DNA errors are scanned electrically

[Elshamah]

Oh by the way, you're going to love this(2 minutes on pubmed can do wonders for your knowledge):
http://www.ncbi.nlm.nih.gov/pubmed/18451863
Life without RNase P.

Abstract
The universality of ribonuclease P (RNase P), the ribonucleoprotein essential for transfer RNA (tRNA) 5' maturation, is challenged in the archaeon Nanoarchaeum equitans. Neither extensive computational analysis of the genome nor biochemical tests in cell extracts revealed the existence of this enzyme. Here we show that the conserved placement of its tRNA gene promoters allows the synthesis of leaderless tRNAs, whose presence was verified by the observation of 5' triphosphorylated mature tRNA species. Initiation of tRNA gene transcription requires a purine, which coincides with the finding that tRNAs with a cytosine in position 1 display unusually extended 5' termini with an extra purine residue. These tRNAs were shown to be substrates for their cognate aminoacyl-tRNA synthetases. These findings demonstrate how nature can cope with the loss of the universal and supposedly ancient RNase P through genomic rearrangement at tRNA genes under the pressure of genome condensation.

Here's an organism living fine without your supposedly absolutely required enzyme.

i already knew about that. Laurence Moran brought it to my knowledge. N. equitans was the first organism to be identified to generate six tRNA isoacceptors via a trans-splicing reaction using tRNA half molecules. So it uses a other mechanism, but it has to splice and cleave the introns together as well. So the need remains.......it can reduce Rnase P, but has to use another reaction, so the mechanism is not really reducable.

 

[Rumraket]

i already knew about that. Laurence Moran brought it to my knowledge. N. equitans was the first organism to be identified to generate six tRNA isoacceptors via a trans-splicing reaction using tRNA half molecules. So it uses a other mechanism, but it has to splice and cleave the introns together as well. So the need remains.......it can reduce Rnase P, but has to use another reaction, so the mechanism is not really reducable.

You copy-pasted this sentence: "N. equitans was the first organism to be identified to generate six tRNA isoacceptors via a trans-splicing reaction using tRNA half molecules."

When you copy-paste stuff, you should correctly note that they are quotes, at minimum by putting it in quotation marks, "stuff here". Or by putting it in an actual quote quote box and giving a reference.
In this case, you got it from here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491384/

It really is quite pathetic that you have to pretend to know stuff that you don't.

 

[Dragan Glas]

Greetings,

Name-dropping as well - "Larry Moran brought it to my attention".

Pardon us for breathing - we are not worthy...

Kindest regards,

James

 

[Elshamah]

i already knew about that. Laurence Moran brought it to my knowledge. N. equitans was the first organism to be identified to generate six tRNA isoacceptors via a trans-splicing reaction using tRNA half molecules. So it uses a other mechanism, but it has to splice and cleave the introns together as well. So the need remains.......it can reduce Rnase P, but has to use another reaction, so the mechanism is not really reducable.

You copy-pasted this sentence: "N. equitans was the first organism to be identified to generate six tRNA isoacceptors via a trans-splicing reaction using tRNA half molecules."

When you copy-paste stuff, you should correctly note that they are quotes, at minimum by putting it in quotation marks, "stuff here". Or by putting it in an actual quote quote box and giving a reference.
In this case, you got it from here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491384/

It really is quite pathetic that you have to pretend to know stuff that you don't.

you think you can avoid the RNA world scenario, by sticking to the metabolism first scenario. You can't. Both are complementary. So you reject the RNA world scenario, what do you want the make of DNA replace with ? furthermore, my answer was not meant as proposing the RNA world , but by pointing out that there are serious challenges to explain the origin of nucleobases by their own, and then, even more, proposing a stepwise build up to ribonucleotides. Thats simply not tenable. In the same manner, as RNase P has no function by its own, if not embedded in the tRNA synthesis process, there is no reason why the individual parts of ribonucleobases would bond together in a highly complex manner if there is no plausible energy source available, or enzymes like phosphodiesterases that could only arise later, since they depend on DNA to be made...... So my contemption still stands, since nobody proved the contrary, that all 3 parts , the nucleobases, sugar and phosphate are essential, irreducible, and cannot arise in a stepwise manner by natural mechanisms.

 

[Rumraket]

You copy-pasted this sentence: "N. equitans was the first organism to be identified to generate six tRNA isoacceptors via a trans-splicing reaction using tRNA half molecules."

When you copy-paste stuff, you should correctly note that they are quotes, at minimum by putting it in quotation marks, "stuff here". Or by putting it in an actual quote quote box and giving a reference.
In this case, you got it from here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491384/

It really is quite pathetic that you have to pretend to know stuff that you don't.

you think you can avoid the RNA world scenario, by sticking to the metabolism first scenario. You can't.

Yes I can. It is amazing that this doesn't sink into your skull.

RNA is biochemically sythesized in chemoautotrophic bacteria, ultimately from H[sub]2[/sub], NO[sub]3[/sub][sup]-[/sup] and CO[sub]2[/sub]. That is the basis of metabolism, with the correct energy sources present and the right catalysts (that would be the enzymes in extant life), the chemical reactions required to make RNA are no longer energetically "uphill", because the local conditions have lowered the activation energy profiles of the basic reactions. That is what catalysts do, and all enzymes are catalysts. The basic metabolic enzymes use metals and mineral cofactors to catalyze these reactions, the true catalyst is therefor usually a metal atom, or small mineral cluster. The surrounding peptide complex usually only acts to discriminate between substrates, or funnel the substrate towards the catalyzing metal in the right angle to enhance the rate of turnover. But fundamentally, the reactions can still take place without the peptides there, the "naked" metal atom is still a catalyst.

Both are complementary.

No they aren't.

So you reject the RNA world scenario, what do you want the make of DNA replace with ?

Can you reformulate the question? It doesn't make sense.

furthermore, my answer was not meant as proposing the RNA world , but by pointing out that there are serious challenges to explain the origin of nucleobases by their own

Yeah, "on their own". I don't believe nucleotides originated "on their own".

Here are some even more serious challenges: There is zero evidence for divine magical creation. No experiment ever has ever demonstrated that supernatural divine magic exists.

You may think various naturalistic scenarios for the origin of life are implausible or untenable, but the alternative you are proposing is literally impossible. It is a violation of the physical laws of the universe.

A gradualistic natural origin is infinitely more plausible than the instantaneous and miraculous origin of a fully functioning organism, with all it's parts in the right places and working from the start, in an instant.

You blather about unlikely stepwise scenarios with molecules assembling a few atoms at a time, but instead you propose the INSTANT creation of an entire fucking organism. How likely is that? Do the math.

Dude, stop fucking talking about "serious problems" and "challenges" when the alternative you want to conclude is the most absurdly unlikely of them all.

, and then, even more, proposing a stepwise build up to ribonucleotides. Thats simply not tenable.

This is coming from the guy who is proposing that magic is the answer.

Can I laugh now?

In the same manner, as RNase P has no function by its own, if not embedded in the tRNA synthesis process,

Provably incorrect as already shown.

there is no reason why the individual parts of ribonucleobases would bond together in a highly complex manner if there is no plausible energy source available, or enzymes like phosphodiesterases

Phosphodiesterase is an enzyme that cleaves DNA, it doesn't make DNA.

Stop using terms you don't know what even mean.

that could only arise later, since they depend on DNA to be made

You don't actually know that.

All you can say is that, in life as we know it, the amino acid sequence of phosphodiesterase enzymes is encoded in DNA sequence.

It does not follow from this, that there cannot be any other way a phosphodiesterase enzyme could arise, than through DNA. It just doesn't follow. In fact we know several non-proteinaceus organic compounds with phosphodiesterase activity.

You are apparently clueless about basic biochemistry principles. Enzymes are merely catalysts that enhance the selectivity and rate of certain chemical reactions. But there are other ways to get those chemical reactions to proceed without these enzymes. They will be less efficient, and they will be less specific, but they still work.

You are operating under this misconception that everything has to work exactly like it does now in life that already exists, but how do you know this is true? You don't, at all. This is just something you assume. All your arguments are based on the assumption there cannot be any other way for life to function than the way life you know it does. What merits this assumption? Nothing at all.

..... So my contemption still stands, since nobody proved the contrary

We don't have to prove the contrary, YOU are the one that has to prove that they ARE essential, irreducible and cannot arise in a stepwise manner.

All you have done is argue that life that depends on them now, cannot live without them, and would cease to function if you took away their DNA. Yes, we all agree, if life dependent on DNA lost it's DNA it would cease to function. Duh!
But is that the only kind of life possible? How could you possibly know?

Unless you have ruled out all other concievable options with some kind of demonstration of their impossibility, all we can is is that we don't know how life as we know it originated. But you have not ruled anything out, all you have done is argue that if life is dependent on DNA, then it needs DNA to be already present. You have done nothing to establish that there are no other kinds of life possible.

 

[Elshamah]

RNA is biochemically sythesized in chemoautotrophic bacteria, ultimately from H[sub]2[/sub], NO[sub]3[/sub][sup]-[/sup] and CO[sub]2[/sub]. That is the basis of metabolism, with the correct energy sources present and the right catalysts (that would be the enzymes in extant life), the chemical reactions required to make RNA are no longer energetically "uphill", because the local conditions have lowered the activation energy profiles of the basic reactions. That is what catalysts do, and all enzymes are catalysts. The basic metabolic enzymes use metals and mineral cofactors to catalyze these reactions, the true catalyst is therefor usually a metal atom, or small mineral cluster. The surrounding peptide complex usually only acts to discriminate between substrates, or funnel the substrate towards the catalyzing metal in the right angle to enhance the rate of turnover. But fundamentally, the reactions can still take place without the peptides there, the "naked" metal atom is still a catalyst.

So where did these chemoautotrophic bacterias come from ? what is their origin ? are they not alive, and their origin must be explained ?

here is a good overview of the problems inherent of metabolism first scenarios :

http://www.godandscience.org/evolution/replicator_vs_metabolism.html

Here are some even more serious challenges: There is zero evidence for divine magical creation. No experiment ever has ever demonstrated that supernatural divine magic exists. Dude, stop fucking talking about "serious problems" and "challenges" when the alternative you want to conclude is the most absurdly unlikely of them all.

I am not Dude. And yours is just a argument from incredulity. If you cancel God as a potent cause of the universe and all in it, you are left with nothing. Nothing causing the physcial universe makes more sense to you ?? You can stick to irrational scenarios. I don't. That would the be the magic of all magics........ah, wait, now you will either answer that 1. you do not believe the universe was caused by nothing, or 2. argue that you don't know...LOL.....

Can I laugh now?

you should rather think about your self delusion...... and if that is what you really want for yourself.

Provably incorrect as already shown.

So Rnase P has a function by its own, if not embedded in the process together with the other parts ?? LOL.....

there is no reason why the individual parts of ribonucleobases would bond together in a highly complex manner if there is no plausible energy source available, or enzymes like phosphodiesterases
Phosphodiesterase is an enzyme that cleaves DNA, it doesn't make DNA.

Where did i say phosphdiesterases MAKE DNA ?? My point was precisely that the bonding of the monomers to polymers is another major hurdle and problem.

It does not follow from this, that there cannot be any other way a phosphodiesterase enzyme could arise, than through DNA. It just doesn't follow.

Russell's teapot much ??!!

In fact we know several non-proteinaceus organic compounds with phosphodiesterase activity.

You are apparently clueless about basic biochemistry principles. Enzymes are merely catalysts that enhance the selectivity and rate of certain chemical reactions. But there are other ways to get those chemical reactions to proceed without these enzymes. They will be less efficient, and they will be less specific, but they still work.

that they work to make the molecules in demand in a prebiotic world is pure speculation.

You are operating under this misconception that everything has to work exactly like it does now in life that already exists, but how do you know this is true? You don't, at all. This is just something you assume. All your arguments are based on the assumption there cannot be any other way for life to function than the way life you know it does. What merits this assumption? Nothing at all.

we know of many parts and things that had to exist right from the beginning as they are know, as for example the genetic code, DNA, RNA, RNA polymerases, DNA and RNA repair mechanisms, the Ribosome, chaperones, just to mention a few.

..... So my contemption still stands, since nobody proved the contrary
We don't have to prove the contrary, YOU are the one that has to prove that they ARE essential, irreducible and cannot arise in a stepwise manner.

I have. You are the one that is incredulous towards my position, and have failed so far to refute my claims in a competent manner and providing compelling scenarios. DNA can not be reduced from nucleotides to nucleosides to nucleobases. DNA is irreducibly complex. You have not falsified or refuted my claim, as the fact is obvious it can't. And the make of nucleobases is still a problem, since enzymes are required that hardly could be ribozymes, as it is as well to make nucleosides, as the lability of glycosidic bonds, and the difficulty of formation of them in a prebiotic world, and as well it is to make ribose, and the possible solvents for phosphorylation. And so the availability of phosphor and actually all required elements in a prebiotic world. And so is the necessity of left handedness. These are formidable unresolved problems.

But is that the only kind of life possible? How could you possibly know?

Again proposing Russells teapot ?? And, well, we do not know of any other life form, than based on DNA, RNA etc ya know.......

Unless you have ruled out all other concievable options with some kind of demonstration of their impossibility

what other concievable options ? viaje dans la maionnaise much again ??

, all we can is is that we don't know how life as we know it originated.

aham.......

As Robert Shapiro wrote :

RNA's building blocks, nucleotides, are complex substances as organic molecules go. They each contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern. Many alternative ways exist for making those connections, yielding thousands of plausible nucleotides that could readily join in place of the standard ones but that are not represented in RNA. That number is itself dwarfed by the hundreds of thousands to millions of stable organic molecules of similar size that are not nucleotides.

a metabolism first scenario is also a simplistic explanation for follwing reasons, citing Shapiro again:

http://www.scientificamerican.com/article/a-simpler-origin-for-life/

A coupling mechanism must link the release of energy to the organization process that produces and sustains life. The release of energy does not necessarily produce a useful result. Chemical energy is released when gasoline is burned within the cylinders of my automobile, but the vehicle will not move unless that energy is used to turn the wheels. A mechanical connection, or coupling, is required. Each day, in our own cells, each of us degrades pounds of a nucleotide called ATP. The energy released by this favorable reaction serves to drive processes that are less favorable but necessary for our biochemistry. Linkage is achieved when the reactions share a common intermediate, and the process is speeded up by the intervention of an enzyme. One assumption of the small-molecule approach is that coupled reactions and primitive catalysts sufficient to get life started exist in nature.

Will we eventually discover a naturalistic explanation for origins in general, and the first life ?

http://elshamah.heavenforum.org/t1508-will-we-eventually-discover-a-naturalistic-explanation-for-first-life

If a certain line of reasoning is not persuasive or convincing, then why do atheists not change their mind because of it? The more evolution papers are published, the less likely the scenario becomes. Some assertions have even been falsified. We should consider the fact that modern biology may have reached its limits on several subjects of biology. All discussions on principal theories and experiments in the field either end in vague suppositions and guesswork, statements of blind faith, made up scenarios, or in a confession of ignorance. Fact is there remains a huge gulf in our understanding… This lack of understanding is not just ignorance about some technical details; it is a big conceptual gap. The reach of the end of the road is evident in the matter of almost all major questions. The major questions of macro change and abiogenesis are very far from being clearly formulated, even understood, and nowhere near being solved, and for most, there is no solution at all at sight. But proponents of evolution firmly believe, one day a solution will be on sight. Istn't that a prima facie of a " evolution of the gap" argument ? We don't know yet, therefore evolution and abiogenesis ? That way, the God hypothesis remains out of the equation in the beginning, and out at the end, and never receives a serious and honest consideration. If the scientific evidence leading towards naturalism providing sactisfactory explanations, why should we not change your minds and look somewhere else ?

 

[Rumraket]

RNA is biochemically sythesized in chemoautotrophic bacteria, ultimately from H[sub]2[/sub], NO[sub]3[/sub][sup]-[/sup] and CO[sub]2[/sub]. That is the basis of metabolism, with the correct energy sources present and the right catalysts (that would be the enzymes in extant life), the chemical reactions required to make RNA are no longer energetically "uphill", because the local conditions have lowered the activation energy profiles of the basic reactions. That is what catalysts do, and all enzymes are catalysts. The basic metabolic enzymes use metals and mineral cofactors to catalyze these reactions, the true catalyst is therefor usually a metal atom, or small mineral cluster. The surrounding peptide complex usually only acts to discriminate between substrates, or funnel the substrate towards the catalyzing metal in the right angle to enhance the rate of turnover. But fundamentally, the reactions can still take place without the peptides there, the "naked" metal atom is still a catalyst.

So where did these chemoautotrophic bacterias come from ? what is their origin ? are they not alive, and their origin must be explained ?

I'm explaining to you how RNA is synthesized now in extant cells, how the chemistry works. I'm not saying chemoautotrophic bacteria came out of nowhere for fucks sake, please try to follow the discussion.

Here is the point again: RNA is synthesized(now, in your very own cells) by using energy and certain catalysts(to reduce the energy barrier). The energy and the catalysts probably already existed before life(because most of them are actually metal catalysts). The life that exists today is still using the same principles of energy and catalysis to make it's basic constituents as would have existed in the prebiotic environment. At least, there are some good indications that this is so when we analyze the structure and mechanism of the oldest metabolic enzymes.

You have a lot of quotes about how the nonbiological chemical synthesis of RNA is energetically "uphill". All that means is that it takes energy to make RNA, energy that would have already existed under the right conditions. And then there are catalysts, those would be enzymes in extant life, but inorganic minerals and metals on the ancient Earth.

here is a good overview of the problems inherent of metabolism first scenarios :

http://www.godandscience.org/evolution/replicator_vs_metabolism.html

This is old shit that has been superceded long ago. Leslie Orgel and Robert Shapiro died years ago, quite a lot has happened since their original discussions on replicator vs metabolism first scenarios.

Case in point, all the issues erected in that article are dealt with in the alkaline hydrothermal vent theory. So in factual fact, metabolism first does stand on it's own merits.

Here are some even more serious challenges: There is zero evidence for divine magical creation. No experiment ever has ever demonstrated that supernatural divine magic exists. Dude, stop fucking talking about "serious problems" and "challenges" when the alternative you want to conclude is the most absurdly unlikely of them all.

I am not Dude. And yours is just a argument from incredulity.

No, it's an argument from physics. Your "theory" for the origin of life is a violation of everything we know about how the world works.

Yeah, I'm quite incredulous towards the physically impossible and rightfully so. But I'm open to being convinced otherwise with a nice demonstration. Bring on the magic.

If you cancel God as a potent cause of the universe and all in it, you are left with nothing.

Or maybe not, maybe, just like you believe about your god, the universe necessarily exists by it's own nature. That would be a simpler explanation. We don't need to postulate god then.

Nothing causing the physcial universe makes more sense to you ??

What caused your god? Another god?

You can stick to irrational scenarios. I don't.

Yes you do. You simply make shit up: I can't figure it out so oh gee a magic man gone dunnit! *allakhazam*

That would the be the magic of all magics........ah, wait, now you will either answer that 1. you do not believe the universe was caused by nothing, or 2. argue that you don't know...LOL.....

Turns out it's 3. You are special pleading. You believe your god has special properties no other entity has, such as not requiring a cause. But if it's logically possibly not to require a cause, that property could be assigned to the universe.

Theism has lost this argument every time it's been begun. Theism rests inherently on special pleading. Everthing requires a cause except god. Or maybe the universe too. No no, just god because.. well, just because.

Can I laugh now?

you should rather think about your self delusion...... and if that is what you really want for yourself.

I will laugh then. :lol:

Provably incorrect as already shown.

So Rnase P has a function by its own, if not embedded in the process together with the other parts ?? LOL.....

You said RNase P has no function besides modifying tRNA. That is just not correct. I didn't claim RNase P is "just functional" when entirely removed from the organism it belongs to, that's just stupid.

It should tell you something that you have to work so hard to deliberately misunderstand what I write for you to defend your arguments. Notice how I constantly have to correct you on what we are talking about, what words you use mean, what the people you quote are talking about. I have to dumb down what the papers say and so on.

Phosphodiesterase is an enzyme that cleaves DNA, it doesn't make DNA.

Where did i say phosphdiesterases MAKE DNA ?? My point was precisely that the bonding of the monomers to polymers is another major hurdle and problem.

Then why the fuck mention phosphodiesterase enzymes when they CLEAVE the polymers?

It does not follow from this, that there cannot be any other way a phosphodiesterase enzyme could arise, than through DNA. It just doesn't follow.

Russell's teapot much ??!!

You're not making a teapot argument, you're actually claiming you have ruled out that there can be another mechanism. That's what all your quotemines are attempting to establish, that there is no way there can be another mechanism.

You can't have your cake and eat it too. The teapot argument is not about the nonexistence of god, it's about justification for belief in the first place. There is no analogy between your argument against a natural origin of life and Russell's teapot, because unlike Russell you're actually claiming to have ruled out the unknown.

Why do I have to teach you what your own arguments are trying to accomplish? You are flailing around wildly trying to keep your house of cards standing.

In fact we know several non-proteinaceus organic compounds with phosphodiesterase activity.

You are apparently clueless about basic biochemistry principles. Enzymes are merely catalysts that enhance the selectivity and rate of certain chemical reactions. But there are other ways to get those chemical reactions to proceed without these enzymes. They will be less efficient, and they will be less specific, but they still work.

that they work to make the molecules in demand in a prebiotic world is pure speculation.

What molecules are in demand, and how do you know? If you say RNA or DNA, you are assuming the first life or the first metabolism must be like life that exists now. But why must it be so? How do you know?

You are operating under this misconception that everything has to work exactly like it does now in life that already exists, but how do you know this is true? You don't, at all. This is just something you assume. All your arguments are based on the assumption there cannot be any other way for life to function than the way life you know it does. What merits this assumption? Nothing at all.

we know of many parts and things that had to exist right from the beginning as they are know, as for example the genetic code, DNA, RNA, RNA polymerases, DNA and RNA repair mechanisms, the Ribosome, chaperones, just to mention a few.

Blind assertions. Prove it, prove it for every one.

Prove that there cannot be a form of life without the genetic code.
Prove that there cannot be a form of life without DNA.
Prove that there cannot be a form of life without RNA.
Prove that there cannot be a form of life without RNA-polymerase.
Prove that there cannot be a form of life without the Ribosome.
Prove that there cannot be a form of life without chaperones.
Prove that there cannot be a form of life without DNA repair mechanisms.

Notice how you're not making a Russell's Teapot argument here, you are actually claiming to know the teapot doesn't and cannot exist. Okay, prove it!

We don't have to prove the contrary, YOU are the one that has to prove that they ARE essential, irreducible and cannot arise in a stepwise manner.

I have.

No you have not. All you have done is argued on the basis of life as we know it, using quotes from scientists telling us that life as we know it have certain parts that are necessary for their function as they are now.

You are using these quotes to try to prove that there cannot be another form of life that is different from the way life is now. Prove it.

You are the one that is incredulous towards my position

Yes, of course I'm incredulous towards your position. You have not met your burden of proof.

You are the one claiming to know how life originated, and that it not only wasn't a natural origin, that a natural origin is impossible and so instead it was a supernatural origin.

On what basis have you claimed this? A lot of quotes about how life as we know it works. But none of your quotes say there is no other form of life possible, so you simply cannot conclude that we must go to a supernatural origin.

Non sequitur - It doesn't follow. Your whole case is build on a fundamental error in classic Aristotelian logic.

and have failed so far to refute my claims in a competent manner and providing compelling scenarios.

Compelling according to whom? You?

I'm not here to try to compel you to do anything. It is clear to me from our previous 3 or 4 encounters that nothing but religion compels you. I don't care about what you believe, but I care about correcting your many mistakes in logic and reasoning, and making sure any person who comes to this thread to read your many quotemines becomes aware that they are indeed quotemines.

DNA can not be reduced from nucleotides to nucleosides to nucleobases.

Yes it can, it just stops being DNA when you split it up into it's constituents.

But since what you probably mean to say is that DNA is required for life, please demonstrate that there cannot be a form of life without DNA.

DNA is irreducibly complex.

Irrelevant, irreducibly complex entities can evolve. Easily. And have been observed to do so.

You have not falsified or refuted my claim, as the fact is obvious it can't.

Yes I have. The Lenski long-term evolution experiment has produced irreducibly complex metabolic pathways as I already explained to you. But you ignored it.

So irreducible complexity is not only a bad argument against evolution, it's actually evidence for evolution. Evolution predicts that irreducibly complex structures will arise.

And the make of nucleobases is still a problem, since enzymes are required that hardly could be ribozymes
, as it is as well to make nucleosides, as the lability of glycosidic bonds, and the difficulty of formation of them in a prebiotic world, and as well it is to make ribose, and the possible solvents for phosphorylation. And so the availability of phosphor and actually all required elements in a prebiotic world. And so is the necessity of left handedness. These are formidable unresolved problems.

All of this is an argument from ignorance, built on the premise that the mechanism of synthesis of RNA is something like the scenarios envisioned by primordial soupists. What merits this premise in the first place? Nothing.

But is that the only kind of life possible? How could you possibly know?

Again proposing Russells teapot ?? And, well, we do not know of any other life form, than based on DNA, RNA etc ya know.......

But you're NOT making a Teapot argument. Remember, you claimed these things are required for life, that they had to exist right from the beginning.

we know of many parts and things that had to exist right from the beginning as they are know, as for example the genetic code, DNA, RNA, RNA polymerases, DNA and RNA repair mechanisms, the Ribosome, chaperones, just to mention a few. - You

You're not just claiming we have no good reason to believe these things aren't required, you're claiming they are required.

Unless you have ruled out all other concievable options with some kind of demonstration of their impossibility

what other concievable options ? viaje dans la maionnaise much again ??

Oh, all the options I mentioned.

Life without DNA, RNA and proteins. You're claiming they are required and no other life is possible. Prove it.

all we can is is that we don't know how life as we know it originated.

aham.......

As Robert Shapiro wrote :

RNA's building blocks, nucleotides, are complex substances as organic molecules go. They each contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern. Many alternative ways exist for making those connections, yielding thousands of plausible nucleotides that could readily join in place of the standard ones but that are not represented in RNA. That number is itself dwarfed by the hundreds of thousands to millions of stable organic molecules of similar size that are not nucleotides.

This quote you mindlessly offer is utterly fucking irrelevant to the part of my response you quote. Can you even read?

Robert Shapiro, here offering arguments against an RNA-first scenario, is not talking about the general idea of other possible forms of life. So what the fuck is this quote supposed to achieve when it is irrelevant to the statement of mine you quote?

a metabolism first scenario is also a simplistic explanation for follwing reasons, citing Shapiro again:

http://www.scientificamerican.com/article/a-simpler-origin-for-life/

Your popular press article contains no citation of Shapiro that says "metabolism first is simplistic". But even if it was, simplistic does not entail false, so what the fuck is your statement supposed to convey? It would also be idiotic to suggest Robert Shapiro, one of the founders of modern metabolism-first theorizing, is somehow suggesting his own theory specifically erected to solve the problems of the RNA-world is somehow false.

You seem to have a severe problem comprehending the relevance and purpose of all these quotes you have collected and mindlessly copy-paste here. I suggest you take a few months off and train your reading comprehension in english. I would also recommend you supplement your training in basic reading comprehension with some courses in elementary logic. You seem to be exceedingly bad at both.

A coupling mechanism must link the release of energy to the organization process that produces and sustains life. The release of energy does not necessarily produce a useful result. Chemical energy is released when gasoline is burned within the cylinders of my automobile, but the vehicle will not move unless that energy is used to turn the wheels. A mechanical connection, or coupling, is required. Each day, in our own cells, each of us degrades pounds of a nucleotide called ATP. The energy released by this favorable reaction serves to drive processes that are less favorable but necessary for our biochemistry. Linkage is achieved when the reactions share a common intermediate, and the process is speeded up by the intervention of an enzyme. One assumption of the small-molecule approach is that coupled reactions and primitive catalysts sufficient to get life started exist in nature.

Yes, this is all a good overview of what is required from a metabolism-first scenario. Robert Shapiro was a great scientist and he was right when he wrote this stuff. I respect his work a lot.

He would be rolling around in his grave if he knew how much bullshit creationists are spewing about his work and how they are constantly abusing is excellent arguments agains the RNA world to conclude that any natural origin of life must be impossible. You should be ashamed of yourself.

Will we eventually discover a naturalistic explanation for origins in general, and the first life ?

http://elshamah.heavenforum.org/t1508-will-we-eventually-discover-a-naturalistic-explanation-for-first-life

You pose this question and then answer it with a link to your own conclusion on your own website full of quotemines you have collected but don't even understand. This is would be funny if it wasn't so sad.

Kids, Elsamah is your brain on religionism. Just say no!

 

[Elshamah]

I'm explaining to you how RNA is synthesized now in extant cells, how the chemistry works. I'm not saying chemoautotrophic bacteria came out of nowhere for fucks sake, please try to follow the discussion.

before you bring them into the discussion as a solution, you need to explain their origin. Unless you cant do that, all you say will be meaningless.

Here is the point again: RNA is synthesized(now, in your very own cells) by using energy and certain catalysts(to reduce the energy barrier). The energy and the catalysts probably already existed before life

probably. aham. the sophistry begins... LOL.... so not mentioning bacterias anymore ??

(because most of them are actually metal catalysts). The life that exists today is still using the same principles of energy and catalysis to make it's basic constituents as would have existed in the prebiotic environment. At least, there are some good indications that this is so when we analyze the structure and mechanism of the oldest metabolic enzymes.

but today we use mitochondria, and atp synthase for ATP production... explain their origin...... LOL.

You have a lot of quotes about how the nonbiological chemical synthesis of RNA is energetically "uphill". All that means is that it takes energy to make RNA, energy that would have already existed under the right conditions.

it does not take only energy. RNA must be synthesized, and the building blocks must be available.

http://elshamah.heavenforum.org/t2024-the-rna-world-and-the-origins-of-life#3454

And then there are catalysts, those would be enzymes in extant life, but inorganic minerals and metals on the ancient Earth.

I have already provided good reasons why its unlikely that RNA, and so DNA, would arise in the prebiotic world. Now you are just demonstrating incredulity.

This is old shit that has been superceded long ago. Leslie Orgel and Robert Shapiro died years ago, quite a lot has happened since their original discussions on replicator vs metabolism first scenarios.

No kidding. So have their objections been overcome ? If so, how ??

Case in point, all the issues erected in that article are dealt with in the alkaline hydrothermal vent theory. So in factual fact, metabolism first does stand on it's own merits.

So you still believe blindly that your sodium-proton antiporter could have been simple, and arise naturally ?? LOL.....

Yeah, I'm quite incredulous towards the physically impossible and rightfully so. But I'm open to being convinced otherwise with a nice demonstration. Bring on the magic.

But you are not incredulous towards the idea that the universe could have self caused itself, or come into existence by nothing ? LOL.....

Or maybe not, maybe, just like you believe about your god, the universe necessarily exists by it's own nature. That would be a simpler explanation. We don't need to postulate god then.

It seems the absurdity of such a claim is not evident to you ?? Show me something that self caused itself.

What caused your god? Another god?

a uncaused eternal God has no cause.

Yes you do. You simply make shit up: I can't figure it out so oh gee a magic man gone dunnit! *allakhazam*

So you are making shit up characterizing my arguments in a way i never formulated them. Your ignorance goes strong here.

Turns out it's 3. You are special pleading. You believe your god has special properties no other entity has, such as not requiring a cause. But if it's logically possibly not to require a cause, that property could be assigned to the universe.

ahhm. The old debunked arguments..... pffff.

Its not special pleading to say God is eternal, since this is exactly what the atheist has traditionally said about the universe: It is eternal and uncaused. The problem is that we have good evidence that the universe is not eternal but had a beginning, and so the atheist is backed into the corner of saying the universe sprang into being without a cause, which is absurd.



If logic does not account for justifiable special pleading then such logic is clearly flawed.

Of course an Infinite Creator Who created everything would involve a justifiable special pleading. Such Creator would not be like the rest of us.

It is as simple as seeing the difference between an Infinite Being (notice I didn't say "existence") and billions of "finite beings."

The One Infinite Being is clearly different. The One Infinite Being Who created all existence is quite different than those finite beings who are created by such Being.

It is as easy as seeing the difference between "those who have a beginning" who are finite verses an "Infinite Creator" Who has no beginning and alone possesses the attribute of Aseity.

In theology there are several (what we call) incommunicable attributes of God. 1. would be omniscience. 2. omnipresence. 3. omnisapience 4. Asiety 5. immutability 6. I would include omnitemporal being. There are others.

You see, only God is infinite everywhere. Only God is the Creator of the universe. Everyone else is different.

This is why we have something as basic as justifiable special pleading to account for this every clear difference between an Infinite Creator Who created everything.... and all other finite existences.

http://elshamah.heavenforum.org/t1539-is-attributing-eternity-to-god-special-pleading?highlight=special+pleading

Theism has lost this argument every time it's been begun.

Only in your wishful thinkiing.

Theism rests inherently on special pleading. Everthing requires a cause except god. Or maybe the universe too. No no, just god because.. well, just because.

Its evident that something must exist without a cause, since from absolutely nothing, nothing comes.

I didn't claim RNase P is "just functional" when entirely removed from the organism it belongs to, that's just stupid.

Thats however exactly the problem you have to explain. It had only function after fully operatonal, and duly embedded in the tRNA biogenesis pathway. So why should natural step by step mechanisms make it in the first place ?

Where did i say phosphdiesterases MAKE DNA ?? My point was precisely that the bonding of the monomers to polymers is another major hurdle and problem.

Then why the fuck mention phosphodiesterase enzymes when they CLEAVE the polymers? [/quote]

Because thats not the ONLY thing they do. Just read on Wiki about what else they are involved in.

You're not making a teapot argument, you're actually claiming you have ruled out that there can be another mechanism.

As long as science does not find a other use, why should i make one up ?

That's what all your quotemines are attempting to establish, that there is no way there can be another mechanism.

I have not said ther CANT be another mechanism. I have said we should not invent one, if there is no evidence that there is one.

You can't have your cake and eat it too. The teapot argument is not about the nonexistence of god, it's about justification for belief in the first place.

Thats precisely what i addressed. You believe the enzyme has eventually another function without evidence.

Why do I have to teach you.............

You have not teached me anything so far, and thats neither the reason i debate with you.

what your own arguments are trying to accomplish? You are flailing around wildly trying to keep your house of cards standing.

Nah. My house stands firm and on solid ground. Projecting much ??!!

You are apparently clueless about basic biochemistry principles.

How much clue or no clue i have is irrelevant. Relevant is if my arguments stand, and if there is ground for refutation. So far, you have miserably failed ..... try harder LOL.

Prove that there cannot be a form of life without the genetic code.
Prove that there cannot be a form of life without DNA.
Prove that there cannot be a form of life without RNA.
Prove that there cannot be a form of life without RNA-polymerase.
Prove that there cannot be a form of life without the Ribosome.
Prove that there cannot be a form of life without chaperones.
Prove that there cannot be a form of life without DNA repair mechanisms.

Russells teapot much ? LOL...

Notice how you're not making a Russell's Teapot argument here, you are actually claiming to know the teapot doesn't and cannot exist. Okay, prove it!

you make the claim, you provide evidence. Thats how a rational discourse works. Teaching you the basics, hah ?? .....

No you have not. All you have done is argued on the basis of life as we know it, using quotes from scientists telling us that life as we know it have certain parts that are necessary for their function as they are now.

well, then show me that life could have begun without tRNA. Good luck with that.

You are using these quotes to try to prove that there cannot be another form of life that is different from the way life is now. Prove it.

I dont have to prove that. All i can do, and i have done so, is showing that tRNA hardly could arise by natural means. As long as you cannot provide a better explanation by natural means, all you do, is empty blabbering.

Yes, of course I'm incredulous towards your position. You have not met your burden of proof.

I dont have to prove anything. Providing a better explanation is enough.

You are the one claiming to know how life originated, and that it not only wasn't a natural origin, that a natural origin is impossible and so instead it was a supernatural origin.

On what basis have you claimed this? A lot of quotes about how life as we know it works. But none of your quotes say there is no other form of life possible, so you simply cannot conclude that we must go to a supernatural origin.

Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information, irreducible and interdependent biological systems.
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information, irreducible and interdependent systems of all sorts.
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information and irreducible complexity in the cell, and interdependence of proteins, organelles, and bodyparts, and even of animals and plants, aka moths and flowers, for example.

Compelling according to whom? You?

yes.

then why are you debating me in the first place ?? LOL.....

I'm not here to try to compel you to do anything. It is clear to me from our previous 3 or 4 encounters that nothing but religion compels you.

Bollocks. I have not written about religion, but science, and how the scientific evidence provides hard evidence for a designer/creator.

I don't care about what you believe, but I care about correcting your many mistakes in logic and reasoning

Pretentiuous much ?

DNA can not be reduced from nucleotides to nucleosides to nucleobases.
Yes it can, it just stops being DNA when you split it up into it's constituents.

thats precisely my point. DNA cannot be reduced further. the 3 parts are essential. And it will not exercise its funciton anymore. And since it cannot arise in a stepwise naturalistic manner, the argument that DNA is IC is granted.

But since what you probably mean to say is that DNA is required for life, please demonstrate that there cannot be a form of life without DNA.

Russells teapot again ?? If you think there can be life not based on DNA, its you to demonstrate it.

Irrelevant, irreducibly complex entities can evolve. Easily. And have been observed to do so.

If they can evolve, they are not IC anymore. It seems you are becoming more desperate , providing such strawman arguments ?

Yes I have. The Lenski long-term evolution experiment has produced irreducibly complex metabolic pathways as I already explained to you. But you ignored it.

What does THAT now have to do with DNA, ??? All Lenskys experiments have shown, is a total failure of macro evolution.

So irreducible complexity is not only a bad argument against evolution, it's actually evidence for evolution. Evolution predicts that irreducibly complex structures will arise.

LOL.... IC is the oposit of evolution. IF its IC, evolution is falsified. :lol:

All of this is an argument from ignorance, built on the premise that the mechanism of synthesis of RNA is something like the scenarios envisioned by primordial soupists. What merits this premise in the first place? Nothing.

No argument from ignorance, but based on decades of experiments. To be honest, i am becoming just bored now, so i will leave it at this for now. I will not respond to the rest of your post.

 

[Rumraket]

I'm explaining to you how RNA is synthesized now in extant cells, how the chemistry works. I'm not saying chemoautotrophic bacteria came out of nowhere for fucks sake, please try to follow the discussion.

before you bring them into the discussion as a solution, you need to explain their origin. Unless you cant do that, all you say will be meaningless.

Here is the point again: RNA is synthesized(now, in your very own cells) by using energy and certain catalysts(to reduce the energy barrier). The energy and the catalysts probably already existed before life

probably. aham. the sophistry begins... LOL.... so not mentioning bacterias anymore ??

Are you illiterate? What country are you from? You seem to have a very hard time understanding english.

Let's go over it again, this time step by step.

Inside your cells, now, RNA is synthesized from simple precursors. Do you understand this?
Your own cells can make, and are making, RNA, through chemistry. They make the ribose, they make the nucleobases, they link the triphosphates on, they make the glycosidic bond between C[sub]1[/sub] on Ribose and the Nitrogen atom on the nucleobase.

Can I get a confirmation that you understand this simple thing? Your cells make RNA. Do you agree?

 

[Rumraket]

If they can evolve, they are not IC anymore.

That's not what irreducible complexity means and not how Michael Behe defined it.

Irreducible complexity is supposed to be an argument against evolution, not a definition of the impossibility of evolution. Do you understand the difference?

If IC merely meant: Cannot evolve - then it stops being an argument against evolution and just becomes a tautology. That means you could restate it as: That which cannot evolve, cannot evolve. Well duh!

But that is the very statement that is being contested, is it in fact true that "IC" systems cannot evolve? If they can, then IC is not a good argument against evolution.

 

[Dragan Glas]

Greetings,

Of course an Infinite Creator Who created everything would involve a justifiable special pleading. Such Creator would not be like the rest of us.

It is as simple as seeing the difference between an Infinite Being (notice I didn't say "existence") and billions of "finite beings."

The One Infinite Being is clearly different. The One Infinite Being Who created all existence is quite different than those finite beings who are created by such Being.

It is as easy as seeing the difference between "those who have a beginning" who are finite verses an "Infinite Creator" Who has no beginning and alone possesses the attribute of Aseity.

In theology there are several (what we call) incommunicable attributes of God. 1. would be omniscience. 2. omnipresence. 3. omnisapience 4. Asiety 5. immutability 6. I would include omnitemporal being. There are others.

You see, only God is infinite everywhere. Only God is the Creator of the universe. Everyone else is different.

This is why we have something as basic as justifiable special pleading to account for this every clear difference between an Infinite Creator Who created everything.... and all other finite existences.

Do you believe that God has all those attributes?

[And it's "aseity".]

Kindest regards,

James

 

[Rumraket]

I have not written about religion, but science, and how the scientific evidence provides hard evidence for a designer/creator.

That is not only oxymoronic, it is a fucking lie.

This is why we have something as basic as justifiable special pleading

"Justifiable special pleading". This is where I just point and laugh. :lol:

 

[Rumraket]

I'm explaining to you how RNA is synthesized now in extant cells, how the chemistry works. I'm not saying chemoautotrophic bacteria came out of nowhere for fucks sake, please try to follow the discussion.

before you bring them into the discussion as a solution, you need to explain their origin. Unless you cant do that, all you say will be meaningless.

The evidence that you can't follow the discussion is starting to form a mountain-range on this forum.

Look, let me try to cut it down into small easy to swallow pieces and lay it all out so you see where I'm going with this.

You are concerned about the origin of RNA, right?
You have a lot of quotes about how difficult it is to synthesize RNA without the aid of life, right? I can do that work for you, without having to copy-paste anything. Because I actually know this subject by heart.

Researchers who first proposed the RNA world hypothesis, got to work on the theory by trying to come up with some way RNA could be synthesized without the aid of life from simple precursors like hydrogencyanide (HCN) and formaldehyde (CH[sub]2[/sub]O). Mostly because there was and still is some evidence that these molecules(HCN and CH[sub]2[/sub]O) could have existed on the early Earth. They have, after all, been detected in space.

Formaldehyde was envisioned to be used to make the ribose-sugar(through the formose reaction), and hydrogencyanide to make the nucleobases. Many elaborate schemes were tested, and they were all heavily criticized by other researchers, because the conditions that allowed the synthesis of ribose, were different from the conditions to make the nucleobases. Also because the yields were low and the conditions interfered with to get more pure product mixes. So already at the start, there was the problem of two mutually incompatible chemical reactions required to produce two of the constituents of RNA, not to mention issues of yield and interfering side-reactions when the conditions weren't manipulated.

Furthermore, to link the nucleobase to ribose required a very special and hard-to-get-to-work-properly-reaction, to catalyze the formation of a glycosidic bond. That is, the particular bond between C[sub]1[/sub] in ribose and a particular N-atom in the nucleobase.

All these reactions, while individually, could be envisioned to be possible in some prebiotic environment, but even then there were problems like concentration and the stability of the products under the conditions at which they were made.
Even worse, when looked at collectively, it was clear that for RNA to be made in prebiotic environments like lakes or atmospherically, it would require at least three individual types of environments in close proximity to each other, so that the environment that produced ribose somehow never interfered with the environment that made the bases, and the environment that linked ribose to the nucleobase, never interfered with the two others.

The whole idea was, not to put too fine a point on it, fucking absurd. This quickly became clear to many of the researchers, one of them Robert Shapiro who you love to quotemine to no end. He pointed out many of these issues as much as 20 fucking years ago at least. He also happened to know how cells make RNA and that cellulalar anabolism is ultimately based on simple metabolic processes catalysed by some extremely old enzymes with interesting properties. This lead him and others to start postulating various "metabolism first" type theories instead. Though at the time these were very speculative and undeveloped. They were merely ideas and no hard data or work had been done to try to link cellular metabolism to any possible prebiotic environment.

Okay so, clearly RNA doesn't just spontaneously appear in the prebiotic environment, at least not through the formose reaction combined with the spontaneous conversion of HCN into the bases. Some, in my opinion no longer entirely rational researchers, still believe they can get this shit to work and have postulated so-called "discontinous synthesis" models of prebiotic RNA formation.
See for example: Asphalt, Water, and the Prebiotic Synthesis of Ribose, Ribonucleosides, and RNA.
In my view these people have in some sense lost their rational senses and have become obsessed with the idea that RNA must precede everything, perhaps because the idea of a self-replicator kick-starting life is easy to grasp and intuitively appealing. Perhaps partially because of an overemphasis on genetics as the basis of life and so on. There are so many problems with this theory one could write half a book discussing them all. Environment A produces compound A1 that is flushed into environment B with another compound B1 in it, in which they are both combined to make compound C etc. etc.
Do such a combination of environments exist anywhere today? No. Is there good reason to think this combination of environments would exist on the early Earth and happen to produce all these compounds in the right order, in sufficient quantities, continuously at such a high rate that the products would accumulate before they broke down etc. etc.? No.

Okay, so, how the fuck is RNA made in the most basic** primary producers* that live today, you say?
* (by primary producers I mean organisms that don't get their energy or carbon from any other living organisms, they get it all from inorganic, non-biological sources)
** (And by most basic I mean the types of organisms that are most like the type of organisms we can reconstruct from phylogenetics at the root of the tree of life, something around the time of the universal common ancestor).

Turns out RNA is actually made, at bottom, from CO[sub]2[/sub]and amino acids (the amino acids are made from CO[sub]2[/sub] and NH[sub]3[/sub]/NO[sub]3[/sub][sup]-[/sup]). The ribose is produced by some sort of Acetyl-CoA or reductive citric acid cycle-pathway through multiple reductions of CO[sub]2[/sub], catalyzed enzymes with metal clusters as cofactors:

(I adapted this picture from this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685469/)

So the way RNA is made in life is very different from the way it was envisioned to be made outside of life by the "prebiotic RNA-world"-chemists.

How come life can make RNA in the first place? What is it that makes it possible for an organism to make RNA? Energy and catalysts. Energy to drive the chemical reactions, catalysts to promote specific ones to happen at higher rates than others (make them "thermodynamically favored").

What kind of energy and what catalysts? This is where it gets interesting. The energy ultimately comes from the proton-motive force. The disequilibrium in the concentration of protons between the inner and outer cell-membrane is driving the formation of compounds with the well-known high-energy phosphate bonds in ATP (through the ATP-synthase of course), that can be used by other chemical reactions if the right catalysts are present. (It turns out there is a natural environment known, with a significant proton gradient that is sustained over millenia: Alkaline hydrothermal vents)

Anyway, in this sense the phosphates in ATP function like a sort of chemical "tag" that can be attached to another molecule (become phosphorylated), so it becomes energetically favored for further modification. It often just takes a catalyst to kick the molecule into a further conversion when it has become "charged" with the phosphate group.

And the catalysts that act to make CO[sub]2[/sub] and the nitrogen compounds into cellular carbon and amino acids, what are those? Well in life today they are specific protein enzymes with special metal-clusters as their cofactors. Metals like Iron, Nickel, Magnesium, Molybdenum, Tungsten and a few others. Metals that would have existed in pretty good quantities in the ocean on the early Earth.

What is the role of these metal cofactors I hear you say? (well you don't, because you are an unquestioning religionut so I'm going to explain this for some one else who wants to know it). A good analogy would be to say they function like small spot-welders that the proteins can grab and use to "zap" other molecules into a conversion of some sort.

Basically metals like to move electrons around, metals are almost always charged and ready to let go of, or take up, electrons. That's why most metals are good conductors, the outer shell electrons can move relatively freely between the atoms in a cluster. That's also why metal-clusters make good catalysts in chemistry and biochemistry, when they get close to certain organic molecules they can break or make bonds by stealing electrons or by lending their own.

Okay, so why is there a big fat protein sitting around the metal cofactor? To discriminate between substrates and/or promote specific reactions. The protein basically sits there to prevent unwanted molecules to get close to the "welding spot", and some times the protein can even change the direction at which a certain molecule approaches the metal cofactor, such that when it comes into contact, only a specific chemical bond is near the active site, and so only a specific chemical reaction is promoted.

This ensures that almost always it is only that particular chemical reaction that happens, instead of some other possible reaction the metal could catalyze.

Notice, though, that no enzyme in existence is 100% effective in discriminating between substrates. Sometimes, even for the most high-fidelity enzymes known, an occasional side-reaction still gets catalyzed accidentally. In this sense biochemists like to talk about the degree of "promiscuity" of enzymes. Some enzymes are highly promiscous, and catalyse many different reactions and can work on many different substrates. Phylogenetic reconstructions of the oldest enzymes known, using a special statistical process called ancestral sequence reconstruction, has been used to show many times that the further we go back in time, the more promiscous the enzymes become. This implies the oldest catalysts were highly promiscous and therefore probably less efficient. Curious fact isn't it?

Anyway, getting back to RNA and how it could possibly have been made outside of living cells, before the origin of modern enzymes. Since the actual catalysts that make RNA are metals, and since the surrounding proteins merely act to promote certain reactions above others, it is clear that the chemical reactions that are required could still be catalyzed by the metals, even without the surrounding proteins.

The rate of catalysis will be lower, because many times the molecules to be converted will be hitting the catalyst at the wrong angle(due to the absense of the surrounding protein complex to "guide" the substrate toward the active site in the right way), and so instead another conversion will happen into something different and unrelated to RNA synthesis. But simply as matter of chance, the "right" chemical reactions will still happen.

Back to the matter of the energy. Obviously there would be no ATP synthase and so no ATP before ATP synthase evolved. But remember, the important part of ATP is not the A (Adenosine, the nucleotide), the important part is the phosphate groups. They are the part of the molecule that actually carries the "charge", the energy to "make things happen".
When ATP is used in the chemical synthesis of some energetically "uphill" compound in your cells, what is actually used is the phosphate parts, the chemical bond between the phosphates is where the energy lies. The Adenosine(a purine) part is basically just a "handle" attached to them, so ATP can be detected and transported around the cell instead of having to rely on simple diffusion. So what is needed is merely a carrier of the phosphates, easily synthesized from CO[sub]2[/sub] and capable of easy phosphorylation and phosphorolysis. Turns out a good candidate is acetyl-thioesters, which have been easily synthesized under alkaline hydrothermal conditions.

What else has been synthesized, experimentally without any artificial manipulations of purity or concentration, under alkaline hydrothermal conditions? Ribose. And amino acids.

Now I will openly state that nobody has yet seen RNA synthesized in a single experiment like this. So it is definitely still speculative whether this is possible. But I have two things to say about that, the first of which is that as far as I am aware, actual experiments to mimick the conditions under alkaline hydrothermal vents on the early Earth have only begun within the last 10 years or so, are only worked on by two laboratories in the world(as far as I know), and in light of the above explained facts, it really doesn't seem all that implausible that a primordial metabolism working with the same metal catalysts used by the enzymes in extant life, acting on the same substrates, could eventually end up producing RNA.

Speculative and unproven. Sure. Should we therefore believe that this is how it happened. No, not until it has been demonstrated. Should we believe it is impossible in the mean time? No. We should just admit that we don't know yet. What we don't have good reason to conclude is what you are trying to do: That it is impossible and that therefore we should believe your pet god did it.

 

[Rumraket]

An excellent and very recent paper, for anyone who is not a deluded religious apologist, but instead interested in trying to understand stuff about recent developments in the field, and who would like to see some stuff on the possible origin of RNA and coded protein synthesis, I can recommend this paper:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390850/
How Amino Acids and Peptides Shaped the RNA World

Abstract
The “RNA world” hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and tRNA are crucial for modern protein synthesis. However, this view is incomplete at best. The modern protein-RNA ribosome most probably is not a distorted form of a “pure RNA ribosome” evolution started out with. Though the oldest center of the ribosome seems “RNA only”, we cannot conclude from this that it ever functioned in an environment without amino acids and/or peptides. Very small RNAs (versatile and stable due to basepairing) and amino acids, as well as dipeptides, coevolved. Remember, it is the amino group of aminoacylated tRNA that attacks peptidyl-tRNA, destroying the bond between peptide and tRNA. This activity of the amino acid part of aminoacyl-tRNA illustrates the centrality of amino acids in life. With the rise of the “RNA world” view of early life, the pendulum seems to have swung too much towards the ribozymatic part of early biochemistry. The necessary presence and activity of amino acids and peptides is in need of highlighting. In this article, we try to bring the role of the peptide component of early life back into focus. We argue that an RNA world completely independent of amino acids never existed.