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.
™ Version 4.2