them. And I can't see early life having the ability
to dicriminate. Hence, I want to limit my diet to a handful
of small inorganic chemicals - CO, HCN, H2CO as the carbon
containing ones - that can easily be recognized and held in
place by transition metal ions. My large organics are all
products of my own biochemistry of cycles. The organics
interact with the metal ions as ligands, and hence have
access to the CO, HCN, and H2CO which are co-ligands.
Thermodynamic free energy for driving the cycles has to come
from redox, perhaps with photo-assist. No "fermentations".

Quoted message said:

I understand that in particular large quantites of cyanide
are produced by UV radiation under presumed primitive
conditions, correct?

I wouldn't call it *large* quantities.

Quoted message said:

The experts among us need to think mostly about early
products of UV radiation etc., and cascades of reaction
products starting from them, rather than more "normal"
chemicals we are used to today. These cascades from UV
etc. events could quickly make whole trees of chemicals
present in significant quantities, causing catalytic
chains to close to form loops rather quickly. Only after
these have been around a long time would, by chance, a
more "normal" catalyst for a more "normal" reaction occur.
(At least that's my intuition.)

My understanding is that the kinds of cascades you are
talking about are precisely what happens in Miller
experiments, and that they are reasonably well understood.
They produce soup or tars, depending on your prejudices. I
don't like that direction - that way lies chaos, with Stuart
Kauffman beaconing us on. I want life to start simple and
then slowly add complexity - not to start complex and then
somehow find order in that chaos.

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Before you showed up, the active OOL posters were Tim
Tyler, who is into Cairns-Smith, and the Borg fellow with
his heat cycles.

The other "origins" posters are probably suffering from
****.******* shell shock ;-)

Quoted message said:

(The naked RNA gene people, are probably a majority, but
they maintain a smug silence.)

I don't know how many of these there actually are.

Organic chemstry in the ocean doesn't seem that promising -
so those "naked gene" folks who have not embraced crystals
seem to either invoke membranes, or catalytic clay surfaces
- or some combination of the two.

Quoted message said:

One of my speculations is that my early lipid organisms
could have had a "cell wall" made of minerals (perhaps
calcium carbonate, iron oxide, or iron pyrite).

It does seem possible - *assuming* that they lived inside
porus rocks.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

Perplexed in Peoria <[email hidden]> wrote or quoted:

Quoted message said:

"Tim Tyler" <[email hidden]> wrote in message

Quoted message said:

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Quoted message said:

Quoted message said:

The ideal digital bowling lane would slope toward the
gutters from the center (the threshold). And it is
this "basin of attraction" feature in the dynamics
that distinguishes digital from analog.

...but surely analog systems can exhibit basins of
attraction as well.

But surely an IDEAL analog system will not. See my reply
to John.

Can't seem to find that reply.

...but - "ideal" or otherwise - surely analog systems can
exhibit things like Lorentz attractors and basins of
attraction - just like any other dynamical system can.

BTW, I'm not sure what "ideal" was intended to mean in
this context.

If an "ideal analog system" is *defined* as being one
with no attractors, then I can't see the utility of such
a concept.
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John Wilkins <[email hidden]> wrote or quoted:

Quoted message said:

William Morse said:

[email hidden] (John Wilkins) wrote in

Quoted message said:

Quoted message said:

Quoted message said:

All data storage in the real world is analogue. The
only difference between analogue and digital is the
fidelty of replication. I think that any evolutionary
process is going to maximise the fidelity to the point
where further improvements would be too costly, no
matter whether it is cultural, biological or
technological. I completely agree with Tim, and would
say that "digital" is, in the real (as opposed to
abstract) world, a name for "very-high-fidelity
reproduction" over analogue substrates.

Umm - whatever happened to your reductionist stance?
Unless you are denying quantum mechanics, or are arguing
for emergent properties, it would seem that your only
logically consistent argument would be that all data
storage in the real world is digital.

You'll have to explain this to me. All I can see is that
if analogue systems can simulate digital ones (and I don't
quite see what the appeal to QM has to do with this - data
storage occurs on macro-level systems here, and it is
agreed by all that they form analogue states of
distribution rather than digital binary states) [...]

Many argue that the world is fundamentally discrete.

Ed Fredkin is one:

digitalphilosophy.orgdigitalphilosophy.orgOpen ↗

I also have a site on the subject:

finitenature.comfinitenature.comOpen ↗

It is not currently known whether physics is best modelled
as being discrete or not.

*If* the universe is discrete, all data storage in the real
world would be fundamentally digital in nature.
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