My "Mother of all Mystery"

[perion666]

I've gotten myself captivated by, what must be, the Mother of All Puzzles. For me it is, anyway.

Here's my problem. Assuming that by hook or crook, by whatever prevailing physical conditions, statistical anomalies, etc, we arrive at a prebiotic point where there exists an assortment of proximate biomolecular compounds with some very interesting capabilities. Many can be chained together into some fabulously intricate 3D structures. Some, by their structural arrangement, even have the built-in capability of information storage and self-replication. Some degree of self-assembly is possible as a result of the various bonding characteristics, structural compatibilities, degree of random associations, etc. There's also a wealth of other elemental ingredients present for the formation of organic compounds. OK - that's great and marvelous and awesome (and not too easy to explain, either) but it's not really all that mysterious. It goes with the nature of the of the various compounds present. For me, the mind bender - the Mother of all Mystery is this: how is it that we go from that intriguing assortment of biomolecular compounds to a situation where we have an information code that prescribes the assembly of the very molecular apparatus that's used to implement the code??? Without the apparatus we just have a sequence of bases. The code needs a particular assortment of code implementations in order that it can be implemented...

Maybe this just reflects my immaturity in dealing with the subject of biochemistry. But, when I look outside the realm of biochemistry I seem to just end up in places where people are debating God vs Evolution or ID vs neo-Darwinism, etc. I get tired of all that bickering. But maybe biochemistry won't pan out for me either - at least, for this particular puzzle. The problem does seem like the chicken/egg scenario from Hell. I'd be interested how others handle this.

[Taffer]

I've gotten myself captivated by, what must be, the Mother of All Puzzles. For me it is, anyway.

Here's my problem. Assuming that by hook or crook, by whatever prevailing physical conditions, statistical anomalies, etc, we arrive at a prebiotic point where there exists an assortment of proximate biomolecular compounds with some very interesting capabilities. Many can be chained together into some fabulously intricate 3D structures. Some, by their structural arrangement, even have the built-in capability of information storage and self-replication. Some degree of self-assembly is possible as a result of the various bonding characteristics, structural compatibilities, degree of random associations, etc. There's also a wealth of other elemental ingredients present for the formation of organic compounds. OK - that's great and marvelous and awesome (and not too easy to explain, either) but it's not really all that mysterious. It goes with the nature of the of the various compounds present. For me, the mind bender - the Mother of all Mystery is this: how is it that we go from that intriguing assortment of biomolecular compounds to a situation where we have an information code that prescribes the assembly of the very molecular apparatus that's used to implement the code??? Without the apparatus we just have a sequence of bases. The code needs a particular assortment of code implementations in order that it can be implemented...

Maybe this just reflects my immaturity in dealing with the subject of biochemistry. But, when I look outside the realm of biochemistry I seem to just end up in places where people are debating God vs Evolution or ID vs neo-Darwinism, etc. I get tired of all that bickering. But maybe biochemistry won't pan out for me either - at least, for this particular puzzle. The problem does seem like the chicken/egg scenario from Hell. I'd be interested how others handle this.

Perhaps your problem comes from assuming that the first "life" looked and behaved in much the same way as modern life does.

There is no reason to suspect that it would.

[fagin]

I've gotten myself captivated by, what must be, the Mother of All Puzzles. For me it is, anyway.

Here's my problem. Assuming that by hook or crook, by whatever prevailing physical conditions, statistical anomalies, etc, we arrive at a prebiotic point where there exists an assortment of proximate biomolecular compounds with some very interesting capabilities. Many can be chained together into some fabulously intricate 3D structures. Some, by their structural arrangement, even have the built-in capability of information storage and self-replication. Some degree of self-assembly is possible as a result of the various bonding characteristics, structural compatibilities, degree of random associations, etc. There's also a wealth of other elemental ingredients present for the formation of organic compounds. OK - that's great and marvelous and awesome (and not too easy to explain, either) but it's not really all that mysterious. It goes with the nature of the of the various compounds present. For me, the mind bender - the Mother of all Mystery is this: how is it that we go from that intriguing assortment of biomolecular compounds to a situation where we have an information code that prescribes the assembly of the very molecular apparatus that's used to implement the code??? Without the apparatus we just have a sequence of bases. The code needs a particular assortment of code implementations in order that it can be implemented...

Maybe this just reflects my immaturity in dealing with the subject of biochemistry. But, when I look outside the realm of biochemistry I seem to just end up in places where people are debating God vs Evolution or ID vs neo-Darwinism, etc. I get tired of all that bickering. But maybe biochemistry won't pan out for me either - at least, for this particular puzzle. The problem does seem like the chicken/egg scenario from Hell. I'd be interested how others handle this.

Read

[Cuddles]

how is it that we go from that intriguing assortment of biomolecular compounds to a situation where we have an information code that prescribes the assembly of the very molecular apparatus that's used to implement the code??? Without the apparatus we just have a sequence of bases. The code needs a particular assortment of code implementations in order that it can be implemented...

Think of it as a catalyst situation. There are many, many different compounds which can catalyse chemical reactions. However, all these reactions can take place without a catalyst as well, they just take much longer. Now, what happens if a compound catalyses its own formation? It could take ages for the first molecule to form, but once it has, it will cause more and more to form very rapidly. The same sort of thing could be true for the precursors of life. At first, it would just be a random mess of organic molecules forming, reacting with each other and breaking up again. However, if at some point a molecule formed which happened to catalyse its own formation, it would spread everywhere. Assuming imperfections in its reproduction, evolution happens and life takes off.

The problem you seem to be having is that you are assuming the initial formation is impossible without the product already being present, leading to problems with chickens and eggs. It isn't. Life may be very unlikely to form without life already present to create it, but it isn't impossible.

Edit: The vast majoity of the arguments you see are simply over the initial probability of a self-catalysing organic (or possibly even inorganic) molecule forming. Obviously, the answer to this just isn't known. We know that surprisingly complex molecules can form very easily in the conditions thought to exist on the early Earth. We even know that they can form in very uninviting places like outer space. What we don't know is exactly what the conditions actually were, or how hard it is to go from what we know can form to actually being life. Fundamental creationists say it is simply impossible and therefore god. Other people say it may be possible, but is unfeasible given the timescales involved, and lean either towards creationism or panspermia and other "it came from somewhere else" ideas. Others say that it's actually not improbable at all and it would be surprising if life didn't exist all over the place.

Edit2: Also bear in mind the argument is never "God vs. evolution", although that is what creationists would like you to think. Evolution says nothing about the origin of life (depending on your definition - some people use a more general definition that would include various non-living systems as well). The actual argument is "God vs. abiogenesis". Creationists like to argue about evolution because it is this that tells us we are no more special than any other form of life. However, even if evolution by natural selection was proven wrong tomorrow, it still would say absolutely nothing about creationism or the origin of life.

[fishbob]

Trillions of molecules, millions of years.

Trial and error.
Repeat.

[Soapy Sam]

The answer to the chicken / egg mystery is (as I'm sure you know) "something a lot like an egg, but more like a reptile egg than a chicken egg". ie the question seems to be an either / or one, but is not.

I'm reasonably confident the solution to your other mystery is similar and explicable in terms of known chemistry, added to fishbob's recipe.

[perion666]

Think of it as a catalyst situation. There are many, many different compounds which can catalyse chemical reactions. However, all these reactions can take place without a catalyst as well, they just take much longer. Now, what happens if a compound catalyses its own formation? It could take ages for the first molecule to form, but once it has, it will cause more and more to form very rapidly. The same sort of thing could be true for the precursors of life... (snipped)
Thanks much for the thoughtful reply. In fact, thanks to all that responded. I see what you're saying regarding with/without catalysts just being a matter of taking longer.

The problem you seem to be having is that you are assuming the initial formation is impossible without the product already being present, leading to problems with chickens and eggs. It isn't. Life may be very unlikely to form without life already present to create it, but it isn't impossible.

It's not the formation of "life", per se, that is giving me difficulty. I understand, or, to be more precise, I assume, that the complex information pathways we see now are not necessarily relevant to understanding prebiotic molecular processes. I'm studying my textbooks (Lehninger and a few others)and trying to understand Gilbert's "RNA World" from the book [PDF version here]. I need to study more, I know, but I still can't see any scenarios that would've conferred upon some group of pre-rRNA base sequences the role of a coding scheme. I understand that there possibly could have been forms of RNA that were capable of not only information storage (that's a given for RNA structure), but also the ability to catalyze peptide bonding and therefor, presumably, synthesize proteins. My mental block isn't in dealing with the possible existence of the hardware capabilities but rather, what determined the sequences - the information - which amino acid gets added next - what constitutes a stop sequence - which and how many bases constitute a functional, transcribable, unit (like a present-day gene), which sequential groups should be transcribed and which skipped - etc??? Let me give an analogy.

For me, the situation is like the printed recipe cards - maybe how to bake a cake or roast a stuffed turkey. Each recipe is an ordered sequence instructions embodied in a symbolic language that can be interpreted and carried out. The recipe makes use of not only the chemistry of the hardware of paper and ink (and the physics of photon emission/absorption) but also, among many other subtleties:

an underlying symbolic language convention whereby the information for each step can be unambiguously represented
some method for extracting and interpreting the information contained in each step - e.g. the act of reading
a coherent order to the steps in each recipe by which a recipe-specific end product will result when performed in that order

The recipes are most certainly physically manifested according to the chemistry of the paper and ink, the physics of the light, etc. However, neither the language convention nor the order of the steps that constitute a recipe have anything to do with chemistry and physics. That's were my puzzlement lies with prebiotic RNA scenarios - its not the possible hardware capabilities - its the software informational aspect that I can't get a handle on. [BTW - this may sound like some intelligent design argument but I'm really not doing that here. I'm genuinely puzzled by all this stuff - for real. My apologies for rambling so long - no need to respond in kind. Just thinking via my typing fingers...]

[Taffer]

See my response.

The life which lead to "life as we know it" need not have used the same mechanisms which life does now.

[perion666]

I did read your response. I'm not talking about "life". I'm talking about RNA information processing functionality before life - long before an entire macro-system such as a cell could exist.

[Taffer]

I did read your response. I'm not talking about "life". I'm talking about RNA information processing functionality before life - long before an entire macro-system such as a cell could exist.

Then why speculate about what could or could not have existed?

Your argument appears to be much like an argument about "irreducible complexity", which has been shown to be flawed.

[BME]

I think that the crux lies in the misconception that follows easily out of the computer analogy: you have a program that is in the end "translated" by the BIOS to certain operations (i am not a computer expert at all). THere is no such thing in tis case; the "information" does not need to be "decoded" or translated into instructions; the RNA molecule(s) hypothesized to be the beginning of "life" are the instructions themselves (ie have catalytic activity)
my 2p
cheers, Bart

[Cuddles]

I'm talking about RNA information processing functionality before life - long before an entire macro-system such as a cell could exist.

Why do you think RNA existed? Why do you think anything processed information? This is what Taffer is saying. The first life, and its precursors, are unlikely to have been the same as anything we can see now. The question of why did transcribe proteins is irrelevant because it (probably) didn't. All that happened was a molecule formed which catalysed it's own production. It's likely that it did this by attatching pieces to itself and joining them up, similar to how RNA and DNA do today, although this isn't the only possibility. But that is all it would have done. At first.

The point is, any function other than reproduction would not have existed. You are having problems because you are assuming that the first life and its precursors did things which they could not possibly have done. The simple answer is that they didn't do them.

[Southwind17]

I did read your response. I'm not talking about "life". I'm talking about RNA information processing functionality before life - long before an entire macro-system such as a cell could exist.

No disrespect to Taffer, but perion, you'll quickly learn, as I have done, which Forum members are sympathetic if not welcoming to your curiosity and are willing to help you learn, and which just enjoy issuing the one-liners and giving you short shrift. The latter, whilst essentially harmless, usually have very fixed misconceptions and erroneous views. My advice is to disregard them politely (ignoring them can work well!) and develop the dialogue with those willing to discuss meaningfully and thoughtfully. That said, I often get tempted to give one-liner exponents short shrift in return, usually with interest(!), for which I often get bombarded with flack. I don't mind that though; I'm thick-skinned and can usually outsmart most with a few carefully crafted home truths which tends to send them crawling back under their stones. Either that or an attritianal war or words ensues, which I'm usually equally happy to entertain. OK, just a few words of advice to try to avoid any disillusionment! Unfortunatley I can't offer any views regarding your puzzlement; you're clearly already way ahead of me! Good luck ;)

[Taffer]

No disrespect to Taffer, but perion, you'll quickly learn, as I have done, which Forum members are sympathetic if not welcoming to your curiosity and are willing to help you learn, and which just enjoy issuing the one-liners and giving you short shrift. The latter, whilst essentially harmless, usually have very fixed misconceptions and erroneous views. My advice is to disregard them politely (ignoring them can work well!) and develop the dialogue with those willing to discuss meaningfully and thoughtfully. That said, I often get tempted to give one-liner exponents short shrift in return, usually with interest(!), for which I often get bombarded with flack. I don't mind that though; I'm thick-skinned and can usually outsmart most with a few carefully crafted home truths which tends to send them crawling back under their stones. Either that or an attritianal war or words ensues, which I'm usually equally happy to entertain. OK, just a few words of advice to try to avoid any disillusionment! Unfortunatley I can't offer any views regarding your puzzlement; you're clearly already way ahead of me! Good luck ;)

I'm curious why you think I have the bolded.

[Southwind17]

I'm curious why you think I have the bolded.

Well, you're certainly harmless, because words can't hurt, at least not if you abide by the Forum Rules. As for the rest, based on the limited number of posts of yours that I can recall reading, I don't. The word 'usually' serves to rule you out Taffer. ;)

[Taffer]

Well, you're certainly harmless, because words can't hurt, at least not if you abide by the Forum Rules. As for the rest, based on the limited number of posts of yours that I can recall reading, I don't. The word 'usually' serves to rule you out Taffer. ;)

And so it should! I didn't spend years of my life and become indebted to hold fixed misconceptions and erroneous views. :p

[perion666]

No disrespect to Taffer, but perion, you'll quickly learn, as I have done, which Forum members are sympathetic if not welcoming to your curiosity and are willing to help you learn, and which just enjoy issuing the one-liners and giving you short shrift. The latter, whilst essentially harmless, usually have very fixed misconceptions and erroneous views. My advice is to disregard them politely (ignoring them can work well!) and develop the dialogue with those willing to discuss meaningfully and thoughtfully. That said, I often get tempted to give one-liner exponents short shrift in return, usually with interest(!), for which I often get bombarded with flack. I don't mind that though; I'm thick-skinned and can usually outsmart most with a few carefully crafted home truths which tends to send them crawling back under their stones. Either that or an attritianal war or words ensues, which I'm usually equally happy to entertain. OK, just a few words of advice to try to avoid any disillusionment! Unfortunatley I can't offer any views regarding your puzzlement; you're clearly already way ahead of me! Good luck ;)

Sorry for starting a fight :duck:

Actually, I haven't disregarded ANYONES' feedback - one-liners or many. Also, I don't mind being criticized or misunderstood. Normally, if I've been misunderstood, then I probably didn't communicate my thoughts accurately. In this case, I don't feel misunderstood. I think I probably just have a naive view of pre-biotic conditions. I'm working on that.

I don't hold any particular view on the origin of life or the "RNA World" theory or any other theories of molecular development. I don't know enough yet to even have an intelligent view. I'm just learning biochemistry and asking questions, unfortunately, out of my current ignorance. I just want to see what others think and maybe learn something from someone more knowledgable of the subject. I'm sure that probably gets annoying for people that really do know more about these things and have dealt with it a zillion times with other newbies. But, I still love biochemistry and hopefully, in a few years or so will have a deeper, more mature understanding. There's so much to learn that it seems impossible to ever get competent with it, but I figure if others can do it then so can I. If not... well, it won't be for lack of effort.

Oh - I appreciate your concern and warnings. I'm OK, though. I've been around and have no illusions or expectations.

Bye...

[Schneibster]

I got a number of what looked like interesting hits with the Google search term, "evolution of prebiotic RNA." Several papers in the first ten hits seem to be focusing on various sorts of prebiotic evolution leading to mRNA and the creation of a genetic code; i.e., the association of particular codons with particular amino acids. If you're learning this stuff right now, you probably have access to a library that might have these papers available for you to read; I would recommend you do so.

The answer, I think, lies in the character of the protein replication mechanism.

ETA: I think there might be some details about the particular way that mRNA becomes attractive to a particular amino acid that might not be arbitrary, but instead dictated by the chemistry involved. Knowing what I do about systems theory, and what I do about quantum mechanics, I strongly suspect that the genetic code is a function of the mRNA. Thanks for that; it's a thought I hadn't had before.

[perion666]

I got a number of what looked like interesting hits with the Google search term, "evolution of prebiotic RNA." Several papers in the first ten hits seem to be focusing on various sorts of prebiotic evolution leading to mRNA and the creation of a genetic code...
Here's some interesting material. The link, below, is a chapter from a book at Cold Spring Harbor entitled "RNA World". Not all chapters are available so I listed the ones that are. Each chapter is a stand-alone paper so there's no loss of continuity by not having access to all the chapters. Just substitute the desired chapter number for "09" in the url. I had to drop the hypertext transport protocol prefix abbreviation from the link since I haven't posted 15 times yet. OK - whatever...

*****//rna.cshl.edu/content/free/chapters/09_rna_world_2nd.pdf.

For other chapters, substitute the chapter number for "09" in the URL. Available chapters are:

01, 03, 04, 06, 07, 09, 12, 13, 14, 15, 18, 21, and 24.

Bye

[BenBurch]

Trillions of molecules, millions of years.

Trial and error.
Repeat.

Billions of planets.

On the planets where it didn't happen, nobody has discussions like this one.