It just so happens that this post contains a number of previous posts, re-
posted within it. Unfortunately this makes the post long and perhaps
tedious! I apologise but I could think of no better way of addressing Brian's
In fact I have had to split it in two because of it's size (39K) , so I have
extracted the science self-correcting part out of the middle of Brian's
post and made it a seprate topic. This will make it easier to read.
On Sun, 09 Jan 2000 19:51:07 -0800, Brian D Harper wrote:
>>SB>are you guys really sure there has actually been a "shift to space"?
>>>Stephen has recently posted abstracts of articles on research being done on
>>>oceanic heat vents and on bacteria found in deep-earth core samples. In
>>>other words abiogenesis research is alive and well on planet earth. It
>>>*would* be interesting to find extra-terrestrial life or evidence of it,
>>>but I think that research is in *addition* rather than *instead of.*
>SJ>*Today's* bacteria are not evidence for the *origin* of life any more than
>>today's vertebrates are:
>>"...the notion that bacteria are primitive....bacteria have undergone a longer
>>evolutionary history than the vertebrates." (Lewontin R.C..., 1995, p167).
>>Corliss, who discovered the first "oceanic heat vent" (ie. hydrothermal
>>vent), believes that all the life around such vents migrated there:
>>"...Corliss and others agree that current life at the vents
>>probably migrated there..." (Bradley W.L. & Thaxton C.B., ..., 1994, p194)
>>Moreover hydrothermal vents are actually a *problem* for the origin of
>>"Stanley L. Miller and his colleague Jeffrey L. Bada...have conducted
>>experiments which indicate that the incredibly hot water inside these vents
>>(frequently exceeding 300 degrees C) would destroy complex organic compounds
....." (Overman D.L...., 1997, p80).
>>This is because the superheated water in hydrothermal vents would
>>*destroy* any organic compounds:
>>"Stanley Miller and Jeffrey Bada...suggest the superheated water inside
>>vents, which sometimes exceeds 572 degrees F, would destroy rather than
>>create complex organic compounds. As a result, Miller actually considers
>>the vents a hindrance to the origin of life." (Bradley W.L. & Thaxton C.B.,
BH>This is indeed an important issue for abiogenesis. If Miller and Bada
>are coreect then this presents a difficulty not just for the
>hydrothermal vent scenario but also for the more traditional view
>which Miller favors (i.e. discharges in atmosphere yielding amino
>acids which accumulate over long times in the oceans etc.) due to
>the relatively rapid circulation of the Earth's early oceans through
Agreed. I have an email from Brian which I have kept, and although it was
private, I am assuming there is nothing confidential about it (after personal
stuff is deleted), which states that the circulation rate through hydrothermal
vents was only "every million years":
Date: Sat, 15 Jul 1995 18:30:49 -0400
To: firstname.lastname@example.org (Stephen Jones)
From: email@example.com (Brian D. Harper)
Subject: Re: Its about time (was Whale problems #2.)
It is difficult to get a short quote from the paper in question which
really captures the various reasons for the very short estimate on the
allowable time for the origin of life. Here is the statement and ref.:
There are a number of reasons to think that life must have arisen
in ten million years or less, based on the known rate of
decomposition of organic compounds. Since we do not know the details
of the processes required for the origin of life, we cannot say
how much less time may have been involved, but a period of
perhaps 10,000 years for such processes is not impossible.
ref: Miller, 1992
This is just one of a number of reasons suggesting a short allowable time
for the origin of life. If I have time, I'll try to put a more detailed
summary together for the reflector. Briefly, some other factors are:
1) Strong geological evidence that life was abundant on Earth 3.8
billion years ago. This same study provides strong evidence that
there never was a primeval soup, i.e. no abiotic kerogen was
found in these rocks. ref: Schidlowski, 1988.
2) Heavy bombardment of the Earth by asteroids began to subside
about 3.8 billion years ago. Maher and Stevenson (1988) estimate
the frequency of major impact events that could have had a
significant influence on the origin of life. For example, events
that could have resulted in "global surface sterilization" were
occuring roughly once every million years about 4 billion years ago
and once every 10 million years about 3.8 billion years ago. Events
that could cause "global surface climatic trauma" were more common.
These were occurring roughly once every million years 3.6 billion
years ago and once every 10 million years about 3.4 billion years
3) At present, the entire volume of the ocean is circulated
through deep sea vents (> 350 C) once every 10 million
years. In ancient times the estimated rate is once
every million years. These extreme conditions would
destroy any amino acids or other organic compounds in
the ocean waters. Ref: Joyce 1988, Miller & Bada 1988.
Item 3 is very controversial and could be overturned. Proponents
of the deep sea hydrothermal vent scenario argue that the vents are
a *source* of amino acids rather than a sink. I was given a recent
reference in support of this but haven't had a chance to look at it
yet. If this turns out to be true, then things will look much brighter
for abiogenesis research since it will also help out with the neutral
============================= references =============================
G. Joyce, 1988, "Hydrothermal Vents too Hot?", _Nature_, <334>:564.
K.A. Maher and D.J. Stevenson, 1988, "Impact Frustration of the Origin
of Life," _Nature_, <331>:612-614.
S.L. Miller, 1992, "The Prebiotic Synthesis of Organic Compounds as a
Step Toward the Origin of Life," in _Major Events in the History
of Life_, J.W. Schopf, ed., pp. 1-28.
S.L. Miller and J.L. Bada, 1988, "Submarine Hot Springs and the Origin
of Life," _Nature_, <334>:609.
M. Schidlowski, "A 3,800-million-year isotopic record of life
from carbon in sedimentary rocks," _Nature_, vol. 333, 26 May
1988, pp. 313-318.
BH>If, on the other hand, the vents are a source rather
>than a sink, then one has a possible counter to the prevailing
>current opinion that the Earth's early atmosphere was probably never
>strongly reducing as was once thought.
Source of what? High pressure water at > 350 degrees C (ie. > 662
degrees F) would presumaby destroy any organic polymers being built up
and any life that got started before it could build up its adaptive
defences which today allow it to live *near* (but not *in*) hydrothermal
[...] Brian's comments about `cover-up' allegations extracted out
into separate post.
BH>OK, back to Miller and Bada. This study sparked an interesting
>controversy which, unfortunately, I haven't kept up with in the
>past few years. I might be able to find the detailed references
>if anyone is interestd. Basically, several people challenged
>Miller's experiment, whether it adequately modelled hydrothermal
>vent conditions. There followed several rounds of point and
>counter-point. Some evidence in favor of Miller's critics is
>a recent paper in <Science> by Koichiro Matsuno and his co-workers
>which I just happenned to stumble across a few months ago:
>Imai, E. et al.,1999. "Elongation of Oligopeptides in a Simulated
>Submarine Hydrothermal System," <Science> 283, 831-833.
>What Matsuno did here was very interesting. He wanted to model
>not just the high temperature (he went up to 350 C) and pressure
>in the vent, but also the quenching that occurs when the water
>leaves the vent. What he did then was cycle between a high temp/
>pressure reactor and a cooling chamber. With repeated cycling
>he was able to convert amino acids into oligopeptides. He was
>further able to synthesize hexaglicine from oligoglycine.
>This would indicate, to me anyway, that the ball is back in
I posted the following on this to the the other list I was on
when it occurred. I presume it was during time I left I had left the
The scenario seems to this sceptic to be highly contrived and they
appear to have tried the experiment towards the end of the grant
period when it looked like they would have to admit no results:
On Wed, 10 Feb 1999 05:46:00 +0800, Stephen Jones wrote:
>Here is a recent origin-of-life experiment article with the usual hype
>from Yahoo at:
>My comments are in square brackets.
>Sunday February 7 1:20 AM ET
>Origin Of Life Breakthrough Born In Japan Snow By Elaine Lies
>NAGAOKA, Japan (Reuters) - Huddled at the foot of soaring
>white peaks and buried deep in snow for months at a time, this rural
>city in Japan's remote snow country hardly looks like a place where
>scientific breakthroughs could occur.
>Yet here, Friday, a team of Japanese researchers announced that
>they have managed to recreate the conditions from which life itself
>may have sprung.
>[This is an implied admission that up till now they hadn't!]
>In a major breakthrough in the never-ending debate about how life
>started, Koichiro Matsuno and colleagues at the Nagaoka
>University of Technology built an artificial system simulating the
>environment at undersea thermal vents, where water heated deep
>below erupts through the seabed into cooler ocean water.
>[One wonders how realistic this "artificial system" was. Here we
>have "deep" "undersea thermal vents" but later on we also have
>"dry and wet conditions...in lagoons"!].
>By this they were able to produce some of the elementary building
>blocks from which proteins, essential to life, are formed.
>[In an earlier paragraph it was "life itself." Now it is just the
>"building blocks" of "proteins" which even themselves are only
>"essential to life" not actually "life itself" ]
>"Man has been asking 'what is life' for thousands of years. But the
>real question is where did life begin," Matsuno told reporters.
>[How can we know where life begins if we don't know what life is?
>Perhaps this is necessary because if Matsuno defined the awesome
>complexity of even the simplest living system, the gap between
>what he had achieved and what was still to be achieved would be
>"For 10 years, underwater hydrothermal vents have been thought to
>be the place where life began -- and we were able to prove it."
>[Eh? He produces merely some building blocks of proteins, and that is
>enough to "prove" that life began in hydrothermal vents?]
>Writing in the journal Science, Matsuno described how his team
>simulated a process called polymerisation, in which complex
>molecules -- in this case oligopeptides, one of the elements that
>make up proteins -- are formed from simpler amino acids.
>[An oligopeptides is a peptide "of less than ten amino acids" (Isaacs
>A., et. al., eds., "Oxford Concise Science Dictionary," 1991, p509).
>This excerpt doesn't say how long the oligopeptides were, what
>exactly they were, and if they are part of proteins found in living
>This process was likely to be repeated numerous times, possibly
>aided by "heating in dry and wet conditions, day-and-night cycles,
>tidal waves (and) dry-wet conditions in lagoons", the authors
>[We later learn the cycles only lasted only "one-minute" which is
>hardly simulating "day-and-night." Thaxton, et. al. point out there
>are major problems with lagoons: "In other words, for these more
>limited zones (e.g., lakes, pools, lagoons), as for the ocean itself,
>it is difficult to imagine significant concentrations of essential
>organic compounds ever accumulating. As we have seen,
>degradative forces need to be taken into account in realistic
>estimates of concentrations, and they have frequently been
>ignored." (Thaxton C.B., Bradley W.L. & Olsen R.L., "The
>Mystery of Life's Origin," 1992, p66)]
>"I asked myself where life originated and said, 'go down to the
>hydrothermal vents in the (primordial) sea'," Matsuno said.
>[This assumes that there *were* hydrothermal vents when life
>originated on Earth 3.7 bya. Miller and Bada point out that
>"superheated water inside vents, which sometimes exceeds 572
>degrees F, would destroy rather than create complex organic
>compounds. As a result, Miller actually considers the vents a
>hindrance to the origin of life." (Bradley W.L. & Thaxton C.B., in
>Moreland J.P. ed., "The Creation Hypothesis", 1994, p194)]
>There, chemical products synthesized in hot vents could re-enter
>the vents after being quenched in the surrounding cold water and
>undergo further reactions.
>[What they don't mention is that 5 out of the 20 amino acids
>essential to life, could not survive such treatment: "Dr. Miller
>remains unconvinced by the proponents of a high-temperature
>origin of life. He has a forceful objection: Many of the essential
>components of living cells are unstable at high temperatures. In a
>paper published this month in The Proceedings of the National
>Academy of Sciences, he reported that constituents of DNA lasted
>as little as 19 days at the temperature of boiling water. "We
>conclude that a high-temperature origin of life may be possible, but
>it cannot involve adenine, uracil, guanine or cytosine," he wrote
>with a touch of acerbity, referring to four of the five main
>components of the nucleic acids DNA and RNA." (Wade N., "Data
>Back Idea Life Began in Inferno," The New York Times, July 31,
>What Matsuno and his team did that was new was build a flow
>reactor that mimicked the cooling and heating parts of the cycle.
>[One wonders why this was necessary. If it was a *realistic*
>simulation why was there would be any need to simulate it?
>All one would need to do is go to where the conditions apply
>naturally, near a hydrothermal vent or a lagoon nearby and harvest
>the polypeptides in vast quantities!]
>The two-chambered flow reactor circulated materials from hot to
>cold environments in roughly one-minute cycles. When they added
>the amino acid glycine, they found that this formed into more
>complex oligopeptide molecules in a stepwise process.
>[Is "one-minute cycles" realistic for hydrothermal vents? Also, was
>the glycine unrealistically pure? Scott points out: "The other
>problems, of selection and purity, are much more severe. Out of all
>the various chemicals being produced in various places throughout
>the earth, how did the ones that could form selfreplicating nucleic
>acids (or self-replicating anything) come together in sufficiently
>pure form to allow each subsequent stage of the chemistry to
>proceed to significant extents? Chemical reactions are notoriously
>sensitive to the presence of 'impurities' chemicals not involved in
>the desired reaction which can interfere with that reaction (by
>promoting side-reactions, by reacting with the desired products,
>and so on. The reactions that take place in complex messy mixtures
>of many different chemicals are certainly not the same ones as occur
>when a few components of the mixtures are purified out and
>combined in isolation." (Scott A., "The Creation of Life: Past,
>Future, Alien," 1986, p97).
>Key to the process was the addition of bivalent copper ions, one of
>many minerals present on the sea floor -- an addition Matsuno said
>"I was at a conference with my good friend Andre Brack, a French
>researcher, and just as I was about to step on a bus, he said 'You
>really should consider bivalent ions.' That was it."
>[And keep the process away from all the other minerals present on
>the sea floor, in case they have the opposite effect?]
>A native of Japan's northernmost island of Hokkaido who attended
>the prestigious Tokyo University, Matsuno, 58, said he has
>wrestled with questions on the origins of life for more than three
>decades, since around the time he received his physics PhD from
>the Massachusetts Institute of Technology.
>But inspiration for his current work came only two years ago.
>"I had a lot of failures, and finally came up with this experimental
>design, basically because nothing else worked."
>[An interesting admission that "nothing else worked"! One wonders
>if in desperation Matsuno just kept making the process less and less
>realistic until *something* publishable happened?]
>The solution came just in time -- the group was about ready to give
>up its research if this last attempt failed.
>The flow reactor itself, a little over one yard high, looks like
>something put together from spare parts in a garage.
>Matsuno said its simplicity was probably why it succeeded.
>"Our biggest problem before was making things too complicated in
>[Reading between the lines it seems that the more realistic the
>simulation was, the less it worked. Only when it was made
>unrealistically simple was some limited success achieved?]
>Although the idea of cutting edge research coming out of a remote
>university -- Nagaoka is 170 miles from Tokyo, the closest
>metropolitan area -- may be surprising, Matsuno and his colleagues
>said this works to their advantage.
>More elite Japanese universities tend to be hierarchical.
>Ei-ichi Imai, the researcher who built the flow reactor, said
>whenever he got stuck on a problem he could just go and casually
>ask some expert for advice.
>"Here, you don't have to spend so much time on other things and
>can think hard about your work."
"Neo-Darwinism has failed as an evolutionary theory that can explain the
origin of species, understood as organisms of distinctive form and
behaviour. In other words, it is not an adequate theory of evolution. What
it does provide is a partial theory of adaptation, or microevolution (small-
scale adaptive changes in organisms)." (Goodwin B., "Neo-Darwinism has
failed as an evolutionary theory", The Times Higher Education
Supplement, May 19, 1995).
Stephen E. Jones | firstname.lastname@example.org | http://www.iinet.net.au/~sejones
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