Reflectporites
On Mon, 18 Sep 2000 11:12:01 -0700, Tedd Hadley wrote:
[...]
>SJ>I have a book on microbiology which doesn't say anything about
>>bacteria eating amino acids and nucleic acids.
TH>Look up putrefactive bacteria or any of those varieties that ferment
>proteins. There are probably thousands of species.
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.
Anyway, it seems that only the chemical called "vitamin B12" can
metabolise (i.e. eat) amino acids:
"Vitamin B12's main role is in the metabolism of amino acids,
molecules which are the building blocks of proteins. Amino acids
consist of an amino group (-NH2) and a carboxylic acid group (-
COOH) separated by a carbon atom that also carries a hydrogen
atom along with another group of atoms, which varies in each type
of amino acid." (Milgrom L., "The assault on B12," New Scientist,
11 September 1993, p.39.
http://archive.newscientist.com/archive.jsp?id=18904300)
and vitamin B12 is made only by a few species of microorganisms:
"Vitamin B12 is made only by a few species of microorganisms.
Many of these live symbiotically in the large intestines of animals,
which is how these animals obtain their daily B12 needs." (Milgrom
L., 1993, p.39)
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>The gut (small & large intenstine, not stomach, by the way) doesn't
>>>have an appreciable quantity of O2 in it (nor nitrogen so
>>>"air" is not the case) but occasionally has small quantities of
>>>bacterial fermentation bioproducts such as hydrogen, carbon
>>>dioxide, and methane.
>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.
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>For most amino acids, such specialized bacteria should see no
>>>difference between abiotic proteins and the "natural" proteins.
>SJ>See above on "chemotaxis". I would need hard evidence of this.
>>
>>I would think it unlikely that modern day bacteria would be
>>attracted to raw amino and nucleic acids.
TH>How the heck do you think dead plant and animal matter decays
>then??
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 don't really think that we'll find a big pile of
>amino acids in some unfortunate's coffin after the appropriate
>decomposition interval?
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), or their chemical
constituents (which apart from carbon are the gases N, H, and O).
[...]
>>TH>Likewise, for the amino acids that do not occur in
>>>life, it would seem that a buildup for any length of time would
>>>represent an energy source to be exploited
>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.
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'?
>SJ>I would consider this unlikely because of the ready supply of cellular
>>materials they can already exploit.
TH>Cellular materials from what or where? What happens when that
>runs out? All the bacteria just die, like that, with a food
>source available right there with only minor chemical differences?
See above on chemotaxis and vitamin B12. If the *right* "food" is not
available (i.e. it is recognised *as* "food") then the bacteria will indeed die.
It is like a cow or a horse would starve to death if all it had to eat was
meat! Or like some animals with specialised diets, e.g. the koala, will starve
to death if leaves that are not the sort it eats are all that is available.
In fact here is a quote which I stumbled on while preparing my current
assignment on the frog's digestive system:
"The food of the frog consists primarily of living insects. These are
usually captured by the specialized extensile tongue. The prey
adheres to sticky secretions on the tongue, which is then withdrawn
into the mouth. Large insects and other bulky prey are pushed into
the mouth by the forefeet. No attention is paid to objects that are
not moving; extension of the tongue is a reflex initiated by a small
spheroidal object moving with a minimum velocity across the retinal
field of vision. A captive frog will starve to death if placed among
hundreds of dead flies." (Boolootian R.A. & Stiles K.A. "College
Zoology," 1981, p.372)
>>TH>In the race between a possible new life precursor from abiotically
>>>produced amino acids and evolution of a new bacterial strain
>>>able to metabolize those amino acids, I'd put my money on the
>>>bacteria every time.
>SJ>Tedd might lose his money. There would be good reasons why bacteria
>>would *not* metabolize amino acids.
TH>Well, given that bacteria now seem to have no problem and that
>amino acids have been available as a potential food source for
>billions of years, my money looks safer than McDonald's stock.
Tedd seems to forget that it has indeed been "billions of years" and if he
believes in evolution, there is no reason why the bacteria *today*, which
have a vast supply of living and dead organisms to eat, have not specialised
on those organisms, and lost (assuming they ever had it) their ability to
directly consume raw amino and nucleic acids.
And as it turns out, it seems that *no* bacteria can directly metabolise
amino acids, and only those few bacteria which can synthesis vitamin B12,
can indirectly metabolise amino acids.
>>>>TH>However, four billion years ago, who knows? Maybe the first
>>>>>life form thrived on a soup of life precursors.
>>>SJ>What "soup" would that be exactly?:
>>TH>Who knows? But, as you point out, probably not prebiotic
>>>soup of Oparin's scenario.
>SJ>If not Oparin's, what "prebiotic soup" then?
>>
>>"The existence of a prebiotic soup is crucial to the whole scheme.
>>Without an abiotic accumulation of the building blocks of the cell
>>no life could ever evolve. If the traditional story is true, therefore,
>>there must have existed for many millions of years a rich mixture of
>>organic compounds in the ancient oceans and some of this material
>>would very likely have been trapped in the sedimentary rocks lain
>>down in the seas of those remote times. 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. Most notable of these rocks are the dawn rocks" of Western
>>Greenland, the earliest dated rocks on Earth, considered to be
>>approaching 3,900 million years old. .... Sediments from many other
>>parts of the world dated variously between 3,900 million years old
>>and 3,500 million years old also show no sign of any abiotically
>>formed organic compounds.
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.
>
>| The simplest interpretation of the carbon isotopic data in Mojzsis
>| et al. (1996) is that the organisms responsible for the light carbon
>| signature in the oldest known terrestrial sediments were metabolically
>| complex, perhaps comprising populations of phosphate-utilizing
>| photoautotrophs and chemoautotrophs. These data may point to the
>| presence of diverse photosynthesizing, methanogenic, and methylotrophic
>| bacteria on Earth before 3850 Ma (Mojzsis and Arrhenius, 1998;
>| Mojzsis et al., 1999b). Not only had life taken firm hold on Earth
>| by the close of the Hadean era, but it also appears to have evolved
>| far enough away from its origin to create an interpretable signature
>| in carbon isotopes.
Thanks to Tedd for the URL. I think I have the GSA article in my foot-
high pile of unfiled photocopies (!), but in any event I definitely have (and I
think I posted to the Reflector at the time) excerpts from the original
NATURE articles referred to in the references:
"Mojzsis, S.J., Arrhenius, G., McKeegan, K.D., Harrison, T.M., Nutman,
A.P., and Friend, C.R.L., 1996, Evidence for life on Earth before 3,800
million years ago: Nature, v. 384, p. 55-59.
Mojzsis, S.J., Harrison, T.M., Arrhenius, G., McKeegan, K.D., and Grove,
M., 1999a, Origin of life from apatite dating? - Reply: Nature, v. 400, p.
127-128."
The short answer is that Tedd is misreading this. As his own quote states it
is a report about the discovery of a "light carbon signature" which "may
point to the presence of diverse photosynthesizing, methanogenic, and
methylotrophic bacteria on Earth before 3850 Ma".
That is, it is a report of the remains of life that was *already in existence*,
not of a *pre*-biotic soup.
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 are 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>In the same way, the origin of life
>>>will very likely require at least as much research because *it
>>>is a lot more difficult than it looks*.
>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;
It is interesting how the evidence to decisively test Darwinist claims is
always missing?
But what *Tedd* claims "doesn't follow logically". Why should "*all*
evidence" be eliminated?
The living world is full of `living fossils' that have hardly changed in the
fossil record. There are fundamental biochemical processes that are
conserved across the whole of biology.
Tedd's own quote above shows that 3.85 bya, some organisms had
metabolic outputs that resemble those of modern day cyanobacteria.
Indeed, they have actually found cyanobacteria fossils that look like these
not all that later. I personally have seen some of the oldest rocks on Earth
in the Pilbara Region of Western Australia which are ~3 byo, and they have
fossilised stromatolite mats in them that look the same as stromatolites
produced by modern day cyanobacteria in the sea only about 500
kilometers away.
TH>2) the number of
>configurations of environments and chemicals is still astronomical.
Again what *Tedd* claims "doesn't follow logically". The "number of
configurations of environments and chemicals" *on the early Earth* is
*not* "astronomical". It is *large* but it is not "astronomical".
Any large problem can be broken down into manageable components and
tested, and those that fail can be eliminated. And any limited successes can
be zeroed in on. With the accumulated knowledge how molecules work
and with the simulating power of supercomputers, they should be able to
do it, "*If* the origin of life was fully naturalistic."
My son can pick locks which really *do* have an "astronomical" number of
combinations. What he does is to systematically vary one number why
keeping all others constant. Eventually something clicks (literally) and he
writes that down and then tests the others. In a very short time he has
found the combination and opened the lock.
If life did originate fully naturalistically on the early Earth then they could
simulate that and systematically test and eliminate those possibilities that
don't work. In fact that is what they have been doing these last 40+ years.
The problem is that *none* of the possibilities work. Which is good
evidence that the origin of life on the early Earth was *not* fully
naturalistic.
[...]
>>TH>There is no shortage of simple-sounding solutions for medical
>>>and abiogenesis research.
>SJ>I regard Tedd's dragging in of the common cold as just a
>>red-herring. There is little or no connection between curing
>>the common cold and demonstrating an abiotic origin of life.
TH>The only connection I wish to stress is that they both seem to
>be simple problems which turn out to be difficult to solve.
>No red-herring.
And as I pointed out they *are* "simple problems which turn out" *not*
"to be difficult to solve" just that they are not *worth* solving. They
already *can* "solve" influenza (which is the same family of virii), because
that is *worth* solving.
>SJ>Anyway, it defeats Tedd's own argumenmt. Researchers have made
>>and are making steady progress in medical research over the last
>>40+ years, but there is no such steady progress being made in
>>abiogenesis. What origin of life reasearchers report is
TH>Heh, post something up to date, not 12 years out of date!
This is another ploy that Darwinists use. They always assume that the
passage of time resolves their problems automatically, so that all they have
to do is ignore a problem long enough and they can declare out "out of
date":
"Evolutionary biologists have a habit of ignoring the most
pertinent criticisms of their theory until they can decently call
them out-of-date. (Berlinski D., "Denying Darwin: David Berlinski
and Critics," Commentary, September 1996, p.26.
http://www.commentarymagazine.com/9609/letters.html)
The fact is that there *is* nothing "up to date". I have been on this List
since 1995 and there has been nothing new in OoL, just more of the same
recycling of old arguments with new hype.
Paul Davies has just written a book on the origin of life and I remember
when he started he was confident he would solve it, and as I have already
posted a few days ago, he finished like the others I quoted, saying that "we
are missing something very fundamental about the whole business" and
"some radically new ideas" are needed:
"When I set out to write this book I was convinced that science was
close to wrapping up the mystery of life's origin. The dramatic
evidence for microbes living deep underground promised to provide
the 'missing link' between the prebiotic world of biochemical soups
and the first primitive cells. And it is true that many scientists
working in this field confidently believe that the major problems of
biogenesis have largely been solved. Several recent books convey
the confident message that life's origin is not really so mysterious
after all. However, I think they are wrong. Having spent a year or
two researching the field I am now of the opinion that there remains
a huge gulf in our understanding. To be sure, we have a good idea
of the where and the when of life's origin, but we are a very long
way from comprehending the how. This gulf in understanding is not
merely ignorance about certain technical details, it is a major
conceptual lacuna. I am not suggesting that life's origin was a
supernatural event, only that we are missing something very
fundamental about the whole business. If it is the case, as so many
experts and commentators suggest, that life is bound to arise given
the right conditions, then something truly amazing is happening in
the universe, something with profound philosophical ramifications.
My personal belief, for what it is worth, is that a fully satisfactory
theory of the origin of life demands some radically new ideas."
(Davies P.C.W., "The Fifth Miracle," 1998, pp.xvi-xvii)
The only problem is that they assume it has to be "new" *naturalistic* "ideas"!
[...]
>>TH>Okay, let's try a little experiment. If you claim we know too
>>>much, I have a simple request. Read the publications at the
>>>following URL and tell me what we know about the conditions of
>>>early earth that should eliminate this research as possible
>>>candidate for origin of simple replicators:
>SJ>The only way to "eliminate" possibilities is to test them all
>>out. There are probably thousands of labs across the world who
>>could divide-and-conquer this problem.
TH>Don't forget that the availability of research grants severely
>constrains this approach.
Especially when trying the same old naturalistic "approach" has failed!
>SJ>It should be a lot easier and cheaper than trying to find life on Mars or
>>Europa. Besides, even if they did find life on another planet, they would
>>still need to work out how it originated.
TH>It sure is easier getting public funding for alien-life form study
>than for abiogenesis.
Virtually all the "public funding" on OoL these days in in NASA's
budget and that's why it has this "alien-life form" spin. It is
even starting to be criticised by other scientists:
---------------------------------------------------------------------------
http://archive.newscientist.com/archive.jsp?id=22500200
New Scientist
Editorial
Don't bet your shirt on life 05 Aug 00
[...]
Since 1996, when scientists found traces of what looked like fossilised
bacteria in Martian meteorite ALH84001, NASA has championed the
search for life in the Universe. No bad thing, you may say. The agency fired
the public's imagination at a time when it faced a hostile US Congress. But
is NASA now relying too much on this search?
Take the surface of Mars, which is covered with what look like river
valleys and flood plains. If there was ever water here, the reasoning goes,
life may not be far below. A few weeks ago, NASA reacted with great
enthusiasm to a photograph that seems to show gullies that have been
freshly cut by water (New Scientist, 1 July, p 6).
Yet this week comes the suggestion from Australia that the Martian
channels were made by carbon dioxide, not water. If true, it greatly reduces
the prospects for life on the planet (see p 6). Separately, Aron Vecht and
Terry Ireland from the University of Greenwich, London, announced an
experiment which shows how a chemical process can make the carbonate
patterns that were taken to be signs of life in ALH84001.
There are many good reasons to explore Mars and our other neighbours-to
help us understand the Earth and the Solar System, to push technology to
its limits and add to the richness of human culture. But relying on a single
raison d'Etre is a dangerous game. NASA needs to broaden its aims and
find other ways to capture the imagination. If it doesn't, it risks getting lost
in space.
[...]
---------------------------------------------------------------------------
TH>I think most folks still see abiogenesis
>as a threat to religious belief.
I am not sure this is true. As I posted the other day, it was originally the
(or at least a) Christian position that life originated spontaneously. There is
nothing in the Bible that says how or even where life originated.
The point about "abiogenesis" being "a threat to religious belief" began
with materialistic-naturalistic science assuming it was simple and that
would validate their whole materialistic-naturalistic program.
But it has backfired on them. They are now aware of large is the gap
between the simplest living system and any non-living system.
Yet they cannot escape now. If the origin of life requires intelligent input,
then the whole materialistic-naturalistic program would collapse:
"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., "Darwin on Trial," 1993, pp.103-104)
>TH>Okay, let's try a little experiment. If you claim we know too
>>much, I have a simple request. Read the publications at the
>>following URL and tell me what we know about the conditions of
>>early earth that should eliminate this research as possible
>>candidate for origin of simple replicators:
>>
>> http://ool.weizmann.ac.il/publications.html
>SJ>Reading a number of "publications" may not be "a simple request".
[...]
TH>Exactly. There is a great deal of material there that you can't
>simply dismiss out of hand because you don't know enough about
>early Earth conditions to rule it out.
I don't "dismiss out of hand" or "rule ...out" *anything* - I am not
a Darwinist!
If Tedd wants to claim something, then let him do so and post his
*evidence* so *everyone* on this List can see it.
TH>We do *not* know too much about abiogenesis, we know too little
>and that is amply demonstrated by the variety of approaches
>being attempted, suggested and often rejected.
Tedd would need to support this claim from the scientific literature
otherwise it sounds too much like something he just made up or has
accepted uncritically from an unreliable source.
I am not claiming that Tedd does not really believe this, but there is no
claim that I am aware of in the OoL literature that "we know too little"
"about abiogenesis".
Indeed in a recent book co-authored by a Professor of Biochemistry
(Weber) claims that because of what we know about the molecular level,
"it is now overwhelmingly likely that life...will be produced and replicated
under laboratory conditions within a fairly short time":
"Until recently, the problem of the origin of life has remained
almost as peripheral among Darwinians as it was for Darwin
himself. The molecular revolution, however, has given
increased saliency to the issue and has suggested experiments that
have uncovered some intriguing facts. Indeed it is now
overwhelmingly likely that life, under some reasonable definition,
will be produced and replicated under laboratory conditions within
a fairly short time. When that happens, the origin of life will cease
being conceived as a one-time event, after the manner of Genesis I,
and will begin to be treated as an expected phenomenon that has
emerged." (Depew D.J. & Weber B.H., "Darwinism Evolving,"
1997, p.400)
The *real* problem is not that OoL researchers don't know enough, but
that they know *too much* and on naturalistic philosophical grounds
refuse to acknowledge what is staring them in the face! That is, the origin
of life was not fully naturalistic but required the input of intelligence.
TH>Now I think most creationists have a different explanation for
>the quantity of abiogenetic research out there and that is:
>
>"It's an atheist conspiracy to make it *appear* to the public
> like much progress is being made when in reality the work is
> mostly fraudulent."
>
>I think, Stephen, this is fairly close to your own belief as
>well, is it not?
I have responded separately in my inaugural "SEJ FAQ" to Tedd's
erroneous claim that I am alleging a "conspiracy" (I am not). I will post this
in a day or two.
I thank Tedd for this long-running thread in case he decides to terminate it.
Maybe I will anyway, unless Tedd responds with something new.
Steve
--------------------------------------------------------------------------
"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. ... Our list of questions is not
entirely haphazard. 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: Systems Dynamics and the Genealogy of Natural
Selection," [1995], MIT Press: Cambridge MA, 1997, Second printing,
p.393. Emphasis in original)
Stephen E. Jones | sejones@iinet.net.au | http://www.iinet.net.au/~sejones
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