Origins and Science

[funyun]

Fine, I am sorry I used words like "attack" instead of "critical analysis." Robert Shapiro uses "a critical analysis" in the title of some of his origin of life publications.

Dude, I don't care if you change it or not just as long as you understand the difference between th words 'attack' and 'critical analysis'. Critical analysis is a good thing, and there is a world of difference between the two.

 

[Arik Soong]

As far as the naturalistic origins of life, I guess I should have elucidated further. It really does not matter to me one whit with regards to whether evolution on Earth has occured via special creation, abiogenesis, Panspermia or as the senior project for a class of hyperdimensional High School students - the evidence that evolution has occured cannot be denied.

I personally, based upon a general acceptance of naturalistic origins skew towards an abiogenetic explanation, but whether that's true or not doesn't effect whether evolution has occured since the biogenetic event - whatever it was. At this point, since semantics is apparently as important a topic around here as paleontology and chemistry, I remain empirically agnostic regarding the advent of life on Earth.

This really proves my statement which is cited from another thread true:

I agree that ID has an unfair advantage, but this is simply because the evidence is in it's favor, for example, we don't rely on "unknown steps" or "future theories" as evidence for our theory. We rely on the data.

I acknowledge evolution is a well supported theory so I am not debating that so this is irrelevent.

So you are not relying on any data for what you currently believe...simply relying on "unknown steps" and "future theories" for evidence. Also about my quote about those people which I mentioned...seriously, if you cannot deal with me, how are you going to deal with people who are knowledgable on cell biology like Mike Gene and other legends of the internet ID movement who has plenty of experience dabating others on the ARN and ISCID message boards which stimulate an intellectually rigorous environment (or use to) if you compare it to the discussion level at CF (no offense). Well, on the ISCID message board, I doubt Edmond's nonsense would be tolerated.

Also about bashing, read Leslie Orgel's paper. Look at his usage of rhetorical questions and he also called Wachtershauser's proposal "imaginary" in a perjoritive way. One could discern his contempt for the iron-sulphur world hypothesis in this publication although he was able to convey it in a formal manner and support his scorn with his knowledge of chemistry. Surely one could sense a contempteous tone in Orgel's paper.

 

[Tomk80]

In light of the last post, I feel it is good to quote myself again, and ask for an answer to my arguments in that quote. Again.

Nobody said all answers regarding abiogenesis have been answered. Nobody said that current theories of abiogenesis are complete and do not have their problems. All current theories of abiogenesis have problems, and only the future will tell whether these problems will be solved. That does not mean that we can't say that some models may seem more likely currently than others.

But problems with one theory are not support for another. That is why arguments of ID are ineffective, because they have no support on their own. They only point out problems with other theories. But even if we discover that all current lines of research regarding abiogenesis are incorrect, this still forms no argument that ID is correct. It only tells us that we still don't know how life came into existence.

 

[HairlessSimian]

Whatever, adenine is not a nucleotide. It is not linked to the 1' carbon of ribose to even form a nucleoside. Well, if you read what Orgel wrote, he spoke of the difficulties of fusing adenine to ribose as the proper form of the nucleoside was only produced in 3% yield.

How much of a yield do you need to get the result? Next to nothing! One molecule!

 

[HairlessSimian]

Hmmm... advocating a metabolism-first scenario. As you have said, you are an organic chemist so you are probably aware that water is a poor medium for polymerization so to avoid this problem, you advocate metabolism-first. So you believe that a version of the Krebs cycle would form sponetaneously? Orgel said that there is no reason to believe that a mineral surface or the intermediates of the cycle (e.g. citrate, isocitrate, acontate, alpha ketoglutarmate, fumarate, malate, oxaloacetate) would catalyze all of the necessary reactions. Surely one mineral might catalyze one reaction of the citric acid cycle (or the reductive version of it) but I doubt that a mineral could catalyze all of the reactions necessary of the citric acid cycle. Well, if I sound inelegant let Leslie Orgel explain: http://www.pnas.org/cgi/content/full/97/23/12503

I heard you said amino acids could do it... how would they replicate without the information being stored on a nucleic acid. The RNA World scenario provides an answer to this but one must believe in the notion of RNA could act as an efficent polymerase and this has not yet been demonstrated despite numerous valient attempts by David Bartel and coworkers. Also, lets not forget about the difficulties inheritant in prebiotic nucleotide synthesis. One difficulty is attaching the correct nitrogen atom of the base (9') to the correct carbon atom to the sugar (1'). If it attached to one, it must be in its furnanose (5 vertice ringed form) instead of the pyranose (6 vertice ring.) If it is attached to the 1' carbon of ribose, it must be in its beta anomer not the alpha anomer.

It appears you've hardly read what I wrote.

 

[HairlessSimian]

So Hairless, you would agree that it is more, for lack of a better word, economical, to have metabolism come first, rather than genetics?

I'm just thinking of what's possible with very simple starting materials. Proteins are simple. Nucleotides are not.

I could be convinced otherwise.

By the way, guys, (I'm gonna sound like dad, now) there is no need to transpose what we know occurs today to the past. For instance, it is possible that genetic information could have been carried by some class of molecule completely foreign to us, which got replaced by the magic of natural selection, never to be seen again. It is also possible that everything was exceeedingly inefficient. Cell division taking hundreds, nay thousands of years. Why not? There weren't any predators, after all. Who was in a rush? Again, once natural selection kicks in, efficiency develops rapidly. But we're talking the first cell, here.

 

[HairlessSimian]

So I see you will have no problem using Robert Shapiro's publications (who is adamently opposed to a nucleic acid first scenario) to bash the views of James Ferris and David Bartel who are both RNA world proponents. Shapiro argued against the plausiblity of cytosine and ribose being prebiotic and he also critically analyzed adenine's prebiotic role (I did not read his publication about adenine though.) So without these components of the nucleotides, then the RNA World has no foundation. For example, deny Ferris of his ribonucleotides, then his montmorillonite clays would have nothing to catalyze. Even with his nucleotides, he could only get 90% of the desired 3'-5' phosphodiester linkages (using adenine deriviates as the activating group since nucleotides without an activating group will not polymerize) with the polynucleotides he synthesized. Do not believe my statistic then here: http://www.mbl.edu/CASSLS/FERRIS.ABS.html.

The great irony here is that implausible was exactly what Life was. What seems implausible to us in the present may have been all there was in the past. In any case, an implausible scenario might certainly be replaced by a less implausible one.

90% 9% 0.9% 0.0000009%
When success in Life can be measured in molecules, yield measured in grams and milligrams matters much less than it does today.

What won't polymerize in someone's reaction flask over the course of hours or days may do a fine job over the course of months or years or decades. Catalyst. No catalyst. Whatever. Don't transpose modern expectations to early biochemistry.
Look at linseed oil. Lousy polymerization substrate. We know of Rembrandt and all the great masters through linseed oil polymerization.
Look at amber. Took ages to form. Same with petroleum, diamonds, any number of inorganic materials we know and enjoy today. Why not Life?

 

[HairlessSimian]

If one cannot answer some sixteen year old kid who has some doubts on a naturalistic origin of life, then how could one call the arguments of ID ineffective.

It's not an either/or situation. Not having solid evidence (yet) of a naturalistic origin does not mean ID is correct.

As I wrote originally, there is much less activity in this field than there could be. Breakthroughs may come. Funding may come. Don't hold your breath but don't suspend logic in the meantime.

 

[Arik Soong]

The great irony here is that implausible was exactly what Life was. What seems implausible to us in the present may have been all there was in the past. In any case, an implausible scenario might certainly be replaced by a less implausible one.

90% 9% 0.9% 0.0000009%
When success in Life can be measured in molecules, yield measured in grams and milligrams matters much less than it does today.

What won't polymerize in someone's reaction flask over the course of hours or days may do a fine job over the course of months or years or decades. Catalyst. No catalyst. Whatever. Don't transpose modern expectations to early biochemistry.
Look at linseed oil. Lousy polymerization substrate. We know of Rembrandt and all the great masters through linseed oil polymerization.
Look at amber. Took ages to form. Same with petroleum, diamonds, any number of inorganic materials we know and enjoy today. Why not Life?

Hmm...do you know what a 2'-5' phosphodiester bond could do? Let's take a look: http://www.pnas.org/cgi/content/abstract/73/4/1149 .
Well, you could download the PDF, but a 2'-5' phosphodiester linkage is quite unstable compared to the 3'-5' "natural" linkages. Usher & McHale state that if a poly A dodecamer (I and II; I has all 3'-5' linkages while II has one 2'-5' linkage which is flanked by five 3'-5' linkages) was placed in the presence of poly U, the triple helix actually increases the rate of the hydrolysis of a 2'-5' bond by 18 fold (for dodecamer II) while the presence of poly U stabilized the 3'-5' bonds by 15 fold (pg. 1153). In addition, when compared to each other, the 2'-5' bond is 900 times more prone to hydrolysis than the 3'-5' bond if they are both in a triple helix (pg. 1152). When not in a triple helix the 2'-5' bond faster compared to the 3'-5' bonds. For dodecamer II (3'-5': 0.0023 hr-1; 2'-5': 0.01 hr-1.)

Lol, time is on your side? The polymerization of nucleotides (assuming they were plausible prebiotic reagents) is theromodynamically uphill; in other words, they do not occur spontaneously. Ferris got around this by attaching an activating group (1-Methyladenine other activating groups that are used include imidazole derivatives but adenine derivitives are more plausible prebiotic reagents and they are better) to the nucleotides. In vivo, DNA/RNA polymerases uses deoxyribonucleotide triphosphates and ribonucleotide triphosphates to provide the energy for the polymerization.
Also hydrolysis is spontaneous so it will be favored over time, thus any polymers formed would breakdown into monomers not the other way around.

Also about not reading what you wrote, could you defend the hypothesis of the TCA cycle again. Tell me how a particular enviroment could do the job of multiple enzymes like aconotase, isocitrate dehydrogenase, alpha ketoglutarate dehydrogenase, succinate dehydrogenase, fumarase, malate dehydrogenase, ect. Of course in the reductive citric acid cycle "dehydrogenase" would not apply as the substrates are being reduced not oxidized. In vivo, Nicoamide adenine dinucleotide + (NAD+) is being reduced while the substrate is being oxidized, during this process NAD+ is converted to NADH as it receives a pair of electrons. In Wachtershauser's scenario H2S acts like NADH as it gives (reduces) a pair of electrons to the intermediates instead of the intermediates being oxidized (like with NAD+ -> NADH.) Of course, this is generously assuming that CO2 could be reduced in a hydrothermal environment.

 

[HairlessSimian]

Hmm...do you know what a 2'-5' phosphodiester bond could do? Let's take a look: http://www.pnas.org/cgi/content/abstract/73/4/1149 .
Well, you could download the PDF, but a 2'-5' phosphodiester linkage is quite unstable compared to the 3'-5' "natural" linkages. Usher & McHale state that if a poly A dodecamer (I and II; I has all 3'-5' linkages while II has one 2'-5' linkage which is flanked by five 3'-5' linkages) was placed in the presence of poly U, the triple helix actually increases the rate of the hydrolysis of a 2'-5' bond by 18 fold (for dodecamer II) while the presence of poly U stabilized the 3'-5' bonds by 15 fold (pg. 1153). In addition, when compared to each other, the 2'-5' bond is 900 times more prone to hydrolysis than the 3'-5' bond if they are both in a triple helix (pg. 1152). When not in a triple helix the 2'-5' bond faster compared to the 3'-5' bonds. For dodecamer II (3'-5': 0.0023 hr-1; 2'-5': 0.01 hr-1.)

What's your point and how does it relate to anything I said? Or are you just dropping randomly chosen facts? I never mentionned 2,5'-linked anything. I questionned the need for a high yield of anything in particular.

In any case, even if this was relevant: so what if polymerization produces mostly 2,5' linkages? You've just pointed out that they won't survive as well, so you'll be left with the more stable linkage dominating. Thermodynamic control. Big deal. I never said the emergence of Life depended on 2,5' linkages. Heck, I didn't even say it depended on nucleotides.

If you can read PNAS articles, why can't you read the posts on your own thread?

Lol, time is on your side? The polymerization of nucleotides (assuming they were plausible prebiotic reagents) is theromodynamically uphill; in other words, they do not occur spontaneously. Ferris got around this by attaching an activating group (1-Methyladenine other activating groups that are used include imidazole derivatives but adenine derivitives are more plausible prebiotic reagents and they are better) to the nucleotides. In vivo, DNA/RNA polymerases uses deoxyribonucleotide triphosphates and ribonucleotide triphosphates to provide the energy for the polymerization.
Also hydrolysis is spontaneous so it will be favored thus over time, any polymers formed would breakdown into monomers.

Phosphate diester polymers, perhaps. I haven't looked at the bond energies. but the linkages are esters after all. But, as I reminded you just now, I never mentionned nucleotides in the first place. False problem. Strawman fallacy.

Consider peptides. That's what I wrote about. Much, much more stable linkages.

Now, just so you can convince me that you actually know what you're talking about: Can you imagine any scenario where a thermodynamically uphill polymerization can occur?

 

[Arik Soong]

What's your point and how does it relate to anything I said? Or are you just dropping randomly chosen facts? I never mentionned 2,5'-linked anything. I questionned the need for a high yield of anything in particular.

In any case, even if this was relevant: so what if polymerization produces mostly 2,5' linkages? You've just pointed out that they won't survive as well, so you'll be left with the more stable linkage dominating. Thermodynamic control. Big deal. I never said the emergence of Life depended on 2,5' linkages. Heck, I didn't even say it depended on nucleotides.

If you can read PNAS articles, why can't you read the posts on your own thread?



Phosphate diester polymers, perhaps. I haven't looked at the bond energies. but the linkages are esters after all. But, as I reminded you just now, I never mentionned nucleotides in the first place. False problem. Strawman fallacy.

Consider peptides. That's what I wrote about. Much, much more stable linkages.

But of course, your OP wasn't a real invitation for people to post their ideas so much as an occasion for you to spout your own. At least, that's how this is all occuring to me.

Now, just so you can convince me that you actually know what you're talking about: Can you imagine any scenario where a thermodynamically uphill polymerization can occur?

Ok, that is true that peptides are have a metastable bond compared to phosphoester linkages but remember their polymerization is uphill too but inevitablely they will break down too. Also, lets not forget about chirality and monofunctional chain terminators like simply carboxylic acids (R'-COOH) which could bond to the growing peptide chain terminating it on one of its growing ends.

I must correct myself, I forgot to mention flavin adenine dinucleotide (FAD/FADH2) which acts as an electron donor too. Succinate dehydrogenase oxidizes succinate and reduces FAD to form FADH2 and also releases a fully oxidized carbon in the form of CO2.

Another example of an energetically uphill polymerization: OMP (orotidine 5-monophosphophate) an intermediate in the biosynthesis of UMP (uridine monophosophate) is formed by attaching the 1' N of orotate to 5- phosphoribosyl-1-pyrophosphate (or PRPP). Since this is an energetically uphill reaction, the pyrophosphate must be hydrolyzed which releases energy to drive the polymerization of orotate to the 1' carbon of ribose to form orotidine 5-monophosphate.

 

[HairlessSimian]

Also about not reading what you wrote, could you defend the hypothesis of the TCA cycle again. Tell me how a particular enviroment could do the job of multiple enzymes like aconotase, isocitrate dehydrogenase, alpha ketoglutarate dehydrogenase, succinate dehydrogenase, fumarase, malate dehydrogenase, ect. Of course in the reductive citric acid cycle "dehydrogenase" would not apply as the substrates are being reduced not oxidized. In vivo, Nicoamide adenine dinucleotide + (NAD+) is being reduced while the substrate is being oxidized, during this process NAD+ is converted to NADH as it receives a pair of electrons. In Wachtershauser's scenario H2S acts like NADH as it gives (reduces) a pair of electrons to the intermediates instead of the intermediates being oxidized (like with NAD+ -> NADH.) Of course, this is generously assuming that CO2 could be reduced in a hydrothermal environment.

I didn't propose a TCA cycle. So much for reading.

In any event, who says you need a TCA cycle in the first cell?

Even if the TCA cycle is it, who says you need for it to be of the same efficiency as that afforded by aconitase and company?

And it's nicotinamide. Why do I get the impression you're talking out of your hat?

 

[Arik Soong]

I didn't propose a TCA cycle. So much for reading.

In any event, who says you need a TCA cycle in the first cell?

Even if the TCA cycle is it, who says you need for it to be of the same efficiency as that afforded by aconitase and company?

And it's nicotinamide. Why do I get the impression you're talking out of your hat?

Arigato, for correcting me I wasn't thinking about spelling when I wrote it. I still have alot more to learn though.

By the way, guys, (I'm gonna sound like dad, now) there is no need to transpose what we know occurs today to the past. For instance, it is possible that genetic information could have been carried by some class of molecule completely foreign to us, which got replaced by the magic of natural selection, never to be seen again. It is also possible that everything was exceeedingly inefficient. Cell division taking hundreds, nay thousands of years. Why not? There weren't any predators, after all. Who was in a rush? Again, once natural selection kicks in, efficiency develops rapidly. But we're talking the first cell, here.

Well, I guess you do not agree with the TCA cycle first proposal but you did mention you believe in some unknown prebiotic replicator so I guess you agree with Orgel's conclusion:

The novel, potentially replicating polymers that have been described up to now, like the nucleic acids, are formed by joining together relatively complex monomeric units. It is hard to see how any could have accumulated on the early earth. A plausible scenario for the origin of life must, therefore, await the discovery of a genetic polymer simpler than RNA and an efficient, potentially prebiotic, synthetic route to the component monomers. The suggestion that relatively pure, complex organic molecules might be made available in large amounts via a self-organizing, autocatalytic cycle might, in principle, help to explain the origin of the component monomers. I have emphasized the implausibility of the suggestion that complicated cycles could self-organize, and the importance of learning more about the potential of surfaces to help organize simpler cycles.

In other words, Orgel acknowledges the inherent difficulty of generating the RNA World de novo (i.e. the first genetic material was RNA without any precursors like TNA, PNA, pRNA, ect. because Orgel acknowledges the experimental difficulties of ribonucleotide synthesis)but to circumvent this difficulty, he postulates the existence of some prebiotic hereditary material which could act as the precursor.

 

[HairlessSimian]

Ok, that is true that peptides are have a metastable bond compared to phosphoester linkages but remember their polymerization is uphill too but inevitablely they will break down too. Also, lets not forget about chirality and monofunctional chain terminators like simply carboxylic acids (R'-COOH) which could bond to the growing peptide chain terminating it on one of its growing ends.

The chirality problem is one reason I prefer peptides to nucleotides. Chiral diversity is better tolerated in proteins than in nucleic acids, don't you agree?

Standard sigma-bond dissociation energies say that amide formation is actually exothermic. Add to that H-bonding energies (favouring water), solvation (difficult to quantify) & resonance (favouring the amide), and I do believe your generalized assertion is wrong.

Now tell me: can you name any non-protein amide polymer? Does it decompose in water?

The chain termination problem is no worse with peptides than what you would get with any other polymerization scheme. It represents one of any number of competing reactions. It is reversible. But, I repeat, yields are not an issue, so competing reactions are not an issue. What counts is what worked, not what didn't work.

Before you continue your "critical analysis" of my idea, let me say again what I said in my first post: this idea is not supported by any experimental evidence other than established chemistry, and is full of holes and unknowns. It is not my day-to-day activity to investigate.

Before you continue your "critical analysis" of any abiogenetic idea, let's hear yours and let us have a go at critiquing it from a scientific POV, then we'll pick our favorite, OK? Or don't you have one?

I must correct myself, I forgot to mention flavin adenine dinucleotide (FAD/FADH2) which acts as an electron donor too. Succinate dehydrogenase oxidizes succinate and reduces FAD to form FADH2 and also releases a fully oxidized carbon in the form of CO2.

Another example of an energetically uphill polymerization: OMP (orotidine 5-monophosphophate) an intermediate in the biosynthesis of UMP (uridine monophosophate) is formed by attaching the 1' N of orotate to 5- phosphoribosyl-1-pyrophosphate (or PRPP). Since this is an energetically uphill reaction, the pyrophosphate must be hydrolyzed which releases energy to drive the polymerization of orotate to the 1' carbon of ribose to form orotidine 5-monophosphate.

This is you trying to sound impressive without a point.

I notice you avoided my question:
Can you imagine any scenario where a thermodynamically uphill polymerization can occur?
Yes or no?

 

[Arik Soong]

The chirality problem is one reason I prefer peptides to nucleotides. Chiral diversity is better tolerated in proteins than in nucleic acids, don't you agree?

Standard sigma-bond dissociation energies say that amide formation is actually exothermic. Add to that H-bonding energies (favouring water), solvation (difficult to quantify) & resonance (favouring the amide), and I do believe your generalized assertion is wrong.

Now tell me: can you name any non-protein amide polymer? Does it decompose in water?

The chain termination problem is no worse with peptides than what you would get with any other polymerization scheme. It represents one of any number of competing reactions. It is reversible. But, I repeat, yields are not an issue, so competing reactions are not an issue. What counts is what worked, not what didn't work.

Before you continue your "critical analysis" of my idea, let me say again what I said in my first post: this idea is not supported by any experimental evidence other than established chemistry, and is full of holes and unknowns. It is not my day-to-day activity to investigate.

Before you continue your "critical analysis" of any abiogenetic idea, let's hear yours and let us have a go at critiquing it from a scientific POV, then we'll pick our favorite, OK? Or don't you have one?



This is you trying to sound impressive without a point.

I notice you avoided my question:
Can you imagine any scenario where a thermodynamically uphill polymerization can occur?
Yes or no?

I do agree that chiral impurity could be tolerated in polypeptides much more than nucleic acids as I do not have a source that says in order for a peptide to be functional it must contain only one enantiomer as I do agree that is just a creationist myth although one does have to acknowledge that a monomer of the wrong chirality destablizes secondary structures. About nucleotides, I am sure you are aware of enantiomeric cross inhibition which if a nucleotide of the wrong chirality is incorporated in template direct synthesis of RNA, the growing strand stops to grow. Chirality is not an impossible problem to solve as there are probably some stereospecific prebiotic reactions that I am not apprised of but chirality should always be considered.

Well, I am not one who pontificates on a subject manner which I do not know of so I could not answer your question about bonding theories. I am not a chemist (I think you see me as some know-it-all sixteen year old based on your pejoritive usage of quotation marks which indicate some contempt in your tone) as I only have an intermediate understanding of some of the concepts. I am only interested in the origin of life as a hobby and I mostly read a plethora of literature on the RNA World and most of that is about ribozyme engineering. In addition, I offer one other "criticism" on your model as one should question that if functional peptides are formed, then how will they replicate? Amino acids do not share the same advantage of nucleobases (i.e. they are able to "recognize" their complementary bases. Of course, this is done because of hydrogen bonding in the nucleobases.) In addition, you have shown how peptide bond synthesis is uphill (in a detailed way I might add ) as it requires about 23 kilojoules (4.184 x 5.5)/mole.


Yes, they are quite common in vivo to answer your question. For example, a polymerase adds nucleotides in the 5'-3' direction using dNTPs or NTPs and releasing pyrophosphate during the polymerization but the real question is how could the high energy precursors form. Well, a metabolism transfers the energy from other organic compounds to the phosphoanhyride bonds of ATP and then nucleoside-diphosphate kinases transfer the one phosphate of ATP to another nucleoside diphosphate. Of course, I am not claiming it is an impossibility as condensing agents or heating could overcome the barrier in a prebiotic environment could form high energy precursors (an example is ATP could be formed prebiotically from AMP with pyrophosphate in the presence of cyanate) also I do remember Wachtershauser & Huber 1998 which they were able to form dipeptides (12.3% yield) and tripeptides (0.003% yield) in an aqueous solution with co-precipated FeS using CO to activate the amino acids. So I renounce any claim (if I made such a claim) that thermodynamically uphill reactions are magically precluded by some law in the universe.

I have no idea how life could arise...I am an agnostic (thus do not accept the theistic hypothesis) because of the problem of evil and accepting a naturalistic origin of life answers why there is suffering and pain in the world as I could see no benevolent force acting in the world today. However, I am sympathetic to intelligent design as I seem to discern a sense of purpose in nature (so I am kind of a pantheist in a way) but I fail to see any evidence for an omnibenevolent entity.

 

[Dr.GH]

The false notion that all "living" molecules are chiral is so common, even among biologists who should know better, that you can win many adult beverages at conferences. All you need to know are the names of some non-chiral peptides found in nature. (I advise bringing photocopied pages from a good intro to biochem book. I use Ables, Frey and Jencks, 766-769).

 

[HairlessSimian]

I do agree that chiral impurity could be tolerated in polypeptides much more than nucleic acids as I do not have a source that says in order for a peptide to be functional it must contain only one enantiomer as I do agree that is just a creationist myth although one does have to acknowledge that a monomer of the wrong chirality destablizes secondary structures. About nucleotides, I am sure you are aware of enantiomeric cross inhibition which if a nucleotide of the wrong chirality is incorporated in template direct synthesis of RNA, the growing strand stops to grow. Chirality is not an impossible problem to solve as there are probably some stereospecific prebiotic reactions that I am not apprised of but chirality should always be considered.

It's true that the wrong chirality in one link of a polypeptide chain can indeed disrupt higher-order structure. So?
Stop making assumptions about pre-biotic biochemistry based on modern biochemistry. Don't assume that modern protein structures were important or necessary in life-to-be.
Stereospecific reactions do NOT generate chirality (absolute stereochemistry) but only relative stereochemistry. Chirality remains a problem, as life made a choice at some point as, selecting L-amino acids and D-sugars, and explaining this will become necessary. But don't look to stereospecific reactions.

Well, I am not one who pontificates on a subject manner which I do not know of so I could not answer your question about bonding theories. I am not a chemist (I think you see me as some know-it-all sixteen year old based on your pejoritive usage of quotation marks which indicate some contempt in your tone) as I only have an intermediate understanding of some of the concepts.

Because I wrote "critical analysis" in quotes? That was a reference to an earlier issue in this thread regaring your use of the word "attack" in claiming that scientists attack each other's theories.
No, the contempt is real but not there. My contempt is for your tendency to show off what you know (or what you think you know), relevant or not. You do it again in your latest post. Absolutely unwarranted regurgitations without a point. That's not what this forum is for. It's for discussion. It's not like you offer these tidbits of knowledge in response to someone's query, nor do you offer them to illuminate some idea, nor do you ask questions of your own. As far as I can tell, you do it to show off.

And it's not like you really understand it either. I asked you a simple question:
Can you imagine any scenario where a thermodynamically uphill polymerization can occur? Yes or no?

You again avoided the question, and I'll bet you'll avoid it again because I don't believe you can answer it. I asked the question to gauge the depth of your understanding, and I'm more and more impressed through your posts with the superficiality of your understanding. Which makes my task different. And makes you look like a poser.

In addition, I offer one other "criticism" on your model as one should question that if functional peptides are formed, then how will they replicate? Amino acids do not share the same advantage of nucleobases (i.e. they are able to "recognize" their complementary bases.

If you had read my first post and post #34, you wouldn't be asking.

Of course, this is done because of hydrogen bonding in the nucleobases.)

Poser.

In addition, you have shown how peptide bond synthesis is uphill (in a detailed way I might add )

Actually, I showed how it was downhill. But you probably don't understand the relationship between bond dissociation energies and stability.

as it requires about 23 kilojoules (4.184 x 5.5)/mole.

Poser.

Yes, they are quite common in vivo to answer your question.

I didn't ask a question that warranted this answer. This is you showing off, again:

For example, a polymerase adds nucleotides in the 5'-3' direction using dNTPs or NTPs and releasing pyrophosphate during the polymerization but the real question is how could the high energy precursors form. Well, a metabolism transfers the energy from other organic compounds to the phosphoanhyride bonds of ATP and then nucleoside-diphosphate kinases transfer the one phosphate of ATP to another nucleoside diphosphate. Of course, I am not claiming it is an impossibility as condensing agents or heating could overcome the barrier in a prebiotic environment could form high energy precursors (an example is ATP could be formed prebiotically from AMP with pyrophosphate in the presence of cyanate) also I do remember Wachtershauser & Huber 1998 which they were able to form dipeptides (12.3% yield) and tripeptides (0.003% yield) in an aqueous solution with co-precipated FeS using CO to activate the amino acids.

Poser.

The question I DID ask was this:
Can you name any non-protein amide polymer? and does it decompose in water?

To which I got no answer.

So I renounce any claim (if I made such a claim) that thermodynamically uphill reactions are magically precluded by some law in the universe.

How soon you forget. Yes, you did make that claim. Which was not untrue. And which is why I prefer spontaneous peptide formation (downhill) to phosphate ester formation. Which you would have read in my post had you actually read it.

I have no idea how life could arise...I am an agnostic (thus do not accept the theistic hypothesis) because of the problem of evil and accepting a naturalistic origin of life answers why there is suffering and pain in the world as I could see no benevolent force acting in the world today. However, I am sympathetic to intelligent design as I seem to discern a sense of purpose in nature (so I am kind of a pantheist in a way) but I fail to see any evidence for an omnibenevolent entity.

The purpose of nature is simply this: reproduction/survival. Selfishness, as Dawkins put it.
Any other "purpose" is entirely imagined.

As I and others have stated earlier, it is not because there is an incomplete explanation as to how life arose that one is compelled to fill the gap with some other, non-scientific explanation. One is so compelled for entirely non-scientific reasons; for emotive ones, largely. Be clear on that. Your sympathy for ID fills an emotive need of your own, and ID will never be needed for scientific reasons until we have positive evidence of the supernatural.

Now please stop trying to impress and answer my questions.

 

[USincognito]

I acknowledge evolution is a well supported theory so I am not debating that so this is irrelevent.

So you are not relying on any data for what you currently believe...simply relying on "unknown steps" and "future theories" for evidence.

I think I made it clear that I remain emiprically agnostic regarding whether abiogenesis, as currently postulated occured or not. I'm not here at CF to argue abiogenesis any more than I am to argue in the apologetical forum whether it requires a deity to create the Universe, because I am empirically agnostic there too. Until I see something more substantive than "could'ves" or "needed toos" I've simply taken my horse out of those races.

So no, I don't rely on the possibility of future discoveries validating the position I currently find most plausable, it's where the evidence here and now leads me to tenuously conclude. And as far as "unkown steps" such as those offered by Behe, but now discredited, which ID option should I accept - those of Moses or those of Sitchen?

And yeah, I'm a security guard with a BA in History/Political Science, with history being a continuing focus of my interest - not microbiology. Does that disqualify me from being involved in the Creation/Evoultion discussion? Feel free to chastize me for not being more knowledgable of genetics, but don't you dare chastize me for lowering the level of discussion when the Discovery Institute would publish - PUBLISH - Jonathan Well's Icons of Evolution.

 

[Tomk80]

And yeah, I'm a security guard with a BA in History/Political Science, with history being a continuing focus of my interest - not microbiology. Does that disqualify me from being involved in the Creation/Evoultion discussion? Feel free to chastize me for not being more knowledgable of genetics, but don't you dare chastize me for lowering the level of discussion when the Discovery Institute would publish - PUBLISH - Jonathan Well's Icons of Evolution.

Quoted for Truth (with a capital T).

 

[Arik Soong]

Hmm...how could I forget about this thread. Of course, letting it die would simply be the best option but how could nice it would be to people like Tom and USIncognito to believe in the nonsense that peptide bond formation is a energetically downhill process. But personally I doubt they would care.

How soon you forget. Yes, you did make that claim. Which was not untrue. And which is why I prefer spontaneous peptide formation (downhill) to phosphate ester formation. Which you would have read in my post had you actually read it.

Lol, spontaneous peptide formation is a nice description of your position. You explicitly state this and I am assailing your assertion. Moreover, the diagram that you invoked seems to agree with my position since it acknowledges that there is a GAIN in free energy with the formation of the peptide bond. You called me a "poser" when I tried to bring this to your attention.



Here is lecture notes from a biochemistry course I found on the internet: http://www.biochem.arizona.edu/classes/bioc462/462a/NOTES/Amino_Acids/amino_acids.htm

Peptide bond formation endergonic (DGo' ~21 kJ/mol)

• peptide bonds metastable in aqueous environment -- equilibrium lies far in direction of hydrolysis, but RATE of hydrolysis very slow in absence of catalyst
• Enzymes that catalyze peptide bond hydrolysis = peptidases or proteases, e.g., (specific examples of proteases) your digestive proteases like trypsin and pepsin

Since peptide bond formation is uphill, it also explains why aminoacyl tRNA synthetases expend ATP when attaching the carboxyl group of an amino acid to the 3' terminus of the appropriate tRNA. (Yes, I do know what I am talking about here!)

Since peptide bond formation is "endergonic" that is it absorbs energy to form, it does not occur spontaneously and the exergonic reverse reaction (hydrolysis) is favored in aqueous solution.


I'll admit I read some of the responses of this thread in a cursory manner but I am questioning the notion that peptide bond formation is spontaneous. If this is not true, an advantage in your origin of life scenario is rendered invalid. If you could not comprehend a simple chemistry fact correctly (e.g. Peptide bond formation is uphill), then what right do you have for criticizing me for trivial spelling errors?



You are probably correct that intelligent design fulfills some emotional need although I find some of Mike Gene's reflections compelling.


Hmm...about my belief in the origin of life Robert Shapiro states my position quite well:

Some future day may yet arrive when all reasonable chemical experiments run to discover a probable origin for life have failed unequivocally. Further, new geological evidence may indicate a sudden appearance of life on the earth. Finally, we may have explored the universe and found no trace of life, or process leading to life, elsewhere. In such a case some scientists might choose to turn to religion for an answer. Others, however, myself included, would attempt to sort out the surviving less probable scientific explanations in the hope of selecting one that was still more likely than the remainder.

I doubt you (or most atheists or agnostics) will convert to Christianity when (I do not know if the event described by Shapiro will occur) that day arrives too.