Reflectorites
On Tue, 03 Oct 2000 11:06:16 -0700, Tedd Hadley wrote:
[...]
>SJ>There is no doubt that bacteria consume "proteins". We are
>>talking about whether *modern day* bacteria would prevent life
>>from arising again. That is , whether modern day bacteria would
>>consume the *precursors* of life, namely raw amino and nucleic
>>acids, so that life could not ever arise again.
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."
[...[
>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."
TH>As I wrote before (which apparently you've ignored) is that
>putrefactive bacteria do the following conversions through
>decarboxylation: lysine -> cadaverine, arginine -> agmatine,
>tyroseine -> tyramine, orithine -> putrescine, histidine ->
>histamine through decarboxylation. Yes, lysine, arginine,
>tyroseine, orithine, and histidine are amino acids.
I have not "ignored" this. I posted counter-evidence against it. The
evidence was that "bacteria" have to use vitamin B12 in this breakdown of
amino acids.
Tedd's just putting arrows (->) between an amino acid and an organic
compound comprised of that amino acid is not necessarily a full
explanation of what happened in that transformation. Most, if not all, such
transformations involve enzyme catalysts and other special conditions.
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.
Of course Tedd would also have to show that this process started with raw
lysine in the first place, and is not part of a larger process of breaking down
polypeptides and if it only occurs in certain specialised contexts, i.e. in the
gut of animals.
[...]
>SJ>So it seems that in today's world amino acids could accumulate so
>>long as "a few species of microorganisms" which could make vitamin
>>B12 did not find them, and the chance of that might be quite good
>>because of these "few species of microorganisms" that can make
>>vitamin B12, "Many of these live symbiotically in the large intestines
>>of animals".
TH>No. Again, how do you think things in nature decay if the process
>requires ubiquitous B12?
The question is not how I (or Tedd) "think things in nature decay" but how
they actually *do* decay. I have quoted from a scientific journal which
indicates that vitamin B12 is essential for bacteria to break down amino
acids.
I therefore assume that "things in nature" do not "decay" right down into
their constituent amino acids, unless something like nematodes (which are
also "ubiquitous") consume them and use bacteria in conjunction with
vitamin B12 in their gut to break them down further.
>>>SJ>According to the above text on page 274, there are *both* aerobic and
>>>>anaerobic bacteria in human and animal intestinal tracts.
>>
>>TH>That sounds right to me.
>SJ>So Tedd's statement above that "The gut ... doesn't have an appreciable
>>quantity of O2 in it" is false in the original context of his statement (or
>>implication) that only anaerobic bacteria lived in the gut?
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.
>SJ>I have already pointed out that "dead plant and animal matter" are
>>not raw amino acids. They are complex organic compounds that the
>>bacteria's "chemotaxis" detects. 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>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.
TH>2) By your logic, a pack of carnivores would eat each other
> as often as they would prey animals. However, they don't
> because there are other evolutionary mechanisms not related
> to simple food detection that prevent cannibalization. It
> is reasonable to expect that similar mechanisms exist in
> bacteria.
This is my very point!
>>TH>You don't really think that we'll find a big pile of
>>>amino acids in some unfortunate's coffin after the appropriate
>>>decomposition interval?
>SJ>Well since bacteria are composed of nucleic acids and proteins
>>(which are in turn composed of "amino acids), if the "coffin" was
>>sealed, and if the "appropriate...interval" was long enough for
>>the bacteria to have all died, then yes, I would expect to find
>>"amino acids" (not necessarily "a big pile" since all living things
>>are mostly air and water),
TH>No, live bacteria will feed on fragments of dead bacteria.
>(Recall this was one hypothetical origin of nucleic acid
>exchange).
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.
[...]
>>>SJ>Is there any evidence that bacteria eat non-biological amino
>>>acids?
>>TH>Well, point me to a source of non-biological amino acids and
>>>I'll check.
>SJ>It was Tedd's point about "amino acids that do not occur in
>>life", not mine.
>>
>>I assumed he meant "non-biological amino acids" but I guess he
>>could have mean "biological amino acids" that were not part of
>>any living organism, i.e. `free-standing'?
TH>No, I understood you to be talking about non-biological amino
>acids -- i.e. those amino acids that do not occur biologically.
>The best way to check if bacteria eat those kinds of amino acids
>would be first to find a source.
OK.
[...]
TH>[Prebiotic soup stuff. Stephen quotes Denton:
>
>SJ>"Yet rocks of great antiquity have been examined over the past
>>two decades and in none of them has any trace of abiotically
>>produced organic compounds been found." ]
>>TH>Further research appears to prove this wrong. See
>>>http://www.uta.edu/geology/geol1425earth_system/images/gaia_chapter_10/
>Early_Life.htm which indicates that there *is* signs of organic
>>>material in those rocks.
[...]
>SJ>The short answer is that Tedd is misreading this.
TH>No, I'm not. Denton uses his statement to pose a serious
>argument against abiogenesis: the earliest rocks show no sign
>of a "soup". However, this argument is flawed in light of later
>research because early rocks actually show that life was already
>started. It remains reasonable to suppose that life would
>consume or contaminate any proposed prebiotic soup.
It is not "reasonable" at all "to suppose that life would consume or
contaminate any proposed prebiotic soup". The products of Miller-Urey
spark chamber experiments are "Beilstein."
"The original experiment was run for a week. As it progressed, the
water in the flask took on first a red and then a yellow-brown color.
After a week the spark was shut off and the contents of the flask
were analyzed by various chemical methods. During the course of
the experiment, the methane had been consumed and the carbon
atoms originally present in it were now distributed among a number
of organic substances. The predominant product was an insoluble
material, made of a network of carbon and other atoms connected
together in an extended, irregular manner. This substance coated
the walls of the apparatus. Material of this type, called tar, resin, or
polymer (a term meaning "many parts"), appears frequently in
organic reactions It constitutes a nuisance, particularly when the
time comes to clean out the equipment. Fifteen percent of the
material had not been converted to tar and could be identified by
chemical means. A list of the compounds present and their amounts
was prepared. In any reaction of this type, the number of products
identified depends primarily upon the patience and skill of the
investigator. Instruments are now available that allow components
to be identified at the level of a few parts per million, or even per
billion. At such levels, many thousands of substances may be
present in the reaction mixture. Harold Urey had been asked, in
advance of Miller's experiment, what he expected would be
produced, and answered "Beilstein." The name refers to a
multivolume handbook which describes millions of organic
compounds. According to Miller, "Urey's reply meant that the
electric discharge would be expected to produce a little of
everything." (Shapiro R., "Origins: A Skeptic's Guide to the Origin
of Life", 1986, p100)
As I pointed out earlier, bacteria only require (and therefore consume) only
a limited range of organic chemicals. Most of the above "Beilstein" would
therefore not be consumed by bacteria.
TH>Denton's argument shows evidence of *no soup*. However, the
>evidence now shows *no* evidence of no soup. See the difference?
There is no "difference". The fact is that there should be evidence of an
oceanic prebiotic soup if there was one, and there isn't. Here's what the
geochemist Brooks says:
"And then what of the 'primitive soup' required for Chemical
Evolution? If such an environment ever existed on Planet Earth for
any appreciable time, it would require relatively large quantities of
nitrogen-containing organic compounds (amino-acids, nucleic acid
bases and so on). It is likely that such nitrogen-rich soups would
have given significant quantities of 'nitrogenous cokes', trapped in
various PreCambrian sediments. (The formation of such 'cokes' is
the normal result obtained by heating organic matter rich in
nitrogenous substances.) No such nitrogen-rich materials have yet
been found in early Pre-Cambrian rocks on this planet. In fact the
opposite seems to be true: the nitrogen content of early
PreCambrian organic matter is relatively low (less than 0.15%).
From this we can be reasonably certain that: there never was any
substantial amount of 'primitive soup' on Earth when ancient
PreCambrian sediments were formed; if such a 'soup' ever existed it
was only for a brief period of time. Subtract from the basic concept
of the Chemical Evolution Theory the ideas of substantial amounts
of 'primitive soup' and a long period of time, and there is very little
left." (Brooks J., "Origins of Life," Lion: Tring, Hertfordshire UK,
1985, p.118)
Note the delusory nature of evolution. It is so infintely plastic that it
can accommodate itself to something that probably didn't even exist!
[...]
>SJ>That is, it is a report of the remains of life that was *already
>>in existence*, not of a *pre*-biotic soup.
TH>A minor point next to the major point I was making,
>as I explain above.
If Tedd now claims this was only "A minor point" that's OK by me.
But then he keeps arguing for it below.
>SJ>In fact it makes it harder to claim that there was a prebiotic
>>soup but it eroded away. If they can find traces of biologically
>>produced products 3.85 bya, then they should be able to find
>>traces of a whole *ocean* of abiotic precursors to life, like
>>the large quantities of the tarry chemicals that ar e the
>>by-product of Miller-Urey type experiments, which allegedly
>>existed just before this, and in fact would have continued on
>>for a long time after since much of it is not consumable by
>>organisms.
TH>Doesn't follow, given 1) we don't have rocks older than 3.85
>bya to check (to my knowledge), 2) life forms would likely
>consume or contaminate any such prebiotic soup.
No. See above.
TH>Remember, these
>rocks have gone through major heat processes. Detecting the
>existence or non-existence of organic compounds appears to be
>limited to detecting the existence or nonexistence of carbon
>signatures. I'm not sure you can easily rule out a
>sort of "biotic" soup from that.
No. See above quote by Brooks about "nitrogenous cokes".
>>>SJ>*If* the origin of life was fully naturalistic it should be
>>>one of the *easiest* problems of evolution to solve. That is
>>>because, if it was solely by undirected natural chemical
>>>processes, there is only a limited number of these (though
>>>large) and it should be fully deterministic and therefore
>>>completely reproducible in a laboratory.
>>TH>That doesn't follow logically. 1) the existence of advanced
>>>life now very likely eliminates all evidence of the proper
>>>configuration of environments and chemicals;
>SJ>It is interesting how the evidence to decisively test Darwinist
>>claims is always missing?
TH>Non sequitur.
No, it's a fact! Whenever it comes to the crunch, Darwinists *always*
claim that the evidence was really there but is now missing. They *never*
consider that maybe their theory is simply *wrong*.
TH>We're not talking about Darwinist claims,
Yes we are (or at least I am). If an evolutionist believes in "fully naturalistic
evolution, involving chance mechanisms guided by natural selection" then
he/she is a Darwinist:
"By Darwinism I mean fully naturalistic evolution, involving chance
mechanisms guided by natural selection." (Johnson P.E., "Darwin
on Trial," 1993, p.4)
I have never yet come across a Naturalistic Evolutionist who does not
depend at some point on "chance mechanisms guided by natural selection"
to get the designing work done, and therefore is not a Darwinist.
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":
"In fact, Justice Scalia used the general term "evolution" exactly as
scientists use it-to include not only biological evolution but also
prebiological or chemical evolution, which seeks to explain how life
first evolved from nonliving chemicals. Biological evolution is just
one major part of a grand naturalistic project, which seeks to
explain the origin of everything from the Big Bang to the present
without allowing any role to a Creator. If Darwinists are to keep
the Creator out of the picture, they have to provide a naturalistic
explanation for the origin of life." (Johnson P.E., 1993, pp.103-
104).
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. ... 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)
[continued]
Steve
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"How do new species arise? Darwin's original idea, that new species arise
gradually from the action of natural selection over time, is now seriously in
doubt. In fact Darwin was disappointingly vague and inexplicit about the
actual mechanics of speciation (despite the title of his magnum opus). The
events which lead to the 'creation' of new species are still largely a puzzle.
Is selection alone strong enough to bring about new, distinct sexually
isolated species in the wild? Is this process necessarily a gradual one, or
may new species arise quite abruptly? The results of thousands of
experiments and observations from nature are ambiguous natural selection
may be strong enough to create adaptations, but some recent experiments
suggest that selection may actually be irrelevant in the origin of species.
There is also a wrangle over the speed at which new species are formed-the
latest results implying that this may be sudden rather than gradual." (Leith
B., "The Descent of Darwin: A Handbook of Doubts about Darwinism,"
Collins: London, 1982, pp.22-23)
Stephen E. Jones | Ph. +61 8 9448 7439 | http://www.iinet.net.au/~sejones
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