An irrelevant "abiogenesis" paper
Julie Thomas
In another thread (on 6/9/99), Ian Musgrave posted a list of abiogenesis
experiments. Such a list conveys the impression that science has
been making tremendous progress in this area. But just how relevant
are these studies to abiogenesis (regardless of their claims)? For today,
let's look at the first study on Ian's reference list (a study that was also
reported in the general new media).
Imai E, Honda H, Hatori K, Brack A, and Matsuno K.(1999 Feb 5).
Elongation of Oligopeptides in a Simulated Submarine Hydrothermal
System. Science , 283, 831-833.
Here is the abstract:
"Oligomerization of a peptide was attempted in a flow reactor that
simulated a submarine hydrothermal system. When fluid containing
glycine repeatedly circulated through the hot and cold regions in the
reactor, oligopeptides were made from glycine. When divalent ions
(such as copper ions) were added under acidic conditions, oligoglycine
was elongated up to a hexaglycine. This observation suggests that
prebiotic monomers could have oligomerized in the vincinity of
submarine hydrothermal vents on the primitive earth."
Put simply, when these researchers ran a solution of glycine
(the simplest biological amino acid) through an apparatus that
mimics submarine hydrothermal vents, they were able to isolate
peptide chains of up to six glycine residues.
According to the researchers, the glycine solution was cycled
between the high temp and low temp chambers every 34 or 78 sec. How
closely this mimics a submarine hydrothermal vent is something
I do not know (after all, they note that the temperature in the high temp
chamber was "increased gradually over 20 min while the soln was cycling).
But what is more relevant is that they begin with a 100 mM glycine
solution "dissolved in pure water." And at this point, the prebiotic
relevance of this experiment is in serious question. Why dissolve the glycine
in "pure water" rather than sterile sea water given the purpose of this
experiment was as follows:
"We constructed a flow reactor that simulated the pressure and
temperature conditions of the hydrothermal circulation of water in
order to examine the likelihood of synthesizing oligopeptides from
monomeric amino acids."
This rationale, of course, falls under the first sentence of the study:
"The onset of polymerization must have been a major step in the
chemical evolution that formed the precursors of life."
But when you are dealing with a fairly concentrated solution of pure
glycine (10^-1 M) dissolved pure water , you are dealing with
something that is already invested with a fair amount of artificial
specificity (estimates of amino acid concentrations in the prebiotic
ocean have ranged from 10^-7 to 10^-12 M and these of course were
not dissolved in "pure water"). And this form of artificial specificity
does *not* mimic the natural world. Of course I could be wrong and
am open to correction if someone has a paper showing where geochemistry
alone produces pure 100 mM glycine in pure water from a natural solution.
Again, why didn't these researchers use sterile sea water if they want to
mimic what takes place in the sea? Better yet, why didn't they begin
with some of the soup produced by a Miller/Urey discharge apparatus
instead of a pure solution of 100 mM glycine?
Now, when these conditions were used and the flow apparatus was
run for 30 minutes, most of the glycine still remained as monomers.
The most common product was diketopiperazine (figure 2 in the paper).
The other less common reactant products were strings of two glycines,
then three glycines. That is, nothing larger that a chain of three glycines
was seen. Furthermore, from the figure we see saturation curves,
where the diglycine and triglycines appear to reach a maximum synthesis
point after 6-7 min. That is, whether you run the reaction for 10 min
or 30 min, we still obtain the same amounts of diglycine and triglycine.
I should also point out that the authors explained the temperature of
the high-temp chamber was varied from 110 degree to 350 degree C.
They then note:
"The results of interest were obtained for temperatures ranging
roughly between 200 and 250 degree C."
Apparently, no oligos formed at temperatures below or higher
than this range.
So what does this experiment tell us? If we begin with 100 mM glycine
dissolved in pure water, and circulate between cold and hot temperatures
(where hot is specifically 200-250 degree), we can get three glycines to
link up at about 0.5 mM conc after about 7 minutes of circulation. But
if we circulate for a longer time, we don't get any chains longer than 3
and we don't get a higher concentration of triglycines.
Next, the authors added 10 mM CuCl2 to the glycine solution and
lowered the pH to 2.5. Now, they got chains of glycine 2,4, and 6
residues long. But nothing longer.
What interests me here is why 10 mM CuCl2? Why pH 2.5?
While the authors' abstract makes it sound like they tested
a variety of "divalent ions (such as copper ions)", their report
gives no indication whatsoever than anything else than
CuCl2 was used. To me, these sound like reaction conditions
which were arrived at by trial and error. Why is this significant?
Because it suggests many other conditions were tried and did
not work, meaning that to get 6 glycines to hook up (and no
more), we apparently need a solution of 100 mM glycine and
10 mM CuCl2 dissolved in pure water, pH 2.5, cycling between
hot and cold every 34 sec, where the temp was gradually raised
to 200-250 degree.
Sometimes what catches my eye in a scientific paper is not
what is reported, but what is not reported. And this paper
has a whopper. Let's set the context to see this.
First, the researchers design an apparatus to mimic submarine
vents. That's an investment of time, energy, and funds.
Secondly, the experimental system is very simple to use and run.
Simply prepare your solution, load it into the apparatus and then
periodically remove small samples that are easily monitored by
HPLC.
Thirdly, the objective of this whole experiment was again
as follows:
"We constructed a flow reactor that simulated the pressure and
temperature conditions of the hydrothermal circulation of water in
order to examine the likelihood of synthesizing oligopeptides from
monomeric amino acids."
Put these three things together and what is obviously missing?
Here's a hint. After explaining their results, the authors conclude
with the following paragraph:
"As monomers of biological significance, both amino acids and
nucleotide molecules can potentially accommodate stepwise
polymerization schemes into themselves [for instance, by repeating
the cycle of hydrolysis and elongation]. From an evolutionary
perspective, a more pressing issue in this regard is how to
implement such schemes. Stepwise synthesis of oligoglycine
in our flow reactor seems to suggest that submarine hydrothermal
vents in the Archean ocean could have readily facilitated the
multiplicative oligomerization of these monomers, even in
the absence of ribosomes or ribozymes."
Have you figured out what is missing yet?
Before getting to the missing whopper, it should be pointed
out the authors do at least phrase their findings in a scientifically
proper manner. That is, these results "seem to suggest" something
"could" happen. Contrast this attitude to the apologists for
abiogenesis.
Okay, back to what's missing. Is it the fact that nothing larger
than a oligopeptide of only six monomers was formed? That is
a good observation, for why don't we see longer peptides? After
all, if six is the limit, this doesn't seem all that biologically
relevant. But this isn't the biggie.
What's painfully missing are the experiments using other
amino acids or a mixture of amino acids. These would be
very easy experiments to run. Just mix up a solution of
arginine, asparatic acid, glycine, and valine and run it
through the chamber. Or simply use pure solutions of
an amino acid other than glycine. So why weren't these
experiments done? They would not involve a lot of
extra work. And they would make the work far more
successful in light of its intended objectives and conclusions.
Think about it. You go through the trouble of designing this
apparatus and set up an experimental system that is very
simple to run. You could test all kinds of mixtures, but
you only test a solution of pure glycine?
Of course, it is possible that these researchers are in fact
doing these types of experiments right now. We'll have to
wait and see, but keep in mind that it should be easy to put
out another paper in the next year or two reporting on this
(since the experiments would be just as simple to do and
even more important).
Here's the bottom line as I see it. Imai et al. show some mildly
interesting chemistry concerning glycine oligomerization.
That is, using some rather artificially specified conditions, they
show you can string together a small concentration of 6 glycine
residues. By itself, these results might find a home in some
not-widely-read chemistry journal, but by asserting this sheds
some light on abiogenesis, it gets published in _Science_ (perhaps
the most widely read science journal) and is even picked up
by the press. Like I have said before, when it comes to
abiogenesis, skepticism in the scientific community is a
strange concept. :)
Of course, one might also think that 40 years after the Miller/Urey
studies _Science_ would be publishing something a tad
more significant about abiogenesis. One can almost hear the
faint whisper of those straws being grasped.
--
Donald E. Flood
Julie Thomas <iz...@cleveland.Freenet.Edu> wrote in message news:7kh4g1$4jn$1...@alexander.INS.CWRU.Edu...
>
>
>
> In another thread (on 6/9/99), Ian Musgrave posted a list of abiogenesis
> experiments. Such a list conveys the impression that science has
> been making tremendous progress in this area. But just how relevant
> are these studies to abiogenesis (regardless of their claims)? For today,
> let's look at the first study on Ian's reference list (a study that was also
> reported in the general new media).
>
> Imai E, Honda H, Hatori K, Brack A, and Matsuno K.(1999 Feb 5).
> Elongation of Oligopeptides in a Simulated Submarine Hydrothermal
> System. Science , 283, 831-833.
<Big Snip>
> Here's the bottom line as I see it. Imai et al. show some mildly
> interesting chemistry concerning glycine oligomerization.
> That is, using some rather artificially specified conditions, they
> show you can string together a small concentration of 6 glycine
> residues. By itself, these results might find a home in some
> not-widely-read chemistry journal, but by asserting this sheds
> some light on abiogenesis, it gets published in _Science_ (perhaps
> the most widely read science journal) and is even picked up
> by the press. Like I have said before, when it comes to
> abiogenesis, skepticism in the scientific community is a
> strange concept. :)
>
> Of course, one might also think that 40 years after the Miller/Urey
> studies _Science_ would be publishing something a tad
> more significant about abiogenesis. One can almost hear the
> faint whisper of those straws being grasped.
>
Julie,
Why don't you send a letter or commentary to Science, detailing
your "concerns"? Perhaps the editors will you invite into a technical
discussion with the authors of this paper. I would very enjoy reading
a technical dialogue on this paper!
Don
Mitchell Coffey
"Donald E. Flood" <Don.E...@wcom.com> wrote:
>
> Julie Thomas <iz...@cleveland.Freenet.Edu> wrote in message
news:7kh4g1$4jn$1...@alexander.INS.CWRU.Edu...
> Julie,
>
> Why don't you send a letter or commentary to Science, detailing
> your "concerns"? Perhaps the editors will you invite into a technical
> discussion with the authors of this paper. I would very enjoy reading
> a technical dialogue on this paper!
>
> Don
Well, for one, "she" would have to use "her" real name.
--
Mitchell Coffey
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