From: frank@Cookie.secapl.com (Frank Adams)
Subject: Re: nano-replicator assumptions
Date: Mon, 28 Sep 1992 20:07:23 GMT
Organization: Security APL, Inc.

In article <snodgras.717492181@crash> snodgras@crash.cts.com (John Snodgrass) writes:
>       In article <1992Sep22.183733.39095@Cookie.secapl.com>
>frank@Cookie.secapl.com (Frank Adams) writes:
>>       I think the plurality of molecular biologists believe that
>>DNA evolved from earlier systems involving RNA but not DNA.  A
>>strand of RNA (with perhaps some restrictions on the base pairs)
>>in a soup of amino acids is a self-replicating system.
>>Simulations of the conditions believed to have existed in the
>>early history of the Earth produce soups of amino acids, so this
>>is no way an artificial environment.
>
>       RNA is a 'alphabetic' molecule. It was designed (or
>evolved if you like) because it had the property that a large
>number of different types of molecules could be put together from
>a small number of parts

Designed or evolved makes a great deal of difference.  It seems to me that
you are greatly overgeneralizing from the way the human design process
works.  We tend to design things with *a* purpose in mind; only where
required do we adopt multi-purpose parts.  Evolution, by contrast, makes
multi-use the norm; only in special cases does a part specialize to a single
purpose; and even then, it is quite likely to acquire additional purposes in
the course of further evolution.  Consider the human mouth, for example: it
has long functioned for both eating and breathing; more recently, it has
added talking to its repertoire.

RNA evolved because it was (in the environment where it came into existence)
self-replicating as well a store for information.

>>       The question of how RNA first came into existence is a
>>very interesting one, which we can't answer yet.  Based on our
>>current understanding, "just chance" seems unlikely to be the
>>answer.  (The chances against are a bit too long, but only by a
>>few orders of magnitude; the chance of a cell coming into
>>existence by chance are too small by many orders of magnitude.)
>
>       There is no such thing as "just chance".

Even if you believe the universe is deterministic, this is an unreasonable
statement.  If you shuffle a deck of cards repeatedly, eventually you will
get all four aces on top of the deck.  When this happens, it is most
reasonable to describe it as happening by chance.  There are all sorts of
physical processes involved in the shuffling operation, but they did not in
any interesting way cause the particular arrangement of the cards.

Similarly, if you put a bunch of chemicals with the right elements into
solution, with an external energy source to keep them within a certain
energy range, eventually any given molecule formed from those elements will
form.  In some cases, it will take a fraction of a second; in others, the
average waiting time will be 10^100 years or longer.  This is the only sense
of "chance" needed for my comments above.

>The much
>misunderstood notion of "probability" is just a mathematical
>method for describing events which are not understood and cannot
>be predicted any other way (but through tabulation). Probability by
>definition explains nothing. (QM people should face up to this.)

This is wrong, but irrelevant to the current discussion.

>>       However, there is no reason to think that RNA did not
>>evolve from some still simpler self-replicating system, for which
>>"just chance" is an appropriate explanation.  This is an
>>interesting research question.
>
>       RNA does not reduce to a simpler system, i.e. the way a
>vertebrate reduces (evolutionarily) to an invertebrate.

I'm not sure what "the way a vertebrate reduces to an invertebrate" means.
Vertebrates developed from invertebrates (primarily) by addition of a
backbone; however, amphibians and reptiles developed from fish as much by
loss of the gills as by addition of the lungs.

If you mean only that vertebrates developed only from modification of
invertebrates, while RNA did not develop from modification of some earlier
system, you may be right.  On the other hand, RNA may have developed in just
this way; we don't know what the precursor was, so we don't know how it
happened.

What seems nearly certain is that the precursor is not still around as an
independent system, and is quite likely not around at all.

> What happened was that something else
>evolved, and learned to store more and more complex information
>in RNA  or DNA (if one came first). One of the biggest advantages
>of doing this is obviously in the ease with which this stored info
>is transferred to offspring -- requiring only a simple copying
>mechanism. This would give such systems tremendous advantage over
>complex systems which must copy their functionality unit by unit.
>Eventually, becoming increasing dependent on this information, it
>would be discovered that allowing mutation of this information itself
>was a successful strategy -- up to a point.

More likely, the older system created RNA by accident: similar molecules
provided some sort of evolutionary advantage, and random mutation then
created RNA itself.  At that point the game was up; the RNA outsurvived its
progenitor, and made it extinct.

Also, increasing mutability is unlikely.  Chemical reactions are inherently
chaotic; one would expect a precursor to suffer from too much mutation
rather than not enough.  Indeed, a lower mutation rate may have been the
very advantage that RNA had over its predecesser -- just as DNA has a lower
mutation rate than RNA.

A simple test here: if the system started out with no ability to mutate, it
cannot evolve one.  If it starts with too much tendency to mutate, it can
evolve less.  Of course, there is an optimal mutation rate for a given
context, and reducing it below this rate will be selected against.

> At any rate, controlled mutation of this
>storage information itself would become an important aspect of evolution.
>But initially it was the mutation of the underlying system. This
>type of mutation must still be occurring today, needless to say, or
>at least that is a testable hypothesis.

What evidence do you have for such a thing?

>>       Such an RNA self-replicating system will evolve just as
>>DNA does: by mutations changing the base pairs.  This will affect
>>the formation of proteins around the RNA, which will favor or
>>disfavor the replication of the RNA; hence natural selection
>>drives the evolution.
>
>       A block or string of material with no internal
>organization is not a system. RNA was created _by_ a system to be
>easy to copy, and this is why biologists have been able to copy
>it: they just use a similar procedure to the one the cell uses.
>This has led to the erroneous notion that it is self-replicating.

A system is what acts like a system.  What reason do you have to doubt the
experimental results, other than an a priori belief that it must be wrong?

>>       Different parts of the DNA make themselves differentially
>>available for transcription by RNA, thus directly affecting what
>>proteins get created.
>
>       Are you suggesting the DNA molecule is "aware" that
>certain things need to be accomplished, and subsequently
>initiates them? If not, then why are you suggesting DNA plays an
>active role?

I don't think *any* part of the cell is "aware" of *anything*.  Maybe your
problem is that you think the opposite.

>       The 'evidence' cited in the current literature would
>not contradict a central control system. But tell me this: how is
>it thought various messenger molecules like RNA know where to go
>once they are formed? [...] How is this physical motion controlled by a
>chain of nucleotides?

What makes you think that these molecules *do* know where to go?  By and
large, molecules created in a cell move around in no particular pattern.
When they get to an appropriate receptor (i.e., a place where they are
capable of having a chemical reaction) they react.

>>       We have two broad classes of control systems: hierarchical
>>and feedback. A "purely" hierarchical control system runs into
>>the problem of infinite regress: [...remaining possibilities
>>deleted]
>
>       Why is infinite (or indefinate) regress rejected out of hand?

Several reasons, which you won't like:

First, it is philosophically distasteful.  It denies the possibility of ever
*really* answer the question, "how does this work"?  Consider a sequence of
statements, where the nth statement is "statement n+1 is true". There is no
way to assess the truth value of such a sequence; if the statements are true,
they're true; if they're false, they're false.  Similarly, given such an
infinite regress of systems, consider each system works because the next one
works.  But it would be just as consistent if each fails because the next
fails.  (Such philosophical considerations are not final; if there was
strong evidence for an infinite regress -- 10 or so levels having been
discovered, with no end in sight -- it would nevertheless be a good working
hypothesis.)

Second, an infinite regress of physical systems entails infinitely small
physical systems.  Quantum mechanics (I told you you wouldn't like it) tells
us that there is an effective lower limit to the size of a physical system.

> What is known about the structure of the material world
>which, even if you find the word 'infinite' distasteful, makes
>you think that there is not regress at least beyond the level of
>the cell we can currently view?

A priori, there is no particular reason why the cell should be the base
case.  But, in fact, we have a plausible outline of a theory of how, in
fact, the control system of the cell is based on feedback, and is not
hierarchical.  Thus, assuming that this is the basic level of explanation is
the most plausible.

>Isn't this just the current mechanistic paradigm in physics?

The idea that the universe is essentially mechanistic has been fundamental
to the development of physics at least since the time of Gallileo.  For it
to be overturned now would be without precedent in the history of science.

>Do you think it would be
>non-constructive for molecular biologists to wonder if they have
>the full explanation with DNA?

Not at all.  Such "wonderings" are the basis for the advancement of science.
So far, the DNA theory of biological organization has withstood every
challenge.  That's what successful theories do.

>>       The paradigm shift I'm talking involves the ideas of
>>non-linear systems, complex feedback, chaos, self-organizing
>>systems, strange attractors, and so forth.  It looks to me like
>>you are the one that doesn't want to accept the new paradigm, and
>>so rejects its validity.
>
>       No. The properties listed above are the result of the
>interaction of the complex systems nature is made of.

No.  This sort of complex behavior emerges from very simple systems.  This
is a mathematical fact.

You might argue that it has no application to the real world; that complex
behavior in the real world always arises from the "complex control systems
interact[ing], each intent on maintaining the identity of its own system".
But this ignores the fact that much real-world behavior is like the behavior
of the mathematical systems.  It ignores the fact that our best models of
many complex systems (like the weather) have chaotic behavior like that of
more simple mathematical models, and this behavior is like the actual system
being modelled.  In short, it is a dogmatic assertion in the teeth of the
evidence.
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