Are the sugars ribose and deoxyribose self assembling

My original question deals with cellular self assembly. If ribose and deoxyribose are not self assembling molecules then it becomes difficult for a cell to self assemble. By the way if you don't think cells arose spontaneously then How did they get here? What would actually be pressuring these early cell prototypes you cited. And by the way this is a line of questioning I am coming up with on my own. I do have citations for the cell self assembly but not the ribose or deoxyribose. That's why I started this thread to see what's out there. I will look up your citations and get back to you but I do work and have a family so the fact that I didn't repond yesterday was that I just got your reply today.

No, your original question deals with abiotic synthesis of complex sugars - ribose and deoxyribose. I pointed out in my response that abiotic synthesis of ribose is problematic. RNA was therefore probably NOT the first replicator, and DNA came afterward RNA, possibly from a modification of dsRNA. PNA is a much liklier precursor/early replicator because it is easy to synthesize chemically from precursors that were putatively available on the early Earth (the very pyrmidine and purine bases found in Miller's original experiment, as well as abiotically spark-synthesized ethylene diamine monoacetic acid backbone). It doesn't require pentose sugars or phosphate groups. One form of PNA can self-catalyze. It has been shown to be capable of catalyzing a simple RNA homolog. etc. It isn't definitive, and it hasn't been completely shown to be self replicating, but does appear highly indicative - especially in the presence of mineral catalysts or templates. See, for example, Miller, SL, 1997, "Peptide nucleic acids and prebiotic chemistry" Nature Structural Biology 3:167-169.Which of course, has nothing to do with cells or cellular self assembly - which is where you've now moved the goal posts.{edited to add citation}[This message has been edited by Quetzal, 11-19-2003]

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my point is that if we can't design it intellegently, why would anyone think that it could happen by chance. It's amazing to me that scientists would look the the stars and accept any nonrandom signal, no matter how small, as proof of intellegence in the solar system. Yet we are confronted with every cell on earth that is filled with more nonrandom information, which would fill thousands of pages of books, and we try to expain it all away.

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1) Scientists don't just accept any nonrandom signal. For example, pulsars aren't random, they're nice and orderly. But they're natural. Now if we saw a pulsar counting in primes, that would be something altogether different. 2) As I mentioned, when we artificially induce evolution (such as creating the "laws of virtual physics" in genetic algorithms), the virtual organisms become complex - often *incredibly* complex. I suggest you download and run Avida for a bit, and then tell me if you can understand how an organism a number of generations down the road is managing to self replicate. Especially when they develop specialized parasites (using a "prey" algorithm to run their replication code for them), it can be incredibly difficult to decipher - just like real organisms.3) Much of the difficulty that we see in real organisms is needless complexity - the type that you get from genetic algorithms, but not from design. Why on earth, for example, are the genes for our blue and green cones in our eyes close together, but red is far away? DNA is all what programmers refer to as "spaghetti code"

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My original point of this thread was to see if anyone knows research about the sugar ribose or deoxyribose. Since they are part of every living thing we are aware of, if they can only be produced in living things (like Glucose) then it presents a real problem.

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Oh, they can be produced by nonliving things just fine - noone doubts that. The questions related to this are:1) How long do they last? Most sugars would have a halflife, in earth's prebiotic oceans, of a few hundred years.2) Were the first self replicators sugar based, like DNA and RNA? Very doubtful. Sugars are likely a later addition to a hypercycle that was initiated by a simple replicating ligase, or perhaps PNA as Quetzal has been referring to (I'm not familiar with that, I'm going to have to read up on it. ).------------------
"Illuminant light,
illuminate me."[This message has been edited by Rei, 11-19-2003]

Just a quick correction: Actually, one experiment I read indicated that ribose, for example, decomposed in 73 minutes! at 100 C, and 34 years at 0 C. (I don't have the citation handy).Also: PNA stands for peptide nucleic acid. It is a very cool molecule. Here's a sample of current thinking on PNA: Nelson KE, Levy M, Miller SL, 2001, "Peptide nucleic acids rather than RNA may have been the first genetic molecule", PNAS 97: 3868—3871.

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Numerous problems exist with the current thinking of RNA as the first genetic material. No plausible prebiotic processes have yet been demonstrated to produce the nucleosides or nucleotides or for efficient two-way nonenzymatic replication. Peptide nucleic acid (PNA) is a promising precursor to RNA, consisting of N-(2-aminoethyl)glycine (AEG) and the adenine, uracil, guanine, and cytosine-N-acetic acids. However, PNA has not yet been demonstrated to be prebiotic. We show here that AEG is produced directly in electric discharge reactions from CH4, N2, NH3, and H2O. Electric discharges also produce ethylenediamine, as do NH4CN polymerizations. AEG is produced from the robust Strecker synthesis with ethylenediamine. The NH4CN polymerization in the presence of glycine leads to the adenine and guanine-N 9-acetic acids, and the cytosine and uracil-N 1-acetic acids are produced in high yield from the reaction of cyanoacetaldehyde with hydantoic acid, rather than urea. Preliminary experiments suggest that AEG may polymerize rapidly at 100C to give the polypeptide backbone of PNA. The ease of synthesis of the components of PNA and possibility of polymerization of AEG reinforce the possibility that PNA may have been the first genetic material.

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Another possible precursor is pyranosyl-RNA (which has the ribose synthesis problem, although is way more stable than normal RNA), and threose nucleic acid (TNA) - on an a-L-threofuranosyl backbone - but which also has the phosphodiester bond problem that PNA eliminates. So I like PNA much more.

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Actually, one experiment I read indicated that ribose, for example, decomposed in 73 minutes! at 100 C, and 34 years at 0 C. (I don't have the citation handy).

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It depends on the sugar and temperature, although in general I think you are correct - it's going to be in tens of years at moderate temperatures, not hundreds (and significantly shorter when hot). I was thinking more along the lines of some of the pyrimidine half lives (which, too, are temperature sensitive).Interesting information on PNA, by the way. Basically, it's a chain of amino acids bonded to purine and pyrimidine groups, correct? Sounds fairly reasonable, both are fairly easy to produce in a prebiotic environment.------------------
"Illuminant light,
illuminate me."

This involves intellegence and a computer to read the program. To be anologous to what I have said you would need the program to write itself, and even though it is non-living, the computer to assemble itself. The question is how do you get it started? From your point of view, without intellegence.

this is my original question If you notice the last part of the post is a follow up question about abiogenesis.

Thanks for clearing that up. My searches led me to the Palestine National Authority. Nice reading but not much science there.

What research do you base this on. That was what I wanted to know in the first sentence of my first post on this thread. Can you provide any citations?

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This involves intellegence and a computer to read the program. To be anologous to what I have said you would need the program to write itself, and even though it is non-living, the computer to assemble itself.

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You're not quite grasping this, so I'll have to reiterate: the program basically creates new virtual laws of physics. They can be quite similar to our laws of physics (such as Framsticks), or utterly different (such as Avida). Depending on the program, you either start with no life or incredibly simple life. Following the virtual laws of physics that you create, the life forms go on their own, and end up far more advanced and complex. They evolve, and often tremendously. I hope you're understanding this: an intelligence creates the environment that the virtual life exists in, and sometimes the earliest life (depending on the program); the life manages itself - and evolves, often in ways that the programmer generally never would have dreamed of (such as Tierra and Avida parasitism), and typically ending with a level of complexity that makes deciphering a very, very difficult challenge.You could use this to argue for the presence of God who created the universe, but not for the presence of a worldview in which evolution doesn't occur - because it does, and quite amazingly in sims. And here's why it does.

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The question is how do you get it started? From your point of view, without intellegence.

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Complexity arises from simplicity all the time. Complex rules create complex behavior. Simple rules create simple behavior. But simple rules, applied iteratively, often create very complex behavior. Are you familair with the Mandelbrought set, for example? It's an incredibly simple rule, but when applied iteratively, it produces an amazing degree of complexity, the further you zoom in. This phenomina is visible everywhere from the weather to fractals to population models and more.Seing as how simple self replicators have formed in programs like Conway's Game of Life even with our limited computing power, the question is not whether a hypercycle can begin in an arbitrary universe - the only question that remains is whether one did in this universe.------------------
"Illuminant light,
illuminate me."

Prebiotic synthesis of autocatalytic products from formaldehyde-derived sugars
Rates of decomposition of ribose and other sugars: implications for chemical evolution
Serine Flavors the Primordial Soup
(i could go on if you'd like with more articles that mention the synthesis ).Basically, most prebiotic sugars would form from various aldehydes. After all, sugars are polyhydroxy aldehydes or keytones. Sugars have also been found in space. (see also this for sugar in a nebula).This paper is an interesting read as well, on that subject: Molecules in Space.------------------
"Illuminant light,
illuminate me."

My understanding of the Miller/Urey experiment was that it produced very little of the building blocks of life.These spark-discharge experiments (and various "fine-tunings" since then) have produced various organic substances ...namely:
A. 85% of the product was a brown, insoluble tar or "polymer" made of hydrocarbons and other atoms interconnected in an irregular mass, with no known biological relevance to the origin of life.
(A chemist in a laboratory might be able to set up the right conditions to convert the "tarry sludge" into biogenic compounds such as amino acids, nucleotides and lipids, --but there is as yet no indication that any such "converting-conditions" may have existed anywhere in nature.)
B. 4% of the product was the simplest of the carboxylic acids, formic acid (comprised of five atoms) --which is found in good concentrations in ants, but has no known role in the origin of life.
C. 2.7% was equal parts (0.9% each) of three more caboxylic acids (not amino acids), which are different arrangements of 13 atoms (3 carbons, 7 hydrogens, 1 nitrogen, and 2 oxygens), and have no known or conjectured relevance to the origin of life.
D. 2.1% was glycine, which is possibly significant, because it is one of the 20 amino acids, which are used in biology to construct the proteins of living organisms ---glycine is the simplest amino acid.
E. 0.85% was the Left-handed (L-)form of the amino acid alanine. Alanine is also one of biology's 20 amino acids (the second simplest), which is produced in both of it's mirror-image forms (of stereochemistry); but only the L-form is used in the proteins of living things;
F. and 0.85% of the product was the Right-handed (R-)form of alanine, however, the R-form of any amino acid is destructive to the proper construction and function of life.
G. 0.5% was acetic acid, another carboxylic acid, which gives vinegar its pungency, but which is (so far as anyone knows) irrelevant to any origin-of-life processes,
H. 0.026% was another of the simplest amino acids ---which was only 260 parts per million of the product.
I. Several more of life's 20 amino acids were produced in ever smaller trace amounts ---and only half of each of those trace amounts was the useful L-form, while the other half was the destructive R-form.
J. Recently, trace amounts of the five bases of DNA and RNA have been detected ...but only about 2 parts per million. --However, even though the chemicals were present for the production of a "nucleoside" (which is the combination of a DNA base plus a sugar), no nucleosides have ever formed in any amount.
--Furthermore, not one nucleotide has ever formed (of course), because this would involve the addition of a phosphate onto a nucleoside (which has never formed) --and the nucleotide is actually the basic building block of DNA and RNA.
Also the Miller/urey experiment can’t produce any of these if free oxygen is present which is why it was left out.Also in the absence of oxygen wouldn’t unltraviolet light break down any formation of life’s building blocks. If PNA is not prebiotic then it really doesn’t provide much hope does it?

I understand your point. If you plug information into a computer program you can get complexity depending on the program you select. What I am saying is that is artificially creating an environment which can’t possibly simulate actual living conditions, and requires an intelligence. Therefore agreed Creationists, or intelligent designers, never, or shouldn’t, deny that microevolution can happen. I have no doubt that all dogs came from a common dog ancestor. I have no doubt that bacteria can develop resistance to antibiotics. You would have to be an idiot and totally blind to not agree with that. So if we discuss microevolution, no problem. My problem always comes when we make a gigantic leap and say that since a bacteria can become resistant, its obvious that it can become a tree. Back to my original thread, thanks. This is the kind of information I am looking for.

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Creationists, or intelligent designers, never, or shouldnt, deny that microevolution can happen. I have no doubt that all dogs came from a common dog ancestor. I have no doubt that bacteria can develop resistance to antibiotics. You would have to be an idiot and totally blind to not agree with that. So if we discuss microevolution, no problem. My problem always comes when we make a gigantic leap and say that since a bacteria can become resistant, its obvious that it can become a tree.

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Before you classify all genetic algorithms have achieved as microevolution, I suggest you read on the current state of what has occurred, given what starting conditions, whether it's randomly linked cubes which evolve to fight over an object, or hyperparasites (parasites upon parasites) developing to steal resources away from their competitors in Tierra. For a real world example, are these just microevolution? What about (can't find the paper on short notice) a single cellular organism developing into a multicellular organism in the middle of a laboratory experiment?------------------
"Illuminant light,
illuminate me."