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Source: (consider it)
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Thread: Abiogenesis
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EtymologicalEvangelical
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# 15091
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Posted
On the 'Evidence' thread some weeks ago there were the following exchanges:
Here:
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Originally posted by EtymologicalEvangelical
quote:
Originally posted by Marvin the Martian
You seem fairly sure that abiogenesis can't happen. What evidence do you have to support that belief?
Because of the chicken and egg scenario of protein / DNA production, which is convincing evidence that abiogenesis is impossible. The "RNA world" theory doesn't answer this, because RNA still has to be decoded by specific proteins that are themselves coded for by the information in RNA. This is an example of irreducible complexity, requiring the immediate appearance of a fully formed complex system, that could not have come into being in stages, which abiogenesis requires.
Here:
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Originally posted by ken
quote:
Originally posted by EtymologicalEvangelical
The "RNA world" theory doesn't answer this, because RNA still has to be decoded by specific proteins that are themselves coded for by the information in RNA.
If I understand what you are saying then I'm pretty sure you are entirely wrong about this - maybe you would want to start another thread in Dead Horses to explain what you actually mean by it.
Here:
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Originally posted by Karl: Liberal Backslider
No one is stupid enough to propose that a protein assembled itself in one go. Was it you who earlier totally misunderstood RNA world and thought it needed proteins to work? Might it be worth spending more time reading papers on research into abiogenesis and less reading ID proponents telling you it's all bullshit? Just a thought.
And...
Here:
quote:
Originally posted by EtymologicalEvangelical
Perhaps you would be so kind as to explain to me the function(s) of ribosomal proteins, and why (I assume) you think that such functions were, at one time, unnecessary.
I look forward to your answer, which I will compare with peer reviewed scholarship.
(I realise this is a DH subject, so I expect this thread will be moved. Otherwise we will have to open a new thread down there, as admin may advise).
There was the beginnings of a discussion about abiogenesis and the RNA World theory, but which never came to anything. I made a comment about RNA being dependent on proteins and this was questioned. As you can see, I asked for clarification as to the function of ribosomal proteins, and for an explanation as to why they were considered unnecessary at the advent of first life.
Perhaps someone might like to try to answer my question?
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You can argue with a man who says, 'Rice is unwholesome': but you neither can nor need argue with a man who says, 'Rice is unwholesome, but I'm not saying this is true'. CS Lewis
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Karl: Liberal Backslider
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# 76
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Posted
Proteins, ribosomal or otherwise, are irrelevant to the RNAworld hypothesis; RNA replication is proposed to have been catalysed by Ribozymes - enzymes themselves conposed of RNA, not protein.
Robozymes can therefore catalyse their own replication, thus avoiding the chicken and egg protein enzyme/coding for protein enzyme issue posed by the DNA.
Nucleic acids coding for proteins comes later.
[ 21. February 2013, 11:10: Message edited by: Karl: Liberal Backslider ]
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Might as well ask the bloody cat.
Posts: 17938 | From: Chesterfield | Registered: May 2001
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EtymologicalEvangelical
Shipmate
# 15091
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Posted
quote:
Originally posted by Karl: Liberal Backslider
Proteins, ribosomal or otherwise, are irrelevant to the RNAworld hypothesis; RNA replication is proposed to have been catalysed by Ribozymes - enzymes themselves conposed of RNA, not protein.
Robozymes can therefore catalyse their own replication, thus avoiding the chicken and egg protein enzyme/coding for protein enzyme issue posed by the DNA.
Nucleic acids coding for proteins comes later.
This article summarises your position:
quote:
Perhaps the strongest evidence for the RNA World Hypothesis is the fact that the ribosome, a large molecular complex that assembles proteins, is a ribozyme. Although the ribosome is made up of both RNA and protein components, structural and biochemical analyses revealed that the mechanisms central for translation (the process of assembling a peptide chain based on a RNA sequence) is catalyzed by RNA, not protein. This suggests that the use of RNA by early lifeforms to carry out chemical reactions preceded the use of proteins.
However, that assumes that ribosomal proteins can simply be ignored as unnecessary for translation. Note that the article uses the phrase "central for translation". 'Central' does not imply that there are no secondary functions on which translation relies.
There is a pdf article entitled "Ribosomal Proteins: Role in Ribosomal Functions" by Stelzl, Connell, Nierhaus and Wittmann-Liebold, which I can't seem to link to, but which you can find through Google and then access through www.researchgate.net . This article concludes as follows:
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In the 1970s the generally accepted view was that ribosomal proteins were the functionally active part in the ribosome and rRNA was essentially a scaffold, keeping the proteins in a position for optimal function. In the 1980s the pendulum swung in the opposite direction: now the proteins were thought to have mainly a scaffolding function, controlling and stabilizing the three-dimensional fold of the rRNAs for optimal function. The reason for this change was that an impressive wealth of data showed a direct involvement of rRNAs in distinct ribosomal functions. Examples are the Shine–Dalgarno interactions during initiation of protein synthesis of bacterial ribosomes, the presence of 16S rRNA sequences in the decoding centre and 23S rRNA sequences in the peptidyltransferase centre. However, one can argue for a direct participation of ribosomal proteins with the same stringency, for example the participitation of ribosomal proteins S12, S4 and S5 in the accuracy of the decoding process, L7/L12 in the binding of elongation factors and the possible role of L4 in controlling the nascent peptide chain’s access to the tunnel. The truth might be in the middle as is so often the case. Certainly, the interplay of both ribosomal proteins and rRNA is a prerequisite for optimal functioning of the ribosomal machine. But even if we restrict our view to the essential core functions of the ribosome such as decoding, peptide bond formation and translocation, proteins and RNA might be equally important.
In the light of this, it is rather hard to understand how essential functions of a ribosome can simply be dispensed with, in order to construct an entirely speculative scenario in an unknown environment in the early Earth.
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You can argue with a man who says, 'Rice is unwholesome': but you neither can nor need argue with a man who says, 'Rice is unwholesome, but I'm not saying this is true'. CS Lewis
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Karl: Liberal Backslider
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# 76
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Posted
Because RNA has been observed to self-replicate under certain circumstances.
The second article is pretty much irrelevant - it describes how ribosomes work in existing DNA based organisms and does not address what is or is not possible.
Yes, proteins are absolutely essential for ribosomes to work in DNA based organisms such as we see today. However, that's quite different from what may be possible in an RNA world. It's a bit like observing that a sound box, tuning pegs, frets and so on are necessary for a guitar to work - that does not mean that a single stretched string cannot vibrate without these - simply that that's not all there is to guitars.
The details of ribosomal function are hardly pertinent to early replicators which are not theorised to have had them.
[ 21. February 2013, 13:19: Message edited by: Karl: Liberal Backslider ]
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Might as well ask the bloody cat.
Posts: 17938 | From: Chesterfield | Registered: May 2001
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EtymologicalEvangelical
Shipmate
# 15091
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Posted
quote:
Originally posted by Karl: Liberal Backslider
Because RNA has been observed to self-replicate under certain circumstances.
Link to peer reviewed paper, please.
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You can argue with a man who says, 'Rice is unwholesome': but you neither can nor need argue with a man who says, 'Rice is unwholesome, but I'm not saying this is true'. CS Lewis
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Crœsos
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# 238
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Posted
quote:
Originally posted by EtymologicalEvangelical:
quote:
Originally posted by Karl: Liberal Backslider
Because RNA has been observed to self-replicate under certain circumstances.
Link to peer reviewed paper, please.
So sorry to hear the Google machine is broken where you live.
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Humani nil a me alienum puto
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EtymologicalEvangelical
Shipmate
# 15091
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Posted
quote:
Originally posted by Croesos
So sorry to hear the Google machine is broken where you live.
Ah, I see. I have to do the work of investigating the evidence for other people's claims, do I?
No. I think I will wait for Karl to support his own assertion.
(Although funnily enough, earlier in the thread I did actually link to an article which supported his view, but which clearly stated that it was the ribosome which was required for the RNA World Hypothesis. Shall I remind you?
quote:
Perhaps the strongest evidence for the RNA World Hypothesis is the fact that the ribosome, a large molecular complex that assembles proteins, is a ribozyme. Although the ribosome is made up of both RNA and protein components, structural and biochemical analyses revealed that the mechanisms central for translation (the process of assembling a peptide chain based on a RNA sequence) is catalyzed by RNA, not protein. This suggests that the use of RNA by early lifeforms to carry out chemical reactions preceded the use of proteins.
And they have even kindly produced an interactive diagram, that enables the viewer to remove those pesky proteins from the ribosome, as if to suggest that the ribosome can function without them!)
[ 21. February 2013, 13:53: Message edited by: EtymologicalEvangelical ]
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You can argue with a man who says, 'Rice is unwholesome': but you neither can nor need argue with a man who says, 'Rice is unwholesome, but I'm not saying this is true'. CS Lewis
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Karl: Liberal Backslider
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# 76
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Posted
quote:
Originally posted by EtymologicalEvangelical:
quote:
Originally posted by Croesos
So sorry to hear the Google machine is broken where you live.
Ah, I see. I have to do the work of investigating the evidence for other people's claims, do I?
No. I think I will wait for Karl to support his own assertion.
(Although funnily enough, earlier in the thread I did actually link to an article which supported his view, but which clearly stated that it was the ribosome which was required for the RNA World Hypothesis. Shall I remind you?
quote:
Perhaps the strongest evidence for the RNA World Hypothesis is the fact that the ribosome, a large molecular complex that assembles proteins, is a ribozyme. Although the ribosome is made up of both RNA and protein components, structural and biochemical analyses revealed that the mechanisms central for translation (the process of assembling a peptide chain based on a RNA sequence) is catalyzed by RNA, not protein. This suggests that the use of RNA by early lifeforms to carry out chemical reactions preceded the use of proteins.
And they even kindly produce an interactive diagram, that enables the viewer to remove those pesky proteins from the ribosome, as if to suggest that the ribosome can function without proteins!)
You're misunderstanding the point there. A ribosome is indeed a ribozyme. However, not all ribozymes are ribosomes; ribozymes without proteins can and do exist and it is they which are essential to RNA world, not ribosomes. The hypothesis is that the protein/RNA ribosome we have today is a development of the RNA only ribozyme of the RNA world.
Ribosomes are essential for translation - i.e. the formation of proteins, but they are not essential for replication of RNA, which is all that the RNA world hypothesis is about, and which can be done by RNA only, protein free, primitive ribozymes.
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Might as well ask the bloody cat.
Posts: 17938 | From: Chesterfield | Registered: May 2001
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ken
Ship's Roundhead
# 2460
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Posted
Some suggestive facts and some background First, the enzymes that replicate RNA and DNA, and that translate DNA to protein are themselves mostly made of protein, but the parts that do the actual work - that are in contact with the RNA and DNA and read it or write it - are nearly always made of RNA. In all known life RNA literally makes protein, protein does not make RNA. The ribosomes, the little molecular machines that build proteins, are mostly made of RNA and they use transfer RNA to carry the amino acids around and add them to the growing protein.
But its not just ribosomes. Most proteins are closely associated with or bound to non-protein molecules which we can call "ligands". Proteins often depend on the ligands for their structure and function. Many, probably most, enzymes have "cofactors" or "co-enzymes", non-protein molecules that are necessary for function. Almost anything found in life can be an enzyme cofactor, but the most common are metal ions and small organic molecules, very often nucleotides, known as co-enzymes. Nucleotides are three-part molecules made up of either a purine or a pyrimidine (called a "base"), a simple sugar molecule (such as ribose or deoxyridose), and one or more phosphate ions (which are acidic). RNA and DNA are polymers made of lots of nucleotides. In many enzymes the thing that actually does the work is one of these cofactors. It is as if the cofactor is a tool, and the protein a workbench or jig, something that brings the work to the tool (or the tool to the work) and provides a local microenvironment needed to do the job. The most common cofactors include adenine, and very often the protein binds on to the adenine portion of these molecules, as if it was a sort of general-purpose handle that proteins can use to manipulate many other compounds.
And thirdly, our metabolisms are also built round nucleotides, many (but not all) the same ones that are in RNA and DNA. The most important is adenine, the "A" in the genetic code, which is used in adenosine phosphates, adenosine mono-phosphate(AMP), di-phospate (ADP), and tri-phosphate (ATP), the last being the single most commonly used molecule to transfer metabolic energy. Its at the centre of nearly every biochemical parthway found in life. The next most common is probably nicotinamide adenine dinucleotide, NAD, and its phosphate NADP, also made of adenine (which is a purine base), and the nicotinamide (AKA nicacin) which is very similar to pyrimidine. That is exactly the same molecules that are the most common enzyme cofactors, and also the same things that RNA and DNA are made of.
Proteins are often called the "fundamental building blocks of life" or some such thing. They are from a structural point of view, our bodies are largely built of them, but not fromn a functional point of view. Our metabolisms are based round purines and pyramidines. Purine nucleotides and nucleosides (most often containing adenine) are found at the heart of the most fundamental metabolic, genetic, and signalling systems in all known life. Another analogy might be a house. The structure is made of bricks and timber but the other things in the house - kitchen equipment, tools, TVs, books, plumbing, people, pets, furniture, whatever, is made of all osrts of other things. In livign cells the gross structure is made or proteins and carbohydrates, but most of the gubbins tht does the actual work is nucleotide. You can imagine a metabolism similar to the way life works nowdays without proteins, you can't imagine one without nucleoitides.
Proteins amost certainly aren't fundament iIn an evolutionary sense either. If our current DNA/RNA/Protein biological world really was preceded by an RNA world in which RNA functioned for both catalysis and replication then it is likely that organisms reliant on ribozymes for catalysis would have to have made use of many cofactors to supply characters which RNA (chemically much more limited than proteins) could not. If that is so, then early evolutionary history of enzymes would have included the gradual replacement of ribozyme structures by protein structures. The original RNA might have been cut away until all that was left was a small cofactors, or else leaving previous cofactors in place. In other words the tools are the same as they used to be, but the nucleotide workbenches have been replaced by upgraded protein ones.
Since then there seems to have been a partial replacement of those cofactors by amino-acid determined active sites. But this process was never completed, so many cofactors remain, perhaps as evolutionary fossils of the previous state.Not all enzymes use co-factors, and it seems that almost any biological reaction can be accomplished without them. Many proteins bind purines and other substrates without cofactors being involved. . If the RNA world hypothesis is true these are examples of proteins whose active sites have entirely replaced some putative ancestral cofactor with amino acids. But many others still use nucleotide cofactors.
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Ken
L’amor che move il sole e l’altre stelle.
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Crœsos
Shipmate
# 238
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Posted
quote:
Originally posted by EtymologicalEvangelical:
Link to peer reviewed paper, please.
quote:
Originally posted by EtymologicalEvangelical:
(Although funnily enough, earlier in the thread I did actually link to an article which supported his view, but which clearly stated that it was the ribosome which was required for the RNA World Hypothesis.
Funnily enough, that website isn't peer reviewed! Why expect one standard from those you're debating and apply a different one to yourself?
[ 21. February 2013, 14:03: Message edited by: Crœsos ]
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Humani nil a me alienum puto
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EtymologicalEvangelical
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# 15091
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Posted
Karl -
Thanks for those links.
The first one is rather strange. One of the comments beneath it expressed a view I agree with:
quote:
Headline is wrong: if biologists had created a self-replicating RNA, it could replicate 100% of itself, not 50%.
As for the Joyce article, I can only access the abstract, but I have access to a critique of Joyce's work, so I will look that up and get back to you.
quote:
So what's the actual thrust of your question? What the ribosomal protein function in RNA world is? The answer is there isn't one. Whether the RNA world hypothesis is sound? Who knows; there's not a lot of settled science in this area.
The general point of this thread is that it's a follow up to another thread. See the OP.
I am not convinced that the chicken and egg dilemma of abiogenesis has been overcome.
quote:
Originally posted by Croesos
Funnily enough, that website isn't peer reviewed! Why expect one standard from those you're debating and apply a different one to yourself?
Fair enough. You 'win' that one. Give yourself a big pat on the back.
(And I assume you think that that article is wrong?)
[ 21. February 2013, 14:07: Message edited by: EtymologicalEvangelical ]
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You can argue with a man who says, 'Rice is unwholesome': but you neither can nor need argue with a man who says, 'Rice is unwholesome, but I'm not saying this is true'. CS Lewis
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ken
Ship's Roundhead
# 2460
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Posted
Also, this isn't neccessarily anything to do with abiogenesis. The hypothesised RNA world might have included some very sophisticated living things. Well, biochemically sophisticated, I doubt if they wrote grand operas or grew bodies much more complicated than a layer of slime. Its plausible, persuasive even, that such living thigns might be ancestral to living things like ourselves. But they weren't neccessarily the first living things. In fact they almost certainly weren't.
The normal techniques of evolutionary biology are based on comparison. We look at living things to see what they have in common and what's different. We infer things about their common ancestor from what they have in common, and we infer things about their subsequent history from what is different. But we can't use those techniques to see beyond the common ancestor, and we can't use them to look outside the tree.
All known life is related, and - metabolically at any rate - the last universal ancestors were something like modern bacteria. We can make infomed speculations about what the immidiate ancestors of those universal ancestors were like but the further back we go the more speculative it gets. So we can never be as sure about the nature of these RNA world organisms as we are about our ancestral bacteria. And we can't see anythign at all about organisms that have left no descendents. So its quite possible ther were all sorts of other liiving things at the time - but they are invisible to biology.
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Ken
L’amor che move il sole e l’altre stelle.
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Karl: Liberal Backslider
Shipmate
# 76
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Posted
Overcome? No, but if you're trying to hint at "which came first! Aha! Therefore God!" then you do need to demonstrate that it's fundamentally insoluble.
Personally, given that most of what we know indicatesthat the universe and life came about via naturalistic processes, I don't quite see why God would create a universe that didn't quite work and therefore required the sort of tinkering that would be inherently undiscoverable by scientific means and always remain a mystery - like the Far Side cartoon with "And then a miracle happens" in the middle of the formula. Is God not able to make a universe which develops according to its own parameters in the way he wants and to the ends he's decreed?
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Might as well ask the bloody cat.
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ken
Ship's Roundhead
# 2460
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Posted
quote:
Originally posted by EtymologicalEvangelical:
I am not convinced that the chicken and egg dilemma of abiogenesis has been overcome.
And you never will be because something that does not exist can never be overcome.
And, as I said, the RNA world hypothesis isn't really relevant, because its already a complicated set of living processes.
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Ken
L’amor che move il sole e l’altre stelle.
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agingjb
Shipmate
# 16555
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Posted
Proteins are astonishingly versatile, but the one thing they don't do is replicate other proteins, polypeptide sequences, on their own.
I've often wondered if a meta-ribosome could be constructed artificially that could take proteins and duplicate them without the whole genetic code, DNA, RNA mechanism. And would that be significant, or possibly catastrophic, for the biosphere.
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Refraction Villanelles
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