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Re: Here's Some More Evidence For You

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Christopher A. Lee wrote:
> 
> On Mon, 07 Mar 2016 21:34:00 -0500, Moses
> <noone@here.not-valid-address> wrote:
> 
> >Christopher A. Lee wrote:
> >
> >>  Moses wrote:
> >
> >> >> >> You looked at it, and perhaps skimmed it. But you didn't read it.
> >
> >> >> >> They metabolised and reproduced.
> >
> >
> >> >> >that flavins may be found in the bubbles and flavins have metabolic activities in living cells,
> >> >> >does not suggest that these bubbles are using flavins to feed themselves. they are not. these
> >
> >> >> What "bubbles" were you lying about?
> >
> >> >the proteinoid microspheres are bubbles,
> >
> >> READ THE PRESENTATION, AND LOOK AT THE MICRO-PHOTOGRAPHS.
> 
> Clearly, you didn't.

> >there's another glaring problem with the relevance of the Fox work. not that it isn't interesting work, but

> >the miller-urey type experiments produces the amino acids glycine and alanine in approximately 2% yield
> >[1.05%] and [0.75%] respectively, depending on the amount of carbon supplied as methane. More complex
> >amino acids such as glutamic acid and leucine are produced in smaller amounts about 0.026% of the total

> So frikking what?

> Fox used a different method of amino acid formation than Miller and
> Urey.

> He produced amino acids using heat and silica sand as a catalyst, not
> an electrical discharge.


and the proportions are generally identical, the reason being that it is in the nature  of the products themselves
and not the exact method for obtaining them. glycine and alanine simply form more readily due to their structures,
and the others, including glutamic and aspartic form in much smaller proportions by these methods.
this is part of the "non-randomness" of the chemistry. 

you may like to peruse this instead of your harbinger presentation

Molecular Evolution and Protobiology
By Matsuno, Dose, Harada and Rohlfing

and that's Kaoru Harada who worked with Fox, he gives a fairly detailed first hand account of the studies in question.



> Modern abiogenesis researchers consider this a more likely way in the
> pre-biotic world. The current favourite theory is that it happened
> around undersea thermal vents, The sea bed provides the sand and the
> vents provide the heat. With currents and tides contributing my moving
> the intermediate products between zones having different temperatures,
> etc.

thermal vents are not 1000 C more about 350 C but 

Stability of Biomolecules at High Temperatures
A thermophilic origin of life is not a new idea. It was first suggested
by Harvey [138], who argued that the first life forms were het-
erotrophic thermophiles that had originated in hot springs such as
those found in Yellowstone Park. As underlined by Harvey, the one
advantage of high temperatures is that the chemical reactions could
go faster and the primitive enzymes could have been less efficient.
However, high temperatures are destructive to organic compounds.
Hence, the price paid is loss of biochemical compounds to decomposition.
Although some progress has been made in synthesizing small
molecules under hydrothermal vent type conditions, the larger trend
for biomolecules at high-temperature conditions is decomposition. As
has been demonstrated by various authors, most biological molecules
have half-lives to hydrolysis on the order of minutes to seconds at
the high temperatures associated with hydrothermal vents. As noted
above, ribose and other sugars are very thermolabile compounds [79].
The stability of ribose and other sugars is problematic, but pyrimidines
and purines, and many amino acids, are nearly as labile. At 100 °C
the half-life for deamination of cytosine is 21 days, and 204 days for
adenine [139,140]. Some amino acids are stable, for example, alanine
with a half-life for decarboxylation of approximately 19,000 years
at 100 °C, but serine decarboxylates to ethanolamine with a half-life of
320 days [141]. White [142] measured the decomposition of various com-
pounds at 250 °C and pH 7 and found half-lives of amino acids from 7.5 s
to 278 min, half-lives for peptide bonds from <1min to 11.8 min,
half-lives for glycoside cleavage in nucleosides from <1s to 1.3 min,
decomposition of nucleobases from 15 to 57min, and half-lives for
phosphate esters from 2.3 to 420 min. It should be borne in mind
that the half-lives for polymers would be even shorter as there
are so many potential breakage points in a polymer. Thus, while
the vents may serve as synthesis sites for simpler compounds such
as acetate or more refractory organic compounds such as fatty acids,
it is unlikely they played a major role in synthesizing most
biochemicals or their polymers.

350°C submarine vents do not seem to presently synthesize organic
compounds, more likely they decompose them in a time span ranging
from seconds to a few hours. Thus, the origin of life in the vents is
improbable. This does not imply that the hydrothermal springs were a
negligible factor on the primitive Earth. If the mineral assemblages
were sufficiently reducing, the rocks near the vents may have been
a source of atmospheric CH4 or H2. As stated earlier, the concentra-
tions of biomolecules which could have accumulated on the primitive
Earth is governed largely by the rates of production and the rates
of destruction. Submarine hydrothermal vents would have also been
important in the destruction rather than in the synthesis of organic
compounds, thus fixing the upper limit for the organic compound
concentration in the primitive oceans. Although it is presently not
possible to state which compounds were essential for the origin of life,
it does seem possible to preclude certain environments if even fairly
simple organic compounds were involved [143].
//////
79. Larralde, R., M. Robertson and S. Miller.
Rates of decomposition of ribose and other sugars:
implications for chemical evolution. Proceedings of
the National Academy of Sciences USA, 92:8158–60, 1995.
138. Harvey, R. Enzymes of thermal algae. Science, 60:481–2, 1924.
139. Garrett, E. and J. Tsau. Solvolyses of cytosine and cytidine.
Journal of Pharmaceutical Sciences, 61(7):1052–61, 1972.
140. Shapiro, R. The prebiotic role of adenine:
a critical analysis. Origins of Life and Evolution
of the Biosphere, 25:83–98, 1995.
141. Vallentyne, J. Biogeochemistry of organic matter.
II. Thermal reaction kinetics and transformation products
of amino compounds. Geochimica et Cosmochimica Acta, 28:157–88, 1964.
142. White, R. Hydrolytic stability of biomolecules
at high temperatures and its implication for life at 250°
C. Nature, 310(5976):430–2, 1984.
143. Cleaves, H. and J. Chalmers. Extremophiles may
be irrelevant to the origin of life. Astrobiology, 4(1):1–9, 2004.
144. Oró, J. Comets and the formation of biochemical
compounds on the primitive Earth. Nature, 190:442–3, 1961.
/////



> And modern abiogenesis researchers still use protocells.


you can use whatever you like, but the Fox experiment is not "natural" for the reasons i have outlined.

and you want amino acids produced in water to majically be ejected from the water
on to some hot surface where they can dry out and form melts in the necessary 
proportions which are not teh proportions found by "natrualistic" experiments.




> >that's an 80 to 1 abundance of glycine and alanine to the rest, which includes glutamic
> >the actual proportions may be even greater.

> So what?

see Harada; the melts must be in proportions that favor glutamic and aspartic acid because those are the ones that actually melt.
but they are also formed "naturally" in much -smaller- amounts. barring a miracle, there is no natural tendency for the proportions
 to pan out as teh Fox experiment would dictate.



> >[from harbinger Fox note] speaking of the decomposition which occurs when you heat amino acids
> >
> >\\\\
> >"We learned that we could avoid the decomposition if we included in the mixture to be heated
> >a sufficient proportion of one or both of two amino acids: aspartic acid and/or glutamic acid."    /lysine also works
> >\\\

> And?

and you get nothing unless glutamic or aspartic or lysine are present in great excess of all the others 
and this is not found in the methods which produce them in the first place.

not natural.



> >this part of the experiment cannot be carried out in aqueous solution because the production
> >of water in the polymerization process makes the reaction non-spontaneous
> >
> >[amino acid] + [amino acid]  <===> [amino acid polymer] + water
> >                                    free energy favors reactants

> Even if that were true, so what?

it is true, that's -why- they use the melts, maybe you should try looking at something else
 -besides- your "simplistic"[your words] presentation at harbinger. these reactions do -not- 
proceed in aqueous solution hot or cold.


> >so, the reason for the excessive proportions of those particular acids is that, aspartic lysine glutamic acids
> >form melts when heated, and the melts constitute the solvent system where the other amino acids may form co-polymers
> >with the solvent system. meaning when you form a melt with aspartic lysine or glutamic acids you can then dope in
> >other amino acids and the reaction proceeds in a 'non-aqueous' environment/solvent system.

> >glycine alanine and all the rest do not form melts.

> And?

and if you do Not have excessive amounts of glutamic or aspartic you do Not get the melts which are the non-aqueous solvent system.


> >trouble here is that the "natural" abundance of amino acids formed by the electrical discharge experiments
> >show a glaring =poverty= of the amino acids that form melts, and which must be employed in =excess= proportion
> >in the Fox experiment.

> THAT'S NOT HOW HE GOT THE AMINO ACIDS, imbecile.

look it up, you get essentially the same proportions.

mostly alanine and glycine and much more trace proportions of glutamic and aspartic and all the rest.
they a few more amino acids apparently, but the major projucts and major proportions didn't change.


> >so, our "experimenter" must step in and alter the natural abundance to get his experiment to proceed.

> Fox had thermal proteins _before_ he and his team discovered that the
> mixture required aspartic and/or glutamic acid. This was the result of
> investigating why some of the mixtures _didn't_ produce thermal
> proteins while others did.

most didn't because most amino acids do not form melts. the ones that reacted were teh ones that formed melts.
and they did Not just take a raw sample from the production experiments and start heating it up, they did experiments that produced amino acids
and then did separate experiments in heating dried amino acids that they had refined and sorted  out.


> >these proportions are not "natural" as shown from the electrical discharge experiments and so,
> >nullify the Fox experiment as not a naturalistic reproduction of pre-biotic chemistry.

> Even if that were true, so what?

it is true, the proportions are altered to fit the necessities of the second experiment.


> What you don't seem to grasp, is that this does not actually matter.
> Because three billion years after the earliest life appeared, we don't
> know exactly what the pre-biotic chemistry was, we can only guess.


so now we're back to "i don't know but i insist this happened anyway cuz if suits my fantasies" routine


> This research does, however, show that life can form naturally.

does not, it shows how an experimenter can take dried amino acids and manipulate the proportions to such an extent 
that a reaction will occur that =probably= will not take place under purely "natural" conditions.

see, i said "probably" because it's possible some unseen hand interfered just like your experimenter




> >> >and another trouble is, the starting materials which are clean dried purified amino
> >> >acids in very specific proportions do not occur "naturally" and you have to rig
> >> >the experiment and then make up stories after the fact to make those conditions
> >> >conform to some imaginary earth conditions.

> >> Where did the presentation say anything about "clean, dried, purified
> >> amino acids in specific proportions?

> >the initial part of the experiment is carried out by heating dried amino acids in a melt,
> >because the reaction doesn't go in aqueous solution. there's your "dried" part;

> Where did the presentation say that?

if we must confine ourselves to that "simplistic" presentation, then you do not get to insinuate that these bubbles manipulated nucleic acids
because that is nowhere to be found in your simplistic presentation.


> Hint: it didn't.

see Kaoru Harada book, he's a bit more detailed.


> >and as he says;

> >"We learned that we could avoid the decomposition if we included in the mixture to be heated
> >a sufficient proportion of one or both of two amino acids: aspartic acid and/or glutamic acid."

> >a "sufficient proportion"

> And?

and they set the experiment up using unnatural proportions


> >in other words, he has to rig the proportions to get a favorable result and in this case,
> >the proportions do not match the proportions of the miller-urey and herrera type experiments.


> He already had thermal proteins _before_ he investigated why some
> mixtures worked and others didn't.



> Why do you imagine experiments like Herrera's, Miller's and Urey's,
> and Fox's always yielded exactly the same mixture in exactly the same
> proportions?

because it is the ease of formation of some amino acids over the others as they are Not "random" some of
 the amino acids form more readily than others because of =their= structures alanine and glycine are in 
the "most readily formed" category and aspartic and glutamic are in teh "much less readily formed category
but, in the -second- part, the heating of the dried acids, these natural abundances are reversed and altered to fit.
a nifty bit of gesticulation and prestidigitation, to be sure, but "not natural" to also be certain.


> >fails the "natural" test.

> Even if that were true, so what?

be=cause= these experiments -claim- to be trying to mimic the naturally occuring event sequences.

> Nobody is insisting that it actually happened this way more than three
> billion years ago. That would take a time machine.

 it certainly isn't a "natural" representation as it would claim to be.

it's not just the preporturous notion that amino acids will be formed in water and be in some sort of "soup" can,
and then, be vomited up onto the dry land and have the water driven off in a cool place so as not to destroy 
the molecules, and then, the neatly dried acids, sit and wait for the sun to bake them into a melt wherupon 
-rain- water, hot rain water, that must have a certain ionic strength as found in -sea water- washes out 
the proteinoids forming microspheres but yet manages to also provide this wonderful "soup" can of "nutrients"
 and phosphates and ATP   and they all lived happily ever after.

remember to start your stories with "once upon a time"

at least themn i'll be able to eat my milk and cookies and fall asleep to the neat bedtime stories.

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Re: Here's Some More Evidence For You Moses <moses@sinai.55> - 2016-03-05 20:14 -0500
  Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-05 20:18 -0600
    Re: Here's Some More Evidence For You Gordon <gordonlr@swbell.net> - 2016-03-05 20:36 -0600
      Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-05 20:49 -0600
        Re: Here's Some More Evidence For You "%" <persent@gmail.com> - 2016-03-05 19:52 -0700
    Re: Here's Some More Evidence For You Moses <moses@sinai.6y> - 2016-03-05 22:48 -0500
      Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-05 22:44 -0600
        Re: Here's Some More Evidence For You Moses <moses@sinai.56> - 2016-03-05 23:48 -0500
          Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-05 23:38 -0600
            Re: Here's Some More Evidence For You Moses <moses@sinai.56> - 2016-03-06 02:51 -0500
              Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-06 02:03 -0600
                Re: Here's Some More Evidence For You Moses <moses@sinai.56> - 2016-03-06 03:25 -0500
                Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-06 09:45 -0600
                Re: Here's Some More Evidence For You Moses <moses@sinai.54> - 2016-03-06 11:58 -0500
                Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-06 14:31 -0600
                Re: Here's Some More Evidence For You Moses <noone@here.not-valid-address> - 2016-03-07 21:34 -0500
                Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-08 01:14 -0600
                Re: Here's Some More Evidence For You Moses <noone@here.not-valid-address> - 2016-03-08 03:13 -0500
                Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-08 04:35 -0600
                Re: Here's Some More Evidence For You Moses <noone@here.not-valid-address> - 2016-03-08 06:10 -0500
                Re: Here's Some More Evidence For You Moses <noone@here.not-valid-address> - 2016-03-08 06:48 -0500
                Re: Here's Some More Evidence For You Moses <noone@here.not-valid-address> - 2016-03-08 07:42 -0500
                Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-08 10:41 -0600
                Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-08 10:30 -0600
                Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-08 10:29 -0600
                Re: Here's Some More Evidence For You Malte Runz <noyouare@notgetting.it> - 2016-03-09 01:12 +0100
                Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-08 19:18 -0600
              Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-06 18:00 -0600
      Re: Here's Some More Evidence For You Moses <moses@sinai.56> - 2016-03-05 23:44 -0500
  Re: Here's Some More Evidence For You Malte Runz <forget@it.nw> - 2016-03-06 12:01 +0100
    Re: Here's Some More Evidence For You Moses <moses@sinai.56> - 2016-03-06 07:29 -0500
      Re: Here's Some More Evidence For You Smiler <smiler@jo.king> - 2016-03-06 19:20 +0000
        Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-06 13:56 -0600
          Re: Here's Some More Evidence For You Gordon <gordonlr@swbell.net> - 2016-03-06 14:27 -0600
            Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-06 14:35 -0600
        Re: Here's Some More Evidence For You Gordon <gordonlr@swbell.net> - 2016-03-06 14:33 -0600
          Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-06 14:47 -0600
          Re: Here's Some More Evidence For You Smiler <smiler@jo.king> - 2016-03-07 20:23 +0000
      Re: Here's Some More Evidence For You Malte Runz <noyouare@notgetting.it> - 2016-03-06 20:53 +0100
        Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-06 14:07 -0600
        Re: Here's Some More Evidence For You Moses <noone@here.not-valid-address> - 2016-03-07 22:17 -0500
          Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-08 01:20 -0600
          Re: Here's Some More Evidence For You Jeanne Douglas <hlwdjsd2@NOSPAMgmail.com> - 2016-03-07 23:37 -0800
          Re: Here's Some More Evidence For You Malte Runz <noyouare@notgetting.it> - 2016-03-08 23:15 +0100
            Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-08 16:56 -0600
      Re: Here's Some More Evidence For You Cloud Hobbit <youngblood2949@gmail.com> - 2016-03-08 17:22 -0800
        Re: Here's Some More Evidence For You "%" <persent@gmail.com> - 2016-03-08 18:25 -0700
    Re: Here's Some More Evidence For You Jeanne Douglas <hlwdjsd2@NOSPAMgmail.com> - 2016-03-06 05:07 -0800
      Re: Here's Some More Evidence For You Malte Runz <noyouare@notgetting.it> - 2016-03-06 17:08 +0100
        Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-06 11:00 -0600
    Re: Here's Some More Evidence For You Christopher A. Lee <c.lee@fairpoint.net> - 2016-03-06 09:50 -0600
      Re: Here's Some More Evidence For You Malte Runz <noyouare@notgetting.it> - 2016-03-06 23:01 +0100
        Re: Here's Some More Evidence For You Don Martin <drdonmartin@comcast.net> - 2016-03-07 18:30 -0500

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