Critique on Calilasseia's "The Emergence Of Life On Earth"

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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#21  Postby Katherine » Mar 04, 2010 1:13 pm

95Theses wrote:
i'm just bookmarking so I can watch the resulting carpet bombing.


And I am busy preparing a crack squadron of my finest cleaners! The street sweepers can't arrive until tomorrow... typical! :roll:

However, everything else is ready.... :mrgreen:
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#22  Postby rainbow » Mar 04, 2010 3:15 pm

Katherine wrote:
95Theses wrote:
i'm just bookmarking so I can watch the resulting carpet bombing.


And I am busy preparing a crack squadron of my finest cleaners! The street sweepers can't arrive until tomorrow... typical! :roll:

However, everything else is ready.... :mrgreen:


One would expect that this would be the meat in the sandwich:
However, amino acids are not the only molecules required for life, important though they are. Some form of self-replicating molecule, providing the basis of an inheritance mechanism, is required. Given the difficulties involved in synthesising DNA as a total synthesis, researchers turned to RNA instead, a molecule that still forms the basis of the genomes of numerous extant taxonomic Families of viruses today. RNA, being easier to synthesise, was considered a natural first choice for the basis of primordial genomes, and thus, attention turned to the synthesis of RNA under prebiotic conditions. This was soon found not only to be possible, but to be readily achievable in the laboratory, and indeed, catalysis plays a role in these experiments. Natural clays formed from a mineral called montmorillonite provide a ready natural catalyst that would have been present in quantity on a prebiotic Earth, and the catalytic chemistry of RNA formation whilst adsorbed to such clays is now a standard part of the scientific literature[22- 42].

Unfortunately there is no explanation of how we get from the simple molecules formed in the Miller-Urey experiments to something rather complex such as RNA. Certainly there isn't a shred of evidence to show that RNA forms if you add some montmorillonite to a Miller-Urey reactor.
It is somewhat more complicated than that, and the statement:
This was soon found not only to be possible, but to be readily achievable in the laboratory, and indeed, catalysis plays a role in these experiments.
- glosses over the actual problems involved.
How were the reagents formed?
What were they and how could they have got to the concentrations required to make a nucleotide?
How did they get purified to the point where the required reactions were not overwhelmed by side reactions?
How did one step get to the next?
Really we need a bit of detail here, rather than just waving at 20 or so scientific papers, in the hope that the answers may be contained in there somewhere.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#23  Postby skintbuthappy » Mar 04, 2010 4:36 pm

:popcorn:

Yeah, baby. Is there a :tinhat: smiley, too? :ask:
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#24  Postby hackenslash » Mar 04, 2010 4:53 pm

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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#25  Postby skintbuthappy » Mar 04, 2010 4:54 pm

hackenslash wrote:Image


No way, Hack: that's just a smiley with an iced gem on its head! :nono:
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#26  Postby Mononoke » Mar 04, 2010 4:56 pm

Maybe life was brought to earth by the reapers, so that they can harvest our DNA to replicate themselves.


[Reveal] Spoiler:
The reapers are a race giant techno-organic squid
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#27  Postby Imp » Mar 04, 2010 5:13 pm

:popcorn:
Even creationism evolves - Mr P (Grizby)
:offtopic:

THWOTH wrote:Devil spawn kitty killer! :mad:
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#28  Postby OgreMkV » Mar 04, 2010 5:19 pm

Should I start now or wait until Cali gets here. I mean, rainbow's already contradicted himself once, so I'd hate to let that slide. I'd also point out some recent research which shows that two of rainbow's points are moot.

Just out of curiousity rainbow, why don't you do this research to show us that it's impossible?
Even if you disprove evolution, it does not mean that ID or your religion is correct.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#29  Postby skintbuthappy » Mar 04, 2010 5:21 pm

OgreMkV wrote:Should I start now or wait until Cali gets here. I mean, rainbow's already contradicted himself once, so I'd hate to let that slide. I'd also point out some recent research which shows that two of rainbow's points are moot.

Just out of curiousity rainbow, why don't you do this research to show us that it's impossible?



I don't think it would be rude, just to have a little nibble...
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#30  Postby Katherine » Mar 04, 2010 5:33 pm

rainbow wrote:One would expect that this would be the meat in the sandwich:


Please dispose of sandwich remains in the bins provided! :mrgreen:
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#31  Postby OgreMkV » Mar 04, 2010 6:17 pm

http://www.sciencedaily.com/releases/2010/01/100108101433.htm

This article (popular) describes how the metabolism first hypothesis is unsound.

http://www.sciencedaily.com/releases/2010/02/100222162009.htm popular
Rebecca M. Turk, Nataliya V. Chumachenko, and Michael Yarus. Multiple translational products from a five-nucleotide ribozyme. Proceedings of the National Academy of Sciences, Published online February 22, 2010 DOI: 10.1073/pnas.0912895107 http://www.pnas.org/content/early/2010/02/12/0912895107.full.pdf+html journal reference

This article descibes how RNAs that are only 5 bases long can be fully functioning protein catalyst.

from the Discussion

Further, these particular reactions are central to metabolism,
resembling the substrate and product of biological aminoacyltRNA
synthesis. Transaminoacylation in this work is performed
more simply than elsewhere (9, 12, 17). In addition, observation
of RNA-peptide products provides the simplest polypeptide
synthesis from aminoacyl adenylate (12, 18, 19), or from any
other substrate, in the absence of protein catalysts. Essential intermediates
in protein biosynthesis therefore arise surprisingly
easily in the presence of very short RNAs.


So this simple 5 nucleotide RNA chain can catalyze the essential intermediates. In other words, it shows that more of the steps from chemistry to biology are possible than we had before.


The ultimate importance of these observations may lie partly
in the unknown number of other reactions that can be accelerated
by comparably small RNAs. This is because for each such minuscule
RNA reaction, there is a prima facie case that it would
become accessible even after the most primitive ribonucleotide
polymerization.


So if one RNA only 5 nuceotides long can do this kind of work... why can't more. The search is on!


To see this, consider that, to pick every possible RNA pentamer
sequence from arbitrary pentamers (with probability 0.9975),
one needs only accumulate 4.1 × 10−18 gm of RNA. To possess
every tetramer (with probability 0.9975) from a pool of arbitrary
tetramers, one would need 3.4 × 10−18 gm RNA. In a real polymerization,
one would have a distribution of lengths; nonetheless,
with only attograms of total RNA of distributed short lengths
from some geochemical source, one would have not only our
ribozyme, but every activity of comparable size.


So you only need 0.00000000000000000041 grams of RNA to have every possible (0.9975) combination of RNA pentamer. Which could provide huge number of catalytic reactions.


As an illustration, the ribozymic complexes characterized here
demonstrate that aminoacyl-RNA and peptidyl-RNAs could
have appeared in the presence of ≥9 nucleotides of polymeric
RNA, with six of these free to vary to other base pairs. We have
previously estimated that a population containing about 1 ng of
arbitrary-sequence RNA would be required before useful ribozymes
and other active RNA structures would probably occur
among this population
(20). This follows the so-called axiom of
origin (21), which estimates that theRNAworld would begin when
the amount of RNA exceeds the threshold for occurrence of ribozymes.
The finding of nine-nucleotide active centers reduces the
threshold for ribozyme activity about 7 orders of magnitude, to a
level much more easily breached by undirected geochemical syntheses
,
or by RNA-catalyzed RNA synthesis itself (22–24).


my emphasis

Hey look, 'undirected geochemical syntheses'! :lol:


The most intriguing possibility raised by these results is that an
RNA reaction center for phosphoester transfer may exist somewhere
near this size. This would make the polymerase/replicase
needed to initiate Darwinian evolution of RNAs, the founding
event of the RNA world, much more likely. On one hand, with
this few ribonucleotides to dispose in space, there may not be
other similar nucleotide structures that are both stable and capable
of catalysis. On the other hand, for obvious reasons, it will be
extraordinarily important to look


Hmmm... future work that can be done using the concepts in this paper. Something ID has never done.

I hope this isn't too deep. I'll be happy to explain further.

edit: correct quotes
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#32  Postby Jie » Mar 04, 2010 10:38 pm

Hmm... this looks like it's getting interesting! :popcorn:
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#33  Postby Mononoke » Mar 05, 2010 3:43 am

Nobody is interested in my giant alien DNA farm hypothesis :whine:
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#34  Postby tnjrp » Mar 05, 2010 6:25 am

Well, first of all you wrong about the source. It was in fact the Elder Things that inadvertly created the life on Earth :fsm:

Other than that, it's all well and good to subscribe to that abiogenesis couldn't happen on Earth, at least without some helpful direction (in this case meaning specifically something that is done by a purposeful if not necessarily intelligent agent working for the goal of achieving either abiogenesis or implantation of pre-existent life). One would then only need to think of a solution for where the one(s) that did the directing originated. Are there other places in the universe where abiogenesis in fact does occur -- and if so, what are they? -- or is this direction of extra-universal origin? Or something yet more exotic.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#35  Postby rainbow » Mar 05, 2010 7:43 am

OgreMkV wrote:http://www.sciencedaily.com/releases/2010/01/100108101433.htm

This article (popular) describes how the metabolism first hypothesis is unsound.

http://www.sciencedaily.com/releases/2010/02/100222162009.htm popular
Rebecca M. Turk, Nataliya V. Chumachenko, and Michael Yarus. Multiple translational products from a five-nucleotide ribozyme. Proceedings of the National Academy of Sciences, Published online February 22, 2010 DOI: 10.1073/pnas.0912895107 http://www.pnas.org/content/early/2010/02/12/0912895107.full.pdf+html journal reference

This article descibes how RNAs that are only 5 bases long can be fully functioning protein catalyst.

from the Discussion

Further, these particular reactions are central to metabolism,
resembling the substrate and product of biological aminoacyltRNA
synthesis. Transaminoacylation in this work is performed
more simply than elsewhere (9, 12, 17). In addition, observation
of RNA-peptide products provides the simplest polypeptide
synthesis from aminoacyl adenylate (12, 18, 19), or from any
other substrate, in the absence of protein catalysts. Essential intermediates
in protein biosynthesis therefore arise surprisingly
easily in the presence of very short RNAs.


So this simple 5 nucleotide RNA chain can catalyze the essential intermediates. In other words, it shows that more of the steps from chemistry to biology are possible than we had before.


The ultimate importance of these observations may lie partly
in the unknown number of other reactions that can be accelerated
by comparably small RNAs. This is because for each such minuscule
RNA reaction, there is a prima facie case that it would
become accessible even after the most primitive ribonucleotide
polymerization.


So if one RNA only 5 nuceotides long can do this kind of work... why can't more. The search is on!


To see this, consider that, to pick every possible RNA pentamer
sequence from arbitrary pentamers (with probability 0.9975),
one needs only accumulate 4.1 × 10−18 gm of RNA. To possess
every tetramer (with probability 0.9975) from a pool of arbitrary
tetramers, one would need 3.4 × 10−18 gm RNA. In a real polymerization,
one would have a distribution of lengths; nonetheless,
with only attograms of total RNA of distributed short lengths
from some geochemical source, one would have not only our
ribozyme, but every activity of comparable size.


So you only need 0.00000000000000000041 grams of RNA to have every possible (0.9975) combination of RNA pentamer. Which could provide huge number of catalytic reactions.


As an illustration, the ribozymic complexes characterized here
demonstrate that aminoacyl-RNA and peptidyl-RNAs could
have appeared in the presence of ≥9 nucleotides of polymeric
RNA, with six of these free to vary to other base pairs. We have
previously estimated that a population containing about 1 ng of
arbitrary-sequence RNA would be required before useful ribozymes
and other active RNA structures would probably occur
among this population
(20). This follows the so-called axiom of
origin (21), which estimates that theRNAworld would begin when
the amount of RNA exceeds the threshold for occurrence of ribozymes.
The finding of nine-nucleotide active centers reduces the
threshold for ribozyme activity about 7 orders of magnitude, to a
level much more easily breached by undirected geochemical syntheses
,
or by RNA-catalyzed RNA synthesis itself (22–24).


my emphasis

Hey look, 'undirected geochemical syntheses'! :lol:


The most intriguing possibility raised by these results is that an
RNA reaction center for phosphoester transfer may exist somewhere
near this size. This would make the polymerase/replicase
needed to initiate Darwinian evolution of RNAs, the founding
event of the RNA world, much more likely. On one hand, with
this few ribonucleotides to dispose in space, there may not be
other similar nucleotide structures that are both stable and capable
of catalysis. On the other hand, for obvious reasons, it will be
extraordinarily important to look


Hmmm... future work that can be done using the concepts in this paper. Something ID has never done.

I hope this isn't too deep. I'll be happy to explain further.

edit: correct quotes


Thank you Ogre, that is an interesting post.
Please could you open a new thread on it, since to discuss it further here would derail this thread?
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#36  Postby rainbow » Mar 05, 2010 1:18 pm

Mononoke wrote:Nobody is interested in my giant alien DNA farm hypothesis :whine:

Of course we are, but you do need to open a new thread on it :dance:

Having established that RNA was synthesisable under prebiotic conditions, researchers then turned to the matter of establishing the existence of self-replicating species of RNA molecules. This was duly successful[30, 43, 45 - 47], establishing that such species could have arisen among the extant RNA molecules being synthesised on a prebiotic Earth, and of course, once one self-replicating species exists, the process of evolution can begin, which has also since been demonstrated to apply to replicating RNAs in appropriate laboratory experiments[48].

It is rather unclear what is meant by 'synthesisable'. If it means that some of the steps have been shown to be possible by laboratory experiments, then it is entirely correct. What it certainly not the case, is that it is possible to set up a reactor set to prebiotic conditions, and then have any measurable yield of RNA.
Of course the term 'self-replicating species of RNA molecules' needs a bit of explanation. This doesn't mean as it might be assumed that these RNA molecules will simply copy themselves if left in a solution of prebiotic soup. They can make copies of themselves if they are fed with high concentrations of nucleotides under the right conditions and purity.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#37  Postby rainbow » Mar 05, 2010 1:49 pm

tnjrp wrote:Well, first of all you wrong about the source. It was in fact the Elder Things that inadvertly created the life on Earth :fsm:


:tongue:

Once a self-replicating molecule that can form the basis of an inheritance mechanism exists, the next stage scientists postulate to be required is encapsulation within some sort of selectively permeable membrane. The molecules of choice for these membrane are lipids, which have been demonstrated repeatedly in the laboratory to undergo spontaneous self-organisation into various structures, such as bilayer sheets, micelles and liposomes. Indeed, in the case of phospholipids, they can be stimulated to self-organise by the simple process of agitating the solution within which they are suspended - literally, shake the bottle[49 - 53].

Yes, it really is that easy. However 'lipids' describes a very large range of compounds, not all of which show the self organisational ability of phospholipids. There is no evidence that phospholipids could've formed under prebiotic conditions.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#38  Postby OgreMkV » Mar 05, 2010 2:14 pm

rainbow,

I'm not sure what you're driving at here. You seem intent on picking apart every little bit. However, these experiments and the 79 odd papers that Cali referenced show that it is possible, whatever other concerns you might have.

You can sit here and blather on about the details for years and it won't matter a hill of beans.

If you want to show that these events could not have occured, then you must do one of the following:

A) show that the experiments are flawed somehow. Not just say they are flawed, but show in such a way that the thousand odd abiogenesis researchers are wrong about some aspect of a pre-biotic Earth. You can't just 'claim' it's not so. You have to show it. These scientists have been doing this work for a long time and the chemical makeup of the pre-biotic Earth is pretty well known, though recent research does indicate there was more hydrogen so the atmosphere was more reducing that suspected.

B) show that there is a flaw in the chemistry. You are confused by how chemistry occurs and seem to think that it cannot occur without intelligent intervention. So, you would have to show that there is a difference between chemistry that is directed and chemistry that is non-directed (see your other thread).

Those papers and the summary presented by Cali are not the ramblings of men (much like your own ramblings), but the results of (sometimes) decades of efforts to crack one of the central mysteries of the Earth. I fully expect that you will not understand this concept.

Why not present what you think happened or better yet, do some research and publish the results.

BTW: Read my sig.

BBTW: (this took about 15 seconds on google by putting in the words "prebiotic phospholipid" Try doing some research before spouting off about things you don't understand.

http://www.nature.com/nature/journal/v266/n5597/abs/266078a0.html Synthesis of phospholipids and membranes in prebiotic conditions
W. R. HARGREAVES, S. J. MULVIHILL & D. W. DEAMER
Department of Zoology, University of California, Davis, California 95616
IT is generally agreed that stable membranes were prerequisite to the assembly of the earliest self-replicating systems1−4. Phospholipids, which are ubiquitous in biological membranes and which self-assemble in aqueous environments into stable lipid bilayers and vesicles4, are obvious candidates for prebiotic membrane components. We report here the abiotic synthesis of various lipids, including membranogenic phospholipids.


http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6THS-4985K18-1G&_user=10&_coverDate=09%2F01%2F2003&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1234759390&_rerunOrigin=google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=d1d869008b06a942c69e857c81eaf264
Toward higher polyprenols under ‘prebiotic’ conditions

Laurent Désaubry, a, , Yoichi Nakatania and Guy Ourissona
aUMR 7509, Université Louis Pasteur, CNRS, Centre de Neurochimie, 5 rue Blaise Pascal, F-67084 Strasbourg, France

Abstract
Geraniol and isomers (C10) can be obtained by the condensation of C5 monoprenols at room temperature in the presence of montmorillonite K-10. It is also possible to obtain farnesol (C15) and isomers by condensation of geraniol with isopentenol. Despite the low yields achieved, these findings support the hypothesis that polyprenyl phosphates may have been formed in prebiotic conditions, and served as constituents of primitive membranes.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#39  Postby RPizzle » Mar 05, 2010 2:58 pm

Wait, didn't rainbow say in a thread moons ago that he was a chemist or had a degree in chemistry?

Edit: I could be wrong though.

Edit 2: Yeah, he is a chemist. http://forum.richarddawkins.net/viewtopic.php?f=4&t=97990&start=159
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#40  Postby rainbow » Mar 05, 2010 3:10 pm

OgreMkV wrote:rainbow,

I'm not sure what you're driving at here. You seem intent on picking apart every little bit.


Clearly you don't understand the meaning of a 'Critique'. The definition is available on the internet if you're not sure.

I will however try to explain it to you in my own words:

It is an evaluation of another work, not necessarily critical. It does however examine in detail the arguments presented and offers a comment on them.
It is NOT intended as argument for another point of view. If I wish to present an alternative Thesis, I've done this elsewhere.
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