At 11:07 PM 11/12/2000, you wrote:
>[...]
>
> >>>DNAunion: Second, you have glazed over some of the most important steps
>on the way to
>life: how the first self-replicators arose.
>
> >>>Chris: Actually, I've dealt with this in previous posts…
>
>**************************
>DNAunion: Okay, but not in the one to which I was replying. In addition, if
>I remember correctly now, your explanations were similar to those you present
>in this post of yours - which are still vague in that they deal with
>nameless, hypothetical entities that might do this or that. For example:
>
>"A simple A-B template molecule such that A attracts and holds another B, and
>the B attracts and holds another A, until there is *both* another A and B,
>which then join and break free from the original molecule will work."
>
>"I don't actually know, of course, how the original replicator molecules
>might have occurred, or even what they might have been"
>
>"However, I'd bet that a good chemistry-simulating program could find a fair
>number of them quite rapidly."
>
>You later state in your most-recent post that you know that more was
>obviously needed to generate life than mere energy flowing though the
>prebiotic "biosphere", but you still omitted that fact from your post to
>which I was replying: you mentioned only the open-system thermodynamics part.
>
>Okay, I promise to be more amiable in the rest of my post.
>******************
>
> >>>Chris: … though by no means exhaustively. Self-replicating
> molecules are
>not exactly uncommon.
>
>******************
>DNAunion: I am unaware of any known natural self-replicating molecule (they
>are very uncommon in nature, if they exist at all). Note the even DNA is not
>self-replicating (I bring this up because it is sometimes incorrectly stated
>that DNA replicates itself).
Chris
Actually, you do know of such molecules: DNA. You may also be aware of
prions. However, even a water molecule can be self-reproducing in the right
chemical circumstances (i.e., it triggers the production of other water
molecules).
>******************
>
> >>>Chris: Even slightly *evolving* self-replicating molecules have been
>observed (in laboratory research, admittedly).
>
>******************
>DNAunion: I would like more details. The main in vitro ("test tube")
>evolution experiments I am familiar with use PCR to amplify the selected
>molecules. That is "cheating": the molecules being studied in such
>experiments do not qualify as self-replicating. (I will briefly address the
>32-amino-acid "self-replicating" peptide in response to your next statement).
>******************
>
> >>>Chris: A simple A-B template molecule such that A attracts and holds
>another B, and the B attracts and holds another A, until there is *both*
>another A and B, which then join and break free from the original molecule
>will work.
>
>******************
>DNAunion: This sounds exactly like the 32-aa "self-replicating" peptide that
>a fair amount of people bring up (A could be the 15-aa "half", B the 17-aa
>"half", and AB the full 32-aa peptide). I won't repeat all the points I
>brought up in another post, but suffice it to say that the full 32-aa peptide
>(AB) was powerless to create the two halves (A and B) it was made from: the
>researches had to continually produce and feed the full 32-aa peptide (AB)
>the 15-aa (A) and 17-aa (B) halves that it would then pair with and bond
>together. This is not self-replication.
Actually, it is. Assembling pieces to make a copy of oneself is
self-replication. Probably *nothing* starts from scratch. Even the
self-replication of a water molecule requires the existence of
already-assembled oxygen and hydrogen atoms; it will not work with just
free electrons, protons, and neutrons.
DNA is not self-replicating in the sense of starting from individual,
separate atoms, either. It works from existing structures, which may be
more or less complex.
Perhaps what you mean is that such molecules are not self-replicating in
the sense of not depending on *human* intervention. That's true, but not
relevant. The question is: *Can* molecules, given suitable conditions,
cause/trigger the production of more of themselves?
As DNA and other molecules prove, they can.
I got my example from an article in Scientific American some years ago. I
don't remember the names of the components used.
>*******************
>
> >>>Chris: I don't actually know, of course, how the original replicator
>molecules might have occurred, or even what they might have been.
>
>*******************
>DNAunion: No one knows how they could have occurred (you are in good company
>there!). From what I have read, it basically comes down to chance: for
>example, trillions of trillions of randomly-generated RNA molecules were
>somehow "pumped out" by some "prebiotic RNA manufacturing plant" until two
>that could function as RNA replicases arose, close enough in space and time
>to find each other, and one copied the other, and one of the then 3 copies
>copied one of the others producing 4 RNA replicases, etc.
>
>What the first self-replicators *might have* been include (1) RNA replicases
>(probably the predominant school of thought, but it *might* be slipping a
>bit), (2) PNA replicators (since RNA itself does not look very prebiotic, OOL
>researchers have started looking for simpler backbone systems), (3) pRNA
>replicators (the pyranosyl - 5 carbons in the ring - form of ribose is
>apparently easier to make prebiotically than the furanosyl - 4 carbons in the
>ring - kind found in RNA), (4) peptide replicators (though it would then
>become difficult to explain the reverse flow of information, from protein
>into nucleic acids), or (5) inroganic replicators (such as Cairns-Smith's
>"clays", but they have largely been ignored and considered irrelevant).
>*******************
Chris
The clay idea is interesting, if it can provide a "scaffold" of sorts for
more nearly true replicators, but, it seems implausible to me, too, over
all. However, I've not studied it and don't have much of the requisite
background. However, other crystallization processes of non-clays might
also need to be considered.
> >>>Chris: However, I'd bet that a good chemistry-simulating program could
>find a fair number of them quite rapidly (to be followed by real-world
>testing, of course).
>
>*******************
>DNAunion: I am glad to hear you say that they should go past mere
>simulations: that they need to actually do something in the lab to try to
>confirm their model instead of simply assuming it is an accurate
>representation of the real world.
Chris
Science must always reach back to the empirical world for confirmation and
correction. Otherwise, the slightest mistake gets magnified as time goes
on, and won't be corrected until way later than is necessary (and perhaps
after some disasters).
>Many people I have debated (for example,
>in relation to the "lipid world" computer model) seem to feel confident that
>if a computer model shows X can happen, well then by golly it obviously can;
>and if the computer model shows that Y cannot happen, well then by golly Y
>obviously can't.
Chris
This was one of the big mistakes of Schutzenberger. Since *his* model did
not work, he assumed that *no* model would work. You can only make such
claims on the basis of a model if you have fully validated that you are
modeling the theory to be modeled. Schutzenberger had little or no concern
for the appropriateness of his model for testing evolutionary theory (even
evolutionary theory of 35 years ago).
>As someone who has programmed computers for years (as you,
>Chris, appear possibly to be also), I am aware of discrepancies that commonly
>exist between reality and computer models. In fact, something I just posted
>here today about near-zero gravity allowing for heat to flow from cold to hot
>was not allowed by computer models - but it actually occurred in nature. The
>Science article I quoted went on to say that when the programmer made
>adjustments to his code, by figuratively canceling out gravity in the
>computer model to match the "absence" of gravity (microgravity) in the Mir
>space station, that it THEN gave the correct result.
>********************
Chris
Interesting. Heat can flow from cold to hot anyway in special cases (via
quantum "randomness"), but I assume that this was not such a case. I will
look for the post. (I say "randomness" in quotes because I don't really
believe in randomness in an absolute or metaphysical sense; I gave it up
for absolutely strict determinism in the '70's, and it has changed my
life. ;-) Of course, this does not mean that I reject the
quantum-level observations or the mathematical descriptions that organize
them; I reject only the standard *interpretation* of these facts and
descriptions).
> >>>Chris Cogan: (I understand that one such program has recently been
>written in the programming language Prolog, which is a remarkable tool in
>itself, aside from the power of some of the programs written in it).
>
>********************
>DNAunion: As I expressed above, I will wait until the actual lab work is
>done to validate such a model.
>
>Second, even if it does generate self-replicators, we would still need to ask
>whether of not they were prebiotically-plausible.
Chris
*That's* the big problem with the molecules in the article I mentioned
above. I don't think they would occur pre-biotically (though I don't
remember enough of the article to be sure).
The point of the Prolog program above is that it is a general chemistry
simulator that actually works for fairly complex molecules, so it would
make a good "search engine" to do at least preliminary searches of
"molecule-space" to find likely suspects.
>It would do OOL
>researchers no good at all if all the computer program came up with were
>things like multimeric proteins consisting of three dissimilar subunits, each
>400 or 500 amino acids in size.
Chris
Yeah. That would be useless for OOL purposes, I think.
>********************
>
>[...]
>
>**********************
>DNAunion: NEW STUFF.
>
>Since we are discussing origin of life stuff again, I recently read something
>I would like to point out and comment on.
>
>In the chapter being quoted from, David Deamer has just presented several
>paragraphs of detail concerning the following summary. This detail material
>has been omitted for brevity's sake.
>
>"To summarize, an abundant source of long-chain hydrocarbon components of
>prebiotic membranes is not obvious. On the other hand, one might argue that
>because the origin of cellular life absolutely requires lipidlike hydrocarbon
>derivatives, such molecules must have been available on the early Earth from
>a yet unknown source." (David Deamer, Membrane Compartments in Prebiotic
>Evolution, Chapter 8 of The Molecular Origins of Life: Assembling Pieces of
>the Puzzle, edited by Andre Brack, Cambridge University Press, 1998, p194)
>
>Can anyone else see the circular reasoning in this? If not, let me give you
>an analogy.
>
>PROSECUTOR: Ladies and gentlemen of the jury, the state believes that Mrs.
>Jones' disappearance is not due to her being abducted by a stranger, but
>rather is due to her husband's discarding her body after he savagely killed
>her. Let it first be noted that the state can't present any actual evidence
>that shows Mrs. Jones is dead, but we strongly suspect so: call it a working
>assumption. In addition, we don't have a murder weapon with Mr. Jones'
>fingerprints on it, despite our best searches. But we argue that since Mrs.
>Jones could not have been murdered by her elderly husband without a murder
>weapon being involved, then we can assume that the murder weapon with his
>fingerprints does exist somewhere, and that we just haven't come across it
>yet. The state asks that you sentence Mr. Jones to life in prison without
>the opportunity for parole for his committing of such a brutal and
>unthinkable act."
>
>Okay, a bit over-dramatic (to say the least), but I think everyone gets the
>point. Take away the preexisting assumption that Mrs. Jones was murdered (or
>analogously, that life arose here on Earth) and the assumption based on it -
>that a murder weapon with Mr. Jones' fingerprints on it must exist (or
>analogously, that an abundant source of long-chain hydrocarbon components
>must have existed) is unfounded, meaningless, and bankrupt. If one is trying
>to demonstrate a basic, underlying assumption, then one shouldn't use
>assumptions drawn solely from that final underlying assumption that he or she
>is trying to validate to argue into existence, from thin air, evidence that
>supports any part of that final underlying assumption.
Chris
I don't see that the argument is circular at all, but rather that it is
*not* an argument but an admission of incompleteness, and admission that,
if the hypothesis is to be ultimately upheld, there will have to be found
some way for the requisite "lipidlike hydrocarbon derivatives" to arise.
This is another avenue to research. Maybe it will be found that they can't
arise under conditions we can reasonably suppose might have existed, but
maybe it will be found that they *can* arise naturally in those conditions.
Right now, who knows?
Also, I'm not at all convinced that they are necessary for the origin of
cellular life, though they might be necessary for the origin of the kind of
cellular life that *we* are familiar with. We need to be careful not to
*assume* that the first life on Earth was much like any life we know today.
This archive was generated by hypermail 2b29 : Mon Nov 13 2000 - 21:12:45 EST