Murchison Meteor Questions

Um, try actually reading the article.Here's what they say:

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We have also investigated the hydrolysis of the supernatant at pH 8, which is a more reasonable model of primitive oceanic conditions, and found that the adenine yield is comparable to that obtained with acid hydrolysis (approximately 0.1%).

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This means that they did a hydrolosis at pH 8 for adenine, and the adenine yield (how much they got) at this pH was comparable to the amount of adenine they got when performing the hydrolosis with an acid solution of .1%.So no, it does not take a 95% formic acid solution to hyrdolize adenine.

Kuresu:Yeah... duh again!

Kuresu:Uh, I think they mean that the adenine yield is .1%But you're right, it doesn't take 95% formic acid to hydrolyze (watch your spelling, it's not hyrdrolyze ) but lower pH (higher concentrations) yeild more adenine faster and also degrade it.Do I have that right?Edited by Rob, : No reason given.

Does the part where they state that a pH of 8 yielded a comparable amount of adenine to the higher acidic solution they were using confuse you?That is, they state:
pH of 8 = comparable yield
lower pH (higher acidity) = ~ 0.1% yieldYou're right with the the percentage being yield instead of acid concentration.Also, the abstract states that shorter hydrolytic periods give higher yields of adenine (less time for adenine to be degraded) if done with a solution that has high acidity (such as with 6 N HCl).With a pH of 8, longer hydrolytic periods do not appreciably decrease the yield because adenine is more stable.In that sense you may be right. However, cut down the period of hydrolosis (in a solution with high pH, of course) and you can get higher yields than either the solution of ph 8 or the short period of hydrolosis.By the way, if you're going to quote my single misspelling, at least misspell it properly. I typed "hyrdolize", not "hyrdrolize".

Let's review again.http://www.lpi.usra.edu/meetings/lpsc2004/pdf/1022.pdf

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Sample Preparation and Sublimation Experiments: A powdered sample of the Murchison meteorite (104 mg) was sealed in a clean test tube with 1 mL of 95% formic acid (Sigma-Aldrich) and incubated in a heating block set at 100C for 24 h.

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HPLC Results and Discussion: Prior to sublimation heating, the Murchison formic acid extract eluted as several small HPLC peaks with retention times similar to adenine, guanine, hypoxanthine, and xanthine, and possibly uracil (Fig. 1a). A large unidentified peak in the chromatogram with a retention time of ~ 5 min and showing significant tailing, made it difficult to accurately quantify these nucelobases, especially uracil, in the Murchison formic acid extract. However, this large non-volatile organic component was removed after sublimation of the Murchison formic acid extract at 450C and peaks corresponding to adenine, hypoxanthine, xanthine and uracil were readily identified (Fig. 1c).

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Table 1. Recovery of Nucleobases from Murchison
Meteorite Formic Acid Extracts (in ppb).
Nucleobase     This Study*    Schwartz [3,4]
--------------------------------------------
Adenine            204             267
Cytosine          < 11        < 30,000
Thymine          < 255             < 3
Guanine           < 16             234
Uracil             145              63
Hypoxanthine       232             215
Xanthine           356             530
*sublimed at 450C for 5 min

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Not hydrolyzed, not subject to high HCl conditions that cause observed degradation of adenine. Identified adenine, hypoxanthine, and xanthine, both before and after sublimation at 450.The only processing involved is the 24 hours in 95% formic acid, and you are suggesting that this process both formed AND degraded adenine. Put it together and took it apart.Enjoy.Edited by RAZD, : .

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Razd:Well of course!After all of the ground we covered???I see that we must endure more revisiting of the criticism. Well I suppose it is a good time for a summation thus far...The paper in question: http://www.lpi.usra.edu/meetings/lpsc2004/pdf/1022.pdfGlavin and Bada: Right there, you have the three problems with these extractions:1. heat

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2. pH

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3. further hydrolysis of adenine and guanine to produce hypoxanthine and xanthine.I can sum all of those problems in one question: How long was the sample exposed to the very low pH level associated with a 95% solution concentration of formic acid, while it was mixed, sealed, and before being placed in the heating block?1. The temperature in the heating block is irrelevant.Glavin and Bada: They tell us that adenine synthesis from HCN is innefficient at 100C. But they leave out the fact, that adenine synthesis is independant of temperatures between -80C and 100C (the temperature range that the sample would have been while being mixed, sealed and put into the heating block). The amount of time in question here, must be known, if the results are to be thoroughly peer reveiwed.Notice that HCN is an abbreviation for NH4CN below...Here is the relevant work by Miller that adresses the temperature and hydrolysis: ( http://exobio.ucsd.edu/miller_99.htm )2. The pH and ammount time given for hydrolysis. [qs]The original studies by Or and Kimball (1961) showed that the 6 N HCl hydrolysis of the NH4CN polymerization supernatant greatly increased the adenine yield. However, this hydrolysis also decomposes adenine and other purines. Therefore, we have measured the yields from an NH4CN polymerization as a function of hydrolysis time, and found that shorter hydrolytic periods give higher yields of adenine. We have also investigated the hydrolysis of the supernatant at pH 8, which is a more reasonable model of primitive oceanic conditions, and found that the adenine yield is comparable to that obtained with acid hydrolysis (approximately 0.1%). The yield of adenine does not decline at longer hydrolysis times because of the greater stability of adenine at pH 8.[qs] ( An Investigation of Prebiotic Purine Synthesis from the Hydrolysis of HCN Polymers - NASA/ADS )To answer one of your questions Razd, the relevant issue here is the pH, not the type of acid used. Both Hydrochloric acid HCL and Formic acid HCOOH have the hydrogen available for hydrolysis of NH4CN HCN to produce adenine.So although adenine quickly synthesizes at lower pH levels (high concentrations), the yield is low because of the continued hydrolysis of the purines, which leads us to criticism #3.3. Hydrolysis of adenine and guanine into hypoxanthine and xanthine.Glavin and Bada:Now that is very interesting, because footnote [5] will take you to another paper by Glavin and Bada: http://astrobiology.gsfc.nasa.gov/Glavin_PSS.pdfNote that the paper get's results only from E Coli cells, but nothing from the murchison tests: But, in that paper is the following: Ain't much to glean from footnote [5]. And it says noting about formic acid being used to prepare the samples. It actually refers to sample prep as pertaining to sodium hydroxide NaOH, which is a stong alkaline.The answer to this issue of the presense of hypoxanthne and xanthine is very simple; they are the bi-products of the hydrolysis of adenine and guanine respectively. And that is what we would expect from a strong acid concentration such as 95% formic acid, and 6 N HCL.So just as was said in our other paper above: Here is what Stanley Miller had to say in 1998: ( Just a moment... )Glavin and Bada make it out to be about thermal deamination durring sublimation. But the issue is hydrolysis and pH before being put into the heating block, not durring incubation or sublimation.There are some big problems with the Murchison extractions!Which brings a 4th criticism...Was this paper peer reviewed? Or does it take a truck driver with a high school education, to do a thorough and objective job of moderating the work of men with 'doctorates'?Buyer beware... there's a whole lot of selling going on in pre-biotic chemistry... but there's no engine under the hood.

Can you not read? Once they put the extract in the test tube and sealed it it went straight into the incubator. By the way, there was no mixing. More reading comprehension problems. Tell me, is 100C the same as between -80C and 100C? No, it's not. 100C is just outside that range. The key word here is between. This means that yield of adenine is independent of tempurate when T is -79 to 99 degrees centigrade. So far, no problem. {ABE: actually, there is a problem. See following post by Percy explaining the difference between HCN and NH₄CN /ABE}Your next statement is a little odd. It is known. As soon as the sample was prepared, it was placed into the incubator. Now then, since time of hydrolosis and pH are the only variables at this stage (before being placed into the incubator), and given that we know that short periods of hydrolosis actually increase the yield, what else could the result be but a potentially higher yield of adenine (though this would be very slight, if at all, due to the lack of time from when the mixture was prepared to when it was placed in an incubator. I'd say 2 minutes max, probably less to put all the pieces together).By the way, you're quoting the wrong study by Miller. What you have is something from 99. This is the study my Miller that they cite:
Just a moment...
Just a moment... (pdf full text) And that's your problem. Rob--this stuff is mostly above my head. I've had more education on this that you have. I can get a hell of a lot more education if I really wanted to. So what makes you think that you can really challenge these people? How can you be sure you aren't screwing things up? And you have, remember? Like when you said a high pH was an acid, or that high concentrations lead to high pH levels (or something similar), or like when you claimed satellites don't exist in nature (which would remove the earth and the moon from existence, and yet here they are). Just in this post you have several mistakes--you quote the wrong source (though you have the right paper later on, oddly enough), and you claim the sample was mixed, when there is nothing in that paper to suggest they were mixed. Any review you do wouldn't qualify as peer review. Review, yes, peer, no.I'll leave the rest of this (and more of the same, no doubt) to RAZD.Edited by kuresu, : No reason given.

I don't think so. HCN is hydrogen cyanide, while NH₄CN is ammonium cyanide. Miller writes that the production of adenine from NH₄CN is independent of temperature between -80^oC and 100^oC, while Glavin and Bada write that the production of adenine from HCN is highly temperature dependent and inefficient at 100^oC. While many origin of life researchers believe that HCN played a key role, Miller speculates that NH₄CN might be a more likely candidate because it produces adenine more efficiently than HCN.But the main point is that you're comparing apples and oranges. HCN and NH₄CN have different properties. Yesterday you didn't know whether an acid is low or high pH, and today you're qualified to perform peer-review of technical papers on prebiotic chemistry? The effort you're making to understand these technical papers is admirable, but I think you can save yourself a lot of time and effort if you recognize that you're attempting the impossible, proving a negative. Even if you prove that it was utterly impossible for any adenine whatsoever to have ever come from the Murchison meteorite either directly or indirectly, you've only got all the rest of the possible sources of adenine left to eliminate, both those we're aware of and those not yet known.Even if science is forced to finally give up and admit that it just can't figure out where adenine came from, an answer of "I don't know" is not evidence of God.You see, conclusions aren't reached from what we don't know. They're reached from what we do know. You won't find God in missing adenine. If you want evidence of God, seek it in something he did.--Percy

Rob, look again. Step (3) only applies to half the sample. I am talking about the other half that was NOT hydrolized. They still found hypoxanthine and xanthine. Probably less time than it took you to type this silly comment. Lab experiments are run under very controlled conditions, and are not like baking in the kitchen. Each sample would be mixed, sealed and placed in the block, and the formic acid was likely pre-heated to 100C ... but feel free to contact them and ask. You are now basically claiming that the adenine, hypoxanthine and xanthine were produced instantaneously during the few seconds of mixing and sealing. And you still haven't addressed the issue of the same process that produces adenine also breaks it down according to your conception.Others have pointed out the error of conflating HCN with NH₄CN -- these are not "abbreviations" but chemical formulas for the compounds, compounds with different characteristics and reactions to conditions. Here's a clue google the formulas. Which doesn't apply to the half of the sample that is only subject to 95% formic acid at 100C -- no NH₄CN, no HCN, and no hydrolysis. You don't know what hydrolysis is. Hydrolysis - Wikipedia

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Hydrolysis is a chemical reaction or process in which a chemical compound reacts with water.[1][2] This is the type of reaction that is used to break down polymers. Water is added in this reaction.

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In inorganic chemistry, the word is often applied to solutions of salts and the reactions by which they are converted to new ionic species or to precipitates (oxides, hydroxides, or salts). The addition of a molecule of water to a chemical compound, without forming any other products is usually known as hydration, rather than hydrolysis.

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It has nothing to do with the acid used, and once again: I am talking about the half of the sample that was not subjected to hydrolysis. Yes, they are talking about the process with pure nucleobase mixtures rather than the unknowns in the Murchison meteor. They found that in those studies that "deamination of the nucleobases did not occur" -- and they KNOW this from having started with the pure nucleobase mixtures. What they are saying is that under those condition adenine did not degrade into hypoxanthine and xanthine. Those same condition DO apply to the Murchison meteor extraction, because they used the same process. This is how scientists evaluate other possibilities. Only when you understand squat about the processes. And the fact that we are still talking about the half of the sample that was NOT subject to HCl and hydrolysis still identified adenine, hypoxanthine and xanthine. It was published in a peer review journal, ie it was reviewed by people that know what they are talking about. Given the several rather substantial errors and miscomprehensions that are the basis of your "truckdriver review" I am not concerned with your "conclusions" as they appear to be based on the conflation of every single negative comment or comment of concern in every single article you can find related to the issue whether it really applies to the study or not.Now let's get back to the issue of the sample that is only subject to 95% formic acid extraction at 100C that identified adenine, hypoxanthine and xanthine. Without HCl. Without hydrolysis. Without fanfare. You quoted that and then said And never addressed the issue.That issue has still not been addressed by you. Once again for clarity the issue is: One single, simple process where we are still talking about the half of the sample that was NOT subject to HCl - or NH₄CN - and NOT subject to hydrolysis still identify adenine, hypoxanthine and xanthine.The fact that several different processes identify adenine, hypoxanthine and xanthine in very similar relative quantities should be enough to give you pause in your claim that these are being manufactured during the sampling process, as the different processes used would have very different capabilities.Enjoy.

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I see I still have much to learn...Percy:I cannot claim to understand all of the chemistry, but there is a strong connection between the two. NH4CN has an additional nitrogen and 4 hydrogens it appears. Both have the cyanideI assumed the abbriviation because of Millers heading in the article: ( http://exobio.ucsd.edu/miller_99.htm )I have to ask why does he use HCN in place of NH4CN in the header?At the moment the chemistry involved is out of my reach but something tells me that there is more to it than you think, though maybe less than I think.Percy: Er... actually I keep telling you that I am not trying to prove a negative. It is you (or those in your field) who have to find the positive proof to support the theories.My other big embarrassment came from not knowing that hydrolysis has to do with water specifically.I have one question about that for you and razd. 95% formic acid... what does that mean? 95% formic acid with water being the other 5%?I want to better understand the chemistry of water hyrdrolysis and the olgiomerization of peptides. Seems that hydrolysis and oligomerization is strongly linked, yet reducing other agents that are anhydrous produces the same results.Sorry for my ignorance, but I am not convinced that you guys really know either. I'd appriciate the assitance of a Doddy or Matt P whether I am right or wrong. Just dumb it down for all of us (or at least me)...I am going to have to take a big step back for now...Good job boys!Edited by Rob, : No reason given.

Rob, Er... actually you are. Is it not your contention that adenine cannot form naturally under earthly conditions?Mark

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There are 10 kinds of people in this world; those that understand binary, & those that don't

mark24:No mark...If you'll take the time to read the OP, the question is whether adenine was extracted or synthesized from the Murchison samples.However... elsewhere I have reminded folks that adenine is sythesized in the living machinery of the cell. That is empirical fact.So there is no mystery as to it's origins really. It is manufactured by biological organisms themselves.My only point has been that there has been no empircal proof thus far, of adenine synthesis in nature apart from biological organisms.

So, either adenine was accidentally synthesized during a fairly simple chemical process OR adenine was originally present on the meteorite? It also seems to be an irrelevant fact. Either answer to your main question seems to be that adenine is easily synthesized outside the cell. If you learn nothing else, could you please learn to stop using the word "proof"?

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No, of course you can't, but you do anyway, claiming truck drivers make better peer reviewers of papers on prebiotic chemistry than scientists. Why do you say such things? CO₂ (carbon dioxide) and CO (carbon monoxide) are even more similar, but look at the difference in their behaviors. Carbon monoxide is fatal at concentrations above 0.04%, while we actually exhale carbon dioxide without any ill effects. A difference of a single atom in a molecule can make an enormous difference in its properties. Miller had previously done research regarding HCN polymerization, and then he later did a reinvestigation that focused more on NH₄CN polymerization. I agree that the heading is less than clear to us laypeople, but it may make perfect sense to those working in the field. Then what's the point of arguing that adenine couldn't have come from the Murchison meteorite? In science you don't find proof, you find evidence. There's no such thing as proof in science. Evidence we have, proof we don't, which is okay since nothing in science has proof. It would be nice if you really wanted to develop a better understanding of chemistry, but reading a basic chemistry textbook might be a better starting point than technical papers on prebiotic chemistry.But let's get real. You're only really interested in chemistry to the extent that it helps you reinforce your preformed conclusions about abiogenesis. Any approach that starts with a conclusion and then goes on a scouting junket for supporting evidence is bound to end up as poorly as you keep ending up *OVER AND OVER AND OVER AGAIN*!Instead of starting with a conclusion, such as, "The production of adenine on the early earth is impossible," start with a question, such as, "Can any possible production avenues for adenine on the early earth be identified?" Then, at least, you'd be getting off on the right scientific foot.--PercyEdited by Percy, : Typo.

From my perspective you appear to be doing quite a good job presenting your arguments. I continue to monitor your manner of dialog as well as your counterparts and it appears that for the most part all are doing fine. The only reason I'm citing the above now is to caution you that it's these kinds of remarks that begin to make problems for the creationist minority folks like you, me and others which likely you're aware of by now.The science educated people we debate and dialog with in science have invested a great amount of expense and time into acquiring the knowledge they have. You, I and others who believe science is mistaken in some of their conclusions need not compromise our positions so long as we feel we can support them but being the minority we get along better when we are all the more careful to show due respect in the threads for the science professionals.I hope you don't mind some constructive criticism. You're a valuable asset to the creo team here with the potential of doing exploits as the prophet Daniel put it in the 12th chapter. I want to do what I can to help your PR here in the science arena where your presence is appreciated by all so far as I can see. Edited by AdminBuzsaw, : edit to update signature modification

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For ideological balance on the EvC admin team as a Biblical creationist.