In a message dated 5/31/99 11:17:38 PM Mountain Daylight Time,
chadwicka@swau.edu writes:
>
> At 06:45 PM 5/31/99 EDT, Kevin wrote:
>
> >Then why would you consider sugar to be a biochemical impurity if sand is
> >not? Are you saying that a mixture of amino acids that contains sand is
> >still a mixture of pure amino acids? If so, explain how. If not, then
> >explain how this doesn't count as working with impure amino acids.
>
> Sure it is still a pure mixture of amino acids.
>
So if I mixed 8 grams of sand with 1 gram of combined amino acids in a beaker
of water, you are saying that I would have a pure mixture of amino acids?
Most chemists I know would call that an impure mixture, since you have
something other than amino acids in the solution with them.
>
> The reaction vessel is
> after all made from sand, yet you don't classify that as an impurity.
>
I would if it interfered with the biochemical reaction. Besides, glass may
be chemically similar to sand, but it is a different kind of substance from
sand. This is especially true of the glass used in chemical glassware, which
is formulated to be as inert as humanly possible. Sand is not inert; even if
it does not react chemically it could still serve as a physical matrix to
help concentrate the amino acids and facilitate their polymerization. Or
prevent it.
>
> I
> would consider an impurity something that has a chance of interfering with
> a biochemical reaction.
>
Biochemically speaking an impurity is anything you don't want in your
reaction mixture, whether it is known to interfere with the reaction or not.
Some things you cannot help having in your mixture, like the glass walls of
the reaction vessel or the usual amounts of salts and metal ions found in
commercially prepared chemicals; others you can help, like sand or ground
basalt or sugar. But whether it interferes or not, if you don't want it in
your mixture, it's an impurity.
>
> I know of no reactions that will occur between an
> amino acid and quartz. Thus putting sand into a reaction vessel is no more
> meaningful than performing the reaction in a glass vessel.
>
Rohlfing has done the experiments that demonstrate you are incorrect. Let me
quote to you what Rohlfing had to say about this: "In synthesizing
proteinoids, mixtures of **pure** amino acids are almost invariably used. In
many natural situations, amino acids would be greatly contaminated with other
organic compounds and with inorganic, geological matter. Such materials
could influence the polymerization process [cf. the role of clays in other
model syntheses]." (Emphasis in original.) So Rohlfing had the same concern
you did: what if the amino acids were not pure? In his experiments he
discovered that inorganic matter either has no affect or (in the case of
sand) actually enhanced polymerization. Since all these experiments were
done in glass reaction vessels, yet only when sand was actually added to the
reaction mixture was any enhancement of polymerization seen, it would appear
that Rohlfing has demonstrated that putting sand into a reaction vessel is
indeed much more meaningful than performing the reaction in a glass vessel.
Fox and Dose report that other people have contaminated mixtures of amino
acids with either inorganic or organic materials and have also discovered
that polymerization can still occur. So the point is again that purity is
irrelevant.
>
> It is simply a
> straw man to divert attention away from the fact that the experiment is
> being done under thoroughly unrealistic conditions for the primitive earth.
>
How are they unrealistic? You've never answered that question. Tell me what
part of the basic mechanism of thermal copolymerization would be impossible
on the primitive earth.
>
> Sand is not a biochemical impurity.
>
Of course it is; no biochemist would deliberately add sand to an experiment,
because he or she would have no idea what affect that could have. Why add
something that you don't know what it will do? And don't invoke glass as the
sand in all biochemical reactions. Glass may be made of silicon, but it's
not sand, and in any event no biochemist would use glassware that he or she
thought might interfere with his or her reactions.
>
> You do this: Take purified amino acids and heat them to 200 degrees....
>
That temperature is only necessary to make lysine-rich proteinoids. For
other types you can use as low as 120 degrees C. (Actually, you can go as
low as 65 degrees; see later).
>
> ...in a test tube (use an oil bath). Try
> the reaction with pure amino acids in various concentrations and then when
> you find an amino acid mix that yields a clear amber liquid, try the same
> concentration of amino acids (the one that worked) with a pinch of sugar
> added. Then tell me what happens when you use an impure mixture of amino
> acids.
>
That experiment has already been done, Art, as I told you in my last post.
The people who did it still got proteinoids. See Fox and Dose for references
and details.
>
> This is an experiment that you can do in an hour. You don't need
> to cite authorities or give references. You can do it yourself.
>
I could, but I don't see why that should be necessary. Unless it is your
claim that the published research is fraudulent, these experiments have
already been done by others, repeatly, over the last 15 years at least.
Heck, even high school students are repeating them.
>
> I have many times, with many different mixtures.
>
And this research is published in what journal? If unpublished you should at
least be able to tell me what results you got. I would also like to see
copies of your research notes on these experiments. I could use them in my
review paper.
>
> I want to hear what you think of
> paleobiogeochemistry when you have done the experiments yourself.
>
I don't understand why that is so important to you. I trust the research
that has already been published in peer reviewed journals and which has been
reproduced by others over the past 30 years. I don't need to reproduce it
all myself to believe it. Based on their results people like Fox, Dose,
Harada, Rohlfing and Matsuno say that it is easy. Why should I doubt them,
especially when I can read their research reports and see for myself just how
easy it is.
>
> There
> are many chemicals, including many amino acids that are unstable at the
> temperatures needed to make polymers.
>
Yes and no. Before the experiments had actually been done, it was assumed,
based on experience with aqueous solutions, that biomicromolecules like amino
acids and nucleotides and sugars were heat labile. (Rohlfing describes it as
a "misconception".) However, the reason why that is true for aqueous
solutions is the high temperatures promote hydrolysis of the micromolecules.
In the absence of water, however, experiment has shown that these
micromolecules are remarkably stable. Both sugars and nucleotides have been
thermally polymerized into polysaccharides and polynucleotides. Amino acids
undergo chemical changes at higher temperature, but these are not
decomposition changes. Instead the amino acids are changing into special
anhydrous derivatives. It is during this process that polymerization takes
place, through a series of steps that regenerates the amino acid form as they
polymerize.
>
> Unless you have glu and asp present
> to melt, the other amino acids will be destroyed by the heat.
>
Actually the amino acids are not destroyed; if they do not polymerize they
simply convert into one of several different kinds of derivatives, which then
aggregate to form the tar. Glutamate and aspartate (and also lysine) happen
to form imide and lactam derivatives that when melted act as a solvent that
stabilizes the structures of the other amino acids and thereby facilitate
polymerization. Glycine by itself can also promote polymerization, but it
does so at lower temperatures by macroscopic solid phase synthesis. Since
every known simulated prebiotic environment produces glycine, glutamate and
aspartate, and most produce lysine, the key amino acids needed to facilitate
polymerization should have been quite common. And since even the amounts
produced in a Miller-style scenario can form proteinoids, proteinoids should
also have been common.:
>
> Of course,
> you can get the reaction to occur no matter what relative perportion of glu
> and asp you have, as long as it is enough to form a melt first that will
> solubilize the other amino acids.
>
That is a key point that needs to be stressed: you don't need to melt amino
acids to get them to polymerize. Rohlfing has shown that thermal
copolymerization of amino acids can occur at temperatures as low as 65
degrees C. It takes longer -- about 80 days to get several grams -- but as
Rohlfing has pointed out time was one commodity the prebiotic earth had in
abundance. Since these temperatures are too low for amino acids to either
decompose or derivitize, your concern regarding stability becomes moot.
Also, at these lower temperatures glycine alone can facilitate
polymerization, and glycine is produced in huge amounts even in the Miller
scenario.
>
> But try leaving them out, and you will
> find out why they have to be there in sufficient quantity to form the
> liquid for the melt.
>
As I said, you don't need to melt amino acids to get them to polymerize.
Also, no one has ever denied that glycine, glutamate, aspartate or lysine
need to be present in order to achieve polymerization. However, since even
very small amounts of glutamate or aspartate will facilitate polymerization,
and since at least two of these four essential amino acids are produced by
any simulated prebiotic scenario so far tested, this requirement is not a
problem.
>
> Again, these are all simple experiments you can do in
> an afternoon, while you are doing your other work. No need to guess.
>
I'm not guessing; I am repeating the results of research published in
peer-reviewed journals, research you continue to ignore.
>
> Try
> mixing all of the chemicals produced in the Miller experiment in dry form
> together and heat to 200 degrees C. That will be a good test of whether it
> is important to use pure amino acids in the proper ratios.
>
That test has already been done, Art; I cited the paper which described it in
my original post. The results are that you still get proteinoids, so you do
not need to use "pure amino acids in the proper ratios" (there is no proper
ratio; any ratio of amino acids will work as long as you have glycine,
glutamate, aspartate or lysine present).
>
> Remember, this is supposed to be easy...it happened so often that it
> generated life, but without chemists or pure chemicals.
>
So far the research has shown that it is indeed very easy.
>
> As to getting the amino acids onto the hot lava for the polymerization
> reaction, no sweat.
>
No one ever said you needed "hot lava"; your are letting your sarcasm make
you silly.
>
> Simply boil away 100,000 to 1,000,000 liters of ocean
> water to get 1 gram of amino acids....
>
Now you are being ridiculous. No one every said you needed to boil away an
entire ocean or even a good part of it. All you would need is for a pond or
a small lake to evaporate, just as ponds or lakes tend to do today in arid
environments. And you don't need a gram of amino acids to make proteinoids.
>
> ...without cooling the rock below 200 degrees....
>
As I explained above the rocks could be as cool as 65 degrees, perhaps even
cooler. But you don't need rocks that are heated geothermally. In deserts
today the sun shining on rocks can heat them up to 90 degrees C.
>
> ...and while preventing rain from washing them back into the ocean
> before you have heated them to 200 degrees for long enough for
> polymerization to occur, but not long enough for them to be carbonized.
>
If the temperature is less than 100 degrees carbonization is not a problem.
As for rain, that is not a problem if you have a seasonal pond in an arid
region subject to alternating wet/dry seasons. If such an area also happens
to have some geothermal activity, so much the better.
>
> But be sure they are all amino acids and no other molecules that might
> start a carbonization reaction leading to tar....
>
Amino acid tar is not produced by carbonization, as I explained above. Amino
acids can thermally polymerize in the presence of sugars, hydrocarbons and
nucleotides, not to mention other organic as well as inorganic material.
Thermal polymerization can occur at temperatures under 100 degrees, thus
eliminating the carbonization problem.
>
> ...and that the ratio is such
> that glu and asp are the predominant forms (remember...no biochemists there
> to control the additions)....
>
There is no need for biochemists. The prebiotic environment by itself would
produce enough aspartate, glutamate, glycine and/or lysine to allow
polymerization. And neither glutamate nor aspartate have to predominate;
amounts less than 1% of total is enough to allow polymerization. Glycine by
itself is enough to allow polymerization.
>
> ...and that the temperature reaches 200 degrees but
> doesn't exceed that by enough to destroy what you have produced.
>
You don't need a temperature of 200 degrees; temperatures between 50 and 125
degrees would be sufficient, and the sun shining on rocks would be enough to
heat them to these temperatures.
>
> Just find me a realistic way to get pure amino acids in high enough
> concentrations in the primitive ocean and we will move on.
>
What's holding us back is that you continue to repeat the same strawman
arguments over and over again because you refuse to acknowledge the research
that refutes your arguments. This last sentence is a case in point. Let me
take each issue one at a time:
Pure amino acids -- The research shows that purity is irrelevent; that amino
acids contaminated by organic and inorganic material can still form
proteinoids.
High enough concentrations -- The research shows that aqueous concentration
is irrelevent; once the water evaporates the dry amino acids will have
infinite concentration.
Primitive ocean -- The research shows that an ocean is unnecessary. All you
need is a pond or small lake, a lagoon, a spring, rain-fed pools; in other
words any body of water that can periodically dry up, leaving behind
anhydrous amino acids that are then baked by the sun until they polymerize, a
body of water that then periodically refills to rehydrate the proteinoids.
Kevin L. O'Brien