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Author Topic:   Murchison Meteor Questions
Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
Joined: 06-01-2006


Message 38 of 216 (422135)
09-16-2007 2:08 AM
Reply to: Message 36 by kuresu
09-16-2007 12:16 AM


Re: Let's not make this a debate on design...
[qs]Kuresu:
Another interesting tidbit:
Initiation of replication begins with the binding of Cdc6/Orc1 to the origin in an ATP independent manner
DNA replication - Wikipedia
Wait, DNA replication without ATP!?!?
But in this case, that is only pertaining to intiation. There are an incredible number of processes involved before and after; all of which are necessary for replication.
Although mth (Archaeon Methanobacterium thermoautotrophicum H*) RFC (Replication factor C) differs in organization from its eukaryotic counterpart, it was shown to be functionally similar to eukaryotic RFC in: (i) catalyzing DNA-dependent ATP hydrolysis;
( http://www.jbc.org/cgi/content/abstract/275/10/7327 )
I added the (parenthesis info) in the quote for definition...
This study concurs:
We have recently found that one of the
three Orc1/Cdc6 homologues in S. solfataricus plays a direct
role in origin recognition, binding in an ATP-dependent
manner
to three conserved origin recognition boxes (ORB1,
2 and 3)...
...in order to load on DNA, the PCNA ring must be opened to allow admission of DNA to the central cavity. This
loading of PCNA is mediated by the clamp loader, replication
factor C (RFC), in a reaction that involves the hydrolysis of
ATP (reviewed in [13,14])
...
( http://www.biochemsoctrans.org/bst/031/0674/0310674.pdf )
Though this is quite enjoyable, has anyone seen the topic?
Edited by Rob, : No reason given.

This message is a reply to:
 Message 36 by kuresu, posted 09-16-2007 12:16 AM kuresu has not replied

  
Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
Joined: 06-01-2006


Message 40 of 216 (422140)
09-16-2007 2:33 AM
Reply to: Message 39 by crashfrog
09-16-2007 2:15 AM


Re: Good science
Crashfrog:
I can't have evidence for what is a contradiction in terms. There can't be any such thing as a "pre-biotic organism", because any organism by definition must be biotic.
Kuresu and I already went through this here: http://EvC Forum: Converting raw energy into biological energy -->EvC Forum: Converting raw energy into biological energy
And here: http://EvC Forum: Converting raw energy into biological energy -->EvC Forum: Converting raw energy into biological energy
Organism:
Merriam Websters 1 : a complex structure of interdependent and subordinate elements whose relations and properties are largely determined by their function in the whole.
en.wikipedia.org/wiki/ In biology and ecology, an organism (in Greek organon = instrument) is an assembly of molecules that influence each other in such a way that they function as a more or less stable whole and have properties of life.
That's exactly what prebiotic chemistry seeks to uncover... and you're right Crash... it is a contradiction in terms. But you don't seem to realize that you've turned everythng upside-down. You're the ones looking for what is a clearly a contradiction. And you're right again... you have no evidence.
Crash:
It was soley my intent to speak to your misunderstanding about what "falsifiable" actually means. Did you have a comment in response to my remarks on that subject?
No, because I agree with your analysis on the matter. The only difference is that you have it backwards. Your upside-down man...
Come to your senses and live....

This message is a reply to:
 Message 39 by crashfrog, posted 09-16-2007 2:15 AM crashfrog has replied

Replies to this message:
 Message 41 by crashfrog, posted 09-16-2007 3:14 AM Rob has not replied
 Message 44 by Percy, posted 09-16-2007 9:21 AM Rob has replied

  
Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
Joined: 06-01-2006


Message 45 of 216 (422186)
09-16-2007 11:11 AM
Reply to: Message 42 by RAZD
09-16-2007 7:40 AM


Re: There is nothing 'self' about replication. It takes a system!
Razd:
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.
There are moments like these... they happen often with certian members of EVC. And I for one would like to see moderator action. That's what a moderator in a debate would do for the audience.
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.
And then he accuses me of moving the goalpost. Pehpas it is so clear to the audience that it doesn't need to be pointed out...
Maybe it is my responsibility to simply ignore him.
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.
Razd:
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?

Well, we know that adenine can be sythesiszed by HCN. That is what Miller called 'the rock of faith'. You do remember the ground we've already covered?
As for the other molecules... I don't know if there is a rocess of sysnthesis for them or not.
I do know this; Glavin and Bada realize that the previous study used a mixture of pure nucleobases and therefore may not be a sufficient control to using mixtures of Murchison, who's chemical composition contains 'unknowns'. there is a lot of mystery surrounding Murchison. And a lot of disagreement. I think that is why some, like MattP, have decided it best to look elswhere for evidence of pre-biotic precursors.
As for controversy on Murchison (in this case the issue of chiralty) consider this article entitled, 'Murchison's Amino Acids: Tainted Evidence?': http://www.astrobio.net/news/modules.php?op=modload&name=...
Razd:
Further, IF it was formed, THEN there were still the molecules from which it was formed available for the formation of adenine.
Now that I can agree with...
But your side has no bilogically plausible explanations for constructing a self replicating cycle without invoking environments that are destructive to life. If you could find life on other planets or mooons with different environments then you'd have something. But if you'll take the time to watch documentaries like 'The Privilaged Planet': https://www.youtube.com/watch?v=tQdxRj49m5c , you'll see that life shouldn't even exist here in terms of probability. And the conclusions are based upon actual evidence.
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 the other point is that you guys are the ones who always lecture about evidence. Your 'the superior and disciplined methodological naturalists' among us simple folk, who demand to see evidence of everything. But you have none.
Percy is trying to make it sound as if I am arguing against a negative to infer design. That is not so... it is Kuresu and JavaMan who brought up design in this thread. I only discussed it in defense.
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.
Got any?

This message is a reply to:
 Message 42 by RAZD, posted 09-16-2007 7:40 AM RAZD has replied

Replies to this message:
 Message 51 by RAZD, posted 09-16-2007 5:29 PM Rob has replied

  
Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
Joined: 06-01-2006


Message 46 of 216 (422188)
09-16-2007 11:22 AM
Reply to: Message 44 by Percy
09-16-2007 9:21 AM


Re: Good science
Percy, what are yu talking about? I am not trying to infer design by proving a negative. A negative cannot be proven. I amy be relatively idiotic at times, but I am not a complete dolt!
I am simply showing that you have no evidence to stand on. You boys simply assume that life evolved, and did so in a certain way even though there is no evidence for it.
You start out with the assumption that there is a material explanation even without any evidence to support the assumption.
Percy:
By the fundamental nature of the style of argument you're using you cannot prove the insufficiency of natural explanations for abiogenesis. You must therefore take another tack, which is to provide evidence supporting supernatural explanations, which would, of course, be way off-topic. But enumerating things science does not know as if they constituted evidence for the supernatural is merely the old "god-of-the-gaps" argument, and this thread is really just a smokescreen for you to push this argument, which is also off-topic.
I didn't invoke design in this thread, Kuresu did, and I think JavaMan as well. I only defended my position because of their questions. They don't like being questioned in the manner I am doing so here in this thread, so they attempted to put me in the hot-seat and change the paradigm (topic).
My only intent here is to remind you that empiricism requires evidence before the theory is valid. And in the case of abiogenesis there is none. It is actually an assumption in spite of the evidence. And that has nothing to do with design...
I think you're trying to make it sound as if I am doing something that I am not (getting off topic), so as to invoke moderator action. If that is true, you deserve a suspension.
Personally, I suspect your just lost in confusion...
I welcome moderator action here. I tried to warn about it earlier when crash piped in. I saw the writing on the wall.
I am not on trial here. The Murchison extraction procedures are.

This message is a reply to:
 Message 44 by Percy, posted 09-16-2007 9:21 AM Percy has replied

Replies to this message:
 Message 47 by Percy, posted 09-16-2007 2:19 PM Rob has replied

  
Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
Joined: 06-01-2006


Message 48 of 216 (422248)
09-16-2007 4:39 PM
Reply to: Message 47 by Percy
09-16-2007 2:19 PM


Re: Good science
Percy:
You are correct that abiogenesis, the development of life from non-life, assumes natural processes, but that is true of all science.
To be more precise, it is true of the 'current definition' of science (methodological naturalism). But if science were to be objective (as it was historically) it would simply look at the evidence without regard for imposing materialistic expectations. It would be simple empiricism once again, with theories that corrospond to reality.
That used to be what science was under a design paradigm, but the materialist philosophers have taken over...
Empiricism: 2 a : the practice of relying on observation and experiment especially in the natural sciences b.
If you design experiments that are assumed to reflect reality because it makes good sense materially, that is not the same thing as observing real evidence.
The definition of science should be, observation of the facts and the formulating of theory that is coherent and consistent with those facts as proven by experimentation (that is what empiricism is...). That way, you cannot invoke material explanations that are not even rooted in evidence. You guys assume the existence of evidence that does not exist. And then you produce and create experiments to give evidence for you presuppositions.
Methodological naturalism has taken such extreme license, that it has actually abandoned empiricism. And it does so as Lewontin points out, purely on it's a priori commitment to materialism. And that is why the Lewontin quotes were relevant. Because he is absolutely right, in spite of any irrelevant concensus.
Facts are not arrived at by concensus, but by empiricism. And that is what you have abandoned.
Percy:
Getting back to the actual point, what Javaman was saying, and I concur, is that you seem to believe that the absence of adenine in the Murchison meteor is evidence against a natural origin for life.
It leads me to believe that you still don't understand that you're trying to prove a negative.
C'mon Percy... I don't think that an absence of evidence is evidence at all!
It has nothing to do with proving a negative. It has to do with your approach not even being scientific in the historical sense. Your obsolete. There's a 'new revolution'...
"There is tremendous irony and a hideous paradox hiding in the philosophy of the natural sciences in our modern academies. It rejects the founding, and historically scientific view of explanation by design, though many of the founders of modern science used design as their starting presupposition. They rejected this view based upon the lack of current evidence in their own time for a supposed designer. Yet in turn, this modern descendant of the revolutionized institution, invokes material explanations that have no basis in the current evidence of our time."
Before I tell you, do you know who gave that quote Percy?
Kind of reminds me of The Who (if you'll pardon the lighthearted humor). They had a famous line at the end of the song, 'Won't Get Fooled Again':
"Meet the new boss... Same as the old boss!"
Edited by Rob, : No reason given.

This message is a reply to:
 Message 47 by Percy, posted 09-16-2007 2:19 PM Percy has replied

Replies to this message:
 Message 59 by Percy, posted 09-16-2007 9:28 PM Rob has replied
 Message 67 by kuresu, posted 09-17-2007 4:19 AM Rob has replied

  
Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
Joined: 06-01-2006


Message 50 of 216 (422250)
09-16-2007 5:27 PM
Reply to: Message 49 by Ken
09-16-2007 5:08 PM


So far so good as Buzz said...
I also thought the topic was wandering, but in the past I have argued that these topics are all intertwined. So... maybe I'm getting a taste of my own medicine.
I also know that AdminBuzzsaw is keeping a watch over the thread, and so far no foul called (and he is a brother). So... it must be staying close enough to be within parameters. Not to mention that this is Percy's forum, and if anyone has drifted off topic it is he and I.
As for molbiogirl, she is already aware of the thread I assure you. She has thus far not participated for whatever her reasons. It happens. I have not always participated in threads that were in response to me either. I'd just asume not have her around, we already have a Razd .
Anyway we best not get chatty. How about you Ken, have you any thoughts or questions that have yet to be answered?
Edited by Rob, : No reason given.

This message is a reply to:
 Message 49 by Ken, posted 09-16-2007 5:08 PM Ken has not replied

Replies to this message:
 Message 58 by AdminBuzsaw, posted 09-16-2007 9:21 PM Rob has not replied

  
Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
Joined: 06-01-2006


Message 52 of 216 (422271)
09-16-2007 6:29 PM
Reply to: Message 51 by RAZD
09-16-2007 5:29 PM


Re: adenine - the spice from space
You started off with some good questions, the same questions I have myself. And the best one's to question my position. I just cannot answer them with the limited knowledge of chemistry I currently have. I do think I can help you formulate them more accurately. And then perhpas an actual PhD like MattP can hlep us answer them. Though he seems to have stepped aside.
Razd:
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.
That is a bit confused.
I don't know that most studies found adenine. The formic acid extractions found adenine but couldn't be quantified because of the unknown UV barrier. Your either forgetting the data already covered, or rewriting history for late-comers to the thread.
There were at least two water tests, and at least one direct sample test that I cited in the OP that came up negative. And from what I gather, the earliest tests of Murchison were negative btw. It was the later tests that had marginal results, and then Glavin and Bada found a way to supposedly sublime away the unknown barrier to reveal adenine; but it requires the additional acid prep over and above the initial incubation.
The other tests that found adenine used very hot HCL extraction methods.
Razd:
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.
I wandered the same thing... but Glavin and BAda mentioned the possibility, so I assmue that in some of these exchanges chemically, the HCN itself must be possible to produce durring the extraction. The other question is about temperature. 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).
I not only do not understand the effect this might have on the experiment, I also do not know (and assume they do not either, as they invoked the possibility) if the unknown composites in murchison could have skewed the results...
Now for some of your other comments:
Razd:
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.
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.
And you never answered my first question on the matter: Where did these scientists get these molecules? Were they taken from existing biological life? Or were they designed in the lab? Either way, it doesn't prove anything pertaining to abiotic chemistry. It's an illusion perforemd by modern magicians and though the crowds may marvel at your genius; count me out!
Razd:
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.
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.
The rest of your reply concerns mobiogirl's professer Rainer Glaser. I already covered this with her at the end of the last thread. My exuberance to refute her earned me a suspension since we were supposed to be giving summaries. Evidently she didn't know that and continued to offer debate points.
She also took his word for it based on authority. But glaser is running beyond the evidence.
Razd:
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.
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 deja vu!) It's a debate with molbiogirl all over agian:
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 explainsigns 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.
I am going to be sick (Percy, a 'puke emoticon' would be nice for moments like this)...
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 (Findings? Don't they mean 'theories') 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...
(btw had to point out that it needs the first step first. That's why it's called first. No self involved...)
...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.
Too bad it's just a computer model. Seems to need a lot of wiggling to me...
Theory is not evidence Razd. Nor are models. We call that theory too. Evidence is what you need the theory to match. That is what empiricism is...
This stuff is not empiricism. This is methodological naturalism run amuck! It's not scientific. It's scientific theory in a world of it's own design.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.

This message is a reply to:
 Message 51 by RAZD, posted 09-16-2007 5:29 PM RAZD has replied

Replies to this message:
 Message 55 by RAZD, posted 09-16-2007 8:21 PM Rob has replied

  
Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
Joined: 06-01-2006


Message 53 of 216 (422273)
09-16-2007 6:34 PM
Reply to: Message 49 by Ken
09-16-2007 5:08 PM


Ken:
RAZD seems to be the only ongoing participant arguing for the accuracy of the tests that claim to have found adenine.
Have you seen his citations that I have analyzed above? Strange evidence.
It's a revisiting of the debate here (deja vu): http://EvC Forum: Converting raw energy into biological energy -->EvC Forum: Converting raw energy into biological energy

This message is a reply to:
 Message 49 by Ken, posted 09-16-2007 5:08 PM Ken has not replied

  
Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
Joined: 06-01-2006


Message 57 of 216 (422334)
09-16-2007 9:11 PM
Reply to: Message 55 by RAZD
09-16-2007 8:21 PM


Re: adenine - the spice from space
Razd:
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 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...
Let's assume for simplicity that you yourself performed the experiments you cited for self replicating molecules:
You were not able to watch a natural self replicating cycle. If you were, then you could repeat the experiment as per your analogy. Instead, you have assumed the self-replication as per your a priori commitment to materialism. And then, you have proceded to construct (or design) an aparatus to show that it could occur without design. Beyond the self defeating aspects, you've proven nothing but the extraordinary lengths some will go to avoid the actual scientific method of empericism.
I know your having a hard time with this, so I'll put it another way...
You are assuming evidence that is not appearent, and then performing an experiment to supposedly verify and reproduce it. But you've reproduced nothing! You've only produced what your bias leads you to believe beforehand. And you've done so under environmental conditions that are irrelevant to the facts as we know them to be today. And under biological conditions that are irrelevant to the chiral aspects of all living organisms. You've found racemic mixtures that are irrelevant to chiral mixtures.
Razd:
Racemeic is irrelevant at this point (it's not part of the original topic and could easily be a topic on it's own).
One of your weaknesses, is that you don't read what has been presented to you.
From the OP:
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.
I think it's later at this point eh? I knew it would come up. MattP made reference to it serveral posts ago, and he was certainly on topic!
In order to believe what you do, you must go outside of science (empericism) and into the realm of metaphysics that are based upon materialist presuppositions. It may be valid, but it is not science. It cannot be proven, and it cannot be tested.
You have no evidence other than the evidence that is manufactured by design.
Razd:
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.
We've benn thorugh this logical fallacy already Razd...
Of course it doesn't necessarily mean that they wouldn't. But it certainly doesn't mean they occurred naturally. You assume that they did only because of your materialistic bias. That's not science or the evidence science requires based upon your won definition. Yours is a philosophical argument not a scientific one.
Science is supposed to be empirical. Anything less is only tentative theory, not proven science. It is called faith Razd. And you have deep faith in your worldview. That's ok... I do too in my own.
Do, you, understand, the, words, that, are, coming, out, of, my, fingers?
Razd:
The point remains that studies have found adenine: explain the results.
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.
It's not proof Razd. It's compelling, yet speculative. It's tentative, not emperical.
Razd:
Note you "highlighted" the following too, this time with my highlight:
"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?"
Well professor Glaser is obvioulsy a believer. But he doesn't bother to tell his audience about the questions surrounding the extraction process that are raised even by the scientists themselves. And why should he? They already believe the results even before they've been shown. They're methodological naturalists remember?
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.

This message is a reply to:
 Message 55 by RAZD, posted 09-16-2007 8:21 PM RAZD has replied

Replies to this message:
 Message 63 by RAZD, posted 09-16-2007 10:52 PM Rob has replied

  
Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
Joined: 06-01-2006


Message 62 of 216 (422375)
09-16-2007 10:31 PM
Reply to: Message 59 by Percy
09-16-2007 9:28 PM


Re: Good science
I really only need to address your first comment.
Percy: You are correct that abiogenesis, the development of life from non-life, assumes natural processes, but that is true of all science.
Rob: To be more precise, it is true of the 'current definition' of science (methodological naturalism). But if science were to be objective (as it was historically) it would simply look at the evidence without regard for imposing materialistic expectations. It would be simple empiricism once again, with theories that corrospond to reality.
That used to be what science was under a design paradigm, but the materialist philosophers have taken over...
Percy:
You're making things up. Empiricism is the view that reality is what we experience through the senses.
Actually, that would be 'emperical'. It is different from empericism, however they are related. The emperical is the veiw that reality is perceived by the senses.
em·pir·i·cal
Pronunciation: -i-k&l
Variant(s): also em·pir·ic /-ik/
Function: adjective
1 : originating in or based on observation or experience
2 : relying on experience or observation alone often without due regard for system and theory
3 : capable of being verified or disproved by observation or experiment
4 : of or relating to empiricism
As we see, the emperical does not necessarily incorporate both observation and experiment.
But in terms of natural science we are talking about empericism which does incorporate both sense evidence and experimentation.
em·pir·i·cism
Pronunciation: im-'pir-&-"si-z&m, em-
Function: noun
2 a : the practice of relying on observation and experiment especially in the natural sciences b : a tenet arrived at empirically
They say that anything follows from a falsehood. The rest of your post is a good example, though I don't mean that as an insult or that it isn't very confusing for all of us. I had this same confusion earlier. Mark24 and I had to iron out the difficulties.
I already knew what I was referring to here as far as definitions because of that earlier exchange with mark 24 in another thread which can be read here: http://EvC Forum: God caused or uncaused? -->EvC Forum: God caused or uncaused?
It was the philosophers like David Hume that changed the paradigm back in the 16th and 17th centuries Percy. They've confused whole generations since. I've discussed it at length elsewhere in many threads (for example: http://EvC Forum: Great Debate / The Humean Arguments -->EvC Forum: Great Debate / The Humean Arguments ) You aught to try and get hold of the concept.
So because of clever philosophers like Hume, you've got some things backwards Percy. My arguments against you are not doomed to failure, I'm afraid yours are.
I have the grounds of empericism here though I am not invoking them to show design. Abiogenesis does not, and that is what I am attempting to show in this thread. And I believe I have done so effectively.
Though I do not suppose to convince true believers in materialism such as yourself and Razd otherwise, I do believe that any objective readers or audience can perceive the difference.
Edited by Rob, : No reason given.

This message is a reply to:
 Message 59 by Percy, posted 09-16-2007 9:28 PM Percy has replied

Replies to this message:
 Message 68 by JavaMan, posted 09-17-2007 4:31 AM Rob has replied
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Rob 
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Posts: 2297
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Message 65 of 216 (422410)
09-17-2007 12:31 AM
Reply to: Message 63 by RAZD
09-16-2007 10:52 PM


This is going nowhere...
Razd:
... 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.
Well your rock analogy is a bit simplistic Razd...
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...
Razd:
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.
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?
Razd:
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.
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.
Rob:
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.
Razd: 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]
Razd:
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
Well that's strange... because it cearly says in the abstract above that, "The presence of adenine could not be confirmed.'
Razd:
[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
Now this one above takes a closer look. Check the last line in the quote:
quote:
Concentrations ranging from 114-655 ppb of the purines adenine, guanine, hypoxanthine, and xanthine were found to be present in acid extracts. All four biologically significant purines, as well as the pyrimidine uracil have been identified in meteorites. It was concluded that the suite of N-heterocyclic compounds identified in meteorites do not permit a clear distinction between mechanisms of synthesis such as the Fischer-Tropsch type, and other candidates.
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?
Razd:
So that is not conclusive (other than that they identified adenine as well).
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.
But you'd not be a scientist if you said so. You'd be a zealot!
Razd:
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.
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.
Razd:
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.
Well that's a much better argument in my opinion. And it actually mirrors some of the questions I had myself.
But Glavin and Bada do not mention the ideal temperature for adenine synthesis by oligomerization of HCN. They only point out that it is highly temperature dependant and innefficient at 100C.
You're assuming that a higher temperature would lead to higher yeilds, 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.
And we still don't know how the unknown material, or unique composition of substances in the meteor would affect the reactions, if at all.
Preliminary results indicate that the yield of adenine is approximately independent of temperature between -80 and 100C. We have also found that shorter hydrolysis times in 6 M HCl and hydrolysis at pH 8, which is a better prebiotic model, substantially increase the yield of adenine. In addition, there is no decrease in the yield during neutral hydrolysis because of the stability of adenine at pH 8.
( http://exobio.ucsd.edu/miller_99.htm )
Notice also the hydrolysis times for synthesis in HCL (which are relevant to some of the other extractions cited in the OP).
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.

This message is a reply to:
 Message 63 by RAZD, posted 09-16-2007 10:52 PM RAZD has replied

Replies to this message:
 Message 69 by RAZD, posted 09-17-2007 8:33 AM Rob has replied
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Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
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Message 66 of 216 (422414)
09-17-2007 1:15 AM
Reply to: Message 64 by AdminBuzsaw
09-16-2007 11:46 PM


Sorry Buzz... Percy...
So noted... my apologies. I was losing confidence that I could handle the situation. I guess I was just whining...
History seemed to be threatening to repeat itself. So, please note that any strength thus far, is not my own.
They'll be no more about it than that...
Edited by Rob, : No reason given.
Edited by Rob, : No reason given.

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Rob 
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Posts: 2297
Joined: 06-01-2006


Message 71 of 216 (422466)
09-17-2007 9:56 AM
Reply to: Message 69 by RAZD
09-17-2007 8:33 AM


Razd:
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.
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. None of us has seen prebiotic structures (as you are now calling them). They are organized right? Self replicating right?
What Is Life?
It will be necessary to provide a definition of the basic requirements of life before it is possible to suggest what constitutes a minimal form of life. What is life? is a controversial scientific question because it is intimately associated with the particular scenario that the scientist is investigating for the origin of life. He/she does not want a definition that would invalidate their paradigm of the origin of life. The definition of life was the topic of a recent paper by Luisi (1998). He provided a brief review of the definitions put forward over the past 100 years and then focused his discussion on recent definitions. The simplest is, "Life is a self-sustaining chemical system undergoing Darwinian evolution." He proposed a modification of this definition for "adherents of the RNA world" that life is "a population of RNA molecules (a quasi-species) which is able to self-replicate and evolve in the process." I will use the modified definition not only because I am one of those "adherents" but also because it provides a useful metric (RNA) for the size of primitive life. As Luisi noted, this definition implies the presence of an external source of energy and/or reactive nutrients to maintain the life. It also specifies the need for RNA but no other molecular species, but it is likely that some other organics were required.
Many scientists feel that this definition of life is inadequate because it does not require that this first life was protected from the vagaries of the environment on the primitive Earth by a surrounding compartment. This more complicated model of life was defined by Luisi as "a system which is spatially defined by a semipermeable component of its own making and which is self-sustaining by transforming external energy/nutrients by its own process of component production." Here I will also make the assumption that genetic information was also stored in RNA in this model of life. This more elaborate life-form may require additional biomolecules such as proteins for the synthesis of the monomers required for the biopolymers and the membrane.
It should be noted here that other biopolymers are also under consideration as either precursors to the RNA world or alternatives to it. For example, peptides have been synthesized in the laboratory (not by "prebiotic reactions") that are self-replicating by template-directed ligation (Lee et al., 1996; Severin et al., 1997).
I like that last line too. It relates to our discussion on adenine that you enjoyed so much. It's the difference between designing (synthesizing) and extracting (discovering). You obvioulsy have a difficult time percieiving the difference. From your rebellious Zen Desit perspective, you can do pretty much say anything you want eh Razd?
Razd:
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 inclusion of a designer (in this case biochemical engineers) automatically detracts from being 'self'. I suppose it does prove that once a designer designs a self-replicating life form, that said life can then operate relatively autonomously. Others can see this Razd. Only the blind materialists have a problem understanding it.
Razd:
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.
And here is your problem of evidence again. Where does it occur naturally? All you have is the experiment... but what are you trying to reproduce?
You can't reproduce something that has never been observed. You have only produced!
Razd:
I would say that this is fundamental to your misunderstanding of how science operates across the board.
Science tries to confirm the agreement between evidence and theory by testing. Theory is just theory. It only means that it is possible under a given set of laws. For example, just because the bomb worked for Einstein, doesn't mean bombs have been made in nature that are anything like 'the bomb'.
Science is empiricism. Theory is tentative. And theory does not necessarily corrospond to reality. If it did, we wouldn't need science would we?

This message is a reply to:
 Message 69 by RAZD, posted 09-17-2007 8:33 AM RAZD has replied

Replies to this message:
 Message 74 by RAZD, posted 09-17-2007 11:31 AM Rob has replied

  
Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
Joined: 06-01-2006


Message 72 of 216 (422468)
09-17-2007 10:01 AM
Reply to: Message 70 by RAZD
09-17-2007 9:22 AM


Re: adenine again
Razd:
IF the adenine was manufactured in the extraction process, why did they not identify any from Tagish?
Unknown differences (some of the differences are known actually) in composition which affected the reactions.
Go to go to work now...

This message is a reply to:
 Message 70 by RAZD, posted 09-17-2007 9:22 AM RAZD has replied

Replies to this message:
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Rob 
Suspended Member (Idle past 5879 days)
Posts: 2297
Joined: 06-01-2006


Message 76 of 216 (422592)
09-17-2007 8:07 PM
Reply to: Message 67 by kuresu
09-17-2007 4:19 AM


Re: Good science
Kuresu:
So your problem with including the supernatural in science is two-fold: you need verifibale empirical evidence that such exists, and then you need to be able to differentiate between super-caused and natural-caused.
Can you do that? If so, you're the first.
Where in this thread have I invoked the supernatural?
The only thing even hinting at it, are my comments to Razd that biochemical engineers desigining evidence really only proves that design is cabable of creating self replicating systems.
I have been questioning abiogenesis, and the supposed 'evidence' to support it. So let's change a couple words in your statement so that they actually reflect the point of the thread (I'll do that last). I am asking questions. And you are answering by accusing me of doing exactly what you are doing, rather than offering any proof. I gave you proof of replication being dependant upon ATP when you questioned me. Now give me some proof for abiogenesis...
The best part is... it was Razd who offered citation for emperical proof of the fact that intelligence can design. I never brought it up once.
I've not designed this thread for the purpose of defending design. But rather to see how well abiogenesis can be defended when asked to present emperical evidence.
You comment reflected back at you:
So your problem with including the purely theoretical in science is two-fold: you need verifibale empirical evidence that such exists, and then you need to be able to differentiate between designed-caused and natural-caused.

This message is a reply to:
 Message 67 by kuresu, posted 09-17-2007 4:19 AM kuresu has not replied

  
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