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Author Topic:   Murchison Meteor Questions
kuresu
Member (Idle past 1414 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 151 of 216 (423175)
09-20-2007 1:09 AM
Reply to: Message 149 by Rob
09-20-2007 12:58 AM


Re: Summary of the case for adenine
Um, try actually reading the article.

Here's what they say:

quote:
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%).

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.


This message is a reply to:
 Message 149 by Rob, posted 09-20-2007 12:58 AM Rob has responded

Replies to this message:
 Message 153 by Rob, posted 09-20-2007 1:16 AM kuresu has responded

  
Rob 
Suspended Member (Idle past 4750 days)
Posts: 2297
Joined: 06-01-2006


Message 152 of 216 (423176)
09-20-2007 1:11 AM
Reply to: Message 150 by kuresu
09-20-2007 1:02 AM


Re: Summary of the case for adenine
Kuresu:
Uh, no. Higher concentration of an acid in a solution, the lower the pH.

Yeah... duh again!


This message is a reply to:
 Message 150 by kuresu, posted 09-20-2007 1:02 AM kuresu has not yet responded

  
Rob 
Suspended Member (Idle past 4750 days)
Posts: 2297
Joined: 06-01-2006


Message 153 of 216 (423180)
09-20-2007 1:16 AM
Reply to: Message 151 by kuresu
09-20-2007 1:09 AM


Re: Summary of the case for adenine
Kuresu:
Here's what they say:
quote:
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%).

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.

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 :D ) but lower pH (higher concentrations) yeild more adenine faster and also degrade it.

Do I have that right?

Edited by Rob, : No reason given.


This message is a reply to:
 Message 151 by kuresu, posted 09-20-2007 1:09 AM kuresu has responded

Replies to this message:
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kuresu
Member (Idle past 1414 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 154 of 216 (423182)
09-20-2007 1:32 AM
Reply to: Message 153 by Rob
09-20-2007 1:16 AM


Re: Summary of the case for adenine
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% yield

You'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".


This message is a reply to:
 Message 153 by Rob, posted 09-20-2007 1:16 AM Rob has not yet responded

  
RAZD
Member (Idle past 306 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 155 of 216 (423213)
09-20-2007 9:48 AM
Reply to: Message 149 by Rob
09-20-2007 12:58 AM


Re: Summary of the case for adenine
Let's review again.

http://www.lpi.usra.edu/meetings/lpsc2004/pdf/1022.pdf

quote:
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 100ºC for 24 h.

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 450ºC and peaks corresponding to adenine, hypoxanthine, xanthine and uracil were readily identified (Fig. 1c).

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 450ºC for 5 min

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 450º.

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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This message is a reply to:
 Message 149 by Rob, posted 09-20-2007 12:58 AM Rob has responded

Replies to this message:
 Message 156 by Rob, posted 09-21-2007 2:11 AM RAZD has responded

  
Rob 
Suspended Member (Idle past 4750 days)
Posts: 2297
Joined: 06-01-2006


Message 156 of 216 (423291)
09-21-2007 2:11 AM
Reply to: Message 155 by RAZD
09-20-2007 9:48 AM


Problems with Murchison extractions...
Razd:
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 450º.

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?

Well of course!

After all of the ground we covered???

I see that we must endure more revisiting of the criticism. :rolleyes:

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.pdf

Glavin and Bada:

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 100ºC for 24 h.

Right there, you have the three problems with these extractions:

1. heat

2. pH

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:

...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. Although a previous study has shown that
the synthesis of adenine from HCN in acid is highly
temperature dependent and inefficient at 100ºC [8],
we cannot rule out the possibility that some purines
may have been synthesized during formic acid extraction
of Murchison...

They tell us that adenine synthesis from HCN is innefficient at 100ºC. But they leave out the fact, that adenine synthesis is independant of temperatures between -80ºC and 100ºC (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:

A Reinvestigation of A, U, G, and C Production from HCN Polymerizations

We have been investigating the effect of temperature, concentration, and hydrolysis time on adenine synthesis from NH4CN polymerizations.
Preliminary results indicate that the yield of adenine is approximately independent of temperature between -80 and 100°C.

( http://exobio.ucsd.edu/miller_99.htm )

2. The pH and ammount time given for hydrolysis.

[qs]The original studies by Oró 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]
( http://adsabs.harvard.edu/abs/2005OLEB...35...79B )

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:

We found that in previous
formic acid extraction and sublimation experiments
using pure nucleobase mixtures, thermal deamination
of the nucleobases did not occur [5]. Therefore, the
production of hypoxanthine and xanthine by thermal
deamination of adenine and guanine during the
extraction procedure is very unlikely.

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.pdf

Note that the paper get's results only from E Coli cells, but nothing from the murchison tests:

After sublimation of the Murchison meteorite, we were unable to identify any nucleobases, including adenine above the 5 pmol/g level (Table 2) by either HPLC or GC-MS. This result is somewhat surprising since the purines adenine, guanine, hypoxanthine, and xanthine have previously been detected in Murchison meteorite formic acid extracts

But, in that paper is the following:

Although guanine did not sublime from the cells during the experiment, the presence of xanthine in the cold finger extract indicates that some thermal decomposition of guanine to xanthine occurred during the experiment

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:

6 N HCl hydrolysis of the NH4CN polymerization supernatant greatly increased the adenine yield. However, this hydrolysis also decomposes adenine and other purines.

Here is what Stanley Miller had to say in 1998:

We show here that the rapid rates of hydrolysis of the nucleobases A, U, G, C, and T at temperatures much above 0°C would present a major problem in the accumulation of these presumed essential compounds on the early Earth.

Analysis of all samples was performed on a Beckman model 110B HPLC system using a YMC (Kyoto) ODS-AQ analytical reversed-phase column and a Kratos absorbance detector set at 260 nm. The mobile phase for all experiments, except for those involving guanine, was a pH 4.8, 0.1 M phosphate buffer. For guanine, a 0.1 M phosphate, pH 2.5 buffer was used. This provided better separation between guanine and its hydrolysis product xanthine. Products were identified by retention time, coinjection with a known sample, and UV absorption.

Decomposition products were identified when possible. They are: for adenine, hypoxanthine, aminoimidazole carboxamide, and 4,5,6-triaminopyrimidine; for guanine, xanthine; for hypoxanthine, aminoimidazole carboxamide; for cytosine, uracil; for diaminopyrimidine, cytosine, isocytosine, and uracil; and for diaminopurine, guanine, isoguanine, and xanthine. No UV-absorbing products were observed from the decomposition of xanthine and uracil.

( http://www.pnas.org/cgi/content/full/95/14/7933 )

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.

;)


This message is a reply to:
 Message 155 by RAZD, posted 09-20-2007 9:48 AM RAZD has responded

Replies to this message:
 Message 157 by kuresu, posted 09-21-2007 3:08 AM Rob has not yet responded
 Message 158 by Percy, posted 09-21-2007 4:19 AM Rob has responded
 Message 159 by RAZD, posted 09-21-2007 8:43 AM Rob has not yet responded
 Message 165 by AdminBuzsaw, posted 09-21-2007 7:48 PM Rob has not yet responded

  
kuresu
Member (Idle past 1414 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 157 of 216 (423294)
09-21-2007 3:08 AM
Reply to: Message 156 by Rob
09-21-2007 2:11 AM


Re: Problems with Murchison extractions...
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?

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.

they leave out the fact, that adenine synthesis is independant of temperatures between -80ºC and 100ºC

More reading comprehension problems. Tell me, is 100ºC the same as between -80ºC and 100ºC? No, it's not. 100ºC 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.

The amount of time in question here{of placing the mixture in the test tube, sealing it, and placing it in the incubator}, must be known, if the results are to be thoroughly peer reveiwed.

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:
http://www.pnas.org/cgi/content/abstract/95/14/7933
http://www.pnas.org/cgi/reprint/95/14/7933 (pdf full text)

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'?

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.

Was this paper peer reviewed?

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.


This message is a reply to:
 Message 156 by Rob, posted 09-21-2007 2:11 AM Rob has not yet responded

  
Percy
Member
Posts: 20113
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 158 of 216 (423300)
09-21-2007 4:19 AM
Reply to: Message 156 by Rob
09-21-2007 2:11 AM


Re: Problems with Murchison extractions...
Rob writes:

Notice that HCN is an abbreviation for NH4CN below...

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 -80oC and 100oC, while Glavin and Bada write that the production of adenine from HCN is highly temperature dependent and inefficient at 100oC. 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.

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'?

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? :rolleyes:

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


This message is a reply to:
 Message 156 by Rob, posted 09-21-2007 2:11 AM Rob has responded

Replies to this message:
 Message 160 by Rob, posted 09-21-2007 10:04 AM Percy has responded

  
RAZD
Member (Idle past 306 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 159 of 216 (423324)
09-21-2007 8:43 AM
Reply to: Message 156 by Rob
09-21-2007 2:11 AM


Problems with Rob's "truckdriver review"
Rob, look again.

1. heat

2. pH

3. further hydrolysis of adenine and guanine to produce hypoxanthine and xanthine.

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.

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?

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 100ºC ... but feel free to contact them and ask.

1. The temperature in the heating block is irrelevant.

They tell us that adenine synthesis from HCN is innefficient at 100ºC. But they leave out the fact, that adenine synthesis is independant of temperatures between -80ºC and 100ºC (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..:

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.

Here is the relevant work by Miller that adresses the temperature and hydrolysis:
( http://exobio.ucsd.edu/miller_99.htm )

Which doesn't apply to the half of the sample that is only subject to 95% formic acid at 100ºC -- no NH4CN, no HCN, and no hydrolysis.

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.

You don't know what hydrolysis is. :rolleyes:

http://en.wikipedia.org/wiki/Hydrolysis

quote:
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.

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.


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.

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.pdf

Note that the paper get's results only from E Coli cells, but nothing from the murchison tests:

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.

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:

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!

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.

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.

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 100ºC that identified adenine, hypoxanthine and xanthine. Without HCl. Without hydrolysis. Without fanfare.

RAZD Message 155

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 450º.

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.

You quoted that and then said

Well of course!

After all of the ground we covered???

And never addressed the issue.

That issue has still not been addressed by you. Once again for clarity the issue is:

RAZD Message 155

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 450º.

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.

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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compare Fiocruz Genome and fight Muscular Dystrophy with Team EvC! (click)


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This message is a reply to:
 Message 156 by Rob, posted 09-21-2007 2:11 AM Rob has not yet responded

  
Rob 
Suspended Member (Idle past 4750 days)
Posts: 2297
Joined: 06-01-2006


Message 160 of 216 (423329)
09-21-2007 10:04 AM
Reply to: Message 158 by Percy
09-21-2007 4:19 AM


Re: Problems with Murchison extractions...
I see I still have much to learn...

Percy:

Miller writes that the production of adenine from NH4CN is independent of temperature between -80oC and 100oC, while Glavin and Bada write that the production of adenine from HCN is highly temperature dependent and inefficient at 100oC. 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.

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:

A Reinvestigation of A, U, G, and C Production from HCN Polymerizations

We have been investigating the effect of temperature, concentration, and hydrolysis time on adenine synthesis from NH4CN polymerizations.
Preliminary results indicate that the yield of adenine is approximately independent of temperature between -80 and 100°C.


( 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:

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

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 :o 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.


This message is a reply to:
 Message 158 by Percy, posted 09-21-2007 4:19 AM Percy has responded

Replies to this message:
 Message 161 by mark24, posted 09-21-2007 10:19 AM Rob has responded
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mark24
Member (Idle past 4096 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 161 of 216 (423330)
09-21-2007 10:19 AM
Reply to: Message 160 by Rob
09-21-2007 10:04 AM


Re: Problems with Murchison extractions...
Rob,

Er... actually I keep telling you that I am not trying to prove a negative.

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

Mark


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

This message is a reply to:
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Rob 
Suspended Member (Idle past 4750 days)
Posts: 2297
Joined: 06-01-2006


Message 162 of 216 (423335)
09-21-2007 10:56 AM
Reply to: Message 161 by mark24
09-21-2007 10:19 AM


Re: Problems with Murchison extractions...
mark24:
Er... actually you are. Is it not your contention that adenine cannot form naturally under earthly conditions?

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.


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ringo
Member
Posts: 19080
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.0


Message 163 of 216 (423338)
09-21-2007 11:18 AM
Reply to: Message 162 by Rob
09-21-2007 10:56 AM


Rob writes:

... the question is whether adenine was extracted or synthesized from the Murchison samples.

So, either adenine was accidentally synthesized during a fairly simple chemical process OR adenine was originally present on the meteorite?

... elsewhere I have reminded folks that adenine is sythesized in the living machinery of the cell. That is empirical fact.

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.

My only point has been that there has been no empircal proof thus far....

If you learn nothing else, could you please learn to stop using the word "proof"?


“Faith moves mountains, but only knowledge moves them to the right place” -- Joseph Goebbels
-------------
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Percy
Member
Posts: 20113
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 164 of 216 (423373)
09-21-2007 3:23 PM
Reply to: Message 160 by Rob
09-21-2007 10:04 AM


Re: Problems with Murchison extractions...
Rob writes:

I cannot claim to understand all of the chemistry...

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?

...but there is a strong connection between the two. NH4CN has an additional nitrogen and 4 hydrogens it appears.

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.

I have to ask why does he use HCN in place of NH4CN in the header?

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.

Er... actually I keep telling you that I am not trying to prove a negative.

Then what's the point of arguing that adenine couldn't have come from the Murchison meteorite?

It is you (or those in your field) who have to find the positive proof to support the theories.

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.

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.

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.

Sorry for my ignorance, but I am not convinced that you guys really know either.

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.

--Percy

Edited by Percy, : Typo.


This message is a reply to:
 Message 160 by Rob, posted 09-21-2007 10:04 AM Rob has responded

Replies to this message:
 Message 168 by Rob, posted 09-22-2007 12:13 AM Percy has responded
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AdminBuzsaw
Inactive Member


Message 165 of 216 (423399)
09-21-2007 7:48 PM
Reply to: Message 156 by Rob
09-21-2007 2:11 AM


Re: Problems with Murchison extractions...
Rob writes:

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'?

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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