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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 4 of 216 (421748)
09-14-2007 8:23 AM
Reply to: Message 1 by Rob
09-14-2007 12:13 AM


mountains out of molehills
Rob,
Sit back and read again.
Why did they use the word or when later in the article they make it clear that no purines were found other than in formic acid extracts?
Because some of the other compounds listed were found in water extracts.
{abe}
Since Murchison is a significant player in origin of life research, Origin of Life please...
Consider that even if adenine is not shown to be found on the Murchison meteor, that this will not diminish the number of 'organic' compounds that have been found on meteors. It will not disprove the possibility that such compounds formed in space and were transported to the early earth by meteors.
Do all the necessary elements for forming life need to come from meteors? Logically the answer is no.
{/abe}
Enjoy.
Edited by RAZD, : sp
Edited by RAZD, : added

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This message is a reply to:
 Message 1 by Rob, posted 09-14-2007 12:13 AM Rob has not replied

Replies to this message:
 Message 11 by Ken, posted 09-14-2007 12:38 PM RAZD has replied

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


Message 14 of 216 (421792)
09-14-2007 1:51 PM
Reply to: Message 11 by Ken
09-14-2007 12:38 PM


Re: mountains out of molehills
I agree with you that not all of the necessary elements for forming life need to come from meteors, but assuming that life began with naturalistic spontaneous generation, where else would these essential compounds have originated?
I'm afraid that would take this thread off-topic. For some answer though look at RAZD - Building Blocks of Life. This was written in 2005 so it is a little out of date on the progress that has been made since, however it talks about a number of possible chemical "factories" that could produce components of the first replication life system.
So then, if the organic compounds required for life could not have already been present on earth, they must have been introduced.
Logically false conclusion. Please take this post to the above thread for answers that will be more on topic, and I'll explain further if you need it (after reading the article).
Now that the rabbit trail has returned me to the topic, it seems that the assertion "Adenine has been found" by molbiogirl that adenine has been found in meteorites is, at the very least, questionable.
I look at this issue as having (at least) these four possibilities:
  1. there was adenine on the meteor in the sample where it was extracted with water, but not in the sample where it was extracted with acid.
  2. there was adenine on the meteor and it was extracted with water, while the acid extraction result was a false negative due to UV interference (but I would need to know more about this to understand).
  3. there was no adenine on the meteor, and the water extraction result was a false positive due to UV interference (but I would need to know more about this to understand).
  4. adenine was formed during the acid extraction process from other molecules existing on the meteor (as the process involved heat this is also available for the early earth in many areas).
From the article these excerpts:
quote:
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.
We were unable to identify any purines or pyrimidines on the cold finger after heating the Murchison meteorite sample directly at 450C (Fig. 1b). This result is surprising since all of these nucleobases, with the exception of guanine, have previously been sublimed from a pure standard mixture at the same temperature with recoveries ranging from 50 to 85% [5]. The presence of a kerogen-like organic polymer in Murchison may inhibit the sublimation of these nucleobases directly from the meteorite [7].
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.
At this point I don't know enough to know, if you know what I mean.
quote:
These preliminary findings need to be confirmed by gas chromatography mass spectrometry.
In the future, nitrogen isotopic measurements of the nucleobases in Murchison should be carried out in order to firmly establish the origin of these compounds.
Sounds like a plan.
Enjoy.
Edited by RAZD, : corrected #4, added quoted material
Edited by RAZD, : added last quotes.

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


Message 16 of 216 (421808)
09-14-2007 3:40 PM
Reply to: Message 1 by Rob
09-14-2007 12:13 AM


and another thing ...
Purines and triazines in the Murchison meteorite - NASA/ADS
. Drastic extraction conditions (hot 3-6 M HCL) a variety of nitrogen compounds appeared, including adenine (15 ppm), guanine (5ppm), melamine (20 ppm), cyanuric acid (20 to 30 ppm), guanylurea (30 to 45 ppm), and urea (25 ppm) .
Whoah!
. It appears that these compounds are present mainly in macromolecular material. Failure of other investigators to identify these compounds in carboneceous chondrites is attributed to inadequate extraction conditions (water and formic acid rather than HCl).
It’s all about the acid folks . Stanley Miller knew how to do it! Too bad it’s biologically irrelevant.
Using acid to extract molecules is not the same as using an acid environment to form the molecules. The extraction method used is essentially irrelevant to the formation of the molecules (or it's not a valid extraction process).
The first paper referred to the adenine etc being bound to kerogen-like compounds (the other (unidentified) organics?), and this would be consistent with needing stronger extraction methods:
quote:
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.
The presence of a kerogen-like organic polymer in Murchison may inhibit the sublimation of these nucleobases directly from the meteorite [7].
It seems to me that the evidence points to adenine being present on the meteor (along with the other 'biological' molecules noted).
Enjoy.
Edited by RAZD, : end.
Edited by RAZD, : added to last quote

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This message is a reply to:
 Message 1 by Rob, posted 09-14-2007 12:13 AM Rob has replied

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


Message 21 of 216 (421963)
09-15-2007 8:51 AM
Reply to: Message 20 by Rob
09-15-2007 12:10 AM


Re: Scientific Controversy -- or not.
It all started in the last thread. My question was, 'Does anyone have any evidence at all for a pre-biotic organism?'
The answer is no!
And the reason I did, was because we have a whole planet full of emperical evidence for biological organisms.
The answer is we don't know. Viruses could be (evolved) remnants of pre-cellular replicating mechanism (where do you draw the line on life eh?)
The empirical evidence we have from the oldest known rock that could have fossils that we could look at (has not been metamorphized) show life already existing in the form of cyanobacteria very similar to what we know today. This is from rock that is dated to 3.5 billion years old. That means that to find older evidence we need to find either (a) older sedimentary rock or (b) be able to distinguish the product of life processes in metamorphic rock - and there have been some (controversial) attempts at that.
The question is - what would the evidence of pre-biotic life look like in the fossil record then? That's an even tougher nut to crack eh?
We are not here to discuss what I think the actual evidence points to. We are here to see whether there is any evidence for you to point to.
Do you perceive the difference?
Oh yes, definitely. But we are pursuing that actual evidence through a 'methodological naturalist' approach because it is the most likely to deliver reasonable -- and unbiased -- answers to the question "could this have happened?"
Message 19
As to your first comment, that is the question... I'm not so sure yet!
You may want to see my resopnse to MattP in message 18 above. I am asking questions in order to understand it better myself.
Message 18(to Matt)
The kerogen-like compound (or compounds) that the adenine is supposedly bound with (in the meteor) are said to be explained by the experiment with actual kerogen (or humic acid though they're not exactly the same from what I gather) and pure mixtures of adenine.
Is that really an analogous test?
My doubt comes from the fact that we do not have as confined a definition of the meteor composites. Though kerogen and humic acid are also not well defined, can we say with reasonable certainty that a sample of this meteor is analogous?
You see, we have this conglomerate in the metoer, and these acid extractions are said to be simmilar to the more controlled experiments. But how can we be sure that 'unknown' mineral or elemental influences do not substancially change the reactions. I am not well versed in chemistry, and perhaps that is the only difficulty. But even Glavin and his associates said they could not dismiss the possibility. Could the chemical composition of the meteor alter the sensitivity to temperature durring the oligamerization of HNC?
The issue is what the acid can and cannot do in these chemical processes. Formic acid is a relatively weak acid IIRC (compared to HCl or H2SO4 which are strong acids). See Acid Strength for a discussion of what makes acids strong\weak.
If the acid\heat is not strong enough to disrupt the chemical bond of the molecule, then it will extract it, and if this was strong enough to disrupt the bond then we wouldn't be able to find the molecules.
Finally there is a difference between a chemical bond and molecules having an "affinity" for co-existence. There are weak electro-chemical attractions between certain molecules that have a polarized shape, similar to the attraction of ion, but that are not of the strength of molecular bonds. Water is such a molecule, and it forms long chains of weakly bonded molecules.
My doubt comes from the fact that we do not have as confined a definition of the meteor composites. Though kerogen and humic acid are also not well defined, can we say with reasonable certainty that a sample of this meteor is analogous?
What they did was test the hypothesis by using a similar compound and adenine to see if it was possible to inhibit the extraction on anedine (which they now know is in the kerogen), and they were. This means that it is extremely likely it occurred in the meteor composites as well.
Enjoy
Edited by RAZD, : finished

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This message is a reply to:
 Message 20 by Rob, posted 09-15-2007 12:10 AM Rob has replied

Replies to this message:
 Message 22 by Rob, posted 09-15-2007 11:59 AM RAZD has replied
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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 29 of 216 (422109)
09-15-2007 9:17 PM
Reply to: Message 22 by Rob
09-15-2007 11:59 AM


'self' replication is not selfish
Well that's strange... because viruses cannot evolve or replicate without a complete cell.
They evolve when they replicate like any other form of life. That they now use existing cells does not mean they were always so restricted, nor does it compare to what it was like before cellular life evolved. There is one (mimi) virus that is bigger and more complex than the simplest cellular life.
See http://www.the-scientist.com/news/20040506/01/ (used to have full article available).
and Just a moment...
and http://www.usatoday.com/...ce/2003-11-13-new-life-usat_x.htm
Before an oxygen atmosphere things were different.
That is simply false... adding or subtracting one atom (and it's chemical bond) would change the molecule from one substance into another. And just because an acid is strong enough to oligomerize HCN, doesn't mean it will act on all of the bonds.
But in the process of developing an extraction method you would test it for effect on the molecules you would like to extract to make sure you don't change them.
We must consider concentration as well.
This was made perfectly clear in the OP; HLC did not disrupt the bond. They used it because they were unable to find adenine with weak formic acid extraction
If the acid is not strong enough to disrupt the molecular bonds the concentration of the acid is irrelevant in causing disruption of the molecular bonds. They would use increasing strength to disrupt non-molecular bonds until they were able to separate molecules from the kerogen-like substance.
...go read their whole paper in the OP.
I have.
No! Your not talking aobut 'methodological naturalism' really... your talking about empericism. And empericism I agree with. And the answer to the question, 'could this have happened', keeps flashing before you; 'Not in terms that are biologically relevant'.
"Methodological naturalism" is "empiricalism."
BTW: please notice EMPIRE ... EMPIRICAL - similar spelling: see if you can remember the correct spelling (or use a spell check). This error has been pointed out previously (by Percy). Occasional misspellings are no problem, consistent continued error after it has been pointed out is failure to learn.
Abiotic compounds (just like in the Miller experiments) are only life-like. And that is why Murchison is so strikingly simmilar to Miller's experiments. Some take it as confirmation of Miller. I take it as confirmation of abiotic compounds being, well... abiotic!
Pre-biotic compounds are pre-biotic compounds regardless of where they come from and regardless of how they came about.
And as Ken showed you in a very straightforward post with tremendous citation, the environmental conditions necessary to produce them are also not compatible with life; extreme heat, reducing atmospheres, comet and meteor imapacts, volcanoes, and otherwise immensly harsh and dangerous conditions are all invoked to explain the arrival of life.
Except the article did not really address the actual science involved, but someones misinterpretation of it. That is why I directed comments to RAZD - Building Blocks of Life -- rather than take your topic off on a tangent.
The evidence is what you are supposed to examine (ie. the actual biological compounds) You're using your 'method' to theorize evidence that does not actually exist. And let's be clear, there is no evidence for self replicating molecules.
There are several examples of molecules that are self-replicating, some mentioned on RAZD - Building Blocks of Life, and more are discovered every year. This is old news, and denial of the evidence does not make it go away.
Molecules must get energy from elsewhere in order to replicate. And in biology, that comes in the form of ATP. There is no self in replication. It is a system. And that is what makes it so complex.
Currently biological systems get their energy through ATP, but that is an evolved system and it does not mean that the original replicating systems did. Energy comes easily from the sun and the environment, so there is a surplus of energy available. It is a matter of getting a system to use it.
Personally there are times when I am tempted to think that life is itself, emminently unnatural. At the very least, living organisms have qualities that are utterly inexpicable in terms that may explain the environment in which they live. So methodological naturalism may be good in for explaining one system, but we cannot assume without invoking metaphysics that it applies to all systems. But that's another matter and topic really. I just wanted to share my opinion.
And probably good for another topic indeed.
Message 25
If you knew, it would be evidence. The fact is... IF there is evidence, it remains to be seen. And that is equal to no evidence.
What we do have evidence for, is whole systems that we call biological organisms. And they defy material explanation.
It's not that we have no evidence but that we do not have evidence from the time period when life developed .. because it is currently inaccessible. As it sits right now (without new finds of older non-metamorphisized sedimentary rock) we are physically unable to find evidence, because it has been destroyed by the metamorphosis process. This is not the same as being evidence that it could not have developed. What it means is that we don't know.
As for Murchison, I am not conviced that they were found. And the fact that they are racemic, really points to artificial synthesis relative to their biological counterparts.
The parts that can be synthesized outside of biology are not even chiral molecules. They are lifelike only. So even if they were found, we still cannot explain the chiral molecules in biology.
They were formed by chemical processes rather than biological, and that is the whole point eh? These molecules do form by chemical processes. They are pre-biotic molecules, formed by chemical processes and readily available for use in the development of life from these basic building blocks.
Chirality may be just a matter of chance: 50:50 chance that it is one or the other that got used in the original surviving form of life that developed. Or maybe 1 in 3 chance if you include original life that may have been able to use both spins (but used more energy and resources to do so). What you end up with is a post hoc ergo propter hoc argument regarding what just happened to occur.
And there are systems that sort molecules by chirality, so they may have acted as a template for the assembly process in the develpment of life. These too are mentioned on RAZD - Building Blocks of Life. The question is what tangents you want to take your topic off onto, once the issue of finding adenine on the Murchison meteor is settled.
As for Murchison, I am not conviced that they were found.
Why not? Adenine was found wasn't it? Where did it come from?
Enjoy.

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This message is a reply to:
 Message 22 by Rob, posted 09-15-2007 11:59 AM Rob has replied

Replies to this message:
 Message 34 by Rob, posted 09-15-2007 10:42 PM RAZD has replied

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


Message 42 of 216 (422156)
09-16-2007 7:40 AM
Reply to: Message 34 by Rob
09-15-2007 10:42 PM


Re: There is nothing 'self' about replication. It takes a system!
The fact that you would even attempt to use parasites of any kind as a possible example of pre-biotic life is mezmerizing. Don't you see the need for a host organism?
You know what... you're right! The actual evidence (that viruses use host organisms) doesn't necesarily... mean that viruses always used them. But it certainly... doesn't mean they didn't.
If anything, the evidence as it is, would actually promote the idea that they did. They're parasites!
Consider that all parasites evolved from organisms that were not parasites, they did not spring de novo once a host appeared. Look at the evidence of the mimivirus.
You are assuming the existence of non cellular life without any evidence? Yet you lecture me about naturalism and empiricism?
No, I am going on evidence that viruses are as old or older than known life. Read the links.
No razd it doesn't necessarily mean that. But the evidence showing biological systems using ATP, certainly does not suggest otherwise. The actual evidence would tend to point toward processes that can be observed.
Evolved life would tend to use efficient processes in place of less efficient ones, thus new systems would replace original ones. Once the ability to make ATP evolved it would replace other methods of acquiring energy from the environment.
And what does the evidence show?
The evidence shows organisms that convert energy of differing types into ATP.
The evidence shows that modern life forms with the benefit of 3.5 billion years of evolution use ATP. The evidence of early life form energy processes is missing.
So what are you saying Razd? That a group of intelligent designers creating an experiment with very limited conditions and variables, controlling the solution, it's components, and the amount of energy available is akin to proving that it happened in an environment with an almost incalculable number of additional variables?
There is nothing 'self' about those experiments, the molecules actions were utterly dependant upon the designers and the system designed for them.
You said there were no replicating molecules. I showed you a reference to several. All you are doing here is full denial of this evidence. Stop trying to move the goalpost rob.
Not to mention that it presupposes the existence of the molecular material to begin with. There is a whole host of questions I could ask... for example: Were these chiral amino acids taken from existing life?
If not, then what relevance does it have for the evidencial life we see today?
If so, then how does taking from life... prove non-life?
It presupposes that pre-biotic molecules were available, and as we have seen from the Murchison meteor (and other pieces of evidence) they were.
That's funny, because Glavin and Bada seemed to think it was worth mentioning:
This suggests that the purines are either bound to other organics, or were produced (e.g. oligomerization of HCN) during acid extraction.
The full quote is:
quote:
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 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]. Therefore, the production of hypoxanthine and xanthine by thermal deamination of adenine and guanine during the extraction procedure is very unlikely.
There is no contesting the other (not adenine) molecules that were found with the water extraction method, so those were not formed in the acid process. Is it likely that only adenine would be so formed?
Further, IF it was formed, THEN there were still the molecules from which it was formed available for the formation of adenine.
We have evidence from the bottom up in pre-biotic molecules and self-replicating molecular systems, and we have evidence from the top down in viral life forms. The gap in knowledge decreases every day.
Enjoy.

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This message is a reply to:
 Message 34 by Rob, posted 09-15-2007 10:42 PM Rob has replied

Replies to this message:
 Message 45 by Rob, posted 09-16-2007 11:11 AM RAZD has replied

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


Message 51 of 216 (422251)
09-16-2007 5:29 PM
Reply to: Message 45 by Rob
09-16-2007 11:11 AM


adenine - the spice from space
You see, Razd here, says I was talking about 'replicating molecules'. That is false, I was talking about 'self replicating molecules'. Some molecules do replicate with the help of intelligent chemists. But they are not self replicating. That was my point, and that was what I said in my last reply.
If you are going to quibble get the quibble right: the molecules did replicate themselves in the experiments. The "help" provided amounted to creating the environment and then sitting back and watching. The molecules assembled other similar molecules from that environment. That amounts to self replication. To quibble over the use or not of "self" does not detract from the evidence of self-replication in these molecules. Several such experiments have been run, and each one adds to the knowledge of what is required to set up a self-replicating molecular system.
I accused you of "trying to move the goalposts" because your post was essentially rejecting any and all experimental studies involving self-replicating molecules as being tainted by the input of "intelligent chemists" rather than looking at the facts of the self replicating molecules.
Finding excuses to use in ignoring data does not make the data go away.
The point is, that molbiogirl stated emphatically that adenine had been found. That's not the case at all. It's a big- fat- maybe!
And some studies also state that adenine has been found. The fact remains that most studies extracted adenine while one we know of (using water extraction) did not. We also know that there is a very good reason for the water extraction to have failed, that not only was this theoretically possible but it was tested and verified.
The other possibility - that adenine was formed during the extraction process - has not been replicated by a study to show the formation of the amount of adenine extracted from other possible molecules in the meteor. This remains a hypothetical possibility at best. Even in this case you have the easy to assemble building blocks for the adenine molecule delivered to the doorstep of life, so even in this event you cannot rule out delivery of adenine to a pre-biotic earth ... along with the other amino acids used to make DNA and RNA.
This is a big difference from a chemical soup such as creationists and Idologues like to claim was the conditions on earth (like Ken's article).
Well, we know that adenine can be sythesiszed by HCN.
Adenine is formed by combining molecules of HCN into a ring formation: so it is not synthesized by HCN but from it. That would tend to make using HCN for extraction purposes questionable, but you would need to show how it can form adenine under the extraction process.
http://www.ch.ic.ac.uk/rzepa/mim/environmental/html/hcn.htm
quote:
For example, under pressure and with traces of water and ammonia, HCN produces adenine, one of the bases needed to construct DNA.
Were conditions necessary for making adenine from HCN part of the extraction process? If not then it is not likely adenine was made during extraction.
I think they are worried that the lack of evidence points to the counterargument. Well maybe it does, but this thread is not about design... it's about evidence.
And the preponderance of evidence in my opinion is that adenine was on the Murchison meteor.
We can also look at the Lake Tagish meteor: in this case no amino acids were found at all. What this demonstrates is that the material carried by meteors is highly variable.
A logical next question is what other evidence do we have for adenine and the other amino acids being formed in space?
http://astrobiology.arc.nasa.gov/news/expandnews.cfm?id=306
quote:
Instellar clouds may produce a component of DNA
According to an article in New Scientist, researchers in Calcutta claim that interstellar clouds may produce large amounts of adenine. Their findings suggest that the raw materials of life may be common in other planetary systems.
As astronomers have long known, collapsing interstellar clouds produce something else as well: stars, planets, and comets. Adenine may have been present when the Earth condensed from dust and gas.Or, adenine may have been carried on the comets that showered the early Earth. A ready supply of adenine from space may help explain how life began relatively quickly after the Earth formed.
Scientists have found signs that other raw materials for life may be present in space. For example, observations have revealed complex organic molecules in interstellar clouds. Researchers with the NASA Astrobiology Institute have even produced membrane-like structures inside a simulated comet. Evidence from observations, laboratory experiments and computer simulations increasingly suggests that the ingredients for life may be abundant throughout the universe.
Life's Ingredients May Have 'Sprinkled' on Earth | Space
quote:
A new computer model indicates clouds of adenine molecules, a basic component of DNA, can form and survive the harsh conditions of space, and possibly sprinkle onto planets as the stars they orbit travel through a galaxy.
"There may be only a few molecules of adenine per square foot of space, but over millions of years, enough could have accumulated to help make way for life," said study co-author Rainer Glaser, a molecular chemist at the University of Missouri-Columbia.
Glaser and his team's findings are detailed in a recent issue of the journal Astrobiolog
Adenine is one of four "letters" of DNA's alphabet used to store an organism's genetic code. Glaser said the idea that large, two-ringed organic molecules like adenine formed in space may seem outrageous, but current evidence leaves the possibility wide open.
"You can find large molecules in meteorites, including adenine," Glaser said. "We know that adenine can be made elsewhere in the solar system, so why should one consider it impossible to make the building blocks somewhere in interstellar dust?"
Using computer simulations of the cold vacuum of space, Glaser and his colleagues found that hydrogen cyanide (HCN) gas can build adenine. Like pieces in a set of tinker toys, hydrogen cyanide serves as adenine's building blocks; the small molecules bond together into chains and, with a little wiggling, eventually assemble into rings.
Although adenine's first ring needs a tiny energy boost from starlight to form, Glaser said the second ring of the molecule self-assembles without any outside help.
Glaser said adenine's ringed shape helps it absorb and release any excess energy without breaking apart, making it stable enough to form concentrated clouds that planets can drift through.
(color added for emphasis)
Note that says adenine has been found on meteors.
http://www.liebertonline.com/...dfplus/10.1089/ast.2006.0112
quote:
CONCLUSION
One of the major goals of prebiotic chemistry is the search for possible syntheses of the nucleobases and especially of the purine bases (Levy and Miller, 1999). Building on the results of half a century of studies of adenine synthesis by HCN pentamerization, we have discussed mechanisms for possible prebiotic pyrimidine-ring formation of monocyclic HCN-pentamers. The calculations model gas-phase chemistry, and the results primarily inform discussions of adenine synthesis in interstellar space. The primary conclusions are (a) that 5-(N#-formamidinyl)-1H-imidazole- 4-carbonitrile, 6, can serve as a substrate for proton- catalyzed purine formation under photolytic conditions and (b) that N-(4-(iminomethylene)- 1H-imidazol-5(4H)-ylidene)formamidine, 7, can serve as a substrate for uncatalyzed purine formation under photolytic conditions.
Photoexcitation of the initially formed monocyclic HCN-pentamer 5-(N-formamidinyl)-1Himidazole- 4-carbonitrile, 5, provides more than 135 kcal/mol of additional internal energy to 5*. Tautomerization to 7 would convert about one third of the excess internal energy into electronic energy and leave the nascent isomer 7 with just about twice its normal internal energy. Such an isomer 7 might be cool enough to prevent any dissociations, while IR fluorescence dissipates the excess energy. The absence of any sizeable activation barrier for the cyclization 7 # (Z)-2 is remarkable, and it is this feature that allows for the formation of the purine skeleton from 7 without any further activation. The exploration of this chemistry presents a considerable challenge for synthetic chemistry.
Conclusion: adenine forms in space from readily available HCN molecules, thus it is available to be on meteors or on dust that sprinkles down on earth.
The building block is available for life no matter how you cut the evidence pie.
Enjoy.

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This message is a reply to:
 Message 45 by Rob, posted 09-16-2007 11:11 AM Rob has replied

Replies to this message:
 Message 52 by Rob, posted 09-16-2007 6:29 PM RAZD has replied
 Message 54 by Ken, posted 09-16-2007 6:50 PM RAZD has replied

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


Message 55 of 216 (422313)
09-16-2007 8:21 PM
Reply to: Message 52 by Rob
09-16-2007 6:29 PM


Re: adenine - the spice from space
That's right Razd! Maybe it's good enough for you, because you like to see what you want to see but the facts that I supposedly ignore are... that intelligent chemists set up the conditions.
The molecules replicated... big deal. But not by themselves. They are therefore not self-replicating. They are designed.
I can watch an existing rock at the top of the cliff fall, then I can take that rock back to the top of a cliff set it back on the cliff, and watch it fall. There is no difference in the way the rock falls or in the result of the fall. One was a natural the other a "designed" occurrence. In both cases the rock falls under the laws of physics.
Your refusal to accept the results of scientific studies as valid on the basis that the studies were "designed" does not mean that (a) they can not be replicated by someone ignorant of chemistry that follow the same procedure or (b) that the same procedure occurring naturally would not end in the same result. The self-replication was not designed: it was a natural result that proceeded from the initial conditions just like the rock on the cliff. Claiming that "intelligent geologists" and "intelligent physicists" put the rock on top of the cliff so therefore the experiment was "designed" in no way affect the falling of the rock or the result of the falling rock.
This is a totally bogus argument - if not desperate attempt at self-delusion.
I don't know that most studies found adenine.
Okay, let me quantify that for you: most of the ones I have seen, including the ones I have googled. Feel free to present numerous ones where they were looked for and not found (a lot of early ones did not look, so those don't count eh?). Note that there is an explanation for not finding adenine when using water extraction techniques.
The formic acid extractions found adenine but couldn't be quantified because of the unknown UV barrier.
That means they found it but could not get an exact figure on the quantity. The molecule was still there. Note that formic acid is not used to make adenine.
They say that at 100c it is an inneficient reaction. And even though the extraction was incubated at 100c, the sublimation was done at 450c (if I remember right, for 5 minutes).
What this would mean is that the extraction was done at 100c. Once the extraction was complete, then they would heat it to 450c to see what sublimated (and condensed on the "cold finger"). Two different processes.
Well no one is denying that amino acids were found in Murchison, though they are racemic mixtures predominantly. But that is not the same thing as finding purines like adenine.
Well actually the ONLY thing being contested is the existence of adenine: all the other DNA components were there and have not been contested. Racemeic is irrelevant at this point (it's not part of the original topic and could easily be a topic on it's own).
The point remains that studies have found adenine: explain the results. Note that there is an explanation for not finding adenine when using water extraction techniques. Put the two together: adenine was on Murchison.
No Razd... No! Adenine doesn't form in space. Did you read what your own links said? Let me highlight them for you (whoah! I'm having de javu)! it's a debate with molbiogirl all over agian:
Happy highlighting. Note you "highlighted" the following too, this time with my highlight:
quote:
"You can find large molecules in meteorites, including adenine. We know that adenine can be made elsewhere in the solar system, so why should one consider it impossible to make the building blocks somewhere in interstellar dust?"
The model is about interstellar adenine, and not that in our solar system. The model just confirms that it is possible to form adenine in space. Adenine has been found in space. Put the two together.
Enjoy.

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This message is a reply to:
 Message 52 by Rob, posted 09-16-2007 6:29 PM Rob has replied

Replies to this message:
 Message 57 by Rob, posted 09-16-2007 9:11 PM RAZD has replied

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


Message 56 of 216 (422324)
09-16-2007 8:54 PM
Reply to: Message 54 by Ken
09-16-2007 6:50 PM


no -- the other paper
How does stating that nucleic acids were probably later products of evolution lead to being labeled a creationist or IDologue?
What labels it creationist or IDoloque is the source of the article
but now that we have determined Robert Shapiro to be a creationist,
Is this typical? Ignore the creationist\IDologue article you posted two quotes from and go to the one where you posted a tid-bit from?
What I was refering to was the article On the Origins of Life by David Berlinski and posted on "The Center for Science and Culture" which is "a Discovery Institute program" (from their "about CSC" page). Do you think I don't check sources?
Enjoy.
Edited by RAZD, : format
Edited by RAZD, : subtitle

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This message is a reply to:
 Message 54 by Ken, posted 09-16-2007 6:50 PM Ken has replied

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 Message 61 by Ken, posted 09-16-2007 10:03 PM RAZD has not replied

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


Message 63 of 216 (422387)
09-16-2007 10:52 PM
Reply to: Message 57 by Rob
09-16-2007 9:11 PM


Re: adenine - the spice from space
Your analogy is severely flawed. I don't even think you are conscious of your own pea-palming. It's just what you believe! so don't think I am trying to shame you...
... by palming the pea? Hardly. What you fail to realize is that once the rock starts to fall it does not matter whether it was there naturally or placed, the laws of physics take over.
Likewise once the conditions are set up by for the experiment it does not matter if they occurred naturally or were the result of the experimental design, the laws of chemistry take over. The replication of the molecule was a result of the laws of chemistry, not because of the "design" of the experiment.
The fact is that these (and other) self-replicating molecules exist. Denial does not alter that fact. Pretending to hide behind your straw man argument with "intelligent chemists" doesn't alter that fact.
Oligomerization of HCN durring the extraction process just as the study said was possible, but not expected. They cannot be sure becuase the consititution of the Murchison samples is not yet constrained.
That doesn't necessarily explain all the other results though:
quote:
The concentrations of these nucleobases in our extracts ranged from 145 to 356 ppb and are similar to those originally reported by Schwartz and coworkers (see Table 1).
Table 1. ... Nucleobase This Study* Schwartz [3,4]
It seems the extraction system used by Schwartz was similar:
[3] Van der Velden W. and Schwartz A. W. (1977) Geochim. Cosmochim. Acta., 41, 961-968.
Search for purines and pyrimidines in the Murchison meteorite - NASA/ADS
[4] Stoks P. G. and Schwartz A. W. (1981) Geochim. Cosmochim. Acta., 45, 563-569.
Nitrogen-heterocyclic compounds in meteorites: significance and mechanisms of formation - NASA/ADS
So that is not conclusive (other than that they identified adenine as well).
But also see Adenine adsorption on and release from meteorite specimens assessed by surface-enhanced Raman spectroscopy
quote:
The trapping of organic molecules in minerals is considered to be an initial step in the genesis of life. We have previously explored the adsorption of adenine and RNA on clay. We have now used surface-enhanced Raman spectroscopy (SERS) to characterize adenine adsorption on and release from specimens of two meteorites, the Zagami Martian meteorite and the Murchison meteorite. Powdered meteoritic material was incubated with very dilute adenine solutions. An adenine SER response of the resulting supernatant weaker than that of the initial solution indicated that adenine was bound to the meteorite. SER signal with the pellet meant that adenine that was initially adsorbed on it was transferred to the silver colloid SER probe. Adenine adsorption on and release from the Murchison carbonaceous chondrite and the mineral Zagami meteorite depended on the composition of the meteorites. Adenine was much more strongly bound to the Murchison meteorite, which contains bioorganic matter, than to the purely mineral Zagami meteorite.
They added adenine to the Murchison meteor and then had trouble recording it due to the strong bond of the "bioorganic matter" -- that would be confirmation that this material bonded to any adenine on the meteor and prevented the water extraction method from identifying the adenine.
From the original Glavin article again:
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], ...
Thus IF adenine were being made in this process we should see a difference - a marked difference - between the two tests made: it should be higher in proportion when the higher temperature is used.
quote:
Fig. 1. ... (a): UV absorbance (=260 nm) of the formic acid extract from the Murchison meteorite sample, (b): sublimed unextracted meteorite heated at 450C for 5 min, (c): the cold finger residue after heating a formic acid extract of the meteorite at 450C for 5 min, and (d): a serpentine blank carried through the same processing procedures as the Murchison sample.
Only (c) was heated to 450C and adenine is identified in both (a) and (c) -- it is higher in proportion for (a), the lower temperature extraction.
To me that says that adenine was on the meteor and was not significantly made during the extraction process.
Enjoy.

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This message is a reply to:
 Message 57 by Rob, posted 09-16-2007 9:11 PM Rob has replied

Replies to this message:
 Message 65 by Rob, posted 09-17-2007 12:31 AM RAZD has replied

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


Message 69 of 216 (422457)
09-17-2007 8:33 AM
Reply to: Message 65 by Rob
09-17-2007 12:31 AM


Re: This is going nowhere... bouncing ball syndrome?
This is going nowhere...
Yep. You need to make a decision: take the evidence where it leads or stick to your (biased) opinions.
We can all imagine a rock being there to begin with. But we don't all assume that pebiotic organisms existed. It's actually a contradiction in terms, so it could not have existed other than de novo. But de novo excludes evolution as the means to the end. De novo would (as Orgel has said) be a near miracle. I digress...
You not only digress you wrap yourself in a knot trying to make something impossible when it isn't. Nor is it a contradiction in terms to assume prebiotic structures that replicate but do not meet the definition of life, and this certainly has no effect on the behavior of chemicals or rocks in the real world.
What the self-replicating experiments show is that there is a chemical process that can occur, and that when the conditions of that chemical process are met that those molecules will replicate themselves. This is not magic, it is just chemistry operating according to the laws of chemistry. It is no different than the rock.
So on the one hand your assuming the existence (without evidence) of prebiotic organisms. And with the other hand, your creating (designing) the organism (or extracting extremely sophisticated molecular material from modern life) and then protecting it from a real-life environment full of variables and dangers, so as to prove that it could happen without intelligent guidance.
If that's not palming the pea will somebody please tell me what is?
Now you are moving the goalposts again: the original argument was that there were no self-replicating molecules. There are. Now you argue that they don't qualify because they don't meet special conditions that you have added. The claim is not that these molecules necessarily represent actual pre-biotic organisms in the pre-biotic world, just that they are self-replicating molecules. At best they provide us hints about that prebiotic world operation, but there is no necessary relationship.
What they do show without doubt is that chemistry can cause self-replication under certain circumstances, just as physics can cause rocks to fall under certain circumstances.
What they do make impossible are rational logical arguments that there are no self-replicating molecules. Thus the only way you can argue that is by palming the pea.
The only fact, is that molecules designed or extracted by intelligent biochemical engineers are not self anything!
This is going nowhere... I do not understand the difficulty in understanding this.
The molecules self-replicate: they build copies of themselves. Denial does not make that fact go away. This is no different than any other chemical reaction, whether set up in an experiment or occurring naturally.
Go back to the rock example and tell me, once the rock has started falling, whether there is any difference between (a) naturally falling and (b) intentionally placed rock falling: if you cannot tell me what is different in the physical behavior of the rock once it has started falling, then you have no argument other than bluster in your personal incredulity.
I'm going to separate this from Murchison data so that you can rail on about it - to no avail.
I would say that this is fundamental to your misunderstanding of how science operates across the board.
As does your absolute failure\inability\willingness to learn how to spell empirical -- even when you quote the dictionary definition -- speak to your unwillingness to learn.
Enjoy.
Edited by RAZD, : emirical

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This message is a reply to:
 Message 65 by Rob, posted 09-17-2007 12:31 AM Rob has replied

Replies to this message:
 Message 71 by Rob, posted 09-17-2007 9:56 AM RAZD has replied

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


Message 70 of 216 (422463)
09-17-2007 9:22 AM
Reply to: Message 65 by Rob
09-17-2007 12:31 AM


adenine again
Well that's strange... because it cearly says in the abstract above that, "The presence of adenine could not be confirmed.'
This is consistent with other tests that found lower levels of adenine than the other DNA type molecules, and this was in 1977, possibly the first attempt to isolate them.
So they cannot clearly discern it's synthesis from extraction either eh? No wonder Glavin and Bada were covering their bases about the oligomerization of HCN. But they're sure popular fellows in the right circles huh?
Not quite what they said Rob. Again you should read the paper not the abstract. This could be nothing more than scientific tenuousness.
They identified adenine this time though, along with the other DNA type molecules.
If you call not confirming the presence of adenine in the 1st one, and not being able to clearly distinguish methods of synthesis from extraction in the 2nd identification, then yes.
They identified adenine. They could not eliminate possibility of some being formed in process, but they still identified it. Capice?
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.
It answers the question of why water extraction did not find adenine. That can no longer be used as evidence that adenine was not there.
... but as it is, a lower temperature is the more efficient condition for synthesis. And this could have occured as the temperature was raised from anywhere from -80C to 100C. Though then, we would have to ask if the hydrolysis is fast or slow, and have some idea of the time given for possible synthesis.
In the quantities identified. These are people familiar with these processes, and they conclude that they found adenine on the meteor.
Another argument is that we have four meteors that have been studied so far: three where they identified adenine, and one where they did not (Tagish). Using the same extraction procedures, then IF the adenine was manufactured in the extraction process, why did they not identify any from Tagish?
Enjoy.

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RebelAAmericanOZen[Deist
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This message is a reply to:
 Message 65 by Rob, posted 09-17-2007 12:31 AM Rob has replied

Replies to this message:
 Message 72 by Rob, posted 09-17-2007 10:01 AM RAZD has replied

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


Message 74 of 216 (422485)
09-17-2007 11:31 AM
Reply to: Message 71 by Rob
09-17-2007 9:56 AM


But your're not talking about the real world. You're talking about the imaginary (once apon a time) pre-biotic world. And that is different from the real world. Your rock analogy is not analogous, because all of us have seen rocks fall.
When you can either (1) tell me the difference between the two rocks falling or (b) tell me how the molecular self-replication does not follow the rules of chemistry, you will have an argument.
Until then, all you are doing is wasting bandwidth on your argument from ignorance and incredulity.
None of us has seen prebiotic structures (as you are now calling them). They are organized right? Self replicating right?
People have seen self-replicating molecules. Declaring something doesn't happen because you haven't seen it happen just absolutely fails as a logical argument.
Enjoy.

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RebelAAmericanOZen[Deist
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This message is a reply to:
 Message 71 by Rob, posted 09-17-2007 9:56 AM Rob has replied

Replies to this message:
 Message 79 by Rob, posted 09-17-2007 9:25 PM RAZD has replied

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


Message 75 of 216 (422486)
09-17-2007 11:34 AM
Reply to: Message 72 by Rob
09-17-2007 10:01 AM


Re: adenine again
Unknown differences (some of the differences are known actually) in composition which affected the reactions.
God of the gaps argument. You are claiming that the process creates adenine. It did not do so on the Tagish meteor and it did not do so on the serpentine blanks (you know, those control pieces that they put through the same procedure and testing). Thus we know adenine was not synthesized from the extraction process chemicals.
As noted by Percy the presence or absence of adenine on Murchison does not mean that adenine was not available. What we have noted before is that we have either (A) adenine on the meteor of (2) compounds from which adenine is readily synthesized in a simple reduction environment, such as would be readily available in a pre-biotic earth. These are the only remaining explanations for the adenine identified from the Murchison meteor, and in either case adenine is delivered by the meteor from space to earth available for use.
Enjoy.
Edited by RAZD, : last P
Edited by RAZD, : .

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This message is a reply to:
 Message 72 by Rob, posted 09-17-2007 10:01 AM Rob has not replied

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


Message 82 of 216 (422651)
09-17-2007 9:53 PM
Reply to: Message 80 by kuresu
09-17-2007 9:41 PM


before and after ... it's another clue
You know, in Oklo.
And the Oklo natural reactors were discovered after the bomb was developed (and then the physics converted to "peaceful use" with nuclear reactors): they did not need to know that it was natural to develop the process or set in motion the laws of physics that are involved in nuclear reactors and bombs.
The rock continues to fall according to the laws of physics, not disturbed by the philosophical musings of Rob.
Enjoy.

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