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

#61  Postby OgreMkV » Mar 06, 2010 2:23 pm

rainbow wrote:
Lipid World

This theory postulates that the first self-replicating object was lipid-like. It is known that phospholipids form bilayers in water while under agitation– the same structure as in cell membranes. These molecules were not present on early earth, however other amphiphilic long chain molecules also form membranes. Furthermore, these bodies may expand (by insertion of additional lipids), and under excessive expansion may undergo spontaneous splitting which preserves the same size and composition of lipids in the two progenies. The main idea in this theory is that the molecular composition of the lipid bodies is the preliminary way for information storage, and evolution led to the appearance of polymer entities such as RNA or DNA that may store information favorably. Still, no biochemical mechanism has been offered to support the Lipid World theory.

http://www.absoluteastronomy.com/topics/Abiogenesis

Can anyone present any evidence to contradict the statement contained in this article wrt Phospholipids?



As I told you already rainbow. Recent evidence points away from a lipid world hypothesis.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#62  Postby byofrcs » Mar 07, 2010 8:36 am

rainbow wrote:
byofrcs wrote:I like the RNA world. Some expansion on the chiral catalysts (are they random ?) and the steps to autocatalysing RNA (which we have now).

Plus shouldn't we mention the importance of phosphate as a catalyst at a number of stages (e.g. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Matthew W. Powner1, Béatrice Gerland1 & John D. Sutherland).


There is a great deal of elegance in the Sutherland experiment, but it does contradict a lot of other work that has been done on the synthesis of bases and sugars prior to nucleotide synthesis, which brings us to the next part of Cali's paper:
Moreover, research has established that these lipids can encapsulate RNA molecules, and selectively admit the passage of base and sugar molecules to facilitate RNA replication[54, 55].

Ribose sugar isn't that easily formed under prebiotic conditions, and some of the bases are unstable. It remains unanswered as to how they could obtain any significant concentration in the vicinity of the lipids.


Isn't this is where the mackinawite surfaces (proposed in the iron-sulphur world and using GA3P and DHAP) come into play because thus we have routes to an autocatalytic set ?. The presence of large volumes of the surfaces would allow the concentrations even in the adverse conditions of the pre-biotic environment (e.g. acidity in sea and ultraviolet).
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#63  Postby rainbow » Mar 07, 2010 9:07 am

OgreMkV wrote:
rainbow wrote:
Lipid World

This theory postulates that the first self-replicating object was lipid-like. It is known that phospholipids form bilayers in water while under agitation– the same structure as in cell membranes. These molecules were not present on early earth, however other amphiphilic long chain molecules also form membranes. Furthermore, these bodies may expand (by insertion of additional lipids), and under excessive expansion may undergo spontaneous splitting which preserves the same size and composition of lipids in the two progenies. The main idea in this theory is that the molecular composition of the lipid bodies is the preliminary way for information storage, and evolution led to the appearance of polymer entities such as RNA or DNA that may store information favorably. Still, no biochemical mechanism has been offered to support the Lipid World theory.

http://www.absoluteastronomy.com/topics/Abiogenesis

Can anyone present any evidence to contradict the statement contained in this article wrt Phospholipids?



As I told you already rainbow. Recent evidence points away from a lipid world hypothesis.


No, I don't remember - but no matter.
Can we now agree that I was correct in saying earlier ?:
There is no evidence that phospholipids could've formed under prebiotic conditions.

If so, we can move onto some more interesting issues raised by the article.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#64  Postby rainbow » Mar 07, 2010 9:21 am

byofrcs wrote:
Isn't this is where the mackinawite surfaces (proposed in the iron-sulphur world and using GA3P and DHAP) come into play because thus we have routes to an autocatalytic set ?.

Perhaps, but I'm not that familiar with the iron-sulphur or transition metal-sulphide worlds. Do you have any full papers on this?
The presence of large volumes of the surfaces would allow the concentrations even in the adverse conditions of the pre-biotic environment (e.g. acidity in sea and ultraviolet).

You are saying a great deal in very few words!
A surface can increase concentration through adsorbtion by VanderWaals, or other electrostatic forces. That may however immobilise the reagents, rather than promote further reactions. Sometimes the reverse reaction can take place - desorbtion as a result of changes in pH, temperature, etc. Interesting.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#65  Postby OgreMkV » Mar 07, 2010 2:55 pm

rainbow wrote:
OgreMkV wrote:
rainbow wrote:
Lipid World

This theory postulates that the first self-replicating object was lipid-like. It is known that phospholipids form bilayers in water while under agitation– the same structure as in cell membranes. These molecules were not present on early earth, however other amphiphilic long chain molecules also form membranes. Furthermore, these bodies may expand (by insertion of additional lipids), and under excessive expansion may undergo spontaneous splitting which preserves the same size and composition of lipids in the two progenies. The main idea in this theory is that the molecular composition of the lipid bodies is the preliminary way for information storage, and evolution led to the appearance of polymer entities such as RNA or DNA that may store information favorably. Still, no biochemical mechanism has been offered to support the Lipid World theory.

http://www.absoluteastronomy.com/topics/Abiogenesis

Can anyone present any evidence to contradict the statement contained in this article wrt Phospholipids?



As I told you already rainbow. Recent evidence points away from a lipid world hypothesis.


No, I don't remember - but no matter.
Can we now agree that I was correct in saying earlier ?:
There is no evidence that phospholipids could've formed under prebiotic conditions.

If so, we can move onto some more interesting issues raised by the article.


No we cannot agree that it is correct. You have switched statements again.

THe lipid world hypothesis is probably not correct in that lipid based vesicles formed FIRST and the provided an environment where organic and inorganic precursors accumulated.

OTOH, it is trivially easy to show that phosophlipids could have formed under prebiotic conditions.

rainbow, I'm starting to think that you aren't interested in actual evidence.

http://www.nature.com/nature/journal/v266/n5597/abs/266078a0.html
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#66  Postby Tero » Mar 07, 2010 3:07 pm

Carbonyl sulfide is not the most familiar substance even to chemists.
this is because in today's world
"Carbonyl sulfide decomposes in the presence of humidity and bases to carbon monoxide and hydrogen sulfide."
http://en.wikipedia.org/wiki/Carbonyl_sulfide

just a footnote to the first post

the origins of chirality are interesting as well
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#67  Postby rainbow » Mar 09, 2010 8:32 am

OgreMkV wrote:
OTOH, it is trivially easy to show that phosophlipids could have formed under prebiotic conditions.

rainbow, I'm starting to think that you aren't interested in actual evidence.

http://www.nature.com/nature/journal/v266/n5597/abs/266078a0.html


I have asked you for the full paper and YOU have evaded me on this.
I asked whether you had read the entire paper and understood it, but you've evaded answering.

Have you read the full paper?
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#68  Postby Darkchilde » Mar 09, 2010 9:42 am

rainbow wrote:
OgreMkV wrote:
OTOH, it is trivially easy to show that phosophlipids could have formed under prebiotic conditions.

rainbow, I'm starting to think that you aren't interested in actual evidence.

http://www.nature.com/nature/journal/v266/n5597/abs/266078a0.html


I have asked you for the full paper and YOU have evaded me on this.
I asked whether you had read the entire paper and understood it, but you've evaded answering.

Have you read the full paper?


MOD NOTE

Rainbow, once again you are trolling by trying to derail the discussion and making personal comments. This is the last time you will get just a note, reminding you of the actual rules, which you can find here: http://www.rationalskepticism.org/old-announcements/forum-users-agreement-t76.html

Next time, rainbow, you will get a warning.

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

#69  Postby rainbow » Mar 09, 2010 9:51 am

Darkchilde wrote:
rainbow wrote:
OgreMkV wrote:
OTOH, it is trivially easy to show that phosophlipids could have formed under prebiotic conditions.

rainbow, I'm starting to think that you aren't interested in actual evidence.

http://www.nature.com/nature/journal/v266/n5597/abs/266078a0.html


I have asked you for the full paper and YOU have evaded me on this.
I asked whether you had read the entire paper and understood it, but you've evaded answering.

Have you read the full paper?


MOD NOTE

Rainbow, once again you are trolling by trying to derail the discussion and making personal comments. This is the last time you will get just a note, reminding you of the actual rules, which you can find here: http://www.rationalskepticism.org/old-announcements/forum-users-agreement-t76.html

Next time, rainbow, you will get a warning.

END MOD NOTE

Where is the personal comment?
We are discussing a particular paper for which a link has been given for the abstract only.
I am asking Ogre whether he's read the paper, that is a question not a comment.
A question that Ogre refuses to answer. Why?

OgreMkV wrote:rainbow, I'm starting to think that you aren't interested in actual evidence.

...that is a personal comment. It implies that I'm not interested in the actual evidence.
Here I am asking for the actual evidence, and Ogre is refusing to give it.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#70  Postby Darkchilde » Mar 09, 2010 10:03 am

MOD NOTE

rainbow, do not derail any more this discussion by commenting on the moderation. Any more comments on moderation will be binned. If you want you can PM Calilasseia or Durro, who are the other mods of this section.

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

#71  Postby OgreMkV » Mar 09, 2010 2:22 pm

rainbow, go read the paper. If you have a problem with it, I'll be glad to discuss it with you.

Now, I've found some more interesting bits regarding cyanimide. Apparently, this compound is useful both in the formation of ribose sugars (I think we mentioned this before, if not remind me to mention it) and the formation of liposomes.

http://en.wikipedia.org/wiki/Cyanamide
Cyanamide is produced by hydrolysis of calcium cyanamide, which in turn is prepared from calcium carbide via the Frank-Caro process.

CaCN2 + H2O + CO2 → CaCO3 + H2NCN
The conversion is conducted on slurries, consequently most commercial cyanamide is sold as an aqueous solution.

The main reaction exhibited by cyanamide involves additions of protic reagents. Water, hydrogen sulfide, and hydrogen selenide add to give urea, thiourea, and selenourea, respectively:

H2NCN + H2E → H2NC(E)NH2(E = O, S, Se)

http://en.wikipedia.org/wiki/Thiourea
Thioureas are used a building blocks to pyrimidine derivatives. Thus thioureas condense with β-dicarbonyl compounds.[4] The amino group on the thiourea initially condenses with a carbonyl, followed by cyclization and tautomerization. Desulfurization delivers the pyrimidine.


Again, this is just stuff found in a few seconds of searching on google and wiki. It's not like this stuff is hidden.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#72  Postby rainbow » Mar 09, 2010 3:09 pm

OgreMkV wrote:rainbow, go read the paper. If you have a problem with it, I'll be glad to discuss it with you.


I would read it, but I have no access to it. I have explained this to you.
Are you going to share the full paper with us?
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#73  Postby Sityl » Mar 09, 2010 3:16 pm

I will now critique rainbow's critique. This will take 144 posts to complete.

I will do two sentences per post and have no knowledge whatsoever on the subject being discussed, therefore I am perfect to be the one to do the critiquing.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#74  Postby rainbow » Mar 09, 2010 3:20 pm

num1cubfn wrote:I will now critique rainbow's critique. This will take 144 posts to complete.

I will do two sentences per post and have no knowledge whatsoever on the subject being discussed, therefore I am perfect to be the one to do the critiquing.


Certainly. Please open a new thread and do so.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#75  Postby OgreMkV » Mar 09, 2010 3:26 pm

rainbow wrote:
OgreMkV wrote:rainbow, go read the paper. If you have a problem with it, I'll be glad to discuss it with you.


I would read it, but I have no access to it. I have explained this to you.
Are you going to share the full paper with us?


I wasn't planning on it. It's via a paid subscription to Nature and I'm not sure of the copy right laws.

Do you have any objection to the abstract as shown in the link? If not, then just move on. We'll call you 'objecting until you've read the paper'. However, I've got to say, if you object to papers that you haven't read...

Well it's kind of like Behe in the Dover trial. He was presented with a couple dozen books and over 50 articles that he hadn't read, yet he knew that they didn't sufficiently explain why he was wrong.

Please continue. Mayeb your next post will pull up some free papers...
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#76  Postby rainbow » Mar 09, 2010 3:34 pm

OgreMkV wrote:
rainbow wrote:
OgreMkV wrote:rainbow, go read the paper. If you have a problem with it, I'll be glad to discuss it with you.


I would read it, but I have no access to it. I have explained this to you.
Are you going to share the full paper with us?


I wasn't planning on it. It's via a paid subscription to Nature and I'm not sure of the copy right laws.

Do you have any objection to the abstract as shown in the link?


No, why should I?
...but it is only an abstract, and it doesn't give any clue as to what conditions were used and whether significant yields were obtained.

Are you now telling us that you haven't read the full paper?
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#77  Postby OgreMkV » Mar 09, 2010 3:59 pm

I've answered the question about whether I have read the paper. I am not going to post it in its entirety here. If you want to question it, then pay the money, read it and start debunking.

rainbow, let me be perfectly honest here. I don't think you are going to consider any evidence that supports abiogenesis. I think that you have made up your mind and are trying solely to discredit this body of work. Now, considering that all the papers Cali presented and the few additional papers I've presented have already gone through peer-review, the chances of you finding a mistake in them are slim to none.

Based on your previous post, I predict that even if you were presented with an experiment that started from base elements and resulted in a fully functioning protocell, you would thne claim "But how do you know, where you there?"

Abiogenesis is chemistry. I'll repeat this for you: chemistry happens. If the reactions can be shown to happen, then they can happen and did happen at some point. That is the point of all this research, to show that the reactions needed for inorganic compounds to become a living thing can happen.

Now, I'll move the rest of this over to the abiogenesis thread and let you continue your 'critique'.
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#78  Postby eversbane » Mar 09, 2010 5:04 pm

rainbow wrote:
Mazille wrote:So, where is your critique?

What's the hurry?

In the earliest period of the history of the planet, it was a body devoid of life, and conditions on the planet were far from conducive to the appearance of life, particularly during the episode termed "The Late Heavy Bombardment"[1] by scientists, which saw intense bolide impact activity taking place on the planet's surface. Once this episode, and subsequent episodes postulated to have taken place, were complete, the Earth cooled, a solid crust formed, and liquid water in quantity began to appear. Thus, the stage was set for the processes that were to result in the emergence of life.


There is no evidence to support the conclusion that there was no life during the bolide impact period, it is pure speculation.
What is clear is that the bolide impacts would have removed any evidence of life before this period.
...so we simply don't know.

And your point is?
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Re: Critique on Calilasseia's "The Emergence Of Life On Eart

#79  Postby eversbane » Mar 09, 2010 5:22 pm

rainbow wrote:
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

#80  Postby Bathynomus Giganteus » Mar 09, 2010 7:18 pm

I would never be a Cali Critique!
I have no wish to cross swords with Cali as far as Butterflies or yoyo monkeys go, but if he ever wishes to challenge me to a "reverse a 40ft trailer onto a loading bay" competition, then I'm game!
That'll sort the mice from the men! :lol:
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