Re: A Question of Abiogenesis #1

From: Tedd Hadley (hadley@reliant.yxi.com)
Date: Tue Oct 17 2000 - 16:56:08 EDT

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    "Stephen E. Jones" writes
      in message <200010152118.FAA23165@urban.iinet.net.au>:
    > Reflectorites
    >
       
       This particular subthread started when I suggested that bacteria
       and other lifeforms would consume or degrade any amino or nucleic
       acids in nature, thus eliminating the barest possibility that
       abiogenesis could occur from such particles in nature now, if
       it did occur in the past.

       Stephen apparently thinks that bacteria break down only a few
       amino acids, leaving the rest to basically ... just accumulate
       I guess. This seems to defy common sense because if it were
       so, we'd likely be up to our eyeballs in great heaps of amino
       acids from the trillions of life forms that have existed on this
       earth. If Stephen does not believe that, he must believe
       *something* is processing or utilizing those amino acids, in
       which case he must grant that, whatever that is, it would be
       directly interfering with any sort of hypothetical abiogenesis
       process proposed.

       Further, how can Stephen believe that bacteria would not be able
       to utilize compounds that are identical to their own constituent
       parts? Again, it seems to defy common sense.

       These two major problems seem to be overlooked in the mire of
       minor details Stephen raises below.

    > TH>Well, since modern day bacteria not only break down proteins
    > >but amino acids and nucleic acids, it seems quite likely.
    >
    > Not necessarily. If modern day bacteria have to use the complex
    > biomolecule vitamin B12 to do it, it would not "seems quite likely."

       That doesn't follow. Assuming (erroneously) that all putrefactive
       bacteria require B12 to breakdown amino acids, we still observe
       that decay exists anywhere and everywhere life exists, we still
       observe the byproducts of amino acid decarboxlization anywhere
       protein matter is found and thus we conclude that the process
       works just fine, B12 or not.

    >SJ>Anyway, it seems that only the chemical called "vitamin B12" can
    > >>metabolise (i.e. eat) amino acids:
    >
    > TH>That's vitamin B12's role in the human digestive process, yes
    > >(although I suspect it's oversimplification to say that's the
    > >only way amino acids can be metabolized in humans). However,
    > >I'm not sure what this has to do with bacteria. I know B6 is
    > >important in certain bacterial processes but I haven't
    > >heard that B12 is critical for all amino acid breakdown.
    >
    > The New Scientist article indicated vitamin "B12" *was "critical for all
    > amino acid breakdown."
       
       http://archive.newscientist.com/archive.jsp?id=18904300

       This article does not claim that B12 is critical for *all* amino
       acid breakdown, and it does not indicate that B12 is needed for
       decarboxylation -- the process that most bacteria use to break
       down amino acids. In closest context, the article is talking
       about human digestion. Further, the article does not indicate
       that B12 is rare in nature, it simply says that few species
       produce it. Those species, however, can be and are quite
       widespread.

    > TH>Let's take one particular example, B. cadaveris. This bacterium
    > >creates a lysine decarboxylase enzyme which breaks down lysine
    > >into CO2 and cadaverine. B12 is not a participant.
    >
    > Thanks to Tedd for this. He has almost won this one! He will have won
    > when he shows that "B12 is not a participant." The fact that "This
    > bacterium creates a lysine decarboxylase enzyme which breaks down lysine
    > into CO2 and cadaverine" does not mean that "B12 is not a participant"
    > unless he can show *all* the steps in the process and they don't involve
    > vitamin B12.

       I can't show you all the steps in the process since I don't know
       all of them. However, I have read that B12 in bacteria is
       specifically used for transfer of methyl groups in the process
       of demethlyation -- which is not decarboxylation. Thus, by
       elimination, B12 does not appear to take part in amino acid
       decaboxylation.

    > Of course Tedd would also have to show that this process started
    > with raw lysine in the first place,
       
       Irrelevant. Either way the process breaks down raw lysine.

    > and is not part of a larger
    > process of breaking down polypeptides

       That makes absolutely no difference. If a process can break
       down protein into amino acids, and then break down those individual
       amino acids, the process can obviously start with amino acids
       and break those down as well. The decarboxylation process
       above required just two things: lysine and a bacteria-manufactured
       decarboxylase enzyme (itself a protein encoded for by a particular
       gene).

    > and if it only occurs in
    > certain specialised contexts, i.e. in the gut of animals.

       No, anaerobic decay obviously takes place everywhere -- in sand,
       in soil, in water -- anywhere protein can be found.

    <snip>
    >
    > TH>Sorry, I didn't mean to imply that there zero aerobic bacteria
    > >in the gut. The bulk of bacteria in the gut are anaerobic, however,
    > >and they survive because there is not an appreciable quantity of
    > >"air" in the gut.
    >
    > There *must* be "an appreciable quantity of `air' in the gut"
    > if *aerobic* bacteria can "survive" also in it.

       No, that's not logical. The variety and quantity of aerobic
       bacteria do not need an apreciable quantity of air to survive.
       What do you mean by appreciable?

    > TH>You're saying bacteria are raw amino and nucleic acids? I thought
    > >they were complex proteins just like all other life.
    >
    > No. I was trying to use Tedd's words as far as possible. What
    > I am saying that if the `bacteria's chemotaxis detected amino
    > acids themselves, it might try to metabolise them.

    > >SJ>As I pointed out, if the bacteria's chemotaxis detected raw
    > > amino and nucleic acids it might try to cannibalise itself or
    > > other bacteria nearby.
    >
    > TH>Two flaws:
    > >1) bacteria are not "raw" amino and nucleic acids
    > > (Perhaps you should define what you mean by "raw" so we can be clear.)
    >
    > See above. I am well aware that "bacteria are not "raw" amino
    > and nucleic acids". But they are *composed* of proteins (which
    > are amino acids) and nucleic acids. My point was that it would
    > be unlikely that chemotaxis would detect amino and nucleic acids
    > themselves, but would only detect *specific* organic compounds
    > made of mino and nucleic acids.

       And my point is that it would be more likely that chemotaxis
       would detect amino and nucleic acids but other mechanisms
       or methods would prevent cannibalization.

       Chemotaxis relies on small particles that can be transported to
       the surface of the bacteria's sensors. It seems quite obvious
       that undamaged bacteria do not "leak" amino acids, nor would
       a bacteria cell wall seem to generate a false positive.

    <snip>
    > Agreed that "live bacteria will feed on fragments of dead
    > bacteria" but only if, their chemotaxis detects their specific
    > compounds as food. There is no evidence that chemotaxis detects
    > amino and nucleic acids themselves. Tedd's "carnivores" analogy
    > above makes this point.

       But there *is* evidence that chemotaxis detects amino and nucleic
       acids. Why are you so quick to make such an assertion? For
       example:

    |Chemotactic response of Escherichia coli to chemically synthesized amino acids.
    |
    |Hedblom ML, Adler J
    |
    |In Escherichia coli, seven of the commonly occurring amino acids
    |are strong attractants: L-aspartate, L-serine, L-glutamate, L-alanine,
    |L-asparagine, glycine, and L-cysteine, in order of decreasing
    |effectiveness. The chemotactic response to each amino acid attractant
    |is mediated by either methyl-accepting chemotaxis protein I or II,
    |but not by both. Seven of the commonly occurring amino acids are
    |repellents. This work was carried out with chemically synthesized
    |amino acids.

    > TH>[Prebiotic soup stuff. Stephen quotes Denton:
       
       I'm going to let Stephen have the last word on the prebiotic
       soup stuff. Basically I agree there is little evidence for
       the kind of thick, dense ocean of organic soup that was proposed
       several decades back for origins of life. I would not argue
       such a soup could be completely obliterated by life without
       a trace.

       Currently, other theories are in favor, such as more isolated
       pools of organic compounds, mineral templates, etc.

    <snip>
    > It is *Darwinists* who need to "provide a naturalistic explanation for the
    > origin of life" in order to "keep the Creator out of the picture":
       
       No, there is no conspiracy against the Creator. They just don't
       see it necessary. The possibility of aliens must be excluded
       before anyone seriously considers a Creator with a capital
       "C". The best route to your Creator remains through emotional
       experiences in a socially supportive setting.

    <snip Johnson quote>
    > Darwinists have often used the ploy that they are not really
    > talking about the origin of life, but in a recent book a Darwinist
    > has admitted they *should*, if their theory is to be "A general
    > theory of biological evolution ":
    >
    > "A general theory of biological evolution should include within its
    > domain a number of problems that have hitherto resisted solution
    > within the broad confines of the Darwinian, or indeed any other,
    > research tradition. These problems include how life evolved from
    > nonlife; how developmental programs evolve; what impact, if any,
    > developmental dynamics have on the evolution of species; the
    > relation between ecological dynamics and species diversification;
    > and what is the best way of conceiving the mix between pattern and
    > contingency in phylogeny. ...
       
       Most detailed discussions of evolution I've seen mention these.
       There are no shortage of problems in evolution. However, none
       of those problems seems large enough to cast doubt on the overall
       theory.

    > The origins of life, development,
    > ecology, phylogenesis-these are the big questions that people think
    > of when they hear the word *evolution*. It is answers to these
    > questions that people want from evolutionists. That is why they so
    > often feel put off when Darwinians confine themselves to talking
    > about changing gene frequencies in populations and to throwing
    > cold water on ideas about evolutionary direction, meaning, and
    > progress." (Depew D.J. & Weber B.H., "Darwinism Evolving,"
    > 1997, p.393. Emphasis in original)



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