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Author | Topic: Murchison Meteor Questions | |||||||||||||||||||||||||||||||||||||
Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
Note to Admin: I would like leniency for the OP length since this will focus on more technical matters.
A significant portion of the thread: http://EvC Forum: Converting raw energy into biological energy -->EvC Forum: Converting raw energy into biological energy Converting raw Energy into Biological Energy centered on the necessity of adenine in biology. In molbiogirl's last post of the thread she repeated the claims (that turn out to be plentiful) that adenine has been found in the Murchison meteor. I wish to challenge that claim. The number of hits on articles and pages that speak of the Murchison meteor and Stanley Miller in the same breath is amazing. And it’s no coincidence. There are specifically two noticeable similarities between Miller’s experiments and Murchison; chiralty, and the synthesis of adenine or other biological chemicals. Both are as questionable and ambiguous as the Miller experiments that mirror them. I’d like to focus on the synthesis of Purines first. The issue of chiralty can be discussed later. Let’s begin with a quick recap of what Michael Behe said on page 150 of Darwin's Black Box, as it pertains to the artificial synthesis of adenine: Chemists who want to synthesize adenine, however, use completely different routes from that used by cells. Because they involve reactions in oily liquids at extremes of acidity, these conditions would cause the quick demise of any known organism. In the early 1960s scientists who were interested in the origin of life discovered an interesting way to synthesize adenine. They saw that the simple molecules of hydrogen cyanide and ammonia- which are thought to have been plentiful in the early days of earth- will form adenine under the right conditions. The ease of the reaction so impressed Stanley Miller that he called it "the rock of faith" for origin-of-life researchers. But there's a problem lurking in the background: Hydrogen cyanide and ammonia are not used in the biosynthesis of AMP. Here are some excerpts from molbiogirl's own link http://www.lpi.usra.edu/meetings/lpsc2004/pdf/1022.pdf I want to examine this paper in sections, make observations, and ask questions for this thread.
Several purines including adenine, guanine, hypoxanthine, and xanthine, as well as the pyrimidine uracil, have previously been detected in water or formic acid extracts of Murchison using ion-exclusion chromatography and ultraviolet spectroscopy [3,4]. However, even after purification of these extracts, the accurate identification and quantification of nucleobases is difficult due to interfering UV absorbing compounds [3]... 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? In the previous studies, has anyone studying Murchison found adenine in aqueous solutions? Also, they note that the quantification is difficult even after formic acid extracts (ie. Can’t say for sure). Remember that for later . Here’s the acid prep:
...Sample Preparation and Sublimation Experiments: A powdered sample of the Murchison meteorite (104 mg) was sealed in a clean test tube with 1 mL of 95% formic acid (Sigma-Aldrich) and incubated in a heating block set at 100C for 24 h. As a control, 100 mg of crushed serpentine that had been heated in air at 500C for 3 h was processed similarly. Half of the formic acid extract was dried under vacuum, re-dissolved in double-distilled (dd) 0.01 M HCl and analyzed for purines and pyrimidines via HPLC separation with detection by UV absorption ( = 260 nm). The remaining formic acid extracts were then sealed separately under 0.5 Torr air in a quartz glass sublimation apparatus and heated in a tube furnace set at 450C for 5 min. A cold finger, attached to the sublimation tube was kept in liquid nitrogen throughout the entire experiment. After sublimation was complete, the apparatus was removed from the furnace and opened to atmospheric pressure. The residue on the end of the coldfinger was rinsed with 0.01 M HCl, and the resulting solution was analyzed by HPLC... Here’s the non-acid prep:
... In addition, a Murchison meteorite sample (105 mg) that had not been extracted in formic acid, was heated directly inside the sublimation apparatus... Acid results:...Prior to sublimation heating, the Murchison formic acid extract eluted as several small HPLC peaks with retention times similar to adenine, guanine, hypoxanthine, and xanthine, and possibly uracil (Fig. 1a). A large unidentified peak in the chromatogram with a retention time of ~ 5 min and showing significant tailing, made it difficult to accurately quantify these nucelobases, especially uracil, in the Murchison formic acid extract. However, this large non-volatile organic component was removed after sublimation of the Murchison formic acid extract at 450C and peaks corresponding to adenine, hypoxanthine, xanthine and uracil were readily identified (Fig. 1c). We did not detect any guanine after sublimation at this temperature, and although there are no apparent structural reasons for the low sublimation recoveries of guanine relative to other purines such as adenine, this finding is consistent with earlier reports [5,6]. There is another paper I must invoke here about the UV Problem that caused the peak and made the analysis uncertain before sublimation. I do so, because the researchers above, publish this paper as though it is a clearly identified substance. In reality, the Murchison samples are quite complex and not fully understood. Here is a link to the relevant paper: http://www.lpi.usra.edu/meetings/metsoc2004/pdf/5145.pdfI just love the language used (highlighted in bold). And keep in mind that both of these papers are from the same year. So this is not an old paper relative to the extractions in this case. The origin and distribution of purines and pyrimidines in carbonaceous chondrites is not yet constrained. Since nucleobases are difficult to detect in carbonaceous chondrites due to their low abundance and underlying UV absorving material of unknown origin, an optimal extraction and purification procedure is still under development. Back to the original paper:No acid results: ...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].... Interesting . the control sample came up blank! But pure standard mixtures of nucleobases typically produce a positive result. Now here is the key to the puzzle in my opinion. And I suspect this is what a great deal of this thread will revolve around. Check it out:
...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... Wow! Sounds like some of that tentative science Percy was mentioning in the other thread . . What it doesn’t sound like, is the hard fact that molbiogirl has proclaimed it to be. -----------------------------Some other tests and papers with similar results: http://www.crustal.ucsb.edu/.../2005-2006/pdfs/Awards-06.pdf From Page 7:
The biological role of purines and pyrimidines as coding elements of ribonucleic acids (RNA) and deoxyribonucleic acids (DNA) have led to broad interest in the isolation, characterization and formation of these compounds and their related derivatives in meteorites (Folsome et al., 1971, 1973; Hayatsu (1964), Hayatsu et al., 1975; Van der Velden and Schwartz, 1977; Stoks and Schwartz, 1981 a,b, 1982;Pizzarello et al. 2001) .
“Broad interest? Hmm . do I hear motive?
. Geochemical studies of meteorites, especially Murchison, have provided some valuable clues about the mechanism of formation of other important organic compounds such as amino acids, via the Strecker-synthesis (Peltzer and Bada, 1978); however, attempts to establish a mechanism of formation for N-heterocycles remains problematic. The problems encountered in some of the earlier work are, in part, due to very different approaches in isolating and analyzing these N-heterocycles in carbonaceous chondritesFor example, Folsome (1971, 1973) examined charcoal absorbates of hot-water and hot formic acid extracts using GCMS and found mainly 4-hydroxypyrimidine, two isomeric methyl-4-hydroxypyrimidines and some non-biological compounds (e.g. pyrimidines, quinolizine). Curiously, none of the biologically occurring purines or pyrimidines was detected . . Oh how curious! Isn’t it curious? Don’t you think so? Enter; more acid, same article:
. This was followed up by Hayatsu et al. (1975) using both the Folsome et al. extraction method (1971, 1973) and much harsher extraction procedures (acid hydrolysis using 3-6 MHCL or trifluoroacetic acid) coupled to detection by direct probe MS without any further derivatization. They detected aliphatic amines and C2-C6 alkyl pyridines but no 4-hydroxypyrimidines via the Folsome et al. (1973) method. Using the stronger acids, two of the biological purines adenine and guanine were detected as well as the triazines melamine, cyanuric acid, urea and guanylurea, which have no known biological function. ------------------------------------------------------------------------------ Search for purines and pyrimidines in the Murchison meteorite - NASA/ADS
A 1-g interior sample of the Murchison CII meteorite was examined for the presence of purines and pyrimidines by dual-column ion-exclusion chromatography and ultraviolet spectroscopy. Xanthine, not previously reported in meteorites, was found to be the major purine liberated by extraction with formic acid, with a concentration corresponding to 2.3 micrograms per gram of meteorite. Guanine (0.1 ppm) and hypoxanthine (0.04 ppm) were also tentatively identified. The presence of adenine could not be confirmed. ------------------------------------------------------------------------------ Purines and triazines in the Murchison meteorite - NASA/ADS
Two samples of the Murchinson C2 chondrite were analyzed for organic nitrogen compounds, using mass spectrometry in combination with paper and thin-layer chromatography. Under mild extraction conditions (water or formic acid), only alphatic amines and some alkylpyridines were seen...
Same story!
. 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. So, as I said in message 1 of the parent thread OP that spawned this thread: I think that some of you have simply moved past the evidence and take for granted that it is possible based upon your 'methodological naturalist' bias. . So what’s the deal with Murchison? In my opinion, the complex mixture of compounds and the unknowns about Murchison make quantifiable and accurate results questionable. There is much that remains a mystery. For those who have broad interest in constraining the issue and finding adenine . It’s not time to celebrate yet. Since Murchison is a significant player in origin of life research, Origin of Life please... Edited by Rob, : No reason given. Edited by Rob, : No reason given.
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
Javaman:
Anyway, the theory that adenine was formed from basic chemicals in early earth history is only one of the theories about the origin of life. The theory isn't proven yet, and even if it's disproven, that doesn't disprove the general theory of natural biogenesis. I am aware of that. Abiogenensis cannot be disproven. And as Lewontin has said, that is one of the reasons that evolution is hopelessly metaphysical( http://EvC Forum: Converting raw energy into biological energy -->EvC Forum: Converting raw energy into biological energy ) Abiogenesis is as inseperable from evolution as the egg is from the chicken. I don't want any nonsense in this thread about evolution and abiogenesis being different subjects. All you have to do is read your next comment to see that they are inseperable. No one is trying to prove a negative. At least not I. Razd made a simmilar comment about negative proofs. That's not what's going on here. Just pointing out the lack of positive proofs on the part of scientists. Javaman: For example, some scientists believe that adenine must have been created later in the evolution of life, when there were already complex molecules capable of catalysing its manufacture. If this is the case then we wouldn't expect to find adenine in meteorites (except as part of some complex life form). Most excellent observation. I concur... Javaman: By the way, do you have a theory about where adenine came from? Did God create all this biochemical machinery at some point in time and then just let it run? For one thing, we're not going to let this thread turn into a totally different subject. This thread isn't about my beliefs. It's about the beliefs of scientists and the lack of evidence for them (in particular) the Murchison meteor. As for adenine, I don't need a theory. We know where it comes from. It is manufactured in the organisms as you said above. The case I am making here, is that to claim adenine was found in the meteor is false. As you said, the scientists did a pretty good job of laying it out honestly. But at first read, a layman could be convinced that it says otherwise. I really had to study it... Javaman: I'm impressed with your dedication to the cause - reading through a science paper is not the most exciting of tasks. It was actually quite enjoyable! Even if adenine had been found, it wouldn't have meant much to me since the parts are usless until they are put together in the right order. But it hasn't been found, and that means even more considering the adamant posture taken by molbiogirl in the last thread. Edited by Rob, : No reason given.
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
Very good JavaMan. I almost removed the questin becuse I finnaly understood it myself. But it serves the purpose of making others examine it carefully also.
I concluded the same thing Razd did. That certain chemicals were extracted in water, and that the purines were extracted in acid. As I said in the OP, my only reservation about what was said, is that the UV problem isn't clearly understood. For all I know, adenine has been extracted by water extraction elsewhere. I want to read those papers if they can be acessed. There were many papers that I wanted to read, but did not have a subscription to the particular journal. Some of them seemed to indicate problems with Murchison, but I cannot say for certain from only keywords. Here is one I'd like to read but cannot access: http://www.springerlink.com/index/Q710223054212574.pdf
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
I appriciate you contribution Matt. And your answer to the problem of adenine being somewhat 'anti-water soluble' (if I can put it that way) makes sense to me.
You also touched on something Razd said. I want to ask you about it... 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? Seems difficult to pin down form what I have read. I hope I am making myself clear... Let me put it this way also... When we use acids to extract a metal from it's ore for instance, we are extracting an actual element from the oxidizer. But atomically, the element is there. In the case of adenine or any other molecule, we are not dealing with an element. So, when we extract something such as adenine, and it is combined with other molecular material (effectively making it another compound altogether), how can we know if it was there to begin with if we do not understand the processes that led to it's current state? If in the process of extraction, we have altered the molecule so as to essentially synthesize it, then we have not discovered adenine. The question is, 'can we be sure in this case'? I don't think so. It appears emperically fuzzy though compelling. MattP:Adenine is sparingly soluble in water. In life, adenine is made a factor of 100-1000 times more soluble by the addition of ribose and phosphate. Back to ATP we are... I haven't read your paper yet, but will. In your opinion, has adenine been (in spite of the issue of handedness) conclusively found in the murchison meteor establishing it's existence outside of biological organisms? Hope I asked some intelligent (even if possibly sophomoric) questions. Edited by Rob, : No reason given.
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
Razd:
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). As to your first comment, that is the question... I'm not so sure yet! I agree with the second part, but it ties into the first. You may want to see my resopnse to MattP in message 18 above. I am asking questions in order to understand it better myself.
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
JavaMan:
Now, let me ask you some questions. You've seen a bit of what goes on in scientific research now (especially how dull it can be ). So what do you think of this methodologically naturalistic approach to answering the question, 'Does the Murchison meteor contain adenine?'? Do you think it's likely to find the answer one way or the other? Or do you think there's a better way of asking the question? Or maybe you don't think we should be asking the question at all? Aren't you a clever fellow... Well... just so you know, I think it is quite appropriate in this case. Though I do not think one must be a 'methodological naturalist' to be a believer in empiricism. That's why I am asking the questions that I am... 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 empirical evidence for biological organisms. 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? And if anyone wants to debate this, take it to another thread. Been there done that! See here: http://EvC Forum: Converting raw energy into biological energy -->EvC Forum: Converting raw energy into biological energy Edited by Rob, : No reason given. Edited by Rob, : No reason given.
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
Razd:
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?) Well that's strange... because viruses cannot evolve or replicate without a complete cell. What is life? I think you nailed it with your description 'replicating mechanism'. We don't want to get into a debate about the definition of life here. For the record, I believe that the proper definition is an autonomous self replicating system. In fact I found that very definition in a scientific paper while searching for info on Murchison. It confirmed my own thoughts on the matter. This was discussed in the parent thread: http://EvC Forum: Converting raw energy into biological energy -->EvC Forum: Converting raw energy into biological energy Kuresu asked the same question in different words. You can then read my response. Razd: 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). 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. 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. 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 . This was followed up by Hayatsu et al. (1975) using both the Folsome et al. extraction method (1971, 1973) and much harsher extraction procedures (acid hydrolysis using 3-6 MHCL or trifluoroacetic acid) coupled to detection by direct probe MS without any further derivatization. They detected aliphatic amines and C2-C6 alkyl pyridines but no 4-hydroxypyrimidines via the Folsome et al. (1973) method. Using the stronger acids, two of the biological purines adenine and guanine were detected as well as the triazines melamine, cyanuric acid, urea and guanylurea, which have no known biological function. ...go read their whole paper in the OP. Razd: 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?" 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'. As MattP showed in his response. These chondrite samples are clearly not terrestrial in terms of chiralty. They only prove that abiotic processes can produce biological compounds that are "not consistent with terrestrial material, 2) there is not a major handedness to these molecules (both forms are produced in ratios ~50:50, or at most 40:60), and 3) there is a host of decidedly non-biologic organic compounds also detected in extracts." ( http://EvC Forum: Murchison Meteor Questions -->EvC Forum: Murchison Meteor Questions ) 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! 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. And those conditions are not even compatible with each other. We need 'one set' of environmental conditions to show a prodution of one compound, and an entirely different set of conditions for the production of another. I think Occam's razor is haunting you... you are simply supporting the production of evidence, not the examination of existing evidence. 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. 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. 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. Anyway, thanks for your opinions Razd. Perhaps we can all work on the other questions together. Edited by Rob, : No reason given. Edited by Rob, : No reason given. Edited by Rob, : No reason given.
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
MattP:
However, as RAZD has explained in part, the extraction of adenine by formic acid and water from Murchison is not equivalent to the formation of adenine in an artificial laboratory setup. Well why then did Glavin make the following comment in his paper: 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... And I am a little cofused as to the temperature... was it 100c or 450c?
A powdered sample of the Murchison meteorite (104 mg) was sealed in a clean test tube with 1 mL of 95% formic acid (Sigma-Aldrich) and incubated in a heating block set at 100C for 24 h. As a control, 100 mg of crushed serpentine that had been heated in air at 500C for 3 h was processed similarly. Half of the formic acid extract was dried under vacuum, re-dissolved in double-distilled (dd) 0.01 M HCl and analyzed for purines and pyrimidines via HPLC separation with detection by UV absorption ( = 260 nm). The remaining formic acid extracts were then sealed separately under 0.5 Torr air in a quartz glass sublimation apparatus and heated in a tube furnace set at 450C for 5 min. This is very confusing since different temperatures were used at different times. And appearently some samples were exposed to acids of differring strength twice. Any thoughts or observations are welcome...
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
Crashfrog:
You can't disprove a correct theory, except with evidence that doesn't exist I agree wholeheartedly!So, do youhave any evidence for prebiotic organisms that dispove the appearence of design in the biotic organisms in light of their de novo appearence? note to admins.. if the discourse between Crash and I get's prickly, please shut him down. I'd really like to keep things civil. Intelligent questions and intelligent answers. I'll just ignore extreme sarcasm.
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
Rob: 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 asked, was because we have a whole planet full of emperical evidence for biological organisms. Razd: The answer is we don't know. Huh? 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. And that's what this is about... where did we get the parts? 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. How do we take 'natural dust' (if you will) that is racemic, and transform it into chiral molecules and put all of the pieces together? The natural cannot explain the unnatural. If nature builds racemic mixtures, what does that tell you about biology that is chiral?
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
Percy:
All that science can do is offer evidence in support of a hypothesis That would be nice... Percy:By definition, science focuses on the natural. Science investigates the origin of life by natural processes because science investigates all natural phenomena under the assumption that their underlying causes are natural. You are absolutely correct! And that assuption cannot be proven with evidence. Therefore, your method is not scientific since science is supposed to be about evidence. It is a philsophical assumption repleat with bias. Let the evidence speak... As you said, this response (and your own) belongs in another thread. If, as the lead admin and facilitator of this forum, you will not resort to invoking off topic concepts to refute my own on-topic debate points, I will not respond with off topic responses in order to defend myself. Percy, I very much appriciate your promoting this topic, and for the mysterious lifting of my suspension, but do you have anything to contribute to the discussion on the Murchison extrations?
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
Kuresu:
This would require that you too, be civil. Yes, that is right. And looking back, we all have some room to grow. As Buzz said, so far so good. Sorry if I made it sound as if it was a one-sided equation. Clearly it is not. Kuresu: On another note, I find it funny that a lot of pro ID (pro-creo) people argue that there is the appearance of design. Stating "appearance" suggests that it's not necessarily actually designed. Looks aren't everything. Well, at least it is there to see... I mean, if we could see any evidence of an suprisingly simple, self-replicating system other than the incredibly complex biological organisms we do see (one capable of operating directly from energy other than ATP woudl be nice), it would appear to be reasonable to assume that it could have happened guided by nothing other than chemical laws and a little influx of energy. But as it stands generally, a dog looks like a dog, a man looks like a man, a fish looks like a fish, and design looks like design. What does 'undesign' look like? Why did Francis Crick make the comment that, 'we must constantly keep before our minds, that these systems were not designed, but evolved'. I'll tell you why... because they scream of design! Kuresu: Well, is there design or isn't there? Well... do you have any comments regarding the extraction of adenine from the Murchison meteor? Because they appear to be well designed, or perhaps it would be better to say, 'crafted'; to produce a desired result. I answered your questions... but let's not make this a debate about design. Clearly, some things are designed. That is what the evidence indicates. Since the parent thread related to energy conversion, do you have evidence of life that is undesigned and strictly natural by way of eliminating ATP as an energy source? That's what the hoopla about adenine is about... That would at least be more relevant to the topic. Edited by Rob, : No reason given.
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
Razd:
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. I just don't know what to say... 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? I simply am at a loss for words... And what does this mean? Razd: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. You are assuming the existence of non cellular life without any evidence? Yet you lecture me about naturalism and empiricism? 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! Razd: 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. 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. 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. And here you do it again... Razd: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. 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. Razd: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. And what does the evidence show? The evidence shows organisms that convert energy of differing types into ATP. Your argument would be effective if some life converted different energy sources into different biological energy, or directly used a raw source of energy to fuel itself. But that is not the case. All organisms convert energy into ATP. Not a lot of diversity there to suggest evolution. All of your assumptions as to things being different biologically are just that; assumptions. You have no evidence to give. In fact, the evidence itself rebukes you.
Rob: And let's be clear, there is no evidence for self replicating molecules. Razd:There are several examples of molecules that are self-replicating, some mentioned on Thread 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. Just wave your magic wand is that it? I don't think so... From your article: First, a self-replicating 32-amino-acid peptide can autocatalyse its own synthesis by accelerating the amino-bond condensation of 15- and 17-amino-acid fragments in solution (29 Kauffman 1996). Then there is the amino adenosine triacid ester (AATE) that replicates by attracting to one of its ends anester molecule, and to its other end an amino adenosine molecule. These molecules react to form another AATE. The ''parent'' and ''child'' AATE molecules then break apart and can go on to build still more AATE molecules (30 Mallove 1990).These experiments are such convincing demonstrations of self-replication by non-living molecules that even extremely skeptical organizations like AnswerInGenesis (AIG) do not dispute the formation of the phenylalanine, tyrosine, and glycine peptides (31 Sarfati) or that the AATE molecules formed new ones (32 Sarfati 2002). 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. 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? As I said before, there is nothing self about replication. You offer nothing but assumptions and give no evidence to support them. Your materialistic bias is shining for all to see in spite of your clammoring for empiricism. I am stunned!
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
Rob: I'll tell you why... because they scream of design! Kuresu: And such is not the case. Unless you think that life is designed by mutation and natural selection. That's not what I think... I don't think natural selection has anything to select until said organism is there to begin with. You cannot mutate what does not exist. That should be obvious to all... Kuresu: Let me ask you a question rob. Can chemical reactions occur without ATP? Can biochemical reactions occur without ATP? Many of them can of course... but not replication. So without ATP there is no natural selection. So natural selection cannot explain the arrival of ATP as a universal biological necessity.
Regulation of DNA replication is achieved through several mechanisms. Mechanisms of regulation involve the ratio of ATP to ADP, the ratio of DnaA protein to DnaA boxes and the hemimethylation and sequestering of OriC. The ratio of ATP to ADP indicates that the cell has reached a specific size and is ready to divide. This "signal" occurs because in a rich medium, the cell will grow quickly and will have a lot of excess ATP. Furthermore, DnaA binds equally well to ATP or ADP, but only the DnaA-ATP complex is able to initiate replication. Thus, in a fast growing cell, there will be more DnaA-ATP than DnaA-ADP. ( http://dna_replication.totallyexplained.com/ ) Edited by Rob, : No reason given.
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Rob  Suspended Member (Idle past 5879 days) Posts: 2297 Joined: |
Kuresu:
Also note that a very key enyme in DNA replication is DNA polymerase (it doesn't exactly start the process as I understand it, but it makes copying DNA a lot easier). ATP is not, as far as I can tell, a part of DNA polymerase. But then, you're the one claiming that ATP is necessary for DNA replication. How about finding conclusive evidence for that? You're quote doesn't support your position, and the issue of ATP is not addressed by the rest of the article (or even by the wiki).
Kuresu, you do know that Wiki doesn't cover everything right? ATP is involved in multiple functions. I was only giving one example. Do you think I make assertions without having at least some knowledge of what I'm talking about? I may only be a truck driver (and inapropriately impatient at times) but I am not stupid or dishonest. I don't know all of the functions of ATP in biology, but I do know they are effectively endless...
Division of labor--sequential ATP hydrolysis drives assembly of a DNA polymerase sliding clamp around DNA. ( NCBI ) The beta sliding clamp encircles DNA and enables processive replication of the Escherichia coli genome by DNA polymerase III holoenzyme. The clamp loader, gamma complex, assembles beta around DNA in an ATP-fueled reaction. Previous studies have shown that gamma complex opens the beta ring and also interacts with DNA on binding ATP. Here, a rapid kinetic analysis demonstrates that gamma complex hydrolyzes two ATP molecules sequentially when placing beta around DNA. The first ATP is hydrolyzed fast, at 25-30 s(-1), while the second ATP hydrolysis is limited to the steady-state rate of 2 s(-1). This step-wise reaction depends on both primed DNA and beta. DNA alone promotes rapid hydrolysis of two ATP molecules, while beta alone permits hydrolysis of only one ATP. These results suggest that beta inserts a slow step between the two ATP hydrolysis events in clamp assembly, during which the clamp loader may perform work on the clamp. Moreover, one ATP hydrolysis is sufficient for release of beta from the gamma complex. This implies that DNA-dependent hydrolysis of the other ATP is coupled to a separate function, perhaps involving work on DNA. A model is presented in which sequential ATP hydrolysis drives distinct events in the clamp-assembly pathway. We also discuss underlying principles of this step-wise mechanism that may apply to the workings of other ATP-fueled biological machines. Edited by Rob, : No reason given. Edited by Rob, : No reason given.
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