Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 64 (9038 total)
221 online now:
nwr (1 member, 220 visitors)
Newest Member: Barry Deaborough
Post Volume: Total: 885,690 Year: 3,336/14,102 Month: 277/724 Week: 35/91 Day: 3/17 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Murchison Meteor Questions
Rob 
Suspended Member (Idle past 4750 days)
Posts: 2297
Joined: 06-01-2006


Message 1 of 216 (421712)
09-14-2007 12:13 AM


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: www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=90&m=301#310 -->www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=90&m=301#310">http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=90&m=301#310 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 100ºC for 24 h. As
a control, 100 mg of crushed serpentine that had been
heated in air at 500ºC 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 (λ
= 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 450°C 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
450ºC 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.pdf
I 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 450ºC (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 100ºC [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/about/annual_reports/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.

------------------------------------------------------------------------------

http://adsabs.harvard.edu/abs/1977GeCoA..41..961V

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.

------------------------------------------------------------------------------

http://adsabs.harvard.edu/abs/1975GeCoA..39..471H

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.


Replies to this message:
 Message 4 by RAZD, posted 09-14-2007 8:23 AM Rob has not yet responded
 Message 5 by JavaMan, posted 09-14-2007 9:32 AM Rob has responded
 Message 7 by JavaMan, posted 09-14-2007 10:42 AM Rob has responded
 Message 9 by JavaMan, posted 09-14-2007 11:41 AM Rob has responded
 Message 16 by RAZD, posted 09-14-2007 3:40 PM Rob has responded
 Message 17 by Matt P, posted 09-14-2007 4:39 PM Rob has responded
 Message 49 by Ken, posted 09-16-2007 5:08 PM Rob has responded

  
Admin
Director
Posts: 12719
From: EvC Forum
Joined: 06-14-2002


Message 2 of 216 (421744)
09-14-2007 7:53 AM


Thread moved here from the Proposed New Topics forum.

  
Admin
Director
Posts: 12719
From: EvC Forum
Joined: 06-14-2002


Message 3 of 216 (421747)
09-14-2007 7:56 AM


Cautionary Notes
I'd like to issue a couple cautionary notes before discussion begins.

The failure of someone to understand your argument may be as much your own fault as theirs. Please take this into account.

Mistakes and missteps are part and parcel of the human condition. Please take this into account, too.


--Percy
EvC Forum Director

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


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


mountains out of molehills
Rob,

Sit back and read again.

Why did they use the word or when later in the article they make it clear that no purines were found other than in formic acid extracts?

Because some of the other compounds listed were found in water extracts.

{abe}

Since Murchison is a significant player in origin of life research, Origin of Life please...

Consider that even if adenine is not shown to be found on the Murchison meteor, that this will not diminish the number of 'organic' compounds that have been found on meteors. It will not disprove the possibility that such compounds formed in space and were transported to the early earth by meteors.

Do all the necessary elements for forming life need to come from meteors? Logically the answer is no.
{/abe}

Enjoy.

Edited by RAZD, : sp

Edited by RAZD, : added


Join the effort to unravel AIDS/HIV, unfold Proteomes, fight Cancer,
compare Fiocruz Genome and fight Muscular Dystrophy with Team EvC! (click)


we are limited in our ability to understand
by our ability to understand
RebelAAmericanOZen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.

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

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

  
JavaMan
Member (Idle past 1220 days)
Posts: 475
From: York, England
Joined: 08-05-2005


Message 5 of 216 (421755)
09-14-2007 9:32 AM
Reply to: Message 1 by Rob
09-14-2007 12:13 AM


Good science
I'm impressed with your dedication to the cause - reading through a science paper is not the most exciting of tasks :).

But what do you think your analysis has proven? To me the paper looks like good science. They've started off trying to prove that the meteorite contains the chemicals they're looking for, but have come to the conclusion that, despite all their attempts at extraction, they can't conclusively state that the chemicals are present. There's no trying to fix the results to prove what they want.

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.

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).

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?


'I can't even fit all my wife's clothes into a suitcase for travelling. So you want me to believe we're going to put all of the planets and stars and everything into a sandwich bag?' - q3psycho on the Big Bang

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

Replies to this message:
 Message 6 by Rob, posted 09-14-2007 9:59 AM JavaMan has not yet responded

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


Message 6 of 216 (421758)
09-14-2007 9:59 AM
Reply to: Message 5 by JavaMan
09-14-2007 9:32 AM


Re: Good science
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( www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=90&m=258#258 -->www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=90&m=258#258">http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=90&m=258#258 )

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.


This message is a reply to:
 Message 5 by JavaMan, posted 09-14-2007 9:32 AM JavaMan has not yet responded

Replies to this message:
 Message 10 by kuresu, posted 09-14-2007 11:56 AM Rob has not yet responded
 Message 13 by iceage, posted 09-14-2007 1:47 PM Rob has not yet responded
 Message 15 by crashfrog, posted 09-14-2007 2:58 PM Rob has responded
 Message 28 by Percy, posted 09-15-2007 9:11 PM Rob has responded

  
JavaMan
Member (Idle past 1220 days)
Posts: 475
From: York, England
Joined: 08-05-2005


Message 7 of 216 (421762)
09-14-2007 10:42 AM
Reply to: Message 1 by Rob
09-14-2007 12:13 AM


Re: Murchison Meteor Questions
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?

They are saying that other people have found these chemicals in water and formic acid extracts and they provide the references for this previous work (the [3,4] at the end of the sentence).

This is pretty standard form for a scientific paper. The introduction talks about the previous work that's been done in the field and quotes the appropriate references, then the authors explain what new work they're doing. In this case they're trying to improve extraction and isolation techniques for these chemicals:

However, even after purification of these extracts, the
accurate identification and quantification of
nucleobases is difficult due to interfering UV
absorbing compounds [3]. In order to reduce these
effects, we have developed an extraction technique
using sublimation [5] to isolate purines and
pyrimidines from other non-volatile organic
compounds in Murchison acid extracts.


'I can't even fit all my wife's clothes into a suitcase for travelling. So you want me to believe we're going to put all of the planets and stars and everything into a sandwich bag?' - q3psycho on the Big Bang

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

Replies to this message:
 Message 8 by Rob, posted 09-14-2007 10:54 AM JavaMan has not yet responded

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


Message 8 of 216 (421764)
09-14-2007 10:54 AM
Reply to: Message 7 by JavaMan
09-14-2007 10:42 AM


Re: Murchison Meteor Questions
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: www.springerlink.com/index/Q710223054212574.pdf


This message is a reply to:
 Message 7 by JavaMan, posted 09-14-2007 10:42 AM JavaMan has not yet responded

  
JavaMan
Member (Idle past 1220 days)
Posts: 475
From: York, England
Joined: 08-05-2005


Message 9 of 216 (421767)
09-14-2007 11:41 AM
Reply to: Message 1 by Rob
09-14-2007 12:13 AM


Scientific Controversy
From my cursory reading of the literature available, it looks like the question of whether the Murchison meteor contains biological compounds is still a matter of controversy. Some scientists still believe that the compounds that have been found are contaminants.

So, if molbiogirl claimed that adenine has definitely been found in the meteor, then she's overstating the scientific case.

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?


'I can't even fit all my wife's clothes into a suitcase for travelling. So you want me to believe we're going to put all of the planets and stars and everything into a sandwich bag?' - q3psycho on the Big Bang

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

Replies to this message:
 Message 20 by Rob, posted 09-15-2007 12:10 AM JavaMan has not yet responded

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


Message 10 of 216 (421769)
09-14-2007 11:56 AM
Reply to: Message 6 by Rob
09-14-2007 9:59 AM


Re: Good science
as Lewontin has said, that{abiogenesis} is one of the reasons that evolution is hopelessly metaphysical

Really? Can you point out where he says abiogenesis in your quote of Lewontin? All I see is this:
The theory of natural selection is then revealed as metaphysical rather than scientific

Your quote doesn't support your position (that abiogenesis makes evolution hopelessly metaphysical). If you can't even get what he's saying right, why should I trust the rest of your OP?

I don't want any nonsense in this thread about evolution and abiogenesis being different subjects.

Wait, are they the same because both are under "biology"?
Abiogenesis is dealing entirely with biochemistry. And how life got started. Evolution really doesn't need biochemistry. Evolution deals with life after it gets started.

That is why they are two different subjects. One studies how life is started, the other studies how life adapts and evolves (regardless of how life came to be in the first place).

To put them together is to build a strawman.

Now then, I have a question for you Rob. You really want to disprove all this abiogenesis stuff, right? Where's your alternative? Do you have one? Do you have evidence (non-scriptural) to support your alternative? Can your alternative explain the evidence any better than the current theories of abiogenesis?


This message is a reply to:
 Message 6 by Rob, posted 09-14-2007 9:59 AM Rob has not yet responded

  
Ken 
Inactive Suspended Member


Message 11 of 216 (421776)
09-14-2007 12:38 PM
Reply to: Message 4 by RAZD
09-14-2007 8:23 AM


Re: mountains out of molehills
RAZD writes:

Do all the necessary elements for forming life need to come from meteors? Logically the answer is no.

I agree with you that not all of the necessary elements for forming life need to come from meteors, but assuming that life began with naturalistic spontaneous generation, where else would these essential compounds have originated? According to David Berlinski in his commentary on the origins of life (I read it here)

According to the impression generally conveyed in both the popular and the scientific literature, the success of the original Miller-Urey experiment was both absolute and unqualified. This, however, is something of an exaggeration. Shortly after Miller and Urey published their results, a number of experienced geochemists expressed reservations. Miller and Urey had assumed that the pre-biotic atmosphere was one in which hydrogen atoms gave up (reduced) their electrons in order to promote chemical activity. Not so, the geochemists contended. The pre-biotic atmosphere was far more nearly neutral than reductive, with little or no methane and a good deal of carbon dioxide.

Nothing in the intervening years has suggested that these sour geochemists were far wrong. Writing in the 1999 issue of Peptides, B.M. Rode observed blandly that “modern geochemistry assumes that the secondary atmosphere of the primitive earth (i.e., after diffusion of hydrogen and helium into space) . . . consisted mainly of carbon dioxide, nitrogen, water, sulfur dioxide, and even small amounts of oxygen.” This is not an environment calculated to induce excitement.
A recent paper in Science has suggested that previous conjectures about the pre-biotic atmosphere were seriously in error. A few researchers have argued that a reducing atmosphere is not, after all, quite so important to pre-biotic synthesis as previously imagined.

In all this, Miller himself has maintained a far more unyielding and honest perspective. “Either you have a reducing atmosphere,” he has written bluntly, “or you’re not going to have the organic compounds required for life.”

So then, if the organic compounds required for life could not have already been present on earth, they must have been introduced.
In the thread that spawned this one, molbiogirl asserts that this was the case, citing Murchison as evidence, but all the missing pieces are not accounted for.
From the same article:

Among the questions is one concerning the nitrogenous base cytosine (C). Not a trace of the stuff has been found in any meteor. Nothing in comets, either, so far as anyone can tell. It is not buried in the Antarctic. Nor can it be produced by any of the common experiments in pre-biotic chemistry. Beyond the living cell, it has not been found at all.

When, therefore, M.P. Robertson and Stanley Miller announced in Nature in 1995 that they had specified a plausible route for the pre-biotic synthesis of cytosine from cyanoacetaldehyde and urea, the feeling of gratification was very considerable. But it has also been short-lived. In a lengthy and influential review published in the 1999 Proceedings of the National Academy of Science, the New York University chemist Robert Shapiro observed that the reaction on which Robertson and Miller had pinned their hopes, although active enough, ultimately went nowhere. All too quickly, the cytosine that they had synthesized transformed itself into the RNA base uracil (U) by a chemical reaction known as deamination, which is nothing more mysterious than the process of getting rid of one molecule by sending it somewhere else.

Robert Shapiro is not critical of just the synthesis of cytosine, but adenine as well.
In Origins of Life and Evolution of Biospheres he writes:

Many accounts of the origin of life assume that the spontaneous synthesis of a self-replicating nucleic acid could take place readily. Serious chemical obstacles exist, however, which make such an event extremely improbable.
Prebiotic syntheses of adenine from HCN, of D, L-ribose from adenosine, and of adenosine from adenine and D-ribose have in fact been demonstrated. However these procedures use pure starting materials, afford poor yields, and are run under conditions which are not compatible with one another.
Any nucleic acid components which are formed on the primitive earth would tend to hydrolyze by a number of pathways. Their polymerization would be inhibited by the presence of vast numbers of related substances which would react preferentially with them.
It appears likely that nucleic acids were not formed by prebiotic routes, but are later products of evolution.

Now that the rabbit trail has returned me to the topic, it seems that the assertion "Adenine has been found" by molbiogirl that adenine has been found in meteorites is, at the very least, questionable.


This message is a reply to:
 Message 4 by RAZD, posted 09-14-2007 8:23 AM RAZD has responded

Replies to this message:
 Message 14 by RAZD, posted 09-14-2007 1:51 PM Ken has not yet responded
 Message 167 by RAZD, posted 09-21-2007 9:23 PM Ken has not yet responded

  
Coragyps
Member
Posts: 5551
From: Snyder, Texas, USA
Joined: 11-12-2002


Message 12 of 216 (421785)
09-14-2007 1:32 PM


Putting Murchison on the shelf for just a moment, let's have a peek at the Tagish Lake meteorite instead. It was seen to fall, and the first bits were collected from atop the ice of a frozen lake within a week.
The Tagish Lake meteorite fell last year on a frozen lake in Canada and may provide the most pristine material of its kind. Analyses have now shown this carbonaceous chondrite to contain a suite of soluble organic compounds (~100 parts per million) that includes mono- and dicarboxylic acids, dicarboximides, pyridine carboxylic acids, a sulfonic acid, and both aliphatic and aromatic hydrocarbons. The insoluble carbon exhibits exclusive aromatic character, deuterium enrichment, and fullerenes containing "planetary" helium and argon. The findings provide insight into an outcome of early solar chemical evolution that differs from any seen so far in meteorites.

One of those pyridine carboxylic acids is more commonly called niacin: the stuff that's in One-A-Day vitamins.


  
iceage 
Suspended Member (Idle past 4816 days)
Posts: 1024
From: Pacific Northwest
Joined: 09-08-2003


Message 13 of 216 (421791)
09-14-2007 1:47 PM
Reply to: Message 6 by Rob
09-14-2007 9:59 AM


Good science or Bad Quote
.

Edited by iceage, : No reason given.


This message is a reply to:
 Message 6 by Rob, posted 09-14-2007 9:59 AM Rob has not yet responded

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


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


Re: mountains out of molehills
I agree with you that not all of the necessary elements for forming life need to come from meteors, but assuming that life began with naturalistic spontaneous generation, where else would these essential compounds have originated?

I'm afraid that would take this thread off-topic. For some answer though look at RAZD - Building Blocks of Life. This was written in 2005 so it is a little out of date on the progress that has been made since, however it talks about a number of possible chemical "factories" that could produce components of the first replication life system.

So then, if the organic compounds required for life could not have already been present on earth, they must have been introduced.

Logically false conclusion. Please take this post to the above thread for answers that will be more on topic, and I'll explain further if you need it (after reading the article).

Now that the rabbit trail has returned me to the topic, it seems that the assertion "Adenine has been found" by molbiogirl that adenine has been found in meteorites is, at the very least, questionable.

I look at this issue as having (at least) these four possibilities:

  1. there was adenine on the meteor in the sample where it was extracted with water, but not in the sample where it was extracted with acid.
  2. there was adenine on the meteor and it was extracted with water, while the acid extraction result was a false negative due to UV interference (but I would need to know more about this to understand).
  3. there was no adenine on the meteor, and the water extraction result was a false positive due to UV interference (but I would need to know more about this to understand).
  4. adenine was formed during the acid extraction process from other molecules existing on the meteor (as the process involved heat this is also available for the early earth in many areas).

From the article these excerpts:

quote:
A large unidentified peak in the chromatogram with a retention time of ~ 5 min and showing significant tailing, made it difficult to accurately quantify these nucelobases, especially uracil, in the Murchison formic acid extract.

We were unable to identify any purines or pyrimidines on the cold finger after heating the Murchison meteorite sample directly at 450ºC (Fig. 1b). This result is surprising since all of these nucleobases, with the exception of guanine, have previously been sublimed from a pure standard mixture at the same temperature with recoveries ranging from 50 to 85% [5]. The presence of a kerogen-like organic polymer in Murchison may inhibit the sublimation of these nucleobases directly from the meteorite [7].

It is important to emphasize that the purines identified in formic acid extracts of Murchison were not detected in water extracts [4]. This suggests that the purines are either bound to other organics, or were produced (e.g. oligomerization of HCN) during acid extraction.


At this point I don't know enough to know, if you know what I mean.

quote:
These preliminary findings need to be confirmed by gas chromatography mass spectrometry.

In the future, nitrogen isotopic measurements of the nucleobases in Murchison should be carried out in order to firmly establish the origin of these compounds.


Sounds like a plan.

Enjoy.

Edited by RAZD, : corrected #4, added quoted material

Edited by RAZD, : added last quotes.


Join the effort to unravel AIDS/HIV, unfold Proteomes, fight Cancer,
compare Fiocruz Genome and fight Muscular Dystrophy with Team EvC! (click)


we are limited in our ability to understand
by our ability to understand
RebelAAmericanOZen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.

This message is a reply to:
 Message 11 by Ken, posted 09-14-2007 12:38 PM Ken has not yet responded

  
crashfrog
Member (Idle past 368 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 15 of 216 (421800)
09-14-2007 2:58 PM
Reply to: Message 6 by Rob
09-14-2007 9:59 AM


Re: Good science
Abiogenensis cannot be disproven.

It can be disproven. You just have to prove, first, that there's absolutely no life on Planet Earth.

The problem you and Lewontin both seem to have is the fact that you can't seem to tell the difference between theories that can't be disproved because they're unfalsifiable and therefore bad science; and the theories that can't be disproved because they're not wrong.

You can't disprove a correct theory, except with evidence that doesn't exist. Lewontin's objection to the fact that evolution and abiogenesis can't be disproved with the current evidence is meaningless. If abiogenesis and evolution were wrong, there would be abundant evidence that this was so. That's a considerable difference from an unfalsifiable theory like those proposed by creationists, which can't be disproven by any conceivable, hypothetical evidence.


This message is a reply to:
 Message 6 by Rob, posted 09-14-2007 9:59 AM Rob has responded

Replies to this message:
 Message 24 by Rob, posted 09-15-2007 1:24 PM crashfrog has responded

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2021