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Author Topic:   Murchison Meteor Questions
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 183 of 216 (423526)
09-22-2007 5:48 PM
Reply to: Message 177 by Rob
09-22-2007 2:03 PM


Re: The acid test.
I was then trying to find out if anhydrous reduction was equivilant to hydrolyisis. I read all kinds of papers. then I thought, 'Wait a minute... what is that other 5%?'
Hydrolysis may still be an issue...
After asking you about it, I then pointed out that the 95% formic acid obtained from Sigma-Aldrich is indeed 5% water. I figure you found that out before I did, since you didn't respond. Why didn't you or Percy come forward with that information? I suppose I shouldn't assume you knew...
Actually I knew the acid was mixed with water, but I was not concerned about it. There is no hydrolysis in 95% formic acid, because there are no free water molecules in the 95% formic acid solution, or did you not comprehend the point in Message 175:
Sulfuric acid - Wikipedia
quote:
The reaction is best thought of as forming hydronium ions, by
H2SO4 + H2O ’ H3O+ + HSO4-,
and then
HSO4- + H2O ’ H3O+ + SO42-.
Because the hydration of sulfuric acid is thermodynamically favorable, sulfuric acid is an excellent dehydrating agent, and is used to prepare many dried fruits. The affinity of sulfuric acid for water is sufficiently strong that it will remove hydrogen and oxygen atoms from other compounds;
In a "95% Sulfuric Acid" what you would actually have is an ion mixture composed of roughly
  • 92.5% pure Sulfuric Acid (H2SO4 in ion form: H+ + HSO4- + SO42-)
  • 7.5% H3O+ + SO42-
  • 0.0% pure water (either as H2O or ionized as H+ + OH-)
    Similar reactions occur in all concentrated acids (but may be one stage instead of two), and will continue to occur until the acid has fully reacted with the water. After that water molecules will be freely available for hydrolysis of other molecules.
    What part about sulfuric acid being used to suck water out of fruit makes you think there would be water available for hydrolysis? Formic acid at 95% concentration is not much different:
    Formic acid - Wikipedia
    quote:
    Safety
    The hazards of solutions of formic acid depend on the concentration. The following table lists the EU classification of formic acid solutions:
    Concentration
    by weight Classification R-Phrases
    2%-10% Irritant (Xi) R36/38
    10%-90% Corrosive (C) R34
    >90% Corrosive (C) R35

    Avantor is setting science in motion for a better world | Avantor
    quote:
    Safety data for formic acid
    Stability
    Stable. Substances to be avoided include strong bases, strong oxidizing agents and powdered metals, furfuryl alcohol. Combustible. Hygroscopic.
    R34 Causes burns.
    R35 Causes severe burns.
    And just for clarification in case you don't have the picture yet:
    hy·gro·scop·ic -adj. Readily absorbing moisture, as from the atmosphere.
    The 95% formic acid is not going to be making water available to be used for hydrolysis, rather it is going to be absorbing any extra moisture it can find.
    Seriously Rob. Let me repeat again: you do not have any hydrolysis in the 95% formic acid extraction. The water that was mixed with the acid to stabilize it is not water in the solution that remains.
    Again, you fail to explain the existence of adenine, hypoxanthine and xanthine in the extract solution.
    Enjoy.
    Edited by RAZD, : safety class

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  • This message is a reply to:
     Message 177 by Rob, posted 09-22-2007 2:03 PM Rob has replied

    Replies to this message:
     Message 184 by Rob, posted 09-22-2007 6:56 PM RAZD has replied

      
    RAZD
    Member (Idle past 1405 days)
    Posts: 20714
    From: the other end of the sidewalk
    Joined: 03-14-2004


    Message 187 of 216 (423550)
    09-22-2007 8:45 PM
    Reply to: Message 184 by Rob
    09-22-2007 6:56 PM


    Re: The acid test.
    Settle down Rob.
    What's this from Robert shapiro?
    The isolation of adenine and guanine from meteorites has been cited as evidence that these substances might have been available as "raw material" on prebiotic Earth (18). However, acid hydrolyses have been needed to release these materials, and the amounts isolated have been low (17-19).
    ( Just a moment... )
    Don't you mean Prebiotic cytosine synthesis: A critical analysis and implications for the origin of life? The other article is not by Shapiro.
    This article is all about Cytosine and only has the one paragraph on adenine. You remember that the experiment involved both formic acid and hydrolysis.
    That is the comparative study done and referenced by Glavin also:
    It is important to emphasize that the purines identified in formic acid extracts of Murchison were not detected in water extracts [4]. This suggests that the purines are either bound to other organics, or were produced (e.g. oligomerization of HCN) during acid extraction.
    And his footnote 4: [4] Stoks P. G. and ...
    From http://www.lpi.usra.edu/meetings/lpsc2004/pdf/1022.pdf
    Old stuff, Rob. Followed directly by:
    quote:
    Although a previous study has shown that the synthesis of adenine from HCN in acid is highly temperature dependent and inefficient at 100C [8], we cannot rule out the possibility that some purines may have been synthesized during formic acid extraction of Murchison. We found that in previous formic acid extraction and sublimation experiments using pure nucleobase mixtures, thermal deamination of the nucleobases did not occur [5].
    If you remember, this means that you might get adenine but you would not get it degrading to hypoxanthine and xanthene, you need hydrolysis to get the degrading, and you do not have hydrolysis in the half sample that we are talking about.
    The issue is that you cannot get both adenine AND hypoxanthine or xanthene from this process.
    I am sorry to be messing with you Razd, but I simply do not understand the tone.
    What tone? Yours? The biggest problem Rob is that you keep going over old territory as if you haven't understood a single part of it.
    You chastise Percy for taking up precious posts when 50% of the posts (or more) are your repeated assertions that amount to a hill of beans. That bit about self-replicating molecules being due to an intelligent design and unnatural was a particularly amusing waste of time on your part.
    To repeat:
    Message 119 (to Percy)
    The experiments on Murchison, Murray, Orgueil, and Tagish meteors show that either adenine was there on Murchison, Murray, and Orgueil, OR that the materials needed for the ready formation of adenine with a simple acid bath (similar to the extraction process) were on the Murchison, Murray, and Orgueil meteors but not on Tagish.
    Rob has essentially conceded this point:
    Message 45
    Further, IF it was formed, THEN there were still the molecules from which it was formed available for the formation of adenine.
    Now that I can agree with...
    and
    Message 65
    That is true... And good evidence to support the potential of adenine undiscovered. But it still doesn't preclude the adenine from being synthesized rather than extracted.
    And we still don't know how the unknown material, or unique composition of substances in the meteor would affect the reactions, if at all.
    Material that was shown to be "adenine-phylic" enough to prevent extraction of adenine with water, and material from which, logically, the adenine was synthesized IF it did not exist as complete adenine molecules, as the extraction process chemicals (formic acid, for example) are inadequate for forming adenine on their own.
    Which is when you started pulling the nonsense that 5% water in the 95% concentrated formic acid could cause the degradation of adenine into hypoxanthine and xanthine.
    Message 142
    You still end up with these two possibilities:
    (1) adenine is\was present on the meteor and it is degrading into hypoxanthine, and xanthine, the extraction process also causes degradation, OR
    (2) adenine is produced by the extraction process -- from compounds like hypoxanthine, and xanthine -- which at the same time is degrading the adenine it just made into hypoxanthine, and xanthine ... (see any problem here?).
    Given the results of the three different processes noted above, I'll stick with my previous conclusions: the existence of hypoxanthine, and xanthine on the meteor can be taken as evidence that adenine used to be on the meteor in greater quantity than today; that it is extremely highly unlikely that the extraction process both synthesized and degraded adenine ... leading to the conclusion that adenine was on the meteor in the past if it is not there today.
    What I am saying, as I did in the OP:
    ... is that you haven't learned much of anything, or made a point that has not been evident from the start:
    Either adenine existed on the meteor
    OR
    It was easily synthesized from molecules on the meteor.
    In EITHER case adenine was available for pre-biotic earth.
    This has been established since Message 42.
    You in fact concede the point in Message 45 (see above) and again here:
    Message 177
    Can you definitively say that there was absolutely no adenine on the meteor?
    Can you definitively say that there was absolutely no hypoxanthine on the meteor?
    Can you definitively say that there was absolutely no xanthine on the meteor?
    Can you definitively say that these molecules were produced during the process?
    Of course not!
    So stop beating around the bush and accept the results:
    Either adenine existed on the meteor
    OR
    It was easily synthesized from molecules on the meteor.
    In EITHER case adenine was available for pre-biotic earth.
    Or are you going to go around the whole sturm und drang again? You're not questioning Rob, your spinning your wheels trying to find traction for a position that is not supported by the evidence (and not supportable by the evidence, because it relies on the evidence not being there).
    Enjoy.
    Edited by RAZD, : sp

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    This message is a reply to:
     Message 184 by Rob, posted 09-22-2007 6:56 PM Rob has replied

    Replies to this message:
     Message 188 by Rob, posted 09-22-2007 9:06 PM RAZD has replied

      
    RAZD
    Member (Idle past 1405 days)
    Posts: 20714
    From: the other end of the sidewalk
    Joined: 03-14-2004


    Message 189 of 216 (423559)
    09-22-2007 9:28 PM
    Reply to: Message 188 by Rob
    09-22-2007 9:06 PM


    Moving on then ...
    RAZD writes:
    OR
    It was easily synthesized from molecules on the meteor.
    I have no problem accepting that. That is precisely what happened as far as I can tell.
    If that is the case, then the discussion moves on to the problems with the atmospheric models to accomplish the synthesis.
    OR adenine existed on the meteor and synthesis on earth is not necessary.
    However, IF synthesis from HCN rings and polymers similar to hypoxanthine and xanthine in an kerogen-like organic polymer matrix that were delivered by the meteors needs to be done with an acid bath, there are many such available on the surface of the earth today -- in spite of the earth now having an oxidizing atmosphere, and so should be even less of a concern for a pre-biotic earth.
    From Message 14
    quote:
    Does this mean we have no source of acidic environments on earth? We can look at sources of natural acid in todays world to see what they could be like and how prevalent they could be. A google on "acid springs" presents a prolific list of sites, from which I picked (you'll see why):
    UW Bacteriology | Error page
    quote:
    Life at High Temperatures
    by Thomas D. Brock
    Each hot spring is unique. Even springs that look the same differ in characteristics such as temperature, flow rate, and chemistry of the water. One chemical property is so important that it has great influence on the kinds of organisms present: the acidity of the water. Some springs, such as those at Norris and Mud Volcano have very acid, sour-tasting water. They contain sulfuric acid, derived from the sulfur-rich gases emanating from the earth. Acid springs are usually concentrated in special basins, such as that of Sylvan Springs shown below, an important feature at the west end of Gibbon Meadow.
    The microorganisms in the acid springs are entirely different from those in the neutral to alkaline springs. Indeed, the organisms of acid hot springs have two environmental hurdles to overcome, high temperature and acidity. These organisms, called thermoacidophiles, are probably derived from some of the first organisms that arose on this planet.
    ... Most acid springs in Yellowstone have pH values between 2 and 4, and the neutral/alkaline springs have values mostly from 7 to 9. ...
    We also see that the "extremophiles" found in these hot springs are probably closely related to the first kinds of life, and they do not use oxygen in their energy cycle so they could survive in the early atmosphere\environment.
    These hot springs are of geo-thermal origin, a process that was ongoing on early earth up to the period of meteoric impact.
    This would easily replicate what happened during the extraction process of the experiment, thus resulting in adenine being available.
    Piece of cake. Time to move on?
    Enjoy.
    ps -- use less keystrokes: type [qs=RAZD]quotes are easy[/qs] and it becomes:
    RAZD writes:
    quotes are easy
    tip-of-the-day from your friendly neighborhood evilootionist.

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    This message is a reply to:
     Message 188 by Rob, posted 09-22-2007 9:06 PM Rob has replied

    Replies to this message:
     Message 191 by Rob, posted 09-22-2007 10:11 PM RAZD has replied

      
    RAZD
    Member (Idle past 1405 days)
    Posts: 20714
    From: the other end of the sidewalk
    Joined: 03-14-2004


    Message 193 of 216 (423572)
    09-22-2007 11:18 PM
    Reply to: Message 191 by Rob
    09-22-2007 10:11 PM


    Re: Moving on then ...
    razd writes:
    OR adenine existed on the meteor and synthesis on earth is not necessary.
    So you are having a hard time making up your mind?
    Nope, just being sure that both options are fully represented. You can't say the results are {a} or {b} now let's look at only {b} ... (wasn't that your whole point?).
    Razd:
    This would easily replicate what happened during the extraction process of the experiment, thus resulting in adenine being available.
    Unfortunately the same processes that synthesize it, would hydrolyze it further. You need a near neutral pH for stability, and a great deal more adenine than we're discussing here.
    No, you don't need to cover the earth with adenine, you only need adenine in the right place at the right time. Once you have a life process it can produce its own (as you have observed). Apparently it took up to 1 billion years for life to form. Now we know of at least one mechanism for producing adenine.
    And even if there was an explanation (which there is not), it takes more than adenine to make an organism. We've not yet even scratched the surface of this problem. That's just the way it is...
    There is a lot we don't know, but that does not make the task impossible. But as we have seen with the Murchison meteor there is more information every year.
    Let's leave the rest for another thread. It's more than off topic here.
    I thought you were done: adenine available directly or indirectly due to meteor delivery from space does result in adenine on earth.
    Message 1
    In molbiogirl's last post of the thread she repeated the claims (that turn out to be plentiful) that adenine has been found in the Murchison meteor. I wish to challenge that claim.
    So what’s the deal with Murchison? In my opinion, the complex mixture of compounds and the unknowns about Murchison make quantifiable and accurate results questionable. There is much that remains a mystery. For those who have broad interest in constraining the issue and finding adenine . It’s not time to celebrate yet.
    Answer: adenine is available directly or indirectly due to meteor delivery from space.
    Enjoy.

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    we are limited in our ability to understand
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    This message is a reply to:
     Message 191 by Rob, posted 09-22-2007 10:11 PM Rob has replied

    Replies to this message:
     Message 194 by Rob, posted 09-22-2007 11:24 PM RAZD has replied

      
    RAZD
    Member (Idle past 1405 days)
    Posts: 20714
    From: the other end of the sidewalk
    Joined: 03-14-2004


    Message 195 of 216 (423578)
    09-22-2007 11:36 PM
    Reply to: Message 194 by Rob
    09-22-2007 11:24 PM


    Re: Moving on then ...
    What does that have to do with adenine on the Murchison meteor?
    Enjoy.

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    we are limited in our ability to understand
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    RebelAAmericanOZen[Deist
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    This message is a reply to:
     Message 194 by Rob, posted 09-22-2007 11:24 PM Rob has replied

    Replies to this message:
     Message 196 by Rob, posted 09-22-2007 11:48 PM RAZD has replied
     Message 197 by Rob, posted 09-23-2007 12:49 AM RAZD has not replied

      
    RAZD
    Member (Idle past 1405 days)
    Posts: 20714
    From: the other end of the sidewalk
    Joined: 03-14-2004


    Message 200 of 216 (423636)
    09-23-2007 12:33 PM
    Reply to: Message 196 by Rob
    09-22-2007 11:48 PM


    Just the logical fallacy for now
    If artificial synthesis of amino acids results in racemic mixtures, and the extracts of Murchison are the same. Then it lends further credence to the position that the adenine was synthesized rather than extracted.
    All A is B
    B
    Therefore A
    This is a logical fallacy Rob, because there is B that is notA.
    The evidence is that adenine and other prebiotic chemicals are synthesized by natural chemical processes in space, and because they are natural chemical processes like the "artificial synthesis of amino acids" they too would result in racemic mixtures.
    If you had said all natural non-biological chemical synthesis reactions result in racemic mixtures you would have been much closer to the truth. Did you actually read your own article where they explain this?
    Enjoy.
    ps - for the record:
    You don't remember avoiding this already in my message Message 45?
    (modified to provide link to msg - use "peek" to see how)
    I remember saying that chirality was not a big issue in Message 29.
    Why not start a new thread on chirality?

    This message is a reply to:
     Message 196 by Rob, posted 09-22-2007 11:48 PM Rob has replied

    Replies to this message:
     Message 201 by jar, posted 09-23-2007 12:43 PM RAZD has not replied
     Message 202 by Rob, posted 09-23-2007 4:21 PM RAZD has replied

      
    RAZD
    Member (Idle past 1405 days)
    Posts: 20714
    From: the other end of the sidewalk
    Joined: 03-14-2004


    Message 203 of 216 (423685)
    09-23-2007 5:32 PM
    Reply to: Message 202 by Rob
    09-23-2007 4:21 PM


    Yeah, I read it for the third time after putting out here for you again. It made me realize that chiralty in amino acids has little or nothing to do with purines like adenine.
    That's why I said forget it in my second response a bit ago. I began to realize it was comparing apples and oranges. It may be worth discussing in another context, but not as it regards purine extractions of Murchison.
    So discuss it at The Recurrent Problem of Chirality. Note the purines attach to D- chiral sugar in making DNA ...
    Chiralty appears to be irrelevant to Murchison extractions of adenine.
    So are we done here? Time for summary of positions?
    Enjoy.

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    we are limited in our ability to understand
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    RebelAAmericanOZen[Deist
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    to share.

    This message is a reply to:
     Message 202 by Rob, posted 09-23-2007 4:21 PM Rob has replied

    Replies to this message:
     Message 204 by Rob, posted 09-23-2007 5:48 PM RAZD has not replied

      
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